Quantitative trait loci (QTL) related to the grain iron and zinc contents of brown rice were mapped by using a doubled haploid population derived from an intra‐japonica cross between 'Hwaseonchal' and 'Goami 2'. QTL–QTL, background–QTL, and background–background interactions and candidate genes that affect grain iron and zinc contents were preliminarily identified. Twenty‐one iron‐ and zinc‐related QTL were found. The major‐effect QTL qFe7 and qZn7 provided the highest contribution to phenotypic variance for grain iron and zinc contents. The colocation of zinc‐ and iron‐related QTL on chromosomes 1, 4, 7 and 11 may account for the strong correlation between iron and zinc contents. A region on chromosome 7 and epistatic interaction between loci on chromosomes 2 and 10 affected iron content. qZn7 and qZn11.3 exerted additive effects on zinc content. Eleven iron‐ and zinc‐related candidate genes colocated with qFe7, qZn7 and the region on chromosome 7 with an additive effect on iron content. The major‐effect QTL identified here may be useful for breeding biofortified rice.

Some sorghum cultivars are sensitive to organophosphate insecticides, which cause red to purple injury spots and, in severe cases, leaf death. Sensitivity to organophosphates is conditioned by a single locus on chromosome 5. We constructed a high‐density genetic map around the locus, termed osr, using DNA markers, and delimited osr to a 377‐kb region on the short arm of chromosome 5. Sequence analysis of this region predicted 19 gene candidates. Four of the candidates are homologous to a disease resistance NBS‐LRR gene. mRNA‐Seq analysis of gene expression and SNPs from two resistant cultivars (‘JN43’ and ‘Greenleaf’) and one sensitive cultivar (‘Nakei MS3B’) suggest that one or more members of this NBS‐LRR gene family are osr. Our results suggested that the recessive allele of osr results in sensitivity to OP insecticides.

High‐density marker‐based QTL mapping can serve as an effective strategy to identify novel genomic information to facilitate crop improvement. In this study, we genotyped an F2 population (KB12‐1 × PP12‐1) using a RAD‐seq approach and constructed a high‐density linkage map for radish. After a series of filtering procedures were performed, 17,124 SNPs and 3,336 indels with aa × bb genotyping were retained to obtain bin markers. Then, a linkage map comprising a total of 1,221 bin markers in nine linkage groups spanning 1,467.3 cM with an average marker interval of 1.2 cM was constructed. We evaluated the resistance of the F2 mapping population to black rot using F3 progeny, and two major QTLs related to black rot resistance were identified based on this map. Among these QTLs, qBRR2 on Chr.2 explained 26.97% of the phenotypic variation with a LOD score of 11.93, and qBRR7 on Chr.7 accounted for 27.06% of the phenotypic variation with a LOD score of 11.83. The additive effect of qBRR2 was positive (14.97); however, qBRR7 had the opposite effect (−11.99). The high‐density linkage map and the major QTLs qBRR2 and qBRR7 provide new important information for disease resistance gene discovery and utilization in genetic improvement.

Grain legumes being affordable sources of proteins, vitamins and essential micronutrients are key to human nutrition worldwide. However, frequent drought episodes present serious threat to grain legume production worldwide. Advances in legume omics in concert with evolving phenotyping and breeding techniques hold great promise to improve drought response of these crops. These resources could underpin prebreeding efforts to expedite discovery and deployment of novel drought tolerance traits into elite backgrounds. Fast‐track transfer of traits that confer drought tolerance using marker technologies has been demonstrated in grain legumes like chickpea. However, complex genetic architecture of drought tolerance demands embracing more efficient tools like genomic selection (GS) for accelerated trait improvement. Recent studies on GS for addressing complex traits like drought tolerance have yielded encouraging results in these crops. Recently, speed breeding (SB) protocols have also been optimized for the improvement of long‐day/day‐neutral grain legumes. Efficacy of SB protocols with regard to complex traits awaits further evidences though. There remains immense scope for integrating SB with GS and gene editing to deliver drought‐tolerant cultivars.

MicroRNAs (miRNAs) are small non‐coding RNAs (ncRNAs), which are involved in regulation of gene expression in almost all plant and animal systems. In crop plants, a large number of miRNAs are now known, which regulate expression of genes controlling a variety of traits including yield and tolerance to biotic and abiotic stresses. Like protein‐coding genes, miRNA genes (MIRs) and their products (including pri‐miRNAs, pre‐miRNAs or miRNAs themselves) also exhibit sequence variation. This variation affects the corresponding miRNAs in a variety of ways including their own transcription, maturation and target specificity. In this review, we summarize the available information on markers based on sequence variations in MIRs and the corresponding target genes. The association of these markers with agronomic traits of value and their possible use in crop improvement is also discussed using suitable examples.

In recent years, plant molecular research on genetic mapping, gene tagging and cloning, and marker‐assisted selection (MAS) have gained importance in crop improvement programmes. In Capsicum, several inter‐ and intra‐specific genetic maps with wide distribution of markers covering the whole genome have been developed. Recently, whole genome of the hot pepper C. annuum, its wild progenitor C. annuum var. glabriusculum and C. baccatum has been sequenced. The Capsicum genome size has been estimated to be approx. 4× (3.48 Gb) the genome size of cultivated tomato (Solanum lycopersicum L.) (900 Mb). Breeders’ access to the pepper genomic information would facilitate the choice of markers from different linkage groups, thus paving the way for gene cloning and its introgression into the elite breeding lines through MAS. Till date, approx. 20 independently inherited nuclear male sterility (NMS) genes have been reported. Linked markers have been identified for ms1, ms3, ms8, ms10, msk, msc‐1 and an undesignated gene. However, markers tightly linked to ms8 and ms10 are still lacking. Except ms1, ms3, ms8 and ms10, the map position of other NMS genes is not known. In cytoplasmic male sterility (CMS), markers for the mitochondrial gene atp6 have been developed and the gene cloned. Number of markers some very tightly linked to the restorer‐of‐fertility (Rf) gene have been identified. However, the actual map position of the Rf locus is still not determined. Another CMS‐associated nuclear gene “pr” responsible for restoring partial fertility has been identified and tagged. In this review, we have compiled up‐to‐date information about the marker technology relating to the NMS and the CMS‐associated genes in Capsicum. This information can be useful when screening Capsicum germplasm, developing NMS lines through MAS, improving efficiency of the NMS system, transferring rf gene for maintainer line breeding and Rf genes for restorer line breeding in CMS and assessing genetic purity of the hybrid seed.

Pvr4 locus, commonly associated with a co‐dominant CAPS marker, confers monogenic dominant resistance to potyvirus complex in Capsicum spp. Aiming to investigate whether the resistance found in resistant genotypes not bearing Pvr4 marker is due to allelism in the Pvr4 locus, or due to a new locus of the pvr series, segregation analyses of an F2 population obtained from a cross between two pepper lines “Myr‐29‐10” (P1) (resistant to PepYMV, showing a single band of 444 bp, Pvr4/Pvr4) and “PIM‐025” (P2) (resistant to PepYMV, showing a single band of 458 bp, Pvr4+/Pvr4+) were performed. According to the results, there is strong evidence that the locus controlling PepYMV resistance in PIM‐025 (P2) is not Pvr4. These results provide evidence that those resistant genotypes, bearing a susceptible band pattern in the Pvr4 locus (458 bp, Pvr4+/Pvr4+), carry a different gene from those described in the literature up to the present time.

Rice is the most important cereal crop but is sensitive to salinity stress. Increased salinization is progressively reducing rice productivity, escalating calls for research to ensure sustainable food production. The genetic diversity available in cultivars provides a rich resource for discovering genes associated with salt tolerance which has not yet been sufficiently utilized. In this study, 54 QTLs associated with salt tolerance were detected through genome‐wide association study (GWAS) using a core population consisting of 181 cultivars. We detected 17 loci significantly associated with dry weight ratio (DWR) for salt tolerance. In the region of a novel QTL qST‐7.19 on chromosome 7, we identified a candidate gene encoding a multidrug and toxic compound extrusion (MATE) protein and further validated the effect by using near‐isogenic line of the candidate gene. These QTLs and the candidate gene pave the ways for salinity tolerance improvement through molecular breeding.

