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Genome assembly and multi‐omic analyses reveal the mechanisms underlying flower color formation in Torenia fournieri Plant Genome (IF 4.219) Pub Date : 2024-03-15 Jiaxing Song, Haiming Kong, Jing Yang, Jiaxian Jing, Siyu Li, Nan Ma, Rongchen Yang, Yuman Cao, Yafang Wang, Tianming Hu, Peizhi Yang
Torenia fournieri Lind. is an ornamental plant that is popular for its numerous flowers and variety of colors. However, its genomic evolutionary history and the genetic and metabolic bases of flower color formation remain poorly understood. Here, we report the first T. fournieri reference genome, which was resolved to the chromosome scale and was 164.4 Mb in size. Phylogenetic analyses clarified relationships
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Exploring the genomics of abiotic stress tolerance and crop resilience to climate change Plant Genome (IF 4.219) Pub Date : 2024-03-14 Rajeev K. Varshney, Rutwik Barmukh, Alison Bentley, Henry T. Nguyen
Abiotic stresses have a detrimental impact on crop production globally. The escalating frequency and intensity of these stresses, driven by rapid changes in climatic conditions, pose significant challenges to agriculture. This situation is worsened by the burgeoning human population that is projected to heighten the demand for food in the coming years, emphasizing the need for further agricultural
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The ancestral karyotype of the Heliantheae Alliance, herbicide resistance, and human allergens: Insights from the genomes of common and giant ragweed Plant Genome (IF 4.219) Pub Date : 2024-03-14 Martin Laforest, Sara L. Martin, Katherine Bisaillon, Brahim Soufiane, Sydney Meloche, François J. Tardif, Eric Page
Ambrosia artemisiifolia and Ambrosia trifida (Asteraceae) are important pest species and the two greatest sources of aeroallergens globally. Here, we took advantage of a hybrid to simplify genome assembly and present chromosome‐level assemblies for both species. These assemblies show high levels of completeness with Benchmarking Universal Single‐Copy Ortholog (BUSCO) scores of 94.5% for A. artemisiifolia
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Genome‐wide scanning to identify and validate single nucleotide polymorphism markers associated with drought tolerance in spring wheat seedlings Plant Genome (IF 4.219) Pub Date : 2024-03-13 Ahmed Sallam, Mona F. A. Dawood, Diego Jarquín, Elsayed A. Mohamed, Mohamed Y. Hussein, Andreas Börner, Asmaa A. M. Ahmed
Unlike other growth stages of wheat, very few studies on drought tolerance have been done at the seedling stage, and this is due to the complexity and sensitivity of this stage to drought stress resulting from climate change. As a result, the drought tolerance of wheat seedlings is poorly understood and very few genes associated with drought tolerance at this stage were identified. To address this
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Mapping the genetic architecture of low‐temperature stress tolerance in citron watermelon Plant Genome (IF 4.219) Pub Date : 2024-03-11 Dennis N. Katuuramu, Amnon Levi, William P. Wechter
Sweet‐fleshed watermelon (Citrullus lanatus) is an important vegetable crop of the tropical origin. It is widely grown and consumed around the world for its hydration and nutritional quality values. Low‐temperature stress can affect early planting, seedling establishment, and expansion of crop production to new areas. A collection of 122 citron watermelon (Citrullus amarus) accessions were obtained
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Cloning and functional analysis of Gb4CL1 and Gb4CL2 from Ginkgo biloba Plant Genome (IF 4.219) Pub Date : 2024-03-11 Xian Zhou, Jie Cao, Xiao‐Meng Liu, Li‐Na Wang, Wei‐wei Zhang, Jia‐Bao Ye, Feng Xu, Shuiyuan Cheng
4‐Coumarate‐CoA ligase (4CL) gene plays vital roles in plant growth and development, especially the regulation of lignin metabolism and flavonoid synthesis. To investigate the potential function of 4CL in the lignin biosynthesis of Ginkgo biloba, this study identified two 4CL genes, Gb4CL1 and Gb4CL2, from G. biloba genome. Based on the phylogenetic tree analysis, Gb4CL1 and Gb4CL2 protein were classified
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A chromosome‐level genome of mango exclusively from long‐read sequence data Plant Genome (IF 4.219) Pub Date : 2024-03-11 Upendra Kumari Wijesundara, Ardashir Kharabian Masouleh, Agnelo Furtado, Natalie L. Dillon, Robert J. Henry
Improvements in long‐read sequencing techniques have greatly accelerated plant genome sequencing. Current de novo assemblies are routinely achieved by assembling long‐read sequence data into contigs that are assembled to chromosome level by chromatin conformation capture. We report here a chromosome‐level mango genome using only PacBio high‐fidelity (HiFi) long reads. HiFi reads at high coverage (204x)
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Validation of sorghum quality control (QC) markers across African breeding lines Plant Genome (IF 4.219) Pub Date : 2024-02-27 Davis M. Gimode, Grace Ochieng, Santosh Deshpande, Eric O. Manyasa, Clarisse P. Kondombo, Erick O. Mikwa, Millicent O. Avosa, Josephine Sarah Kunguni, Kahiu Ngugi, Patrick Sheunda, McDonald Bright Jumbo, Damaris A. Odeny
