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  • Refining the genetic architecture of flag leaf glaucousness in wheat
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-17
    Tobias Würschum, Simon M. Langer, C. Friedrich H. Longin, Matthew R. Tucker, Willmar L. Leiser

    The cuticle is the plant’s barrier against abiotic and biotic stresses, and the deposition of epicuticular wax crystals results in the scattering of light, an effect termed glaucousness. Here, we dissect the genetic architecture of flag leaf glaucousness in wheat toward a future targeted design of the cuticle.

    更新日期:2020-01-17
  • Natural resistance to Potato virus Y in Solanum tuberosum Group Phureja
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-16
    Lesley Torrance, Graham H. Cowan, Karen McLean, Stuart MacFarlane, Aqeel N. Al-Abedy, Miles Armstrong, Tze-Yin Lim, Ingo Hein, Glenn J. Bryan

    Novel major gene resistance against Potato virus Y in diploid populations of Solanum tuberosum Groups Phureja and Tuberosum was biologically and genetically characterised. Named Ry(o)phu, it mapped to chromosome 9.

    更新日期:2020-01-16
  • Chromosomal location of the crown rust resistance gene Pc98 in cultivated oat ( Avena sativa L.)
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-14
    Jun Zhao, Aida Z. Kebede, Jim G. Menzies, Edyta Paczos-Grzęda, James Chong, Jennifer W. Mitchell Fetch, Aaron D. Beattie, Yuan-Ying Peng, Curt A. McCartney

    Abstract Key message SNP loci linked to the crown rust resistance gene Pc98 were identified by linkage analysis and KASP assays were developed for marker-assisted selection in breeding programs. Abstract Crown rust is among the most damaging diseases of oat and is caused by Puccinia coronata var. avenae f. sp. avenae (Urban and Marková) (Pca). Host resistance is the preferred method to prevent crown rust epidemics. Pc98 is a race-specific, seedling crown rust resistance gene obtained from the wild oat Avena sterilis accession CAV 1979 that is effective at all growth stages of oat. Virulence to Pc98 has been very low in the Pca populations that have been tested. The objectives of this study were to develop SNP markers linked to Pc98 for use in marker-assisted selection and to locate Pc98 on the oat consensus map. The Pc98 gene was mapped using F2:3 populations developed from the crosses Pc98/Bingo and Pc98/Kasztan, where Pc98 is a single-gene line carrying Pc98. Both populations were evaluated in seedling inoculation experiments. Pc98 was mapped relative to Kompetitive Allele-Specific PCR SNP markers in both populations, placing Pc98 on the Mrg20 linkage group of the consensus map. Pc98 was bracketed by two SNP markers GMI_ES22_c3052_382_kom399 and GMI_ES14_lrc18344_662_kom398 in the Pc98/Bingo mapping population with genetic distances of 0.9 cM and 0.3 cM, respectively. Pc98 co-segregated with four SNP markers in the Pc98/Kasztan population, and the closest flanking markers were GMI_DS_LB_6017_kom367 and avgbs2_153634.1.59_kom410 with genetic distances of 0.7 cM and 0.3 cM, respectively. Two SNP loci defined a haplotype that accurately predicted Pc98 status in a diverse group of oat germplasm, which will be valuable for marker-assisted selection of Pc98 in breeding of new oat cultivars.

    更新日期:2020-01-15
  • Genetic characterization and genome-wide association mapping for dwarf bunt resistance in bread wheat accessions from the USDA National Small Grains Collection
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-14
    Tyler Gordon, Rui Wang, David Hole, Harold Bockelman, J. Michael Bonman, Jianli Chen

    Abstract Key message Dwarf bunt-resistant bread wheat accessions and SNP markers associated with DB resistance identified in this study are valuable resources for characterization and deployment of DB resistance in bread wheat. Abstract Dwarf bunt (DB), caused by Tilletia controversa J.G. Kühn, can significantly reduce grain yield and quality on autumn-sown wheat in regions with prolonged snow cover. DB can be managed with the use of resistant cultivars. The objectives of the present study were to characterize DB resistance in a large set of bread wheat accessions from the National Small Grains Collection and use a genome-wide association study approach to identify genetic loci associated with DB resistance. A total of 292 accessions were selected using historical DB resistance data recorded across many trials and years in the Germplasm Resources Information Network (GRIN) and re-tested for DB resistance in replicated field nurseries in Logan, UT, in 2017, 2018, and 2019. Ninety-eight accessions were resistant with DB normalized incidence ≤ 10%, and twenty-eight of these were highly resistant with DB normalized incidence ≤ 1% in both GRIN and the field nurseries. Based on the presence of marker haplotypes of the four published dwarf bunt QTL on 6DS, 6DL, 7AL, and 7DS, highly resistant accessions identified in this study may provide novel resistance and should be further evaluated. This study validated one previously identified QTL on 6DS and identified an additional locus on 6DS. These loci explained 9–15% of the observed phenotypic variation. The resistant accessions and molecular markers identified in the present study may provide valuable resources for characterization and deployment of DB resistance in bread wheat.

    更新日期:2020-01-14
  • A spontaneous wheat- Aegilops longissima translocation carrying Pm66 confers resistance to powdery mildew
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-13
    Huanhuan Li, Zhenjie Dong, Chao Ma, Qing Xia, Xiubin Tian, Sunish Sehgal, Dal-Hoe Koo, Bernd Friebe, Pengtao Ma, Wenxuan Liu

    A spontaneous Robertsonian T4SlS·4BL translocation chromosome carrying Pm66 for powdery mildew resistance was discovered and confirmed by RNA-seq, molecular marker, and in situ hybridization analyses.

    更新日期:2020-01-14
  • Genetic variations of acidity in grape berries are controlled by the interplay between organic acids and potassium
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-13
    Éric Duchêne, Vincent Dumas, Gisèle Butterlin, Nathalie Jaegli, Camille Rustenholz, Aurélie Chauveau, Aurélie Bérard, Marie Christine Le Paslier, Isabelle Gaillard, Didier Merdinoglu

    In a grapevine segregating population, genomic regions governing berry pH were identified, paving the way for breeding new grapevine varieties best adapted to a warming climate.

    更新日期:2020-01-13
  • Identification of molecular markers for the Pc39 gene conferring resistance to crown rust in oat
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-11
    Sylwia Sowa, Edyta Paczos-Grzęda

    Six new PCR-based markers for the Pc39 crown rust resistance gene in Avena sativa L. were developed. Pc39 was mapped to Mrg11 of the oat consensus map using BLASTn analysis.

    更新日期:2020-01-13
  • Fine mapping of the male fertility restoration gene CaRf032 in Capsicum annuum L.
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-10
    Zhenghai Zhang, Yanshu Zhu, Yacong Cao, Hailong Yu, Ruiqin Bai, Hong Zhao, Baoxi Zhang, Lihao Wang

    Abstract Key message A novel strong candidate gene CA00g82510 for the male fertility restoration locus CaRf032 in Capsicum annuum was identified by genome re-sequencing and recombination analysis. Abstract A single dominant locus (CaRf032) for fertility restoration of cytoplasmic male sterility was identified in the strong restorer inbred line IVF2014032 of chili pepper (Capsicum annuum L.). CaRf032 was localized within an 8.81-Mb candidate intervals on chromosome 6 using bulked segregant analysis based on high-throughput sequencing data. Subsequently, the candidate interval was genetically mapped and defined to a 249.41-kb region using an F2 population of 441 individuals generated by crossing the male-sterile line 77013A and the restorer line IVF2014032. To fine map CaRf032, eight newly developed KASP markers were used to genotype 23 recombinants screened from a larger F2 population of 2877 individuals. The CaRf032 locus was localized to a 148.05-kb region between the KASP markers S1402 and S1354, which was predicted to contain 22 open reading frames (ORFs). One ORF with an incomplete sequence was predicted to contain a PPR motif, and its physical position overlapped with the Rf candidate gene CaPPR6_46. The PPR ORF sequence before the gap showed 100% identity with the CA00g82510 locus of the CM334 reference genome. CA00g82510 encodes a protein of 583 amino acids, containing 14 PPR motifs, and shows significantly differential expression between the flower buds of the maintainer line 77013 and the restorer line IVF2014032. These results indicated that CA00g82510 is a strong candidate gene for CaRf032. Five KASP markers, which detected single-nucleotide polymorphisms in CA00g82510 of 77013 and IVF2014032, co-segregated with CaRf032 and showed 64.4% successful genotyping of 38 maintainer and 63 restorer lines.