As one of the main rice establishment methods, direct seeding has the advantages of saving labour and reducing costs for farmers. However, the expansion of direct seeding has been constrained by poorly levelled fields, heavy rainfall and poor drainage after sowing. The development of cultivars with anaerobic germination tolerance could improve or overcome these shortcomings of most rice under flooding conditions. In this study, a japonica‐type rice with anaerobic germination tolerance was suggested as a new genetic source and QTL analysis was carried out to improve adaptation to direct seeding. Three QTLs, qAG1, qAG3 and qAG11, were identified, explaining 13.44%, 6.71% and 14.52% of the phenotypic variance, respectively. In an evaluation of the most effective QTL combination, two QTL combinations (qAG1NP + qAG3PBR + qAG11PBR and qAG1NP + qAG11PBR) showed stable survival rates under submergence of filed condition. Based on the results, we will characterize the candidate genes within the detected target regions in further research, and the lines with advantageous alleles will be used to develop reliable cultivars to support the wide adoption of direct‐seeding practices in japonica rice.

Yellow mosaic disease, caused by wheat yellow mosaic virus (WYMV), is one of the most serious diseases of winter wheat in Japan and China. A single major QTL for WYMV resistance in the Japanese wheat variety 'Yumechikara', designated Q.Ymym, has been mapped on a 43.6 cM linkage block between the two markers Xcfd233 and Xgwm349 on chromosome 2D. We were able to obtain two recombinants within the block, which facilitated reducing the size of the linkage block. The pseudomolecule sequence of 'Chinese Spring' (CS) indicated that the original Q.Ymym region of 43.6 cM corresponded to 68.5 Mb and the narrowed Q.Ymym region represents a size of 27.3 Mb. The sequence features of the Q.Ymym region were unique in comparison with CS sequences, which may have led to the low recombination rate within the block. The Q.Ymym haplotype block was detected in other WYMV‐resistant varieties but not in the susceptible varieties used in this study. The unique sequence structure of the Q.Ymym region allowed the development of co‐dominant markers for use in marker‐assisted selection.

Leaf is the main organ of photosynthetic reaction of plants. Studying the genetic mechanism that affects the leaf shape is very important for the improvement of maize production. In this study, a RIL population, derived from a cross between Ye478 and Qi319, was planted in four different environments, and six leaf morphological traits were measured, including the leaf angle of first leaf above ear, the leaf angle of first leaf below ear, leaf orientation value, leaf area of first leaf above ear, leaf area of ear and leaf area of first leaf below ear. By combining with a genetic map containing 4,602 bin markers, 39 QTLs associated with leaf morphological traits were identified. Among them, four QTLs explained more than 10% of the phenotypic variance, and the QTL qLOV8‐2 which controlled LOV not only had a phenotypic contribution rate of 13.86% but also was detected in four environments, which could be considered as a stable major QTL. These results provide useful information for understanding the molecular mechanisms controlling maize leaf morphological traits.

Sorghum has unique advantage in terms of its climate resilience and its grain composition with beneficial bioactive compounds. It is a very good source of bioactive compounds such as polyphenols and antioxidants. Breeding efforts for end‐use identity‐specific genotypes are required for increased profitability to the farmers. In this study, total polyphenol content (TPC) and free radical scavenging activity (FRSA) were estimated in 60 genotypes, comprising of white and red sorghums, over three years each with two replications. TPC ranged from 55.6 mg/100 g to 553.1 mg/100 g with the highest value in IS 30508. The highest antioxidant activity, measured as free radical scavenging activity, was observed in IS 16151. Though in general TPC and FRSA are high in red sorghums, not all red sorghums have high TPC and scavenging activity. Significant effects of genotype and environment were observed for all the characters. Correlation studies indicated the possibility of developing a high yielding line with high antioxidant activity. The information generated aids in identifying donors to develop end‐use specific genotypes that are suitable as functional foods.

Sweet sorghum (Sorghum bicolor [L.] Moench) is a prospective bioethanol feedstock source. Four high‐biomass and sweet sorghum male lines and three grain sorghum female lines were intercrossed using Design II mating. Parents and hybrids were evaluated to (a) identify genetic sources to improve biofuel traits, and (b) determine the inheritance of biofuel and morpho‐agronomic traits. Total soluble sugars (TSS) per plant were determined using juice weight (JW) and Brix (°Bx). Plant height (PH), biomass (BM) and stalk diameter (SD) were also measured. Mean hybrid performance for PH, JW, TSS and BM was higher than the male parent means. Three male parents exhibited positive and significant general combining ability (GCA) for at least three traits. Among males, PI185672 showed the highest GCA for PH, °Bx and BM, while No. 08 exhibited the greatest GCA for JW and TSS. Most hybrids exhibited overdominance‐driven high‐parent heterosis for all traits except SD. Trait broad‐sense heritability ranged from 0.71 (BM) to 0.93 (PH). Results revealed that biofuel traits could be substantially improved through breeding, which will contribute to enhanced bioethanol production.

Fusarium graminearum could cause serious yield loss of soybean. Host resistance could offer an economical and effective way to control F. graminearum. The aims of this study were to identify and confirm quantitative trait loci (QTLs) underlying resistance to F. graminearum, and to analyse the genetic effects of pyramid resistance QTL on resistance level. A total of 140 F2:14 recombinant inbred lines (RILs) were constructed via the cross between 'Hefeng 25' (moderate resistance to F. graminearum) and 'Conrad' (resistance to F. graminearum). The molecular genetic linkage map was constructed based on 164 simple sequence repeat (SSR) markers. A total of seven QTLs underlying F. graminearum resistance, located on six chromosomes, were identified. Among these seven identified QTLs, beneficial allele of qFG‐1, qFG‐2 and qFG‐3 derived from 'Hefeng 25' and beneficial allele of qFG‐4, qFG‐5, qFG‐6, qFG‐7 derived from 'Conrad'. Of these seven identified QTLs, qFG‐1, qFG‐3, qFG‐4 and qFG‐5 were novel for F. graminearum resistance. Four pairs of QTLs with significant epistatic effects were found. The accumulation of resistance QTL was positively correlated with decreases in disease severity index, which was valuable for improving efficiency of marker‐assistant breeding in F. graminearum resistance.

With an objective of developing the induced mutants for superior productivity and resistance to foliar diseases in peanut, two introgression lines (IL‐3 and IL‐4) derived from ABK genomes of peanut were subjected to gamma and sodium azide mutagenesis. Evaluation of M1, M2 and M3 generations could identify foliar disease resistant and productive mutants. Large‐scale evaluation of M4 mutants during the rainy season of 2017 confirmed the superiority of 12 mutants over the respective parents and the best check (GPBD 4). The selected mutants were resistant to leaf spots (early and late) and rust diseases, and significantly more productive than the parents and GPBD 4. ddRAD‐Sequencing of these mutants identified the single nucleotide polymorphisms (SNPs) when compared to their parents. The genes harbouring these structural mutations were also identified. However, no copy number variations (CNVs) were observed between the mutants and the parents. The selected mutants carried resistant‐type alleles at the marker loci linked to foliar disease resistance. These promising mutants (M8) are currently under initial trials of variety development for commercial release.