Sorghum [Sorghum bicolor (L.) Moench] is a cereal crop of critical importance in the semi‐arid tropics, particularly in Africa where it is second only to maize (Zea mays L.) by area of cultivation. The International Crops Research Institute for the Semi‐Arid Tropics sorghum breeding program for Eastern and Southern Africa is the largest in the region and develops improved varieties for target agro‐ecologies
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A Bayesian optimization R package for multitrait parental selection Plant Genome (IF 4.219) Pub Date : 2024-02-22 Bartolo de J. Villar‐Hernández, Susanne Dreisigacker, Leo Crespo, Paulino Pérez‐Rodríguez, Sergio Pérez‐Elizalde, Fernando Toledo, José Crossa
Selecting and mating parents in conventional phenotypic and genomic selection are crucial. Plant breeding programs aim to improve the economic value of crops, considering multiple traits simultaneously. When traits are negatively correlated and/or when there are missing records in some traits, selection becomes more complex. To address this problem, we propose a multitrait selection approach using
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Approaches and progress in breeding drought‐tolerant maize hybrids for tropical lowlands in west and central Africa Plant Genome (IF 4.219) Pub Date : 2024-02-21 Abebe Menkir, Ibnou Dieng, Melaku Gedil, Wende Mengesha, Muhyideen Oyekunle, Priscillia F. Riberio, Gloria Boakyewaa Adu, Abdoul‐Madjidou Yacoubou, Mmadou Coulibaly, Folusho A. Bankole, John Derera, Bunmi Bossey, Nnanna Unachukwu, Yinka Ilesanmi, Silvestro Meseka
Drought represents a significant production challenge to maize farmers in West and Central Africa, causing substantial economic losses. Breeders at the International Institute of Tropical Agriculture have therefore been developing drought‐tolerant maize varieties to attain high grain yields in rainfed maize production zones. The present review provides a historical overview of the approaches used and
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Genome-wide identification, gene expression and haplotype analysis of the rhomboid-like gene family in wheat (Triticum aestivum L.) Plant Genome (IF 4.219) Pub Date : 2024-02-13 Yanyan Zhang, Xiaoya Huang, Long Zhang, Weidong Gao, Jingfu Ma, Tao Chen, Delong Yang
The rhomboid-like (RBL) gene encodes serine protease, which plays an important role in the response to cell development and diverse stresses. However, genome-wide identification, expression profiles, and haplotype analysis of the RBL family genes have not been performed in wheat (Triticum aestivum L.). This study investigated the phylogeny and diversity of the RBL family genes in the wheat genome through
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Erratum to: Fertilization of grapevine based on gene expression Plant Genome (IF 4.219) Pub Date : 2024-02-10
Cheng Zhang, Haifeng Jia, Jingjue Zeng, Tariq Pervaiz, Zhenqiang Xie, Xudong Zhu, Chen Wang Volume 9, Issue 3, The Plant Genome | First published online July 21, 2016 First published November 1, 2016 | https://doi.org/10.3835/plantgenome2015.09.0083 This article corrects the following: Tariq Pervaiz's name was misspelled as Tariq Perraiz in the published version.
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Multi-locus genome-wide association study reveal genomic regions underlying root system architecture traits in Ethiopian sorghum germplasm Plant Genome (IF 4.219) Pub Date : 2024-02-15 Masarat Elias, Diriba Chere, Dagnachew Lule, Desalegn Serba, Alemu Tirfessa, Dandena Gelmesa, Tesfaye Tesso, Kassahun Bantte, Temesgen M. Menamo
The identification of genomic regions underlying the root system architecture (RSA) is vital for improving crop abiotic stress tolerance. To improve sorghum (Sorghum bicolor L. Moench) for environmental stress tolerance, information on genetic variability and genomic regions linked to RSA traits is paramount. The aim of this study was, therefore, to investigate common quantitative trait nucleotides
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Comparative genomics points to tandem duplications of SAD gene clusters as drivers of increased α-linolenic (ω-3) content in S. hispanica seeds Plant Genome (IF 4.219) Pub Date : 2024-02-10 Tannaz Zare, Jeff F. Paril, Emma M. Barnett, Parwinder Kaur, Rudi Appels, Berit Ebert, Ute Roessner, Alexandre Fournier-Level
Salvia hispanica L. (chia) is a source of abundant ω-3 polyunsaturated fatty acids (ω-3-PUFAs) that are highly beneficial to human health. The genomic basis for this accrued ω-3-PUFA content in this emerging crop was investigated through the assembly and comparative analysis of a chromosome-level reference genome for S. hispanica. The highly contiguous 321.5-Mbp genome assembly covering all six chromosomes
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Genome-wide analysis of PvMADS in common bean and functional characterization of PvMADS31 in Arabidopsis thaliana as a player in abiotic stress responses Plant Genome (IF 4.219) Pub Date : 2024-02-07 Karam Mostafa, Bayram Ali Yerlikaya, Mohamed Farah Abdulla, Abdullah Aydin, Seher Yerlikaya, Musa Kavas