    更新日期:2020-01-11
  • Identification and fine mapping of qSB.A09 , a major QTL that controls shoot branching in Brassica rapa ssp . chinensis Makino
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-09
    Pan Li, Tongbing Su, Bin Zhang, Peirong Li, Xiaoyun Xin, Xiaozhen Yue, Yunyun Cao, Weihong Wang, Xiuyun Zhao, Yangjun Yu, Deshuang Zhang, Shuancang Yu, Fenglan Zhang

    QTL mapping plus bulked segregant analysis revealed a major QTL for shoot branching in non-heading Chinese cabbage. The candidate gene was then identified using sequence alignment and expression analysis.

    更新日期:2020-01-11
  • Improvement of nutrient use efficiency in rice: current toolbox and future perspectives
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-09
    Zhihua Zhang, Shaopei Gao, Chengcai Chu

    Modern agriculture relies heavily on chemical fertilizers, especially in terms of cereal production. The excess application of fertilizers not only increases production cost, but also causes severe environmental problems. As one of the major cereal crops, rice (Oryza sativa L.) provides the staple food for nearly half of population worldwide, especially in developing countries. Therefore, improving rice yield is always the priority for rice breeding. Macronutrients, especially nitrogen (N) and phosphorus (P), are two most important players for the grain yield of rice. However, with economic development and improved living standard, improving nutritional quality such as micronutrient contents in grains has become a new goal in order to solve the “hidden hunger.” Micronutrients, such as iron (Fe), zinc (Zn), and selenium (Se), are critical nutritional elements for human health. Therefore, breeding the rice varieties with improved nutrient use efficiency (NUE) is thought to be one of the most feasible ways to increase both grain yield and nutritional quality with limited fertilizer input. In this review, we summarized the progresses in molecular dissection of genes for NUE by reverse genetics on macronutrients (N and P) and micronutrients (Fe, Zn, and Se), exploring natural variations for improving NUE in rice; and also, the current genetic toolbox and future perspectives for improving rice NUE are discussed.

    更新日期:2020-01-09
  • Correction to: Identification and validation of a major and stably expressed QTL for spikelet number per spike in bread wheat.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Jian Ma,Puyang Ding,Jiajun Liu,Ting Li,Yaya Zou,Ahsan Habib,Yang Mu,Huaping Tang,Qiantao Jiang,Yaxi Liu,Guoyue Chen,Jirui Wang,Mei Deng,Pengfei Qi,Wei Li,Zhien Pu,Youliang Zheng,Yuming Wei,Xiujin Lan

    Unfortunately, the author contribution statement was missed out in the original publication. The complete statement is given below.

    更新日期:2020-01-09
  • Correction to: Alternative splicing of a barley gene results in an excess‑tillering and semi‑dwarf mutant
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-04
    Wei Hua, Cong Tan, Jingzhong Xie, Jinghuan Zhu, Yi Shang, Jianming Yang, Xiao-Qi Zhang, Xiaojian Wu, Junmei Wang, Chengdao Li

    In the original publication of this article, the acknowledgement section has been missed to publish. Now the same has been provided in this correction.

    更新日期:2020-01-09
  • Correction to: Genetic characterization and expression analysis of wheat (Triticum aestivum) line 07OR1074 exhibiting very low polyphenol oxidase (PPO) activity.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    S M Hystad,J M Martin,R A Graybosch,M J Giroux

    The above-mentioned article was published in 2015 with an error in the reverse primer sequence for the PPOA2d1074 marker, which made amplification difficult. The reverse primer was missing a thymine nucleotide at the thirteenth position (GCGGTGCTTCACTTGGT).

    更新日期:2020-01-09
  • High-resolution mapping of a major and consensus quantitative trait locus for oil content to a ~ 0.8-Mb region on chromosome A08 in peanut (Arachis hypogaea L.).
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Nian Liu,Jianbin Guo,Xiaojing Zhou,Bei Wu,Li Huang,Huaiyong Luo,Yuning Chen,Weigang Chen,Yong Lei,Yi Huang,Boshou Liao,Huifang Jiang

    KEY MESSAGE: ddRAD-seq-based high-density genetic map comprising 2595 loci identified a major and consensus QTL with a linked marker in a 0.8-Mb physical interval for oil content in peanut. Enhancing oil content is an important breeding objective in peanut. High-resolution mapping of quantitative trait loci (QTLs) with linked markers could facilitate marker-assisted selection in breeding for target traits. In the present study, a recombined inbred line population (Xuhua 13 × Zhonghua 6) was used to construct a genetic map based on double-digest restriction-site-associated DNA sequencing (ddRAD-seq). The resulting high-density genetic map contained 2595 loci, and spanned a length of 2465.62 cM, with an average distance of 0.95 cM/locus. Seven QTLs for oil content were identified on five linkage groups, including the major and stable QTL qOCA08.1 on chromosome A08 with 10.14-27.19% phenotypic variation explained. The physical interval of qOCA08.1 was further delimited to a ~ 0.8-Mb genomic region where two genes affecting oil synthesis had been annotated. The marker SNPOCA08 was developed targeting the SNP loci associated with oil content and validated in peanut cultivars with diverse oil contents. The major and stable QTL identified in the present study could be further dissected for gene discovery. Furthermore, the tightly linked marker for oil content would be useful in marker-assisted breeding in peanut.

    更新日期:2020-01-09
  • Transcriptomics, chromosome engineering and mapping identify a restorer-of-fertility region in the CMS wheat system msH1.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Cristina Rodríguez-Suárez,Paolo Bagnaresi,Luigi Cattivelli,Fernando Pistón,Almudena Castillo,Azahara C Martín,Sergio G Atienza,Carmen Ramírez,Antonio Martín

    An original RNA-seq mapping strategy, validated with chromosome engineering and physical mapping, identifies candidate genes for fertility restoration in the 6HchS chromosome of Hordeum chilense in the wheat msH1 system. Cytoplasmic male sterility (CMS) is a valuable trait for hybrid seed production. The msH1 CMS system in common wheat results from the incompatibility between the nuclear genome of wheat and the cytoplasm of the wild barley Hordeum chilense. This work aims to identify H. chilense candidate genes for fertility restoration in the msH1 system with a multidisciplinary strategy based on chromosome engineering, differential expression analysis and genome mapping. Alloplasmic isogenic wheat lines differing for fertility, associated with the presence of an acrocentric chromosome Hchac resulting from the rearrangement of the short arms of H. chilense chromosomes 1Hch and 6Hch, were used for transcriptome sequencing. Two novel RNA-seq mapping approaches were designed and compared to identify differentially expressed genes of H. chilense associated with male fertility restoration. Minichromosomes (Hchmi), new smaller reorganizations of the Hchac also restoring fertility, were obtained and used to validate the candidate genes. This strategy was successful identifying a putative restorer-of-fertility region on 6HchS, with six candidate genes, including the ortholog of the barley restorer gene Rfm1. Additionally, transcriptomics gave preliminary insights on sterility and restoration networks showing the importance of energy supply, stress, protein metabolism and RNA processing.

    更新日期:2020-01-09
  • Bin-based genome-wide association analyses improve power and resolution in QTL mapping and identify favorable alleles from multiple parents in a four-way MAGIC rice population.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Zhongmin Han,Gang Hu,Hua Liu,Famao Liang,Lin Yang,Hu Zhao,Qinghua Zhang,Zhixin Li,Qifa Zhang,Yongzhong Xing

    A whole genome bin map was developed for a MAGIC population. Association studies for heading date at bin level exhibited powerful QTL mapping and identified favorable alleles. The presumed advantages of multiparent advanced generation intercross (MAGIC) population in quantitative trait locus (QTL) mapping were not fully utilized in the previous studies in which genome-wide association studies (GWAS) were conducted at only single nucleotide polymorphism level. In this study, we genotyped a rice four-way MAGIC population of 247 F7 lines and their parents by sequencing. A total of 5934 bins with an average length of 65 kb were constructed and covered 97% of the genome. The MAGIC population showed low population structure and balanced parental contributions. A bin-based GWAS for heading date identified 4 QTLs in three environments. Three major QTLs were mapped exactly to the bins where the major heading date genes DTH3, Ghd7.1 and Ghd8 were located. Multiple comparisons showed that different parental alleles had varied genetic effects. Like DTH3, the alleles of the Guichao 2/YJSM, IR34 and Cypress had larger, intermediate and no effects, respectively. Based on comparative sequencing of 8 known heading date genes undetected in this MAGIC population, only Ghd7 exhibited diverse function among parents. The failure in Ghd7 mapping was well explained by its interaction with Hd1 because Ghd7 had no effects on heading date when combined with the nonfunctional hd1 carried by all four parents. Overall, bin-based GWAS have more mapping power and higher resolution with a MAGIC population and provide favorable alleles to breeders. The use of more diversified parents is encouraged to develop a MAGIC population for detecting more QTLs for important agronomical traits.