Cowpea is an important grain legume crop in Africa. Cowpea flowers are capable of self‐fertilization, which might be the most frequent type of reproduction. Nevertheless, the rate of cross‐pollination could vary between 1% and 10%, depending on the populations of bumblebees or domestic bees that are present, the climate and the cultivar. The aim of this study was to identify and assess the efficiency rate of the pollinators of the wild cowpea, Vigna unguiculata subsp. unguiculata var. spontanea, the progenitor of the domesticated cowpea Vigna unguiculata subsp. unguiculata. Pollination study was conducted by observing patches of flowers (average 10–20/m2) from dawn to midday, approximately 05:00–12:30 hr for three years. All insects visiting the flowers were noted and identified to species level, where possible, and their foraging behaviour was monitored. Pollen grain deposit and pod set were estimated using single bee visits on plants with strictly outcrossing flowers. Major flower visitors were large bees of the family Megachilidae and the genus Xylocopa (Apidae, Xylocopinae). Xylocopa caffra (Linnaeus) was the most abundant bee species, accounting for 59% of total bees observed and 58% of total flower visited. Pod set was higher in visits by megachilid bees compared to Xylocopa bees. Within Xylocopa, there is a good correlation between size and efficiency (r = .95, p = .0477), the larger insects being more efficient. Honeybees, small bees (Ceratina and Nomia species) and Lepidopterans also visited flowers but without any effect on pollination. Cowpea pollination system is specialized, and pollinators are restricted to Megachilidae and Xylocopa species. Variation in pollen load deposit and pod set reveals that pollination success depends on the insect species involved and their size. Megachilids are the most efficient pollinators, especially since they are able to promote outcrossing more efficiently than Xylocopa species.

In Arabidopsis thaliana, AtMYB76 is an MYB transcription factor that has been shown to play multiple roles in the biosynthesis of aliphatic glucosinolates and fatty acids. However, in Brassica napus, the role of BnaA10.SOI.a, an AtMYB76 orthologue, in the accumulation of seed lipids remains unclear. In the present study, we obtained the BnaA10.SOI.a coding domain sequence from the Brassica napus cultivar 'Zhongshuang 11' and analysed its conserved protein domain. A subcellular localization experiment in tobacco leaf cells indicated that BnaA10.SOI.a functioned as a transcription factor. Our results demonstrated that the introduction of BnaA10.SOI.a into an Arabidopsis thaliana myb76‐2 mutant could restore wild‐type levels of seed fatty acid content. Moreover, the expression levels of six oil biosynthetic genes in developing seeds of myb76‐2 were restored to wild‐type levels by ectopic expression of BnaA10.SOI.a. These results improve our understanding of the function of BnaA10.SOI.a and provide a potential target for genetic manipulations of B. napus to improve oil quantity in seeds.

In cucumber, the genetic basis of traits under domestication and/or diversifying selection is not well understood. Here, we reported QTL mapping for flowering time and fruit size‐related traits with segregating populations derived from a cultivated × wild cross. Phenotypic data of flowering time (FT), fruit size (FS), fruit number (FN) and fruit weight per plant (FW) were collected in multiple environments. QTL analysis identified 19 QTL for these traits. We found that the major‐effect QTL FT1.1 played an important role in regulating flowering time in cultivated cucumber, whereas the minor‐effect QTL FT6.3 contributed to photoperiod sensitive flowering time during domestication. Two novel consensus FS QTL, FS1.4 and FS2.3, seem to be the targets of selection during breeding for the US processing cucumber. All other FS QTL were co‐localized with previously detected QTL using populations derived from cultivated cucumbers, suggesting that they were under selection during both initial domestication and subsequent improvement. Results from this study also suggested that the wild cucumber is a useful resource for capturing positive transgressive segregation and novel alleles that could be explored in cucumber breeding.

The improvement of sugar‐related factors is associated with root traits in sugar beet. The objectives of the present study were to assess variations of sugar‐ and root yield (RY)‐related traits and to estimate general (GCA) and specific (SCA) combining abilities of several lines, testers and hybrids under various environmental conditions. A line × tester mating design was used to develop 28 hybrids from seven lines × four testers. Presently, root‐ and sugar‐related traits were recorded in parental lines, hybrids and five local ('Pars', 'Torbat' and 'Ekbatan') and international ('Kermit' and 'Tous') check varieties in the eight combinations of location and growing season. Mean RY and sugar yield (SY) were 44.81 t/ha and 7.57 t/ha, respectively. Genotypes tested had 16.91% sugar content (SC) and 13.64% white sugar content (WSC) across trials. No one genotype was found to have high levels for all traits, but several had above mean sugar‐related or RY traits. L7T2 as the best hybrid for RY and SY yielded 37.0% and 34.4% more than the checks’ mean, whereas ratios for the best hybrid (L7T4) for SC and WSC were 8.2% and 4.3%, respectively. Additive variance was significant for all traits, whereas dominance component was only significant for RY. Several parental lines had stable GCA effects with respect to direction and magnitude for WSC, RY and SC in environments. L7 and T2 for RY and SY and L3 and T4 for SC and WSC were identified as the best combiners with high GCA effects, and their use might increase favourable alleles in further breeding programmes for traits tested. Estimated heritability for the combined environments was lower for sugar‐related traits (54.01%–59.39%) compared with those for RY traits (73.68%–74.21%). Overall, given heritability and additive variances estimated the identification of environmentally stable GCA and SCA effects and might help to increase efficiency of selection of superior cultivars with respect to sugar traits.

A mutation causing self‐fertility (SF) in perennial ryegrass was studied at the tetraploid level. The aim of this work was to determine a) whether SF remains functional in a tetraploid population and b) whether the SF mutation expresses dominance in heterozygous pollen grains. A tetraploidized plant carrying SF alleles was self‐pollinated to create a segregating F2 population. In the F2 individuals, pollen compatibility ranged between 38% and 84% showing that SF remained functional. The SF locus genotype was the main determinant of pollen compatibility explaining 78% of the variation. The observed segregation was significantly different from the expected under both SF being dominant or recessive models (P(χ2)≤0.001) and tended to be intermediate between them, indicating partial dominance or additive gene action. The frequency of the different genotypes suggested that pollen grains homozygous for the mutation have a competitive advantage over heterozygous pollen and that pollen compatibility is affected by the interaction with additional loci. The implications of our results for breeding polyploid grasses are discussed.

Besides its popular refreshing value, tea is globally consumed as a potential health beverage. Health benefit traits primarily rely on some regulatory networks of different metabolic pathways. In tea, the trait‐specific simple sequence repeat (SSR) markers are still insufficient, which could be used for marker‐assisted breeding technique. MicroRNAs are endogenous, non‐coding, short RNAs directly involved in regulating gene expressions at the post‐transcriptional level. It has been found that differences in miRNA precursor gene sequences interfere their structure formation and obstruct subsequent function. SSR motifs within the putative miRNA precursor genes have been identified followed by experimental validation of their existence and variation exclusively in tea. Simultaneously, diverse commercial accessions of Indian tea were undergone rigorous phenotyping during three plucking seasons to assess 20 chemotypic traits by high‐throughput techniques. Six miRNA‐SSR marker‐generated bands consisted the putative trait‐associated loci. Newly developed microRNAs (mi408, miR5021a and miR2863) precursor‐derived SSR markers, miSSR‐03, miSSR‐11 and miSSR‐14, executed convincing results in distinguishing tea cultivars with contrasting health benefit traits. This is in accordance with the earlier reports where mi408, miR5021a and miR2863 have been found to be involved in cellular pathways conferring tolerance to oxidative stress. Consequently, these markers can be used further as suitable choice to select promising tea genotypes with sound antioxidant quality.

Soybean mosaic virus (SMV) infections can cause significant reduction in soybean yield and seed quality. Identifying SMV resistance genes in soybean and accordingly breeding resistant soybean varieties is an important approach to control soybean loss caused by SMV. Here, whole genome resequencing was performed on a pair of near‐isogenic line (NIL), one resistant (R) line and one susceptible (S) line to SC3, from Qihuang‐1 (resistant to SC3, RSC3Q) × Nannong 1138‐2 (susceptible to SC3, rSC3Q). Based on the distribution of single nucleotide polymorphisms (SNPs) and InDels in each chromosome, the RSC3Q was mapped to a region between 27.4 and 29.8 Mbp in chromosome 13. Comparing the sequence and transcriptome data between R line and susceptible lines (S line and Willams82) to SC3, three RSC3Q candidate genes (Glyma13g25950, Glyma13g25970 and Glyma13g26380) were identified. Silencing Glyma13g26380 in Qihuang‐1 increased the accumulation of SMV at 6 and 24 hpi. Subsequently, the SMV concentration in silenced plants decreased to the same level as that of the control. Thus, Glyma13g26380 is involved in the early resistance response of Qihuang No. 1 to SC3. These results provide a basis for elucidating the soybean resistance mechanism against SMV and breeding more resistant soybean varieties against SMV.