Changing climatic conditions with rising temperatures and altered precipitation patterns pose significant challenges to agricultural productivity, particularly for common bean crops. Transcription factors (TFs) are crucial regulators that can mitigate the impact of biotic and abiotic stresses on crop production. The MADS-box TFs family has been implicated in various plant physiological processes, including
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Simulations of multiple breeding strategy scenarios in common bean for assessing genomic selection accuracy and model updating Plant Genome (IF 4.219) Pub Date : 2024-02-05 Isabella Chiaravallotti, Jennifer Lin, Vivi Arief, Zulfi Jahufer, Juan M. Osorno, Phil McClean, Diego Jarquin, Valerio Hoyos-Villegas
The aim of this study was to evaluate the accuracy of the ridge regression best linear unbiased prediction model across different traits, parent population sizes, and breeding strategies when estimating breeding values in common bean (Phaseolus vulgaris). Genomic selection was implemented to make selections within a breeding cycle and compared across five different breeding strategies (single seed
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Effects of SNP marker density and training population size on prediction accuracy in alfalfa (Medicago sativa L.) genomic selection Plant Genome (IF 4.219) Pub Date : 2024-01-23 Hu Wang, Yuguang Bai, Bill Biligetu
Effects of individual single-nucleotide polymorphism (SNP) markers and the size of “training” and “test” populations affect prediction accuracy in genomic selection (GS). This study evaluated 11 subsets of 4932 SNPs using six genetic additive methods to understand marker density in GS prediction in alfalfa (Medicago sativa L.). In the GS methods, the effect of “training” to “test” population size was
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Common signatures of selection reveal target loci for breeding across soybean populations Plant Genome (IF 4.219) Pub Date : 2024-01-23 João Paulo Gomes Viana, Arián Avalos, Zhihai Zhang, Randall Nelson, Matthew E. Hudson
Understanding the underlying genetic bases of yield-related selection and distinguishing these changes from genetic drift are critical for both improved understanding and future success of plant breeding. Soybean [Glycine max (L.) Merr.] is a key species for world food security, yet knowledge of the mechanism of selective breeding in soybean, such as the century-long program of artificial selection
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Genome-wide association mapping for field spot blotch resistance in South Asian spring wheat genotypes Plant Genome (IF 4.219) Pub Date : 2024-01-14 Umesh Kamble, Xinyao He, Sudhir Navathe, Manjeet Kumar, Madhu Patial, Muhammad Rezaul Kabir, Gyanendra Singh, Gyanendra Pratap Singh, Arun Kumar Joshi, Pawan Kumar Singh
Spot blotch caused by Bipolaris sorokiniana ((Sacc.) Shoemaker) (teleomorph: Cochliobolus sativus [Ito and Kuribayashi] Drechsler ex Dastur) is an economically important disease of warm and humid regions. The present study focused on identifying resistant genotypes and single-nucleotide polymorphism (SNP) markers associated with spot blotch resistance in a panel of 174 bread spring wheat lines using
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Genomic-wide identification and expression analysis of AP2/ERF transcription factors in Zanthoxylum armatum reveals the candidate genes for the biosynthesis of terpenoids Plant Genome (IF 4.219) Pub Date : 2023-12-21 Xiaomeng Liu, Weiwei Zhang, Ning Tang, Zexiong Chen, Shen Rao, Hua Cheng, Chengrong Luo, Jiabao Ye, Shuiyuan Cheng, Feng Xu
Terpenoids are the main active components in the Zanthoxylum armatum leaves, which have extensive medicinal value. The Z. armatum leaf is the main by-product in the Z. armatum industry. However, the transcription factors involved in the biosynthesis of terpenoids are rarely reported. This study was performed to identify and classify the APETALA2/ethylene-responsive factor (AP2/ERF) gene family of Z
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Research highlights, The Plant Genome, Volume 16, Issue 4 Plant Genome (IF 4.219) Pub Date : 2023-12-20
1 EPIGENOME AND EPITRANSCRIPTOME IN PLANT–ENVIRONMENT INTERACTIONS Understanding how plants react and adapt to different environmental conditions is essential for crop improvement in sustainable agriculture. Recent technological advances have enabled high-throughput profiling of plant epigenome and epi-transcriptome, which are important aspects in gene regulation in plant response to environmental
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Genetic mapping of dynamic control of leaf angle across multiple canopy levels in maize Plant Genome (IF 4.219) Pub Date : 2023-12-20 Matthew J. Dzievit, Xianran Li, Jianming Yu
Optimizing leaf angle and other canopy architecture traits has helped modern maize (Zea mays L.) become adapted to higher planting densities over the last 60 years. Traditional investigations into genetic control of leaf angle have focused on one leaf or the average of multiple leaves; as a result, our understanding of genetic control across multiple canopy levels is still limited. To address this