    更新日期:2020-01-09
  • Improving nutritional quality of rice for human health
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-08
    Mingchao Zhao, Yongjun Lin, Hao Chen

    Abstract Key message This review surveys rice nutritional value, mainly focusing on breeding achievements via adoption of both genetic engineering and non-transgenic strategies to improve key nutrients associated with human health. Abstract Rice (Oryza sativa) is an essential component of the diets and livelihoods of over 3.5 billion people. Polished rice is mostly consumed as staple food, fulfilling daily energy demands and part of the protein requirement. Brown rice is comparatively more nutritious, containing more lipids, minerals, vitamins, dietary fiber, micronutrients, and bioactive compounds. In this article, we review the nutritional facts about rice including the level of γ-aminobutyric acid, resistant starch, lysine, iron, zinc, β-carotene, folate, anthocyanin, various carotenoids, and flavonoids, focusing on their synthesis and metabolism and the advances in their biofortification via adoption of both conventional and genetic engineering strategies. We conclude that besides representing a staple food, rice has the potential to become a source of various essential nutrients or bioactive compounds through appropriate genetic improvements to benefit human health and prevent certain chronic diseases. Finally, we discuss the available, non-genetically engineering strategies for the nutritional improvement of rice, including their main strengths and constraints.

    更新日期:2020-01-08
  • Genomic Breeding of Green Super Rice Varieties and Their Deployment in Asia and Africa
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-08
    Sibin Yu, Jauhar Ali, Chaopu Zhang, Zhikang Li, Qifa Zhang

    The “Green Super Rice” (GSR) project aims to fundamentally transform crop production techniques and promote the development of green agriculture based on functional genomics and breeding of GSR varieties by whole-genome breeding platforms.

    更新日期:2020-01-08
  • Genetic analysis of wheat sensitivity to the ToxB fungal effector from Pyrenophora tritici-repentis , the causal agent of tan spot
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-08
    Beatrice Corsi, Lawrence Percival-Alwyn, Rowena C. Downie, Luca Venturini, Elyce M. Iagallo, Camila Campos Mantello, Charlie McCormick-Barnes, Pao Theen See, Richard P. Oliver, Caroline S. Moffat, James Cockram

    Abstract Key message Genetic mapping of sensitivity to the Pyrenophora tritici-repentis effector ToxB allowed development of a diagnostic genetic marker, and investigation of wheat pedigrees allowed transmission of sensitive alleles to be tracked. Abstract Tan spot, caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis, is a major disease of wheat (Triticum aestivum). Secretion of the P. tritici-repentis effector ToxB is thought to play a part in mediating infection, causing chlorosis of plant tissue. Here, genetic analysis using an association mapping panel (n = 480) and a multiparent advanced generation intercross (MAGIC) population (n founders = 8, n progeny = 643) genotyped with a 90,000 feature single nucleotide polymorphism (SNP) array found ToxB sensitivity to be highly heritable (h2 ≥ 0.9), controlled predominantly by the Tsc2 locus on chromosome 2B. Genetic mapping of Tsc2 delineated a 1921-kb interval containing 104 genes in the reference genome of ToxB-insensitive variety ‘Chinese Spring’. This allowed development of a co-dominant genetic marker for Tsc2 allelic state, diagnostic for ToxB sensitivity in the association mapping panel. Phenotypic and genotypic analysis in a panel of wheat varieties post-dated the association mapping panel further supported the diagnostic nature of the marker. Combining ToxB phenotype and genotypic data with wheat pedigree datasets allowed historic sources of ToxB sensitivity to be tracked, finding the variety ‘Maris Dove’ to likely be the historic source of sensitive Tsc2 alleles in the wheat germplasm surveyed. Exploration of the Tsc2 region gene space in the ToxB-sensitive line ‘Synthetic W7984’ identified candidate genes for future investigation. Additionally, a minor ToxB sensitivity QTL was identified on chromosome 2A. The resources presented here will be of immediate use for marker-assisted selection for ToxB insensitivity and the development of germplasm with additional genetic recombination within the Tsc2 region.

    更新日期:2020-01-08
  • Multi-environment analysis of sorghum breeding trials using additive and dominance genomic relationships
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-06
    Colleen H. Hunt, Ben J. Hayes, Fred A. van Eeuwijk, Emma S. Mace, David R. Jordan

    Abstract Key message Multi-environment models using marker-based kinship information for both additive and dominance effects can accurately predict hybrid performance in different environments. Abstract Sorghum is an important hybrid crop that is grown extensively in many subtropical and tropical regions including Northern NSW and Queensland in Australia. The highly varying weather patterns in the Australian summer months mean that sorghum hybrids exhibit a great deal of variation in yield between locations. To ultimately enable prediction of the outcome of crossing parental lines, both additive effects on yield performance and dominance interaction effects need to be characterised. This paper demonstrates that fitting a linear mixed model that includes both types of effects calculated using genetic markers in relationship matrices improves predictions. Genotype by environment interactions was investigated by comparing FA1 (single-factor analytic) and FA2 (two-factor analytic) structures. The G×E causes a change in hybrid rankings between trials with a difference of up to 25% of the hybrids in the top 10% of each trial. The prediction accuracies increased with the addition of the dominance term (over and above that achieved with an additive effect alone) by an average of 15% and a maximum of 60%. The percentage of dominance of the total genetic variance varied between trials with the trials with higher broad-sense heritability having the greater percentage of dominance. The inclusion of dominance in the factor analytic models improves the accuracy of the additive effects. Breeders selecting high yielding parents for crossing need to be aware of effects due to environment and dominance.

    更新日期:2020-01-06
  • SNP markers for early identification of high molecular weight glutenin subunits (HMW-GSs) in bread wheat
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-06
    Catherine Ravel, Annie Faye, Sarah Ben-Sadoun, Marion Ranoux, Mireille Dardevet, Cécile Dupuits, Florence Exbrayat, Charles Poncet, Pierre Sourdille, Gérard Branlard

    Key message A set of eight SNP markers was developed to facilitate the early selection of HMW-GS alleles in breeding programmes. Abstract In bread wheat (Triticum aestivum), the high molecular weight glutenin subunits (HMW-GSs) are the most important determinants of technological quality. Known to be very diverse, HMW-GSs are encoded by the tightly linked genes Glu-1-1 and Glu-1-2. Alleles that improve the quality of dough have been identified. Up to now, sodium dodecyl sulphate–polyacrylamide gel electrophoresis (SDS-PAGE) of grain proteins is the most widely used for their identification. To facilitate the early selection of HMW-GS alleles in breeding programmes, we developed DNA-based molecular markers. For each accession of a core collection (n = 364 lines) representative of worldwide bread wheat diversity, HMW-GSs were characterized by both genotyping and SDS-PAGE. Based on electrophoresis, we observed at least 8, 22 and 9 different alleles at the Glu-A1, Glu-B1 and Glu-D1 loci, respectively, including new variants. We designed a set of 17 single-nucleotide polymorphism (SNP) markers that were representative of the most frequent SDS-PAGE alleles at each locus. At Glu-A1 and Glu-D1, two and three marker-based haplotypes, respectively, captured the diversity of the SDS-PAGE alleles rather well. Discrepancies were found mainly for the Glu-B1 locus. However, statistical tests revealed that two markers at each Glu-B1 gene and their corresponding haplotypes were more significantly associated with the rheological properties of the dough than were the relevant SDS-PAGE alleles. To conclude, this study demonstrates that the SNP markers developed provide additional information on HMW-GS diversity. Two markers at Glu-A1, four at Glu-B1 and two at Glu-D1 constitute a useful toolbox for breeding wheat to improve end-use value.