The number of drought and low‐N tolerant hybrids with elevated levels of provitamin A (PVA) in sub‐Saharan Africa could increase when PVA genes are optimized and validated for developed drought and low‐N tolerant inbred lines. This study aimed to (a) determine the levels of drought and low‐N tolerance, and PVA concentrations in early maturing PVA‐quality protein maize (QPM) inbred lines, and (b) identify lines harbouring the crtRB1 and LcyE genes as sources of favourable alleles of PVA. Seventy early maturing PVA‐QPM inbreds were evaluated under drought, low‐N and optimal environments in Nigeria for two years. The inbreds were assayed for PVA levels and the presence of PVA genes using allele‐specific PCR markers. Moderate range of PVA contents was observed for the inbreds. Nonetheless, TZEIORQ 55 combined high PVA concentration with drought and low‐N tolerance. The crtRB1‐3′TE primer and the KASP SNP (snpZM0015) consistently identified nine inbreds including TZEIORQ 55 harbouring the favourable alleles of the crtRB1 gene. These inbreds could serve as donor parents of the favourable crtRB1‐3′TE allele for PVA breeding in maize.

Teosinte, an ancestor to modern maize, displays an excellent performance regarding resistance to stress, but its yield potential has rarely been reported. To evaluate the potential contribution of teosinte to maize improvement, two maize–teosinte backcrossed recombination inbred line (RIL) populations and their corresponding test‐cross hybrids were planted for trait assessment. In RN and ZP RIL populations, the average coefficients of variation of 31 agronomic traits were 9.14% (Range, 0.38%‒25.21%) and 6.85% (Range, 0.55%‒27.73%), respectively. The correlation coefficients of 13 common shared traits between RIL populations and test‐cross hybrid populations ranged from 0.10 to 0.60 and from 0.06 to 0.72, respectively. A total of 39 and 3 recombined inbred lines, and 29 and 47 test‐cross hybrids exhibited higher yields than their checks (RP125, Zheng58, CD189 and ZD958) with the BLUP data, respectively. Furthermore, four test‐cross hybrids including RN034/SCML1950, ZP068/Chang7‐2, ZP079/Chang7‐2 and ZP122/Chang7‐2 showed a more stable yield performance, with yield gains of +7.07%, +3.64%, +5.83% and +3.82% over checks, respectively. In conclusion, teosinte could serve as an alien germplasm for maize breeding.

Fusarium head blight is among the most extensively studied fungal diseases of wheat and other small grain cereals due to its impact on yield and quality, but particularly due to its potential to produce mycotoxins, which are harmful to humans and animals. Since our last comprehensive review on QTL mapping and marker‐assisted selection for FHB resistance in wheat in 2009, numerous studies have been conducted to identify, validate or fine‐map resistance QTL. The main aim of this review is to update and summarize findings on FHB resistance breeding of wheat published during the last decade. Furthermore, we compiled a user‐friendly table listing FHB resistance QTL data providing a valuable resource for further FHB resistance research. The role of morphological and phenological traits on FHB resistance and possible consequences for resistance breeding are discussed. This review concentrates current knowledge on breeding for FHB resistance and suggests strategies to enhance resistance by deploying molecular breeding methods, including marker‐assisted and genomic selection.

Broadening the genetic base of elite breeding programmes is crucial for further breeding success. The absence of major adaption genes, however, often masks the grain yield breeding value of genetic resources. We assessed the ability of a hybrid strategy to provide unbiased performance estimates of 21 barley genetic resources. By crossing them to elite tester lines, 25 three‐way hybrids were produced and evaluated together with a part of their parents and eight elite hybrids for important agronomic traits in replicated field trials in four environments. The phenotypic data analyses revealed that the hybrid strategy facilitated to identify promising resources by substantially improving lodging resistance. Combining genotypic data for 5,562 SNPs with the phenotypic data highlighted the potential to boost the diversity of the elite breeding pool via targeted introgression of genetic resources into the male and female heterotic pools. We propose an application of the hybrid strategy for genetic resources of entire genebank collections and to use genome‐wide predictions to support a targeted choice of accessions with high value for barley breeding.

Spot blotch caused by Bipolaris sorokiniana is an important disease in barley worldwide, causing considerable yield losses and reduced grain quality. In order to identify QTL conferring resistance to spot blotch, a highly diverse worldwide barley set comprising 449 accessions was phenotyped for seedling resistance with three isolates (No 31, SH 15 and SB 61) and for adult plant resistance at two locations (Russia and Australia) in two years. Genotyping with the 50 k iSelect barley SNP genotyping chip yielded 33,818 informative markers. Genome‐wide association studies (GWAS) using a compressed mixed linear model, including population structure and kinship, revealed 38 significant marker‐trait associations (MTA) for spot blotch resistance. The MTA corresponded to two major QTL on chromosomes 1H and 7H and a putative new minor QTL on chromosome 7H explaining between 2.79% and 13.67% of the phenotypic variance. A total of 10 and 14 high‐confidence genes were identified in the respective major QTL regions, seven of which have a predicted involvement in pathogen recognition or defence.

Yam (Dioscorea spp.) is an important tuber crop with tremendous potential as a functional food in the tropics and subtropics. However, the crop has not shown progressive productivity gain over decades due to various production constraints. This paper reviews the progress achieved in empirical breeding endeavours and the development, status and application of emerging breeding tools and technologies to translate genetic gains in yam improvement. Significant progress has been made in yam genetic improvement over the years which has led to the identification and development of several improved clones and sources of variability for various economically important traits. Substantial efforts have also been made to develop diverse molecular markers, transcriptome and metabolome profiles of crucial traits, trait mapping and generate reference genome sequences of the key species. However, there seems to be a slow translation of research improvements into widespread applications. These advances and the integration of empirical and emerging methods and technologies into the breeding process will enhance yam breeding efforts and ensure the quick delivery of improved varieties that possess superior agronomic and quality traits.

The genetic behaviour of a yellow‐green leaf sweetpotato mutant, a269, was analysed to prepare for genetic mapping and cloning of this mutant and to elucidate the regulation of its molecular mechanisms. The phenotypic stability of the mutant was observed under natural conditions, and photosynthetic pigments in mature leaves were measured. GN1323 and a269 were crossed and backcrossed. Genetic behaviour was assessed using phenotypic expression and segregation in F1, BC1 and BC2. The a269 leaves were yellow‐green at all stages after germination. The thylakoid lamellae of a269 were disorganized, had incomplete grana and were fewer compared with GN1323. The direct and reciprocal F1 populations had normal leaf colour, whereas the BC2 populations had yellow‐green leaves. Segregation of plants with normal‐ and yellow‐green leaf colour in the four BC1 populations satisfied the backcross segregation ratio of 11 : 1 for auto‐allohexaploids. The a269 mutant is stable, and its trait is controlled by one recessive nuclear locus.

The breeding of new stenospermocarpic seedless grape cultivars is of particular importance to the growing table grape market and grape processing industry. However, the developmental and genetic architectures of soft‐seed and seedlessness traits are unclear. In this study, we performed anatomical, histochemical and gene expression analyses to characterize the morphological and genetic basis of the seed hardness of 'Hongju', a stenospermocarpic soft‐seed grape cultivar developed by crossbreeding maternal 'Italia' and paternal 'Perlon' cultivars. We found intensively lignified medium integument layers in the seeds of hard‐seed cultivars, but these layers were degraded in the stenospermocarpic seedless cultivars beginning 35 days after flowering. The expression of genes related to the lignin and cellulose biosynthesis pathways was downregulated, whereas that of several cell‐wall loosening‐related genes was upregulated in 'Hongju' compared with 'Italia' beginning at 21 days after flowering. These results suggest that transcriptional suppression of the lignin and cellulose biosynthesis pathways coupled with reduced formation of medium integument plays an important role in the development of soft seeds in stenospermocarpic seedless grape cultivars.