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The Plant Genome special section: Epigenome and epitranscriptome in plant–environment interactions Plant Genome (IF 4.219) Pub Date : 2023-12-20 Wai-Shing Yung, Ting-Fung Chan, Fanjiang Kong, Hon-Ming Lam
Understanding how plants interact with the external environment is critical for improving crops' adaptation to environmental stresses and restoring marginal lands to fulfill food demand under the changing climate. In response to environmental cues, plants utilize the dynamic epigenome to modulate and fine-tune the temporal gene expression for development and stress adaptation (Lloyd & Lister, 2022)
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The Plant Genome special section: Grain quality and nutritional genomics for breeding next-generation crops Plant Genome (IF 4.219) Pub Date : 2023-12-20 Manish K. Pandey, Reyazul Rouf Mir, Nese Sreenivasulu
By 2050, the world's population is expected to reach 9.8 billion according to United Nations predictions (https://www.un.org/en/desa/world-population-projected-reach-98-billion-2050-and-112-billion-2100). As a result, crop yields must roughly double in order to feed an expanding global population while still satisfying consumer demands for grain quality and nutrition. In addition to enhancing the nutritional
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A new wild emmer wheat panel allows to map new loci associated with resistance to stem rust at seedling stage Plant Genome (IF 4.219) Pub Date : 2023-12-12 Anna Maria Mastrangelo, Pablo Roncallo, Oadi Matny, Čegan Radim, Brian Steffenson, Viviana Echenique, Jan Šafář, Raffaella Battaglia, Delfina Barabaschi, Luigi Cattivelli, Hakan Özkan, Elisabetta Mazzucotelli
Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major wheat disease worldwide. A collection of 283 wild emmer wheat [Triticum turgidum L. subsp. dicoccoides (Körn. ex Asch. & Graebn.) Thell] accessions, representative of the entire Fertile Crescent region where wild emmer naturally occurs, was assembled, genotyped, and characterized for population structure, genetic diversity
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Identification of diagnostic KASP-SNP markers for routine breeding activities in yam (Dioscorea spp.) Plant Genome (IF 4.219) Pub Date : 2023-12-13 Paterne A. Agre, Lindsay V. Clark, Ana Luisa Garcia-Oliveira, Rajaguru Bohar, Patrick Adebola, Robert Asiedu, Ryohei Terauchi, Asrat Asfaw
Maintaining genetic purity and true-to-type clone identification are important action steps in breeding programs. This study aimed to develop a universal set of kompetitive allele-specific polymerase chain reaction (KASP)-based single nucleotide polymorphism (SNP) markers for routine breeding activities. Ultra-low-density SNP markers were created using an initial set of 173,675 SNPs that were obtained
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Identification of a new Rsg1 allele conferring resistance to multiple greenbug biotypes from barley accessions PI 499276 and PI 566459 Plant Genome (IF 4.219) Pub Date : 2023-12-13 Xiangyang Xu, Dolores Mornhinweg, Guihua Bai, Genqiao Li, Ruolin Bian, Amy Bernardo, J. Scott Armstrong
Greenbug [Schizaphis graminum (Rondani)] is a major insect pest that significantly affects barley production worldwide. The identification of novel greenbug resistance genes is crucial for sustainable barley production and global food security. To identify greenbug resistance genes from a US breeding line PI 499276 and a Chinese cultivar PI 566459, two F6:7 recombinant inbred line (RIL) populations
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The alleles bc-ud and bc-ur (previously bc-4 gene), representing coding mutations within Vps4 AAA+ ATPase ESCRT protein, interact with other genes to condition resistance to BCMV and BCMNV in common bean Plant Genome (IF 4.219) Pub Date : 2023-12-12 Alvaro Soler-Garzón, Phillip E. McClean, Phillip N. Miklas
Bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV) have a damaging impact on global common bean (Phaseolus vulgaris L.) cultivation, causing potential yield losses of over 80%. The primary strategy for controlling these viruses is through host plant resistance. This research aimed to identify and validate structural variations for the bc-ud gene as revealed by long-read sequencing
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Soybean genetics, genomics, and breeding for improving nutritional value and reducing antinutritional traits in food and feed Plant Genome (IF 4.219) Pub Date : 2023-12-12 William M. Singer, Yi-Chen Lee, Zachary Shea, Caio Canella Vieira, Dongho Lee, Xiaoying Li, Mia Cunicelli, Shaila S. Kadam, Mohammad Aamir Waseem Khan, Grover Shannon, M. A. Rouf Mian, Henry T. Nguyen, Bo Zhang
Soybean [Glycine max (L.) Merr.] is a globally important crop due to its valuable seed composition, versatile feed, food, and industrial end-uses, and consistent genetic gain. Successful genetic gain in soybean has led to widespread adaptation and increased value for producers, processors, and consumers. Specific focus on the nutritional quality of soybean seed composition for food and feed has further