    更新日期:2020-01-06
  • Germplasms, genetics and genomics for better control of disastrous wheat Fusarium head blight
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-03
    Zhengqiang Ma, Quan Xie, Guoqiang Li, Haiyan Jia, Jiyang Zhou, Zhongxin Kong, Na Li, Yang Yuan

    Fusarium head blight (FHB), or scab, for its devastating nature to wheat production and food security, has stimulated worldwide attention. Multidisciplinary efforts have been made to fight against FHB for a long time, but the great progress has been achieved only in the genomics era of the past 20 years, particularly in the areas of resistance gene/QTL discovery, resistance mechanism elucidation and molecular breeding for better resistance. This review includes the following nine main sections, (1) FHB incidence, epidemic and impact, (2) causal Fusarium species, distribution and virulence, (3) types of host resistance to FHB, (4) germplasm exploitation for FHB resistance, (5) genetic control of FHB resistance, (6) fine mapping of Fhb1, Fhb2, Fhb4 and Fhb5, (7) cloning of Fhb1, (8) omics-based gene discovery and resistance mechanism study and (9) breeding for better FHB resistance. The advancements that have been made are outstanding and exciting; however, judged by the complicated nature of resistance to hemi-biotrophic pathogens like Fusarium species and lack of immune germplasm, it is still a long way to go to overcome FHB.

    更新日期:2020-01-04
  • Identification of quantitative trait loci for net form net blotch resistance in contemporary barley breeding germplasm from the USA using genome-wide association mapping
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-03
    Anil Adhikari, Brian J. Steffenson, Kevin P. Smith, Madeleine Smith, Ruth Dill-Macky

    Abstract Key message Association mapping study conducted in a population of 3490 elite barley breeding lines from ten barley breeding programs of the USA identified 12 QTLs for resistance/susceptibility to net form of net blotch. Abstract Breeding resistant varieties is the best management strategy for net form of net blotch (NFNB) in barley (Hordeum vulgare L.) caused by Pyrenophora teres f. teres (Ptt). Several resistance QTL have been previously identified in barley via linkage mapping and genome-wide association studies (GWAS). A GWAS conducted in a collection of advanced breeding lines (n = 3490) representing elite germplasm from ten barley breeding programs of the USA identified 42 unique marker-trait associations (MTA) for NFNB resistance. The lines were genotyped with 3072 SNP markers and phenotyped with four Ptt isolates in controlled environment. The lines were used to construct 13 different GWAS panels. Efficient mixed model association method with principal components and kinship was used for GWAS. Significance threshold for MTA was set at a false discovery rate of 0.05. Two, eight, six, one and 25 MTA were identified in chromosomes 1H, 3H, 4H, 5H and 6H, respectively. Based on genetic positions and linkage disequilibrium, these MTA’s correspond to two, three, two, one and four QTLs in chromosome 1H, 3H, 4H, 5H and 6H, respectively. A comparison with previous linkage and GWAS studies revealed several previously identified and novel QTLs. Moreover, different genomic regions were found to be responsible for NFNB resistance in two-row versus six-row germplasm. The germplasm-specific SNP markers with additive effects and allelic distribution is reported to facilitate breeders in selection of markers for MAS to introgress novel net blotch resistance.

    更新日期:2020-01-04
  • Understanding epigenomics based on the rice model
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-02
    Yue Lu, Dao-Xiu Zhou, Yu Zhao

    Abstract Key message The purpose of this paper provides a comprehensive overview of the recent researches on rice epigenomics, including DNA methylation, histone modifications, noncoding RNAs, and three-dimensional genomics. The challenges and perspectives for future research in rice are discussed. Abstract Rice as a model plant for epigenomic studies has much progressed current understanding of epigenetics in plants. Recent results on rice epigenome profiling and three-dimensional chromatin structure studies reveal specific features and implication in gene regulation during rice plant development and adaptation to environmental changes. Results on rice chromatin regulator functions shed light on mechanisms of establishment, recognition, and resetting of epigenomic information in plants. Cloning of several rice epialleles associated with important agronomic traits highlights importance of epigenomic variation in rice plant growth, fitness, and yield. In this review, we summarize and analyze recent advances in rice epigenomics and discuss challenges and directions for future research in the field.

    更新日期:2020-01-04
  • The regulation of zein biosynthesis in maize endosperm
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-02
    Chaobin Li, Rentao Song

    We review the current knowledge regarding the regulation of zein storage proteins biosynthesis and protein body formation, which are crucial processes for the successful accumulation of nutrients in maize kernels.

    更新日期:2020-01-04
  • Appraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-02
    Awais Rasheed, Shigeo Takumi, Muhammad Adeel Hassan, Muhammad Imtiaz, Mohsin Ali, Alex I. Morgunov, Tariq Mahmood, Zhonghu He

    We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries.

    更新日期:2020-01-04
  • Aegilops umbellulata introgression carrying leaf rust and stripe rust resistance genes Lr76 and Yr70 located to 9.47-Mb region on 5DS telomeric end through a combination of chromosome sorting and sequencing
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-02
    Mitaly Bansal, Nikolai M. Adamski, Puneet Inder Toor, Satinder Kaur, István Molnár, Kateřina Holušová, Jan Vrána, Jaroslav Doležel, Miroslav Valárik, Cristobal Uauy, Parveen Chhuneja

    Lr76 and Yr70 have been fine mapped using the sequence of flow-sorted recombinant 5D chromosome from wheat-Ae. umbellulata introgression line. The alien introgression has been delineated to 9.47-Mb region on short arm of wheat chromosome 5D.

    更新日期:2020-01-04
  • Identification of heterotic groups in South-Asian-bred hybrid parents of pearl millet
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-02
    S. K. Gupta, K. Sudarshan Patil, Abhishek Rathore, Dev Vart Yadav, L. D. Sharma, K. D. Mungra, H. T. Patil, Suresh K. Gupta, Ramesh Kumar, Vaibhav Chaudhary, Roma R. Das, Anil Kumar, Vikas Singh, Rakesh K. Srivastava, Rajeev Gupta, M. Boratkar, Rajeev K. Varshney, K. N. Rai, O. P. Yadav

    Pearl millet breeding programs can use this heterotic group information on seed and restorer parents to generate new series of pearl millet hybrids having higher yields than the existing hybrids.

    更新日期:2020-01-04
  • QTL mapping for yield-related traits in wheat based on four RIL populations
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2020-01-02
    Junmei Hu, Xiaoqian Wang, Guangxu Zhang, Peng Jiang, Wuying Chen, Yongchao Hao, Xin Ma, Shoushen Xu, Jizeng Jia, Lingrang Kong, Hongwei Wang

    Abstract Key message Eight environmentally stable QTL for grain yield-related traits were detected by four RIL populations, and two of them were validated by a natural wheat population containing 580 diverse varieties or lines. Abstract Yield and yield-related traits are important factors in wheat breeding. In this study, four RIL populations derived from the cross of one common parent Yanzhan 1 (a Chinese domesticated cultivar) and four donor parents including Hussar (a British domesticated cultivar) and three semi-wild wheat varieties in China were phenotyped for 11 yield-related traits in eight environments. An integrated genetic map containing 2009 single-nucleotide polymorphism (SNP) markers generated from a 90 K SNP array was constructed to conduct quantitative trait loci (QTL) analysis. A total of 161 QTL were identified, including ten QTL for grain yield per plant (GYP) and yield components, 49 QTL for spike-related traits, 43 QTL for flag leaf-related traits, 22 QTL for plant height (PH), and 37 QTL for heading date and flowering date. Eight environmentally stable QTL were validated in individual RIL population where the target QTL was notably detected, and six of them had a significant effect on GYP. Furthermore, Two QTL, QSPS-2A.4 and QSL-4A.1, were also validated in a natural wheat population containing 580 diverse varieties or lines, which provided valuable resources for further fine mapping and genetic improvement in yield in wheat.