Cercospora leaf spot (Cercospora canescens) is a major fungal disease which impedes mungbean production worldwide. Presence of wider host range with existence of pathogenic variability creates intricacy towards host‐pathogen dynamics. Moreover, environmental factors having crucial role in augmenting severity of this disease further complicate disease management. An attempt has been made for unfolding genotype x environment interactions towards identifying and validating durable resistant genotypes against cercospora leaf spot in multi‐environment testing. Preliminary screening with 246 genotypes under artificial epiphytotic condition was conducted to extract out a subset of 22 mungbean genotypes for further evaluation in field testing across six environments consecutively for two years. GGE biplot analysis detected significant environmental influence towards genotypic response and confirmed the presence of non‐crossover interaction with incoherent genotypic response, thus advocating the urgency for multi‐location testing. GGE biplot aptly identified “LGG 460” and “COGG 912” as “ideal” and “desirable” genotypes, respectively having durable resistance and genetic homeostasis and thus suggested for their utilization in future resistance breeding programme in mungbean against cercospora leaf spot.

Late blight (LB), caused by Phytophthora infestans, is one of the most devastating diseases of tomato (Solanum lycopersicum) worldwide. Aggressive pathogen isolates resistant to fungicides have driven research in favour of finding new sources of host resistance for tomato breeding. Recently, we reported S. pimpinellifolium accession PI 270443 exhibiting LB resistance stronger than all commercial LB‐resistant tomato cultivars. The purpose of this study was to examine the inheritance of LB resistance conferred by this accession. An interspecific cross was made between PI 270443 and a LB‐susceptible tomato breeding line and advanced to F10 generation. A total of 166 F9 and corresponding F10 recombinant inbred lines (RILs) were evaluated for response to LB in four replicated greenhouse experiments. Estimates of heritability (h2) of LB resistance, determined by parent–offspring (F9:F10) correlation analysis, ranged from 0.66 to 0.81, with an average of 0.76. The moderately high h2 of LB resistance in PI 270443 suggests the utility of this accession for tomato breeding. Molecular mapping and RNA‐sequencing efforts are underway to identify genes underlying LB resistance in PI 270443.

Flooding stress causes a significant yield reduction in soybean. The early growth of soybean in Korea coincides with the rainy season, potentially exposing to flooding stress. Greenhouse experiments were conducted to map the quantitative trait loci (QTL) for flooding tolerance in soybean and to identify and investigate candidate genes near the QTL hot spots. Flood stress was imposed at V1–V2 stage on a recombinant inbred line population (‘Paldalkong’ × ‘NTS1116’), and leaf chlorophyll content (CC) and shoot dry weight (DW) were measured under control and flooded conditions. The genetic map was constructed using 180K Axiom® SoyaSNP markers. The QTL were analysed under control and flooded conditions as well as for index (ratio of CC or DW under flooded to control, CCI and DWI) and flooding tolerance index (FTI, mean of CCI and DWI). A total of 20 QTL with LOD scores 3.59–19.73 causing 5.8%–33.3% phenotypic variation were identified on nine chromosomes. Chromosomes 10, 12 and 13 harboured relatively more stable QTL. Results of this study could be useful to further understand the genetic basis of soybean's flooding tolerance and applied in breeding programmes.

Plant architecture is an accessible approach to achieving high‐yield potential. The DENSE AND ERECT PANICLE 1 (DEP1) gene regulating panicle morphology, grain number per panicle, and nitrogen uptake and metabolism has been widely used for the breeding of high‐yield rice in northern Chinese japonica varieties. However, there has been no consensus on the genetic effects of dep1 on grain yield and quality under different genetic backgrounds and growing environments. In the present study, we developed two sets of near‐isogenic lines (NILs) of DEP1 (AKI‐dep1, AKI‐DEP1, LG5‐dep1 and LG5‐DEP1), each carrying the DEP1 region from either 'Liaogeng5' (LG5) or 'Akitakomachi' (AKI) in the AKI and LG5 backgrounds. Our results demonstrated that AKI‐dep1/LG5‐dep1 exhibited erect panicle and enhanced grain number per panicle, thereby consequently increasing grain yield, whereas they possessed inferior grain appearance compared with AKI‐DEP1/LG5‐DEP1 in the same background. However, the effects of dep1 on grain processing quality and eating and cooking quality varied with the background. These results provide useful information for high‐yield erect panicle rice breeding by marker‐assisted selection.

Maize grain filling (GF) and grain weight (GW) are closely associated with grain yield. In our study, the ZmARM4 locus affecting GF and GW was identified using a reverse genetics screen of UniformMutator (Mu). First, MutatorDR‐flanking sequence (MuDRFs) was isolated from the mutant by the MuDR‐amplified fragment length polymorphism method, and it was verified by cosegregation (between MuDRFs and phenotype) and linkage analyses. Second, the target gene of the MuDRFs was found to encode the Armadillo domain of the repeat protein gene families and has high expression in the GF stage. Third, association mapping between SNPs in the ZmARM4 region and the GW of 489 maize lines indicated that ZmARM4 is a functional gene that is closely related to GW. Moreover, bioinformatics analysis suggested that ZmARM4 may be relevant for the activity of sucrose transport or the number of cell divisions in endosperm cells. Therefore, ZmARM4 may be used as an important locus for maize GW in molecular breeding.

Seed longevity could significantly determine seed regeneration cycle and greatly affect wheat production. With the 90 K chip assays, a genome‐wide association study was performed to identify seed longevity‐related markers and loci in common wheat. Seed germination ratios (GR) under artificially ageing of 166 wheat accessions across three environments were evaluated to assess seed longevity. Totally, 23 longevity‐related loci were identified in the study, explaining 6.7%–11.4% of the phenotypic variations. Of these, QlgGR.cas‐1A and QlgGR.cas‐2B.2 were deemed as stable loci associated with wheat seed longevity. Fifteen loci were found overlapped with known quantitative trait loci or genes. Besides, QlgGR.cas‐1A, QlgGR.cas‐2B.2, QlgGR.cas‐3D.1, QlgGR.cas‐3D.2, QlgGR.cas‐4A.2, QlgGR.cas‐5A.1, QlgGR.cas‐5A.2 and QlgGR.cas‐6A.1 were colocated with seed dormancy‐related loci. Significant additive effects were obtained for seed longevity by pyramiding favourable alleles. Several candidate genes were found involved in signal transduction and stress resistance pathways by sequencing analysis of significantly longevity‐related molecular markers. These results might provide new sights into the genetic architecture of seed longevity.

Spike density (SD), an important spike morphological trait associated with wheat yield, is the spikelet number per spike (SNS) divided by spike length (SL). In this study, phenotypic data from eight environments were collected and a recombinant inbred line population (RIL) constructed by the wheat line 20828 and the cultivar 'Chuannong16' and a Wheat55K SNP array‐based constructed genetic linkage map were used to identify SD quantitative trait locus (QTL). Correlation between SD and other agronomic traits was calculated. Genes associated with plant growth and development for major loci were predicted. The results showed that 24 QTLs associated with SD were detected in eight environments. Among them, three major QTL, namely QSd.sicau‐5B.2, QSd.sicau‐2D.3 and QSd.sicau‐4B.1, explained up to 35.62%, 14.21% and 11.23% of phenotypic variation, respectively. The positive alleles of them were all derived from 'Chuannong16'. The significant relationships between SD and other agronomic traits were detected and discussed. Taken together, the stably expressed SD QTL under different environments identified in this study provided theoretical guidance for further fine mapping and germplasm improvement.

