The Plant Genome最新文献

{"title":"Identification of diagnostic KASP-SNP markers for routine breeding activities in yam (Dioscorea spp.)","authors":"Paterne A. Agre, Lindsay V. Clark, Ana Luisa Garcia-Oliveira, Rajaguru Bohar, Patrick Adebola, Robert Asiedu, Ryohei Terauchi, Asrat Asfaw","doi":"10.1002/tpg2.20419","DOIUrl":"https://doi.org/10.1002/tpg2.20419","url":null,"abstract":"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 from whole-genome resequencing of 333 diverse white Guinea yam (<i>Dioscorea rotundata</i> Poir) genotypes. From whole-genome resequencing data, 99 putative SNP markers were found and successfully converted to high-throughput KASP genotyping assays. The markers set was validated on 374 genotypes representing six yam species. Out of the 99 markers, 50 were highly polymorphic across the species and could distinguish different yam species and pedigree origins. The selected SNP markers classified the validation population based on the different yam species and identified potential duplicates within yam species. Through penalized analysis, the male parent of progenies involved in polycrosses was successfully predicted and validated. Our research was a trailblazer in validating KASP-based SNP assays for species identification, parental fingerprinting, and quality control (QC) and quality assurance (QA) in yam breeding programs.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138630409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"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","authors":"Alvaro Soler-Garzón, Phillip E. McClean, Phillip N. Miklas","doi":"10.1002/tpg2.20421","DOIUrl":"https://doi.org/10.1002/tpg2.20421","url":null,"abstract":"<i>Bean common mosaic virus</i> (BCMV) and <i>bean common mosaic necrosis virus</i> (BCMNV) have a damaging impact on global common bean (<i>Phaseolus vulgaris</i> 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 <i>bc-u</i>^d gene as revealed by long-read sequencing, develop an efficient DNA marker to assist selection of <i>bc-u</i>^d in snap and dry beans, and examine the interactions between the <i>bc-u</i>^d allele and other BCMV resistance genes. A gene (Phvul.005G125100) model on chromosome Pv05, encoding a vacuolar protein-sorting 4 (Vps4) AAA+ ATPase endosomal sorting complexes required for transport (ESCRT) protein, was identified as the best candidate gene for <i>bc-u</i>^d. An 84-bp repetitive insertion variant within the gene, exhibited 100% co-segregation with the <i>bc-u</i>^d resistance allele across 264 common bean accessions. The 84-bp repetitive insertion was labeled with an indel marker IND_05_36225873 which was useful for tracking the <i>bc-u</i>^d allele across diverse germplasm. A different single nucleotide polymorphism variant within the same candidate gene was associated with the <i>bc-4</i> gene. Segregation in F₂ populations confirmed <i>bc-u</i>^d and <i>bc-4</i> were alleles, so <i>bc-4</i> was renamed <i>bc-u</i>^r to fit gene nomenclature guidelines. The interactions of <i>bc-u</i>^d and <i>bc-u</i>^r with other resistance genes, such as <i>bc-1</i> (receptor-like kinase on Pv03) and <i>bc-2</i> (Vps4 AAA+ ATPase ESCRT protein on Pv11), validated gene combinations in the differential “host groups” effective against specific BCMV/BCMNV “pathogroups.” These findings increase our understanding of the <i>Bc-u</i> locus, and enhance our ability to develop more resilient bean varieties through marker-assisted selection, reducing the impact of BCMV and BCMNV.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"38 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138629547","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Soybean genetics, genomics, and breeding for improving nutritional value and reducing antinutritional traits in food and feed","authors":"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","doi":"10.1002/tpg2.20415","DOIUrl":"https://doi.org/10.1002/tpg2.20415","url":null,"abstract":"Soybean [<i>Glycine max</i> (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 elucidated genetic knowledge and bolstered breeding progress. Seed components are historical and current targets for soybean breeders seeking to improve nutritional quality of soybean. This article reviews genetic and genomic foundations for improvement of nutritionally important traits, such as protein and amino acids, oil and fatty acids, carbohydrates, and specific food-grade considerations; discusses the application of advanced breeding technology such as CRISPR/Cas9 in creating seed composition variations; and provides future directions and breeding recommendations regarding soybean seed composition traits.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"195 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138572367","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A new wild emmer wheat panel allows to map new loci associated with resistance to stem rust at seedling stage","authors":"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","doi":"10.1002/tpg2.20413","DOIUrl":"https://doi.org/10.1002/tpg2.20413","url":null,"abstract":"Wheat stem rust, caused by <i>Puccinia graminis</i> f. sp. <i>tritici</i> (<i>Pgt</i>), is a major wheat disease worldwide. A collection of 283 wild emmer wheat [<i>Triticum turgidum</i> L. subsp<i>. dicoccoides</i> (Körn. ex Asch. &amp; 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, and rate of linkage disequilibrium (LD) decay. Then, the collection was employed for mapping <i>Pgt</i> resistance genes, as a proof of concept of the effectiveness of genome-wide association studies in wild emmer. The collection was evaluated in controlled conditions for reaction to six common <i>Pgt</i> pathotypes (TPMKC, TTTTF, JRCQC, TRTTF, TTKSK/Ug99, and TKTTF). Most resistant accessions originated from the Southern Levant wild emmer lineage, with some showing a resistance reaction toward three to six tested races. Association analysis was conducted considering a 12K polymorphic single-nucleotide polymorphisms dataset, kinship relatedness between accessions, and population structure. Eleven significant marker–trait associations (MTA) were identified across the genome, which explained from 17% to up to 49% of phenotypic variance with an average 1.5 additive effect (based on the 1–9 scoring scale). The identified loci were either effective against single or multiple races. Some MTAs colocalized with known <i>Pgt</i> resistance genes, while others represent novel resistance loci useful for durum and bread wheat prebreeding. Candidate genes with an annotated function related to plant response to pathogens were identified at the regions linked to the resistance and defined according to the estimated small LD (about 126 kb), as typical of wild species.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"79 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138681311","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Use of continuous genotypes for genomic prediction in sugarcane","authors":"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","doi":"10.1002/tpg2.20417","DOIUrl":"https://doi.org/10.1002/tpg2.20417","url":null,"abstract":"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 a single class. In this study, we investigate the use of continuous genotypes as a proxy for allele-dosage in genomic prediction models. The hypothesis is that continuous genotypes could better reflect allele dosage at SNPs linked to mutations affecting target traits, resulting in phenotypic variation. The dataset included genotypes of 1318 clones at 58K SNP markers, with about 26K markers filtered using standard quality controls. Predictions for tonnes of cane per hectare (TCH), commercial cane sugar (CCS), and fiber content (Fiber) were made using parametric, non-parametric, and Bayesian methods. Continuous genotypes increased accuracy by 5%–7% for CCS and Fiber. The pseudo-diploid parametrization performed better for TCH. Reproducing kernel Hilbert spaces model with Gaussian kernel and AK4 (arc-cosine kernel with hidden layer 4) kernel outperformed other methods for TCH and CCS, suggesting that non-additive effects might influence these traits. The prevalence of low-dosage markers in the study may have limited the benefits of approximating allele-dosage information with continuous genotypes in genomic prediction models. Continuous genotypes simplify genomic prediction in polyploid crops, allowing additional markers to be used without adhering to pseudo-diploid inheritance. The approach can particularly benefit high ploidy species or emerging crops with unknown ploidy.","PeriodicalId":501653,"journal":{"name":"The Plant Genome","volume":"3 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-12-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138564181","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}