    更新日期:2020-01-04
  • Structural genome analysis in cultivated potato taxa
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-31
    Maria Kyriakidou, Sai Reddy Achakkagari, José Héctor Gálvez López, Xinyi Zhu, Chen Yu Tang, Helen H. Tai, Noelle L. Anglin, David Ellis, Martina V. Strömvik

    Abstract Key message Twelve potato accessions were selected to represent two principal views on potato taxonomy. The genomes were sequenced and analyzed for structural variation (copy number variation) against three published potato genomes. Abstract The common potato (Solanum tuberosum L.) is an important staple crop with a highly heterozygous and complex tetraploid genome. The other taxa of cultivated potato contain varying ploidy levels (2X–5X), and structural variations are common in the genomes of these species, likely contributing to the diversification or agronomic traits during domestication. Increased understanding of the genomes and genomic variation will aid in the exploration of novel agronomic traits. Thus, sequencing data from twelve potato landraces, representing the four ploidy levels, were used to identify structural genomic variation compared to the two currently available reference genomes, a double monoploid potato genome and a diploid inbred clone of S. chacoense. The results of a copy number variation analysis showed that in the majority of the genomes, while the number of deletions is greater than the number of duplications, the number of duplicated genes is greater than the number of deleted ones. Specific regions in the twelve potato genomes have a high density of CNV events. Further, the auxin-induced SAUR genes (involved in abiotic stress), disease resistance genes and the 2-oxoglutarate/Fe(II)-dependent oxygenase superfamily proteins, among others, had increased copy numbers in these sequenced genomes relative to the references.

    更新日期:2020-01-04
  • Identification of a major dominant gene for race-nonspecific tan spot resistance in wild emmer wheat
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-20
    Justin D. Faris, Megan E. Overlander, Gayan K. Kariyawasam, Arron Carter, Steven S. Xu, Zhaohui Liu

    A single dominant gene found in tetraploid and hexaploid wheat controls broad-spectrum race-nonspecific resistance to the foliar disease tan spot caused by Pyrenophora tritici-repentis.

    更新日期:2020-01-04
  • Phenotypic, genetic, and molecular function of msc - 2 , a genic male sterile mutant in pepper ( Capsicum annuum L.)
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-20
    Qing Cheng, Ting Li, Yixin Ai, Qiaohua Lu, Yihao Wang, Lang Wu, Jinqiu Liu, Liang Sun, Huolin Shen

    Bulked segregant analysis and fine mapping delimited the pepper genic male sterile (msc-2) locus into a 336 kb region on chromosome 5. A strong candidate gene, Capana05g000766, a homolog of AtMS1, was indentified in this region.

    更新日期:2020-01-04
  • Fine mapping of restorer - of - fertility gene based on high-density genetic mapping and collinearity analysis in pepper ( Capsicum annuum L.)
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-20
    Jiaowen Cheng, Yijian Chen, Yafei Hu, Ziyan Zhou, Fang Hu, Jichi Dong, Weili Chen, Junjie Cui, Zhiming Wu, Kailin Hu

    Abstract Key message The pepper restorer-of-fertility (CaRf) gene was fine mapped based on conjoint analysis of recombinants and collinearity between the two pepper reference genomes. Capana06g003028, encoding an Rf-like PPR protein, was proposed as the strongest candidate for pepper CaRf based on sequence comparison and expression analysis. Abstract The cytoplasmic male sterility (CMS)/restorer-of-fertility (Rf) system not only provides an excellent model to dissect genetic interactions between the mitochondria and nucleus but also plays a vital role in high-efficiency hybrid seed production in crops including pepper (Capsicum spp.). Although two important CMS candidate genes, orf507 and Ψatp6-2, have previously been suggested, the pepper Rf gene (CaRf) has not yet been isolated. In this study, a high-density genetic map comprising 7566 SNP markers in 1944 bins was first constructed with the array genotyping results from 317 F2 individuals. Based on this map, the CaRf gene was preliminarily mapped to a region of 1.15 Mb in length at the end of chromosome P6. Then, by means of a conjoint analysis of recombinants and collinearity between the two pepper reference genomes, an important candidate interval with 270.10 kb in length was delimited for CaRf. Finally, Capana06g003028, which encodes an Rf-like PPR protein, was proposed as the strongest candidate for CaRf based on sequence analysis and expression characteristics in sterile and fertile plants. The high-density genetic map and fine mapping results provided here lay a foundation for the application of molecular breeding, as well as cloning and functional analysis of CaRf, in pepper.

    更新日期:2020-01-04
  • Dmc1 is a candidate for temperature tolerance during wheat meiosis
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-18
    Tracie Draeger, Azahara C. Martin, Abdul Kader Alabdullah, Ali Pendle, María-Dolores Rey, Peter Shaw, Graham Moore

    The meiotic recombination gene Dmc1 on wheat chromosome 5D has been identified as a candidate for the maintenance of normal chromosome synapsis and crossover at low and possibly high temperatures.

    更新日期:2020-01-04
  • QTL mapping for grain yield-related traits in bread wheat via SNP-based selective genotyping
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-16
    Li Yang, Dehui Zhao, Zili Meng, Kaijie Xu, Jun Yan, Xianchun Xia, Shuanghe Cao, Yubing Tian, Zhonghu He, Yong Zhang

    We identified four chromosome regions harboring QTL for grain yield-related traits, and breeder-friendly KASP markers were developed and validated for marker-assisted selection.

    更新日期:2020-01-04
  • Genotyping-by-sequencing and multilocation evaluation of two interspecific backcross populations identify QTLs for yield-related traits in pigeonpea
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-16
    Rachit K. Saxena, Sandip Kale, Reyazul Rouf Mir, Nalini Mallikarjuna, Pooja Yadav, Roma Rani Das, Johiruddin Molla, Muniswamy Sonnappa, Anuradha Ghanta, Yamini Narasimhan, Abhishek Rathore, C. V. Sameer Kumar, Rajeev K. Varshney

    This study has identified single-nucleotide polymorphism (SNP) markers associated with nine yield-related traits in pigeonpea by using two backcross populations (BP) developed through interspecific crosses and evaluating them at two locations and 3 years. In both the populations, markers have shown strong segregation distortion; therefore, a quantitative trait locus (QTL) mapping mixed model was used. A total of 86 QTLs explaining 12–21% phenotypic variation were detected in BP-1. On the other hand, 107 QTLs explaining 11–29% phenotypic variation were detected in BP-2. Although most QTLs were environment and trait specific, few stable and consistent QTLs were also detected. Interestingly, 11 QTLs in BP-2 were associated with more than one trait. Among these QTLs, eight QTLs associated with days to 50% flowering and days to 75% maturity were located on CcLG07. One SNP “S7_14185076” marker in BP-2 population has been found associated with four traits, namely days to 50% flowering, days to 75% maturity, primary branches per plant and secondary branches per plant with positive additive effect. Hence, the present study has not only identified QTLs for yield-related traits, but also discovered novel alleles from wild species, which can be used for improvement of traits through genomics-assisted breeding.

    更新日期:2020-01-04
  • Identification and fine mapping of a major locus controlling branching in Brassica napus
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-16
    Bao Li, Jinxiang Gao, Jiao Chen, Zhixin Wang, Wenhao Shen, Bin Yi, Jing Wen, Chaozhi Ma, Jinxiong Shen, Tingdong Fu, Jinxing Tu

    A candidate branching-controlling gene for qDBA09 was identified after delimiting a Brassica napus recessive locus within a 270-kb interval on chromosome A09.

    更新日期:2020-01-04
  • Yield reduction historically associated with the Aegilops ventricosa 7D V introgression is genetically and physically distinct from the eyespot resistance gene Pch1
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-13
    Marianna Pasquariello, Simon Berry, Christopher Burt, Cristobal Uauy, Paul Nicholson

    Abstract Key message Yield penalty and increased grain protein content traits associated with Aegilops ventricosa 7D introgression have been mapped for the first time, and they are physically distinct from the eyespot resistance locus Pch1. Abstract Wheat wild relatives represent an important source of genetic variation, but introgression of agronomically relevant genes, such as for disease resistance, may lead to the simultaneous introduction of genetically linked deleterious traits. Pch1 is a dominant gene, conferring resistance to eyespot and was introgressed to wheat from Aegilops ventricosa as part of a large segment of the 7DV chromosome. This introgression has been associated with a significant yield reduction and a concomitant increase in grain protein content. In this study, we evaluated both traits and their relationship to the location of the Pch1 gene. We found that both QTLs were clearly distinct from the Pch1 gene, being located on a different linkage group to Pch1. In addition, we found that the QTL for increased grain protein content was strong and consistent across field trials, whereas the yield penalty QTL was unstable and environmentally dependent. The yield and grain protein content QTLs were genetically linked and located in the same linkage group. This finding is due in part to the small size of the population, and to the restricted recombination between wheat 7D and Ae. ventricosa 7Dv chromosomes. Although recombination in this interval is rare, it does occur. A recombinant line containing Pch1 and 7D_KASP6, the marker associated with increase in grain protein content, but not Xwmc221, the marker associated with the yield penalty effect, was identified.