One hundred and ninety‐seven wheat accessions from Yellow and Huai Winter Wheat Region (YHW) were evaluated for differences of 14 agronomic traits under low‐ and high‐density plantings. Compared with the high‐density plantings, plant height, neck length, uppermost internode length, flag leaf angle and number of sterile spikelets under the low‐density plantings reduced, while heading date, flowering date, flag leaf length and width, spike length, number of fertile spikelets, grain number per spike, thousand‐kernel weight and grain weight per spike increased. A total of 1,118 markers were detected based on GWAS, and seven QTLs were confirmed. One QTL on chromosomes 5BL and two other QTLs on 5Dl were all tightly associated with flowering date difference. Bioinformatics analysis revealed that two haploblocks in 5Dl were involved, and the Vrn‐D1 locus was located in this interval. A region on chromosome 5B at around 531.5 Mb was significantly associated with plant height difference. Two QTLs including AX‐94840438 (7BL) and AX‐94563647 (7DS) were responsible for neck length or uppermost internode length difference.

An appreciation of the genetic diversity retained in the gene pool of anemone‐type chrysanthemums is needed to drive further genetic improvement of this commercially important ornamental species. Here, a panel of 67 accessions was characterized with respect to both floral morphology, assessed using a set of 12 inflorescence‐associated traits, and to genotype, using sequence‐related amplified polymorphism (SRAP) fingerprinting. Abundant variation and a high level of broad‐sense heritability (>88%) were revealed for all traits except number of tubular floret lobes. Of the possible 66 pairwise inter‐trait combinations, 37 proved to be significantly correlated. A principal component analysis of the trait data showed that the first four principal components explained ~78% of the variance; meanwhile a hierarchical clustering analysis revealed a number of discrete groups reflecting the various cultivated types, but was not predictive of provenance. The SRAP genotyping employed 22 primer combinations and generated 238 informative fragments. A moderately high level of the Jaccard's similarity coefficient (mean 0.67) was calculated for the examined panel. A hierarchical clustering analysis based on the genotypic data revealed four groups, which were clearly reflective of cultivated type; moreover, a comparison of the within‐cluster means for each of the two key anemone‐related traits—tubular floret length and tubular floret length/style length—showed that the genotype‐based clusterings were associated with the anemone levels, albeit imperfectively. A principal coordinate analysis showed that the first two coordinates accounted for about 14% of the total variation. In summary, the present study adds new understanding of the genetic diversity present in the anemone‐type chrysanthemum gene pool, and the findings will lay the foundation for implementing a genotype/phenotype association strategy to reveal the genetic and molecular basis of floral form in this valuable ornamental species.

Small‐grain winter cereal crops can be infected with Fusarium head blight (FHB) leading to mycotoxin contamination and reduction in grain weight and quality. Although a number of studies have investigated the genetic variation of genotypes within each small‐grain cereal, a systematic comparison of the winter crops rye, triticale, durum and bread wheat for their FHB resistance, Fusarium‐damaged kernels (FDK) and deoxynivalenol (DON) contamination across species is still missing. We have therefore evaluated twelve genotypes each of four crops widely varying in their FHB resistance under artificial infection with one DON‐producing F. culmorum isolate at constant spore concentrations and additionally at crop‐specific concentrations in two environments. Rye and triticale were the most resistant crops to FHB followed by bread and durum wheat at constant and crop‐specific spore concentrations. On average, rye accumulated the lowest amount of DON (10.08 mg/kg) in the grains, followed by triticale (15.18 mg/kg) and bread wheat (16.59 mg/kg), while durum wheat had the highest amount (30.68 mg/kg). Genotypic variances within crops were significant (p ≤ .001) in most instances. These results underline the differing importance of breeding for FHB resistance in the different crops.

In this study, we have generated more than 12,000 activation‐tagged mutants in a high‐yielding indica rice variety, 'BPT 5204', employing maize Ac/Ds system. Different transgenic plants obtained were analysed based on expression patterns of green fluorescence protein (GFP), red fluorescence protein (RFP), herbicide (Basta) tolerance and molecular analyses. T1 seeds of pSQ5 and pSQ5‐bar transgenics, when germinated separately on hygromycin (50 mg/L) and phosphinothricin (5 mg/L) containing medium, revealed a segregation of 3 tolerant : 1 susceptible plants. The germinal transposition frequency of Ds element in different T2 progeny of rice plants was found to be about 18.0%. Different stable tagged mutants exhibited marked increases in plant height, number of tillers, leaf size, panicle size, seed size and number of grains per plant. The overall results indicate that the genes associated with these traits are upregulated by the enhancer element in activation‐tagged mutants. As such, the various tagged mutant lines appear promising and serve as a valuable genetic resource for identification of key genes determining different agronomic traits of rice.

Anthracnose (Colletotrichum dematium) is an important disease in spinach (Spinacia oleracea). Sources of resistance must be identified, and molecular tools must be developed to expedite cultivar development. In this study, a diverse collection of 276 spinach accessions was scored for anthracnose disease severity. We then evaluated marker identification approaches by testing how well haplotype‐based trait modelling compares to single markers in identifying strong association signals. Alleles in linkage disequilibrium were tagged in haplotype blocks, and anthracnose‐associated molecular markers were identified using single‐SNP (sSNP), pairwise haplotype (htP) and multi‐marker haplotype (htM) SNP tagging approaches. We identified 49 significantly associated markers distributed on several spinach chromosomes using all methods. The sSNP approach identified 13 markers, while htP identified 24 (~63% more) and htM 34 (~162% more). Of these markers, four were uniquely identified by the sSNP approach, nine by htP and nineteen by htM. The results indicate that resistance to anthracnose is polygenic and that haplotype‐based analysis may have more power than sSNP. Using a combination of these methods can improve the identification of molecular markers for spinach breeding.

Optimizing root systems is one crucial point in drought tolerance breeding of plants. Introducing root‐related traits to breeding programmes is time‐consuming and laborious. Most of the commonly used methods are not suitable to be applied in a larger amount of plants. Here we present a study applying a DNA‐based root phenotyping method (root DNA density; RDD) for phenotyping the root system of maize. Twenty‐one maize inbred lines were investigated in a rain‐out shelter experiment and 19 maize inbred lines in a greenhouse experiment under well‐watered and drought conditions. Beside other commonly used root traits, agronomic traits of the plants were recorded and compared to RDD. Within root traits, RDD showed high significant genotypic variation and the highest repeatabilities of up to 72.4%. In contrast to most agronomic traits, repeatabilities increased under drought conditions. Values showed also good correlations between rain‐out shelter and greenhouse trial, indicating the potential of this method for obtaining comparable results across different environments.

Salinity tolerance of 47 wild barley genotypes and six barley cultivars was evaluated under control and salinity stress (300 mM NaCl) conditions. Shoot and root dry weight (DW), plant height, membrane stability index (MSI), relative water content, survival rate, leaf malondialdehyde (MDA) and proline contents, root and leaf Na, K, Ca and K/Na ratio, and chlorophyll a fluorescence were measured. Salinity stress caused significant increase in the MDA, proline content, Na and Ca concentrations of the roots and leaves, but resulted in a decrease in the other traits. H. spontaneum genotypes were considerably less affected by the salinity than the genotypes of H. vulgare. Plant survivability was negatively correlated with the Na concentration (r =−.66) but positively correlated with the leaf K/Na ratio (r = .67) and MSI (r = .68). Tolerance mechanisms such as ion exclusion (Na) were likely to be present in the wild barley causing K/Na homeostasis as well as the much lower root and shoot Na, resulting in the higher survival rate.

Rapeseed/canola seedlings can be easily damaged by spring frost, which can rupture the cells and kill the plant. Genetic variations for frost tolerance have known to exist within rapeseed/canola gene pool. A genome‐wide association study (GWAS) was conducted using 231 diverged rapeseed/canola germplasm to find the significant markers of the freezing tolerance traits. The genotypes were obtained from 21 countries and comprised of spring, winter and semi‐winter growth types. The genotypes were evaluated in plant growth chamber under simulated freezing conditions. Highly significant genotypic variation was observed for the freezing tolerance. The best three freezing tolerant germplasms (Rubin, KSU‐10, and AR91004) were winter type, while the four most freezing susceptible germplasms (Polo Canada, Prota, Drakkar, and BO‐63) were all spring type. No geographical or growth habit type clusters were identified by structure analysis in this mixed population. One QTL was identified that was located on chromosome A02. Six freezing/abiotic stress tolerance genes have been identified in this study.