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Use of continuous genotypes for genomic prediction in sugarcane Plant Genome (IF 4.219) Pub Date : 2023-12-08 Seema Yadav, Elizabeth M. Ross, Xianming Wei, Shouye Liu, Loan To Nguyen, Owen Powell, Lee T. Hickey, Emily Deomano, Felicity Atkin, Kai P. Voss-Fels, Ben J. Hayes
Genomic selection in sugarcane faces challenges due to limited genomic tools and high genomic complexity, particularly because of its high and variable ploidy. The classification of genotypes for single nucleotide polymorphisms (SNPs) becomes difficult due to the wide range of possible allele dosages. Previous genomic studies in sugarcane used pseudo-diploid genotyping, grouping all heterozygotes into
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Durum wheat heat tolerance loci defined via a north–south gradient Plant Genome (IF 4.219) Pub Date : 2023-12-07 Amadou Tidiane Sall, Hafssa Kabbaj, Sidi ould Ely Menoum, Madiama Cisse, Mulatu Geleta, Rodomiro Ortiz, Filippo M. Bassi
The global production of durum wheat (Triticum durum Desf.) is hindered by a constant rise in the frequency of severe heat stress events. To identify heat-tolerant germplasm, three different germplasm panels (“discovery,” “investigation,” and “validation”) were studied under a range of heat-stressed conditions. Grain yield (GY) and its components were recorded at each site and a heat stress susceptibility
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Transcriptome analysis of iron over-accumulating Arabidopsis genotypes uncover putative novel regulators of systemic and retrograde signaling Plant Genome (IF 4.219) Pub Date : 2023-12-06 Louis Grillet, En-Jung Hsieh, Wolfgang Schmidt
On account of its competence to accept and donate electrons, iron (Fe) is an essential element across all forms of life, including plants. Maintaining Fe homeostasis requires precise orchestration of its uptake, trafficking, and translocation in order to meet the demand for Fe sinks such as plastids. Plants harboring defects in the systemic Fe transporter OPT3 (OLIGOPEPTIDE TRANSPORTER 3) display constitutive
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Precision genetics tools for genetic improvement of banana Plant Genome (IF 4.219) Pub Date : 2023-11-27 Jaindra Nath Tripathi, Valentine Otang Ntui, Leena Tripathi
Banana is an important food security crop for millions of people in the tropics but it faces challenges from diseases and pests. Traditional breeding methods have limitations, prompting the exploration of precision genetic tools like genetic modification and genome editing. Extensive efforts using transgenic approaches have been made to develop improved banana varieties with resistance to banana Xanthomonas
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Genomic and phenotypic characterization of finger millet indicates a complex diversification history Plant Genome (IF 4.219) Pub Date : 2023-11-20 Jon Bančič, Damaris A. Odeny, Henry F. Ojulong, Samuel M. Josiah, Jaap Buntjer, R. Chris Gaynor, Stephen P. Hoad, Gregor Gorjanc, Ian K. Dawson
Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub-genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from
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HaploCatcher: An R package for prediction of haplotypes Plant Genome (IF 4.219) Pub Date : 2023-11-15 Zachary James Winn, Emily Hudson-Arns, Mikayla Hammers, Noah DeWitt, Jeanette Lyerly, Guihua Bai, Paul St. Amand, Punya Nachappa, Scott Haley, Richard Esten Mason
Wheat (Triticum aestivum L.) is crucial to global food security but is often threatened by diseases, pests, and environmental stresses. Wheat-stem sawfly (Cephus cinctus Norton) poses a major threat to food security in the United States, and solid-stem varieties, which carry the stem-solidness locus (Sst1), are the main source of genetic resistance against sawfly. Marker-assisted selection uses molecular
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Characterization of the CMS genetic regulation through comparative complete mitochondrial genome sequencing in Nicotiana tabacum Plant Genome (IF 4.219) Pub Date : 2023-11-14 Dongli He, Yifan Li, Cheng Yuan, Xiaoxiong Pei, Rebecca N. Damaris, Haiqin Yu, Bao Qian, Yong Liu, Bin Yi, Changjun Huang, Jianmin Zeng
Mitochondrial genomes (mitogenomes) of flowering plants vary greatly in structure and size, which can lead to frequent gene mutation, rearrangement, or recombination, then result in the cytoplasmic male sterile (CMS) mutants. In tobacco (Nicotiana tabacum), suaCMS lines are widely used in heterosis breeding; however, the related genetic regulations are not very clear. In this study, the cytological
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Genome scans capture key adaptation and historical hybridization signatures in tetraploid wheat Plant Genome (IF 4.219) Pub Date : 2023-11-16 Demissew Sertse, Jemanesh K. Haile, Ehsan Sari, Valentyna Klymiuk, Amidou N'Diaye, Curtis J. Pozniak, Sylvie Cloutier, Sateesh Kagale
Tetraploid wheats (Triticum turgidum L.), including durum wheat (T. turgidum ssp. durum (Desf.) Husn.), are important crops with high nutritional and cultural values. However, their production is constrained by sensitivity to environmental conditions. In search of adaptive genetic signatures tracing historical selection and hybridization events, we performed genome scans on two datasets: (1) Durum