    更新日期:2020-01-04
  • Fine mapping and candidate gene analysis of a seed glucosinolate content QTL, qGSL - C2 , in rapeseed ( Brassica napus L.)
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-12
    Ying Liu, Xianming Zhou, Min Yan, Pengfei Wang, Hao Wang, Qiang Xin, Liyong Yang, Dengfeng Hong, Guangsheng Yang

    QTL mapping and candidate gene analysis indicate that allelic variations in BnaC2.MYB28 resulted from homeologous exchange and determine difference in seed glucosinolate content.

    更新日期:2020-01-04
  • QTL mapping of resistance to Fusarium oxysporum f. sp. niveum race 2 and Papaya ringspot virus in Citrullus amarus
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-10
    Sandra E. Branham, W. Patrick Wechter, Kai-Shu Ling, Bidisha Chanda, Laura Massey, Guangwei Zhao, Nihat Guner, Marco Bello, Eileen Kabelka, Zhangjun Fei, Amnon Levi

    Abstract Key message A Citrullus amarus mapping population segregating for resistance to Fusarium oxysporum f. sp. niveum race 2 and Papaya ringspot virus was used to identify novel QTL, important for the improvement in watermelon disease resistance. Abstract Multiple disease screens of the USDA Citrullus spp. germplasm collection have highlighted the value of Citrullus amarus (citron melon or wild watermelon) as a resource for enhancing modern watermelon cultivars (Citrullus lanatus) with resistance to a broad range of fungal, bacterial and viral diseases of watermelon. We have generated a genetic population of C. amarus segregating for resistance to two important watermelon diseases: Fusarium wilt (caused by the fungus Fusarium oxysporum f. sp. niveum; Fon race 2) and Papaya ringspot virus-watermelon strain (PRSV-W). QTL mapping of Fon race 2 resistance identified seven significant QTLs, with the major QTL representing a novel genetic source of resistance and an opportunity for gene pyramiding. A single QTL was associated with resistance to PRSV-W, which adhered to expectations of a prior study indicating a single-gene recessive inheritance in watermelon. The resistance loci identified here provide valuable genetic resources for introgression into cultivated watermelon for the improvement in disease resistance.

    更新日期:2020-01-04
  • Genome-wide association analyses reveal the genetic basis of biomass accumulation under symbiotic nitrogen fixation in African soybean
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-12-10
    Davoud Torkamaneh, François-P. Chalifour, Chantal J. Beauchamp, Hesham Agrama, Steve Boahen, Halim Maaroufi, Istvan Rajcan, François Belzile

    Abstract Key message We explored the genetic basis of SNF-related traits through GWAS and identified 40 candidate genes. This study provides fundamental insights into SNF-related traits and will accelerate efforts for SNF breeding. Abstract Symbiotic nitrogen fixation (SNF) increases sustainability by supplying biological nitrogen for crops to enhance yields without damaging the ecosystem. A better understanding of this complex biological process is critical for addressing the triple challenges of food security, environmental degradation, and climate change. Soybean plants, the most important legume worldwide, can form a mutualistic interaction with specialized soil bacteria, bradyrhizobia, to fix atmospheric nitrogen. Here we report a comprehensive genome-wide association study of 11 SNF-related traits using 79K GBS-derived SNPs in 297 African soybeans. We identified 25 QTL regions encompassing 40 putative candidate genes for SNF-related traits including 20 genes with no prior known role in SNF. A line with a large deletion (164 kb), encompassing a QTL region containing a strong candidate gene (CASTOR), exhibited a marked decrease in SNF. This study performed on African soybean lines provides fundamental insights into SNF-related traits and yielded a rich catalog of candidate genes for SNF-related traits that might accelerate future efforts aimed at sustainable agriculture.

    更新日期:2020-01-04
  • Dynamic patterns of circular and linear RNAs in maize hybrid and parental lines.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Zi Luo,Jia Qian,Sijia Chen,Lin Li

    Hybrid vigor, also known as heterosis, has been widely utilized in agronomic production of maize (Zea mays L.) and other crops. However, the molecular mechanisms underlying heterosis are still not fully understood. To provide a more complete understanding of the transcriptomic dynamics associated with heterosis, we collected a comprehensive set of sequence data on linear mRNA transcripts and circular RNAs (circRNAs) from seedling leaves of two widely used maize inbred lines and their F1 hybrid at the V4 growth stage. We detected over 25,000 expressed genes with more than 1200 circRNAs that showed dramatic and distinct variations in expression level across the three genotypes. Although most linear and circular transcripts exhibited additive expression in the hybrid, the expression of circRNAs was more likely to be nonadditive. Interestingly, the levels of linear transcripts and their corresponding circRNAs from the same loci showed a significant relationship and coordinated expression mode across all three genotypes. Notably, in the hybrid, allele-specific expression of linear transcripts was significantly associated with the expression of circRNAs from the same locus, suggesting potential regulatory cross talk between linear and circular transcripts. Our study provides a deeper understanding of dynamic variations for both the linear and circular transcriptome in a classical hybrid triplet of maize.

    更新日期:2019-11-01
  • Predicted genetic gains from introgressing chromosome segments from exotic germplasm into an elite soybean cultivar.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Sushan Ru,Rex Bernardo

    To improve an elite soybean line, introgress longer chromosome segments instead of QTL alleles from exotic germplasm. Broadening the diversity of cultivated soybean [Glycine max (L.) Merrill] through introgression of exotic germplasm has been difficult. Our objectives were to (1) determine if introgressing specific chromosome segments (instead of quantitative trait locus alleles) from exotic soybean germplasm has potential for improving an elite cultivar, and (2) identify strategies to introgress and pyramid exotic chromosome segments into an elite cultivar. We estimated genomewide marker effects for yield and other traits in seven crosses between the elite line IA3023 and seven soybean plant introductions (PIs). We then predicted genetic gains from having ≤ 2 targeted recombinations per linkage group. When introgression was modeled for yield while controlling maturity in the seven PI × IA3023 populations, the predicted yield was 8-25% over the yield of IA3023. Correlated changes in maturity, seed traits, lodging, and plant height were generally small but were in the favorable direction. In contrast, selecting the best recombinant inbred (without targeted recombination) in each of the PI × IA3023 populations led to negative or minimal yield gains over IA3023. In one PI × IA3023 population, introgressing and pyramiding only two linkage groups from recombinant inbreds into IA3023 was predicted to achieve an 8% yield gain over IA3023 without sacrificing the performance for other traits. The probability of inheriting intact chromosomes was high enough to allow introgression and pyramiding of chromosome segments in 5-6 generations. Overall, our study suggested that introgressing specific chromosome segments is an effective way to introduce exotic soybean germplasm into an elite cultivar.

    更新日期:2019-11-01
  • Gb8, a new gene conferring resistance to economically important greenbug biotypes in wheat.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Xiangyang Xu,Genqiao Li,Brett F Carver,J Scott Armstrong

    A new greenbug resistance gene Gb8 conferring broad resistance to US greenbug biotypes was identified in hard red winter wheat line PI 595379-1 and was mapped to the terminal region of chromosome 7DL. Greenbug [Schizaphis graminum (Rondani)] is a worldwide insect pest that poses a serious threat to wheat production. New greenbug resistance genes that can be readily used in wheat breeding are urgently needed. The objective of this study was to characterize a greenbug resistance gene in PI 595379-1, a single plant selection from PI 595379. Genetic analysis of response to greenbug biotype E in an F2:3 population derived from a cross between PI 595379-1 and PI 243735 indicated that a single gene, designated Gb8, conditioned resistance. Linkage analysis placed Gb8 in a 2.7-Mb interval in the terminal bin of chromosome 7DL (7DL3-082-1.0), spanning 595.6 to 598.3 Mb in the Chinese Spring IWGSC RefSeq version 1.0 reference sequence. Gb8 co-segregated with a newly developed SSR marker Xstars508, positioned at 596.4 Mb in the reference sequence. Allelism tests showed that Gb8 was different from three permanently named genes on the same chromosome arm and the estimated genetic distance between Gb8 and Gb3 was 15.35 ± 1.35 cM. Gb8 can be directly used in wheat breeding to enhance greenbug resistance.