Average maize yield per hectare has increased significantly because of the improvement in high‐density tolerance, but little attention has been paid to the genetic mechanism of grain yield response to high planting density. Here, we used a population of 301 recombinant inbred lines (RILs) derived from the cross YE478 × 08–641 to detect quantitative trait loci (QTLs) for 16 yield‐related traits under two planting densities (57,000 and 114,000 plants per ha) across four environments. These yield‐related traits responded differently to high‐density stress. A total of 110 QTLs were observed for these traits: 33 QTLs only under low planting density, 50 QTLs under high planting density and 27 QTLs across both densities. Only two major QTLs, qCD6 and qWKEL2‐2, were identified across low‐ and high‐density treatments. Seven environmentally stable QTLs were also observed containing qED6, qWKEL3, qRN3‐3, qRN7‐2, qRN9‐2 and qRN10 across both densities, as well as qRN9‐1 under low density. In addition, 16 and eight pairs of loci with epistasis interaction (EPI) were detected under low and high planting densities, respectively. Additionally, nine and 17 loci showed QTL × environment interaction (QEI) under low‐ and high‐density conditions, respectively. These interactions are of lesser importance than the main QTL effects. We also observed 26 pleiotropic QTL clusters, and the hotspot region 3.08 concentrated nine QTLs, suggesting its great importance for maize yield. These findings suggested that multiple minor QTLs, loci with EPI and QEI, pleiotropy and the complex network of “crosstalk” among them for yield‐related traits were greatly influenced by plant density, which increases our understanding of the genetic mechanism of yield‐related traits for high‐density tolerance.

Alternaria leaf spot (ALS) caused by Alternaria carthami Chowdhury can cause yield loss up to 90% in safflower (Carthamus tinctorius L.) under severe conditions. Even though a definite source of ALS resistance is not available in cultivated species, a few of the wild species, viz. C. palaestinus and C. lantaus, are known to be tolerant to ALS. Therefore, an attempt was made to introgress Alternaria resistance from these species into cultivated species. F1‐F8 generations of crosses (PI537632 × C. palaestinus), (C. palaestinus × PI537632), (“Nira” × C. palaestinus) and ([MS 6(O) × C. lanatus] × C. palaestinus) were screened against ALS. ALS infection (%) was recorded in field and quantified using Windias Leaf Image Analysis system. Detached leaf technique was used in laboratory to confirm resistance in interspecific selections. Six resistant and 29 moderately resistant interspecific lines resembling mostly cultivated species were developed. Inheritance of ALS resistance indicated involvement of multiple minor alleles having small effects on resistance. The identified resistant lines could provide potential source of resistance to ALS for safflower breeding programmes.

Two dominant, closely linked and complementary genes, Btr1 and Btr2, control rachis brittleness in barley. Recessive mutations in any of these genes turn the fragile rachis (brittle) into a tough rachis phenotype (non‐brittle). The cross of parents with alternative mutations in the btr genes leads to a brittle F1 hybrid that presents grain retention problems. We evaluated rachis fragility through a mechanical test and under natural conditions, in F1 crosses with different compositions at the btr genes. Brittleness was significantly higher in Btr1btr1Btr2btr2 crosses compared to hybrids and inbred parents carrying one of the mutations (btr1btr1Btr2Btr2/Btr1Btr1btr2btr2). This fact could jeopardize the efficient harvest of hybrids bearing alternative mutations, reducing the choice of possible crosses for hybrid barley breeding and hindering the exploitation of potential heterotic patterns. Furthermore, non‐brittle hybrids showed higher brittleness than inbreds, suggesting the presence of other dominant factors affecting the trait. In conclusion, this work encourages a deeper study of the genetic control of the rachis brittleness trait and urges the consideration of rachis tenacity as a target for hybrid barley breeding.

Faba bean has the potential to become a key food and feed protein crop in many areas of the world. The presence of tannins in its seed coat has limited the deployment of this crop as feed and food. The expression of either of the two recessive genes, zt1 and zt2, causes a great reduction of tannins from the seed coat and results in a white flower phenotype. Molecular markers linked to these loci are fundamental tools for speeding up the breeding of low‐tannin varieties. The main aim of this study was to develop and validate a robust molecular marker linked to the zt2 locus. We used 176 recombinant inbred lines of the Disco/2 × ILB 938/2 cross at F6 and genotyped those using 257 SNP (single nucleotide polymorphism) markers. An SNP marker associated with zt2 locus was found on faba bean chromosome 3 and was used to develop a high‐throughput low‐cost KASP (kompetitive allele‐specific PCR) marker. The KASP marker can successfully discriminate low‐tannin faba beans carrying zt2 from those carrying zt1 and wild‐type alleles.

Bacterial wilt of tomato caused by Ralstonia solanacearum species complex (RSSC) causes substantial yield losses in the tropics and subtropics. Disease management options by chemicals are limited, and host resistance is the cheapest and easiest means of control. However, sources of bacterial wilt resistance in tomato are limited. The disease often coincides with higher temperatures in the tropics, and resistance sources that are more heat stable are particularly valuable for breeding of tropically adapted tomato cultivars. The objectives of this study were to identify tomato accessions that demonstrate relatively high bacterial wilt resistance under high temperatures and to identify accessions that may possess QTLs other than Bwr‐6 and Bwr‐12 (two major disease resistance QTLs against bacterial wilt), which could be exploited in future breeding. Sixty‐seven tomato entries reported as bacterial wilt resistant were evaluated in a greenhouse against one strain each of phylotype I (Pss4) and phylotype IIB (Pss1632) of the RSSC (average temperature ≥29°C). Of those, five and 19 were homozygous for Bwr‐6 and Bwr‐12, respectively, and six were homozygous for both QTLs. Bwr‐12 contributed to resistance against phylotype I strain but not against the phylotype II strain. Bwr‐6 contributed to resistance against both phylotype strains. Entries with both QTLs as a group performed relatively better against the phylotype I strain. Entry “94T765‐24‐79”, which lacked Bwr‐6 and Bwr‐12, demonstrated relatively high resistance against the phylotype II strain and may carry new QTL/s. As new bacterial wilt resistance QTLs are mapped and markers designed, pyramiding multiple bacterial wilt resistance QTLs into new varieties should be straightforward, thereby increasing the chances of obtaining stable resistance.

Yellow rust, caused by Puccinia striiformis f. sp. tritici, is one of the most severe wheat disease worldwide. Crop losses have ranged from 10% to 70% and up to 100% in extreme conditions. Eighty‐two resistance genes, designated Yr, have been identified. Among them, Yr17 derived from Aegilops ventricosa and located on chromosome 2A has been widely used in wheat breeding. However, it had been overcome already. Through recombination of the Ae. ventricosa Yr17‐carrying 6Nv chromosome with 2D of wheat, we introduced Yr17 onto chromosome 2D. Then, lines carrying Yr17 on both 2A and 2D were generated. Seedlings of the latter, as well as those carrying a single dose of Yr17 either on 2A or on 2D, were inoculated with virulent or avirulent strains on wheat seedlings. The different genotypes were fully susceptible for the two pathotypes that are virulent on Yr17. In the case of avirulent pathotypes, the Yr17 double dose lines were fully resistant, while those with the Yr17 gene only on either 2A or 2D had intermediate resistance reactions towards one or the other or both pathotypes.

In plants, male sterility (MS) is a specific breeding target trait. With the advancements in agriculture, utilization of heterosis breeding in hybrid production through MS lines has become the main breeding tool of various cross‐pollinated and even self‐pollinated crops. Soybean is an essential source of oil and protein; however, the low yield is a major factor limiting its development. Soybean MS mainly comprises cytoplasmic‐nuclear MS and nuclear/genic MS (NMS/GMS), which can effectively utilize heterosis to improve soybean yield. This review outlines the recent research progress on the development of new genetically MS lines, exploring the underlying molecular mechanism of MS, identification and cloning of MS and fertility restoration genes, and the application of MS lines. We further discussed and prospected the future developmental scenario direction of the soybean MS, based on the previous studies of other crops sterility system. Moreover, this review also provides comprehensive information for better application of MS to soybean breeding programme.