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Genetic dissection of domestication traits in interspecific chickpea populations Plant Genome (IF 4.219) Pub Date : 2023-11-14 Toby E. Newman, Silke Jacques, Christy Grime, Fredrick M. Mobegi, Fiona L. Kamphuis, Yuphin Khentry, Robert Lee, Lars G. Kamphuis
Chickpea (Cicer arietinum) is a pulse crop that provides an integral source of nutrition for human consumption. The close wild relatives Cicer reticulatum and Cicer echinospermum harbor untapped genetic diversity that can be exploited by chickpea breeders to improve domestic varieties. Knowledge of genomic loci that control important chickpea domestication traits will expedite the development of improved
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Accelerating genetic gains for quantitative resistance to verticillium wilt through predictive breeding in strawberry Plant Genome (IF 4.219) Pub Date : 2023-11-14 Mitchell J. Feldmann, Dominique D. A. Pincot, Mishi V. Vachev, Randi A. Famula, Glenn S. Cole, Steven J. Knapp
Verticillium wilt (VW), a devastating vascular wilt disease of strawberry (Fragaria × ananassa), has caused economic losses for nearly a century. This disease is caused by the soil-borne pathogen Verticillium dahliae, which occurs nearly worldwide and causes disease in numerous agriculturally important plants. The development of VW-resistant cultivars is critically important for the sustainability
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Advances and opportunities in unraveling cold-tolerance mechanisms in the world's primary staple food crops Plant Genome (IF 4.219) Pub Date : 2023-11-13 Sofora Jan, Sachin Rustgi, Rutwik Barmukh, Asif B. Shikari, Brenton Leske, Amanuel Bekuma, Darshan Sharma, Wujun Ma, Upendra Kumar, Uttam Kumar, Abhishek Bohra, Rajeev K. Varshney, Reyazul Rouf Mir
Temperatures below or above optimal growth conditions are among the major stressors affecting productivity, end-use quality, and distribution of key staple crops including rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays L.). Among temperature stresses, cold stress induces cellular changes that cause oxidative stress and slowdown metabolism, limit growth, and ultimately reduce crop
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Rapid analysis of hydrogen cyanide in fresh cassava roots using NIRSand machine learning algorithms: Meeting end user demand for low cyanogenic cassava Plant Genome (IF 4.219) Pub Date : 2023-11-08 Michael Kanaabi, Fatumah B. Namakula, Ephraim Nuwamanya, Ismail S. Kayondo, Nicholas Muhumuza, Enoch Wembabazi, Paula Iragaba, Leah Nandudu, Ann Ritah Nanyonjo, Julius Baguma, Williams Esuma, Alfred Ozimati, Mukasa Settumba, Titus Alicai, Angele Ibanda, Robert S. Kawuki
This study focuses on meeting end-users’ demand for cassava (Manihot esculenta Crantz) varieties with low cyanogenic potential (hydrogen cyanide potential [HCN]) by using near-infrared spectrometry (NIRS). This technology provides a fast, accurate, and reliable way to determine sample constituents with minimal sample preparation. The study aims to evaluate the effectiveness of machine learning (ML)
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Genomic analysis and characterization of new loci associated with seed protein and oil content in soybeans Plant Genome (IF 4.219) Pub Date : 2023-11-08 Tri D. Vuong, Liliana Florez-Palacios, Leandro Mozzoni, Michael Clubb, Chuck Quigley, Qijian Song, Shaila Kadam, Yuxuan Yuan, Ting Fung Chan, Mohamed Abdur Rouf Mian, Henry T. Nguyen
Breeding for increased protein without a reduction in oil content in soybeans [Glycine max (L.) Merr.] is a challenge for soybean breeders but an expected goal. Many efforts have been made to develop new soybean varieties with high yield in combination with desirable protein and/or oil traits. An elite line, R05-1415, was reported to be high yielding, high protein, and low oil. Several significant
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A medium-density genotyping platform for cultivated strawberry using DArTag technology Plant Genome (IF 4.219) Pub Date : 2023-11-08 Michael A. Hardigan, Mitchell J. Feldmann, Jason Carling, Anyu Zhu, Andrzej Kilian, Randi A. Famula, Glenn S. Cole, Steven J. Knapp
Genomic prediction in breeding populations containing hundreds to thousands of parents and seedlings is prohibitively expensive with current high-density genetic marker platforms designed for strawberry. We developed mid-density panels of molecular inversion probes (MIPs) to be deployed with the “DArTag” marker platform to provide a low-cost, high-throughput genotyping solution for strawberry genomic
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Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids Plant Genome (IF 4.219) Pub Date : 2023-10-30 Joyce N. Njuguna, Lindsay V. Clark, Alexander E. Lipka, Kossonou G. Anzoua, Larisa Bagmet, Pavel Chebukin, Maria S. Dwiyanti, Elena Dzyubenko, Nicolay Dzyubenko, Bimal Kumar Ghimire, Xiaoli Jin, Douglas A. Johnson, Jens Bonderup Kjeldsen, Hironori Nagano, Ivone de Bem Oliveira, Junhua Peng, Karen Koefoed Petersen, Andrey Sabitov, Eun Soo Seong, Toshihiko Yamada, Ji Hye Yoo, Chang Yeon Yu, Hua Zhao