    更新日期:2019-11-01
  • Molecular mapping of major QTL conferring resistance to orange wheat blossom midge (Sitodiplosis mosellana) in Chinese wheat varieties with selective populations.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Lijing Zhang,Miaomiao Geng,Zhe Zhang,Yue Zhang,Guijun Yan,Shumin Wen,Guiru Liu,Ruihui Wang

    Two novel midge resistance QTL were mapped to a 4.9-Mb interval on chromosome arm 4AL based on the genetic maps constructed with SNP markers. Orange wheat blossom midge (OWBM) is a devastating insect pest affecting wheat production. In order to detect OWBM resistance genes and quantitative trait loci (QTL) for wheat breeding, two recombinant inbred line (RIL) populations were established and used for molecular mapping. A total of seven QTL were detected on chromosomes 2D, 4A, 4D and 7D, respectively, of which positive alleles were all from the resistant parents except for the QTL on 7D. Two stable QTL (QSm.hbau-4A.2-1 and QSm.hbau-4A.2-2) were detected in both populations with the LOD scores ranging from 5.58 to 29.22 under all three environments, and they explained a combined phenotypic variation of 24.4-44.8%. These two novel QTL were mapped to a 4.9-Mb physical interval. The single-nucleotide polymorphism (SNP) markers AX-109543456, AX-108942696 and AX-110928325 were closely linked to the QTL and could be used for marker-assisted selection (MAS) for OWBM resistance in wheat breeding programs.

    更新日期:2019-11-01
  • Genetic architecture of fruit size and shape variation in cucurbits: a comparative perspective.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Yupeng Pan,Yuhui Wang,Cecilia McGregor,Shi Liu,Feishi Luan,Meiling Gao,Yiqun Weng

    The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes CsSUN25-26-27a and CsTRM5 in cucumber, CmOFP1a in melon, and ClSUN25-26-27a in watermelon. In cucurbits, the andromonoecy (for 1-aminocyclopropane-1-carboxylate synthase) and the carpel number (for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.

    更新日期:2019-11-01
  • A genome-wide association study uncovers consistent quantitative trait loci for resistance to Verticillium wilt and Fusarium wilt race 4 in the US Upland cotton.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Abdelraheem Abdelraheem,Hanan Elassbli,Yi Zhu,Vasu Kuraparthy,Lori Hinze,David Stelly,Tom Wedegaertner,Jinfa Zhang

    A high-resolution GWAS detected consistent QTL for resistance to Verticillium wilt and Fusarium wilt race 4 in 376 U.S. Upland cotton accessions based on six independent replicated greenhouse tests. Verticillium wilt (VW, caused by Verticillium dahliae Kleb.) and Fusarium wilt (FOV, caused by Fusarium oxysporum f.sp. vasinfectum Atk. Sny & Hans) are the most important soil-borne fungal diseases in cotton. To augment and refine resistance quantitative trait loci (QTL), we conducted a genome-wide association study (GWAS) using high-density genotyping with the CottonSNP63K array. Resistance of 376 US Upland cotton accessions to a defoliating VW and virulent FOV4 was evaluated in four and two independent replicated greenhouse tests, respectively. A total of 15 and 13 QTL for VW and FOV4 resistances were anchored by 30 (on five chromosomes) and 56 (on six chromosomes) significant single nucleotide polymorphic (SNPs) markers, respectively. QTL on c8, c10, c16, and c21 were consistent in two or more tests for VW resistance, while two QTL on c8 and c14 were consistent for FOV4 resistance in two tests. Two QTL clusters on c16 and c19 were observed for both VW and FOV4 resistance, suggesting that these genomic regions may harbor genes in response to both diseases. Using BLAST search against the sequenced TM-1 genome, 30 and 35 candidate genes were identified on four QTL for VW resistance and on three QTL for FOV4 resistance, respectively. These genomic regions were rich in NBS-LRR genes presented in clusters. The results create opportunities for further studies to determine the correlations of field resistance with these QTL, molecular examinations of VW and FOV4 resistances, marker-assisted selection (MAS) and eventual cloning of QTL for disease resistance in cotton.

    更新日期:2019-11-01
  • Correction to: Recombination between homoeologous chromosomes induced in durum wheat by the Aegilops speltoides Su1-Ph1 suppressor.
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-10-04
    Hao Li,Le Wang,Ming-Cheng Luo,Fang Nie,Yun Zhou,Patrick E McGuire,Assaf Distelfeld,Xiongtao Dai,Chun-Peng Song,Jan Dvorak

    Unfortunately, the 9th author name was incorrectly published in the original publication. The complete correct name is given below.

    更新日期:2019-11-01
  • Correction to: Dissection of two quantitative trait loci with pleiotropic effects on plant height and spike length linked in coupling phase on the short arm of chromosome 2D of common wheat (Triticum aestivum L.).
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-09-26
    Lingling Chai,Zhaoyan Chen,Ruolin Bian,Huijie Zhai,Xuejiao Cheng,Huiru Peng,Yingyin Yao,Zhaorong Hu,Mingming Xin,Weilong Guo,Qixin Sun,Aiju Zhao,Zhongfu Ni

    Theoretical and Applied Genetics.

    更新日期:2019-11-01
  • Novel strategies for genomic prediction of untested single-cross maize hybrids using unbalanced historical data.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    K O G Dias,H P Piepho,L J M Guimarães,P E O Guimarães,S N Parentoni,M O Pinto,R W Noda,J V Magalhães,C T Guimarães,A A F Garcia,M M Pastina

    Weighted outperformed unweighted genomic prediction using an unbalanced dataset representative of a commercial breeding program. Moreover, the use of the two cycles preceding predictions as training set achieved optimal prediction ability. Predicting the performance of untested single-cross hybrids through genomic prediction (GP) is highly desirable to increase genetic gain. Here, we evaluate the predictive ability (PA) of novel genomic strategies to predict single-cross maize hybrids using an unbalanced historical dataset of a tropical breeding program. Field data comprised 949 single-cross hybrids evaluated from 2006 to 2013, representing eight breeding cycles. Hybrid genotypes were inferred based on their parents' genotypes (inbred lines) using single-nucleotide polymorphism markers obtained via genotyping-by-sequencing. GP analyses were fitted using genomic best linear unbiased prediction via a stage-wise approach, considering two distinct cross-validation schemes. Results highlight the importance of taking into account the uncertainty regarding the adjusted means at each step of a stage-wise analysis, due to the highly unbalanced data structure and the expected heterogeneity of variances across years and locations of a commercial breeding program. Further, an increase in the size of the training set was not always advantageous even in the same breeding program. The use of the two cycles preceding predictions achieved optimal PA of untested single-cross hybrids in a forward prediction scenario, which could be used to replace the first step of field screening. Finally, in addition to the practical and theoretical results applied to maize hybrid breeding programs, the stage-wise analysis performed in this study may be applied to any crop historical unbalanced data.

    更新日期:2019-11-01
  • Correction to: Genome-wide SNP discovery for development of high-density genetic map and QTL mapping of ascochyta blight resistance in chickpea (Cicer arietinum L.).
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-04-28
    Amit Deokar,Mandeep Sagi,Bunyamin Tar'an

    Unfortunately there was an error in the name of the gene "Ca-AKL18" in the discussion section.

    更新日期:2019-11-01
  • Recent progress on the molecular breeding of Cucumis sativus L. in China.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Shengjun Feng,Juping Zhang,Zihan Mu,Yuji Wang,Changlong Wen,Tao Wu,Chao Yu,Zheng Li,Huasen Wang

    Molecular breeding of Cucumis sativus L. is based on traditional breeding techniques and modern biological breeding in China. There are opportunities for further breeding improvement by molecular design breeding and the automation of phenotyping technology using untapped sources of genetic diversity. Cucumber (Cucumis sativus L.) is an important vegetable cultivated worldwide. It bears fruits of light fragrance, and crisp texture with high nutrition. China is the largest producer and consumer of cucumber, accounting for 70% of the world's total production. With increasing consumption demand, the production of Cucurbitaceae crops has been increasing yearly. Thus, new cultivars that can produce high-quality cucumber with high yield and easy cultivation are in need. Conventional genetic breeding has played an essential role in cucumber cultivar innovation over the past decades. However, its progress is slow due to the long breeding period, and difficulty in selecting stable genetic characters or genotypes, prompting researchers to apply molecular biotechnologies in cucumber breeding. Here, we first summarize the achievements of conventional cucumber breeding such as crossing and mutagenesis, and then focus on the current status of molecular breeding of cucumber in China, including the progress and achievements on cucumber genomics, molecular mechanism underlying important agronomic traits, and also on the creation of high-quality multi-resistant germplasm resources, new variety breeding and ecological breeding. Future development trends and prospects of cucumber molecular breeding in China are also discussed.