Soybean is a special crop that can utilize N2 in the air via symbioses with Rhizobium spp. The formation of effective nodules is a complex process in which nodulation outer proteins (Nops) are determinants of establishment of a symbiotic relationship. We constructed a Sinorhizobium fredii HH103ΩnopB mutant. A nodulation test showed that the mutant had a negative effect on the Suinong14, ZYD00006, Dongnong594 and Charleston soybean lines. Recombinant inbred soybean lines were independently inoculated with the mutant and wild‐type strains, and five and four quantitative trait loci (QTLs) were identified by analysing the nodule number (NN) and nodule dry weight (NDW), respectively. We chose one QTL that overlapped with other studies and a novel QTL identified in our study and selected six candidate genes for further analysis. The qRT‐PCR analysis showed that only changes in Glyma.17G166200 expression depended on NopB. Further analysis showed that Glyma.17G166200 encoded a protein with a D‐glucose‐binding domain and a serine‐threonine/tyrosine protein kinase catalytic domain that was involved in the abscisic acid (ABA) pathway.

Pyramiding Asian soybean rust (ASR) resistance (Rpp) genes in a single genotype has been shown to increase ASR resistance in soybean. However, it remains unclear which combinations of Rpp genes are superior. Therefore, here, we developed six new Rpp‐pyramided lines carrying different combinations of Rpp genes and evaluated their resistance against 13 Bangladeshi rust (Phakopsora pachyrhizi) isolates (BdRPs) alongside seven previously developed Rpp‐pyramided lines. We found that lines carrying one, two and three Rpp genes had high ASR resistance without sporulation in 13.8%, 35.2% and 73.1% of the assays, respectively. Among the new lines that were developed, those with Rpp3 + Rpp4 and Rpp3 + Rpp4 + Rpp5 had high levels of ASR resistance, while the line containing Rpp2 + Rpp4 + Rpp5 showed immunity phenotype at two weeks after inoculation by the BdRP‐22 infection. Thus, pyramiding larger numbers of Rpp genes confers soybean with a higher level of resistance to ASR pathogens and can produce an immunity phenotype at two weeks after inoculation.

Seed fatty acid content is an important consideration for soybean produced for food, feed, and industrial applications. In this study, MCScanX was used to analyze the entire soybean genome to generate a collinearity block, which was then used to assess the collinearity among the soybean fatty acid quantitative trait loci (QTL) in the SoyBase database. The hub‐QTLs located in the Gm06, Gm07, and Gm10 segments were identified. The Kyoto Encyclopedia of Genes and Genomes and gene ontology databases were used to analyze the genes in hub‐QTL regions, resulting in the identification of 17 candidate genes related to soybean fatty acid content. Two lines with different fatty acid contents and a recurrent parent were selected from a chromosome segment substitution line library for a subsequent quantitative real‐time polymerase chain reaction (qRT‐PCR) assay to verify the candidate gene expression patterns. Four genes were related to the total soybean fatty acid content, while three genes were related to the content of specific fatty acid types. The results of this study may be relevant for the fine mapping of soybean fatty acid QTLs/genes.

Breeding soybeans for higher latitudes requires cultivars with an increased chilling stress tolerance, especially when flowering occurs. Phenotyping in climate chambers to select for this trait is labour‐intensive and requires an optimal allocation of resources due to limited space. We screened a diversity panel of 35 early maturity cultivars and a biparental population of 103 RILs for their cold stress tolerance at flowering stage. Pod number under control and stress conditions is highly heritable and showed only a weak correlation between the two treatments. Based on different testing scenarios, we could show that testing more genotypes with less replicates yields much higher responses to selection and hence should be pursued in such climate‐controlled experiments. We identified quantitative trait loci (QTL) for pod number under both conditions (chromosomes 7 and 13) and a cold tolerance‐specific QTL (chromosome 11). Furthermore, we performed genomic predictions using different test set scenarios and prediction models, showing that genomic prediction is a promising tool to select for cold stress tolerance, particularly if known QTL can be used as fixed effects in the model.

Plant height (PH) of soybean (Glycine max (L.) Merr.) is an important and complex architecture trait significantly related to soybean yield. A natural population of 185 elite soybean accessions was used to identify QTN (quantitative trait nucleotide) and candidate genes of PH through genome‐wide association study (GWAS). A total of 33,149 SNPs were identified based on the Specific Locus Amplified Fragment Sequencing (SLAF‐seq). Finally, 14 signals associated with PH through GWAS were detected, including seven novel SNPs and seven known ones which were overlapped or located in the linked regions of known QTL. Numbers of functional genes located in the 200‐kb genomic region of each peak SNP were found. Furthermore, a total of 103 SNPs based on 28 genes were scanned. Among them, six novel genes containing cis‐acting elements involved in gibberellin or auxin responsiveness were predicted significantly related with PH according to transcript abundance analysis. The identified loci with beneficial alleles and the candidate genes might be useful for studying the molecular mechanisms of soybean PH and further for improving the potential yield of soybean.

Both seed length and seed width are important traits for soybean yield. In the present study, 89 Quantitative trait loci (QTLs) of seed length and 65 QTLs of seed width were collected from published papers and our study. QTLs in this study were evaluated by the soymap2, then totally 23 consensus QTLs were located on 17 linkage groups (LGs) through the meta‐analysis. The minimum confidence interval was 0.28 cM and the mean phenotypic variance (R2) was ranged from 5.33% to 23.36%. To optimize these QTLs based on statistic analysis, overview method was further used to narrow down CI, the number of QTLs was narrowed down to 84. Furthermore, 2,750 candidate genes were screened from the consensus QTL intervals by informatics, a total of 37 genes were found to be associated with seed size. All results could lay a foundation for MAS (Molecular Assisted Selection) and gene cloning.

Inheritance of fertility restorer gene in pigeonpea was studied using F2 and BC1F1 populations derived from cross AL103A × IC245273. It was found to be controlled by single dominant gene. Out of 228 SSR primer pairs, 33 primer pairs showed parental polymorphism, while four primers were found polymorphic in bulk segregant analysis (BSA). These four primers viz., CcM 1615, CcM 0710, CcM 0765 and CcM 1522 were used for genotyping of F2 population and were found to be placed at 3.1, 5.1, 28.1 and 45.8 cM, respectively. Two of them, CcM 1615 and CcM 0710, evinced clear and unambiguous bands for fertility restoration in F2 population. The Rf gene was mapped on linkage group 6 between the SSR markers CcM 1615 and CcM 0710 with the distances of 3.1 and 5.1 cM, respectively. The accuracy of the CcM 1615 was validated in 18 restorers and six maintainer lines. The marker CcM 1615 amplified in majority of male restorer lines with a selection accuracy of 91.66%.

Parents and 318 F8 recombinant inbred lines (RILs) derived from the cross, TAG 24 × ICGV 86031 were evaluated for peanut bud necrosis disease (PBND) resistance and agronomic traits under natural infestation of thrips at a disease hotspot location for 2 years. Significant genotype, environment and genotype × environment interaction effects suggested role of environment in development and spread of the disease. Quantitative trait loci (QTL) analysis using QTL Cartographer identified a total of 14 QTL for six traits of which five QTL were for disease incidence. One quantitative trait locus q60DI located on LG_AhII was identified using both QTL Cartographer and QTL Network. Another QTL q90DI was detected with a high PVE of 12.57 using QTL Cartographer. A total of nine significant additive × additive (AA) interactions were detected for PBND disease incidence and yield traits with two and seven interactions displaying effects in favour of the parental and recombinant genotype combinations, respectively. This is the first attempt on QTL discovery associated with PBND resistance in peanut. Superior RILs identified in the study can be recycled or released as variety following further evaluations.