Discovery and analysis of genetic variants underlying agriculturally important traits are key to molecular breeding of crops. Reduced representation approaches have provided cost-efficient genotyping using next-generation sequencing. However, accurate genotype calling from next-generation sequencing data is challenging, particularly in polyploid species due to their genome complexity. Recently developed
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Genome-wide identification and expression analysis of heat shock protein gene family in cassava Plant Genome (IF 4.219) Pub Date : 2023-10-29 Changyi Wang, Fangfang Ran, Yuwei Zang, Liangwang Liu, Dayong Wang, Yi Min
Heat shock proteins are important molecular chaperones that are involved in plant growth and stress responses. However, members of the Hsp family have been poorly studied in cassava. In this study, 225 MeHsp genes were identified in the cassava genome, and their genetic structures exhibited relatively conserved features within each subfamily. The 225 MeHsp genes showed random chromosomal distribution
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Genome-wide dissection and haplotype analysis identified candidate loci for nitrogen use efficiency under drought conditions in winter wheat Plant Genome (IF 4.219) Pub Date : 2023-10-25 Ahossi Patrice Koua, Md. Nurealam Siddiqui, Katrin Heß, Nikko Klag, Carolyn Mukiri Kambona, Diana Duarte-Delgado, Benedict Chijioke Oyiga, Jens Léon, Agim Ballvora
Climate change causes extreme conditions like prolonged drought, which results in yield reductions due to its effects on nutrient balances such as nitrogen uptake and utilization by plants. Nitrogen (N) is a crucial nutrient element for plant growth and productivity. Understanding the mechanistic basis of nitrogen use efficiency (NUE) under drought conditions is essential to improve wheat (Triticum
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Mapping QTL for vernalization requirement identified adaptive divergence of the candidate gene Flowering Locus C in polyploid Camelina sativa Plant Genome (IF 4.219) Pub Date : 2023-10-26 Raju Chaudhary, Erin E. Higgins, Christina Eynck, Andrew G. Sharpe, Isobel A. P. Parkin
Vernalization requirement is an integral component of flowering in winter-type plants. The availability of winter ecotypes among Camelina species facilitated the mapping of quantitative trait loci (QTL) for vernalization requirement in Camelina sativa. An inter and intraspecific crossing scheme between related Camelina species, where one spring and two different sources of winter-type habit were used
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Identification of robust yield quantitative trait loci derived from cultivated emmer for durum wheat improvement Plant Genome (IF 4.219) Pub Date : 2023-10-24 Amanda R. Peters Haugrud, Jyoti Saini Sharma, Qijun Zhang, Andrew J. Green, Steven S. Xu, Justin D. Faris
Durum wheat (Triticum turgidum ssp. durum L.) is an important world food crop used to make pasta products. Compared to bread wheat (Triticum aestivum L.), fewer studies have been conducted to identify genetic loci governing yield-component traits in durum wheat. A potential source of diversity for durum is its immediate progenitor, cultivated emmer (T. turgidum ssp. dicoccum). We evaluated two biparental
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Understanding role of roots in plant response to drought: Way forward to climate-resilient crops Plant Genome (IF 4.219) Pub Date : 2023-10-18 Anmol Kalra, Shailendra Goel, Ani A. Elias
Drought stress leads to a significant amount of agricultural crop loss. Thus, with changing climatic conditions, it is important to develop resilience measures in agricultural systems against drought stress. Roots play a crucial role in regulating plant development under drought stress. In this review, we have summarized the studies on the role of roots and root-mediated plant responses. We have also
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Analyzing genomic variation in cultivated pumpkins and identification of candidate genes controlling seed traits Plant Genome (IF 4.219) Pub Date : 2023-09-29 Chieh-Ying Lee, Jaw-Fen Wang, Chia-Hui Chang, Chih-Wei Tung
Pumpkins are important vegetable crops widely grown worldwide, and seeds are considered a popular nutraceutical food and an excellent source of protein, oil, and vitamins. Seed size is one of the most important targets for commercial breeding in Cucurbita species; studies have shown that pumpkin seed size variation has a similar trend with fruit size, shape, and seed yield. However, few studies have
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Genomic selection of soybean (Glycine max) for genetic improvement of yield and seed composition in a breeding context Plant Genome (IF 4.219) Pub Date : 2023-09-25 Mark J. Miller, Qijian Song, Zenglu Li