    更新日期:2019-11-01
  • Haplotype structure in commercial maize breeding programs in relation to key founder lines.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Stephanie M Coffman,Matthew B Hufford,Carson M Andorf,Thomas Lübberstedt

    High-density haplotype analysis revealed significant haplotype sharing between ex-PVPs registered from 1976 to 1992 and key maize founders, and uncovered similarities and differences in haplotype sharing patterns by company and heterotic group. Proprietary inbreds developed by the private seed industry have been the major source for driving genetic gain in successful North American maize hybrids for decades. Much of the history of industry germplasm can be traced back to key founder lines, some of which were pivotal in the development of prominent heterotic groups. Previous studies have summarized pedigree-based relationships, genetic diversity and population structure among commercial inbreds with expired Plant Variety Protection (ex-PVP). However, less is known about the extent of haplotype sharing between historical founders and ex-PVPs. A better understanding of the relationships between founders and ex-PVPs provides insight into the haplotype and heterotic group structure among industry germplasm. We performed high-density haplotype analysis with 11.3 million SNPs on 212 maize inbreds, which included 157 ex-PVPs registered 1976-1992 and 55 public lines relevant to PVPs. Among these lines were 12 key founders identified in literature review: 207, A632, B14, B37, B73, LH123HT, LH82, Mo17, Oh43, OH7, PHG39 and Wf9. Our results revealed that, on average, 81.6% of an ex-PVP's genome is shared with at least 1 of these 12 founder lines and more than half when limited to B73, Mo17 and 207. Quantifiable similarities and contrasts among heterotic groups and major US seed industry companies were also observed. The results from this study provide high-resolution haplotype data on ex-PVP germplasm, confirm founder relationship trends observed in previous studies, uncover region-specific haplotype structure differences and demonstrate how haplotype sharing analysis can be used as a tool to explore germplasm diversity.

    更新日期:2019-11-01
  • Characterization and application of a gall midge resistance gene (Gm6) from Oryza sativa 'Kangwenqingzhan'.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Yang Li,Yi Mo,Zhihua Li,Meng Yang,Lihua Tang,Ling Cheng,Yongfu Qiu

    The resistance gene Gm6 was mapped and characterized using near-isogenic and pyramided lines, followed by marker-assisted selection to develop lines with resistance to both gall midge and brown planthopper. The Asian rice gall midge (GM; Orseolia oryzae; Diptera: Cecidomyiidae) is a major destructive pest affecting rice cultivation regions. The characterization of GM-resistance genes and the breeding of resistant varieties are together considered the most efficient strategy for managing this insect. Here, the Gm6 resistance gene derived from the Kangwenqingzhan (KW) variety was found to be located on the long arm of chromosome 4 using the F2 population of 9311/KW. The region was narrowed to a 90-kb segment flanked by the markers YW91 and YW3-4 using backcrossing populations. Based on no-choice feeding and host choice tests, GM development and growth in near-isogenic lines (NILs) were severely restricted compared to that in the 9311 control. On day 8, the average GM body length was 0.69 mm and 0.56 mm on NILs and 9311, respectively, and the differences were more significant at later time points. However, GM insects exhibited no host preference between NILs and 9311, and there was normal egg hatching on the resistant plants. We developed pyramided lines carrying BPH27, BPH36, and Gm6 by crossing and backcrossing with marker-assisted selection. These lines were similar to the KW parent in terms of agronomic traits while also exhibiting high resistance to brown planthopper (BPH) and GM. The present mapping and characterization of Gm6 will facilitate map-based cloning of this important resistance gene and its application in the breeding of insect-resistant rice varieties.

    更新日期:2019-11-01
  • Dissection of complex traits of tomato in the post-genome era.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Shuai Sun,Xiaotian Wang,Ketao Wang,Xia Cui

    We present the main advances of dissection of complex traits in tomato by omics, the genes identified to control complex traits and the application of CRISPR/Cas9 in tomato breeding. Complex traits are believed to be under the control of multiple genes, each with different effects and interaction with environmental factors. Advance development of sequencing and molecular technologies has enabled the recognition of the genomic structure of most organisms and the identification of a nearly limitless number of markers that have made it to accelerate the speed of QTL identification and gene cloning. Meanwhile, multiomics have been used to identify the genetic variations among different tomato species, determine the expression profiles of genes in different tissues and at distinct developmental stages, and detect metabolites in different pathways and processes. The combination of these data facilitates to reveal mechanism underlying complex traits. Moreover, mutants generated by mutagens and genome editing provide relatively rich genetic variation for deciphering the complex traits and exploiting them in tomato breeding. In this article, we present the main advances of complex trait dissection in tomato by omics since the release of the tomato genome sequence in 2012. We provide further insight into some tomato complex traits because of the causal genetic variations discovered so far and explore the utilization of CRISPR/Cas9 for the modification of tomato complex traits.

    更新日期:2019-11-01
  • Dissecting the genetics of cold tolerance in a multiparental maize population.
    Theor. Appl. Genet. (IF 3.926) Pub Date : null
    Q Yi,R A Malvar,L Álvarez-Iglesias,B Ordás,Pedro Revilla

    We identify the largest amount of QTLs for cold tolerance in maize; mainly associated with photosynthetic efficiency, which opens new possibilities for genomic selection for cold tolerance in maize. Breeding for cold tolerance in maize is an important objective in temperate areas. The objective was to carry out a highly efficient study of quantitative trait loci (QTLs) for cold tolerance in maize. We evaluated 406 recombinant inbred lines from a multi-parent advanced generation intercross (MAGIC) population in a growth chamber under cold and control conditions, and in the field at early and normal sowing. We recorded cold tolerance-related traits, including the number of days from sowing to emergence, chlorophyll content and maximum quantum efficiency of photosystem II (Fv/Fm). Association mapping was based on genotyping with near one million single nucleotide polymorphism (SNP) markers. We found 858 SNPs significantly associated with all traits, most of them under cold conditions and early sowing. Most QTLs were associated with chlorophyll and Fv/Fm. Many candidate genes coincided between the current research and previous reports. These results suggest that (1) the MAGIC population is an efficient tool for identifying QTLs for cold tolerance; (2) most QTLs for cold tolerance were associated with Fv/Fm; (3) most of these QTLs were located in specific genomic regions, particularly bin 10.04; (4) the current study allows genetically improving cold tolerance with genome-wide selection.

    更新日期:2019-11-01
  • Correction to: Fine mapping and identification of the fuzzless gene GaFzl in DPL972 (Gossypium arboreum).
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2019-06-13
    Xiaoxu Feng,Hailiang Cheng,Dongyun Zuo,Youping Zhang,Qiaolian Wang,Ke Liu,Javaria Ashraf,Qiuhong Yang,Simin Li,Xiaoqin Chen,Guoli Song

    Unfortunately, Figs. 5 and 6 were interchanged in the results section. Figures should swap positions, whereas the legends should stay in the given order.

    更新日期:2019-11-01
  • Correction to: Mapping and characterization of wheat stem rust resistance genes SrTm5 and Sr60 from Triticum monococcum.
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2018-10-13
    Shisheng Chen,Yan Guo,Jordan Briggs,Felix Dubach,Shiaoman Chao,Wenjun Zhang,Matthew N Rouse,Jorge Dubcovsky

    In the original publication, the IWGSC assembly is incorrectly referenced.

    更新日期:2019-11-01
  • Correction to: Development and characterization of a spring hexaploid wheat line with no functional VRN2 genes.
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2018-07-14
    Nestor Kippes,Andrew Chen,Xiaoqin Zhang,Adam J Lukaszewski,Jorge Dubcovsky

    In the original version of this article, PCR fragments and digestion product sizes for the VRN-B2 and VRN-D2 markers were not accurate. The corrected sizes are detailed below.

    更新日期:2019-11-01
  • Correction to: Improving the baking quality of bread wheat by genomic selection in early generations.
    Theor. Appl. Genet. (IF 3.926) Pub Date : 2018-01-18
    Sebastian Michel,Christian Kummer,Martin Gallee,Jakob Hellinger,Christian Ametz,Batuhan Akgöl,Doru Epure,Huseyin Güngör,Franziska Löschenberger,Hermann Buerstmayr

    Unfortunately, the co-author, Dr. Güngör was missed out in the authorship of original publication by mistake and it is updated now.

    更新日期:2019-11-01
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