Genomic selection has been utilized for genetic improvement in both plant and animal breeding and is a favorable technique for quantitative trait development. Within this study, genomic selection was evaluated within a breeding program, using novel validation methods in addition to plant materials and data from a commercial soybean (Glycine max) breeding program. A total of 1501 inbred lines were used
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Near-gapless genome assemblies of Williams 82 and Lee cultivars for accelerating global soybean research Plant Genome (IF 4.219) Pub Date : 2023-09-25 Vanika Garg, Aamir W. Khan, Kevin Fengler, Victor Llaca, Yuxuan Yuan, Tri D. Vuong, Charlotte Harris, Ting-Fung Chan, Hon Ming Lam, Rajeev K. Varshney, Henry T. Nguyen
Complete, gapless telomere-to-telomere chromosome assemblies are a prerequisite for comprehensively investigating the architecture of complex regions, like centromeres or telomeres and removing uncertainties in the order, spacing, and orientation of genes. Using complementary genomics technologies and assembly algorithms, we developed highly contiguous, nearly gapless, genome assemblies for two economically
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Genomic prediction with machine learning in sugarcane, a complex highly polyploid clonally propagated crop with substantial non-additive variation for key traits Plant Genome (IF 4.219) Pub Date : 2023-09-20 Chensong Chen, Owen Powell, Eric Dinglasan, Elizabeth M. Ross, Seema Yadav, Xianming Wei, Felicity Atkin, Emily Deomano, Ben J. Hayes
Sugarcane has a complex, highly polyploid genome with multi-species ancestry. Additive models for genomic prediction of clonal performance might not capture interactions between genes and alleles from different ploidies and ancestral species. As such, genomic prediction in sugarcane presents an interesting case for machine learning (ML) methods, which are purportedly able to deal with high levels of
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Genetic erosion within the Fabada dry bean market class revealed by high-throughput genotyping Plant Genome (IF 4.219) Pub Date : 2023-09-19 Maria Jurado, Carmen García-Fernández, Ana Campa, Juan Jose Ferreira
The Fabada market class within the dry beans has a well-differentiated seed phenotype with very large white seeds. This work investigated the genetic diversity maintained in the seed collections within this market class and possible genetic erosion over the last 30 years. A panel with 100 accessions was maintained in seed collections for 30 years, 57 accessions collected from farmers in 2021, six cultivars
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Genome-wide association study of soluble solids content, flesh color, and fruit shape in citron watermelon Plant Genome (IF 4.219) Pub Date : 2023-09-18 Dennis N. Katuuramu, Amnon Levi, William P. Wechter
Fruit quality traits are crucial determinants of consumers’ willingness to purchase watermelon produce, making them major goals for breeding programs. There is limited information on the genetic underpinnings of fruit quality traits in watermelon. A total of 125 citron watermelon (Citrullus amarus) accessions were genotyped using single nucleotide polymorphisms (SNPs) molecular markers generated via
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Editorial Board Plant Genome (IF 4.219) Pub Date : 2023-09-11
On the cover: Plant breeding efforts on hybrid rye outshining parental lines. Photo credit: Maria Santoro.
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Salinity stress tolerance prediction for biomass-related traits in maize (Zea mays L.) using genome-wide markers Plant Genome (IF 4.219) Pub Date : 2023-09-04 Vishal Singh, Margaret Krause, Devinder Sandhu, Rajandeep S. Sekhon, Amita Kaundal
Maize (Zea mays L.) is the third most important cereal crop after rice (Oryza sativa) and wheat (Triticum aestivum). Salinity stress significantly affects vegetative biomass and grain yield and, therefore, reduces the food and silage productivity of maize. Selecting salt-tolerant genotypes is a cumbersome and time-consuming process that requires meticulous phenotyping. To predict salt tolerance in
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Whole-genome versus per-chromosome targeted recombination: Simulations and predicted gains in maize with an integer programming model Plant Genome (IF 4.219) Pub Date : 2023-09-04 John N. Cameron, Rex Bernardo
Per-chromosome targeted recombination, with one to two recombinations at specific marker intervals on each chromosome, doubles the predicted genetic gains in biparental populations. We developed an integer programing model to identify where a fixed number of targeted recombinations should occur across the whole genome, without restrictions on the number of targeted recombinations on each chromosome
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Research highlights, The Plant Genome, Volume 16, Issue 3 Plant Genome (IF 4.219) Pub Date : 2023-08-31
1 TRANSCRIPTOMICS UNCOVERS FUSARIUM WILT RESISTANCE IN CHICKPEA Fusarium wilt (FW), caused by Fusarium oxysporum f. sp. ciceris (Foc), is a devastating soilborne disease that causes significant yield losses in chickpea worldwide. Management of FW through crop rotation strategies or chemical control is challenging, and thus, resistance breeding is the most cost-effective and environmentally sustainable