Plant GenomePub Date : 2024-12-01Epub Date: 2024-10-15DOI: 10.1002/tpg2.20509
Pilar Muñoz, Francisco Javier Roldán-Guerra, Sujeet Verma, Mario Ruiz-Velázquez, Rocío Torreblanca, Nicolás Oiza, Cristina Castillejo, José F Sánchez-Sevilla, Iraida Amaya
{"title":"Genome-wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits.","authors":"Pilar Muñoz, Francisco Javier Roldán-Guerra, Sujeet Verma, Mario Ruiz-Velázquez, Rocío Torreblanca, Nicolás Oiza, Cristina Castillejo, José F Sánchez-Sevilla, Iraida Amaya","doi":"10.1002/tpg2.20509","DOIUrl":"10.1002/tpg2.20509","url":null,"abstract":"<p><p>Strawberries (Fragaria sp.) are cherished for their organoleptic properties and nutritional value. However, breeding new cultivars involves the simultaneous selection of many agronomic and fruit quality traits, including fruit firmness and extended postharvest life. The strawberry germplasm collection here studied exhibited extensive phenotypic variation in 26 agronomic and fruit quality traits across three consecutive seasons. Phenotypic correlations and principal component analysis revealed relationships among traits and accessions, emphasizing the impact of plant breeding on fruit weight and firmness to the detriment of sugar or vitamin C content. Genetic diversity analysis on 124 accessions using 44,408 markers denoted a population structure divided into six subpopulations still retaining considerable diversity. Genome-wide association studies for the 26 traits unveiled 121 significant marker-trait associations distributed across 95 quantitative trait loci (QTLs). Multiple associations were detected for fruit firmness, a key breeding target, including a prominent locus on chromosome 6A. The candidate gene FaPG1, controlling fruit softening and postharvest shelf life, was identified within this QTL region. Differential expression of FaPG1 confirmed its role as the primary contributor to natural variation in fruit firmness. A kompetitive allele-specific PCR assay based on the single nucleotide polymorphism (SNP) AX-184242253, associated with the 6A QTL, predicts a substantial increase in fruit firmness, validating its utility for marker-assisted selection. In essence, this comprehensive study provides insights into the phenotypic and genetic landscape of the strawberry collection and lays a robust foundation for propelling the development of superior strawberry cultivars through precision breeding.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20509"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628880/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478518","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-12-01Epub Date: 2024-10-15DOI: 10.1002/tpg2.20515
Velma Okaron, James Mwololo, Davis M Gimode, David K Okello, Millicent Avosa, Josh Clevenger, Walid Korani, Mildred Ochwo Ssemakula, Thomas L Odong, Damaris A Odeny
{"title":"Using cross-country datasets for association mapping in Arachis hypogaea L.","authors":"Velma Okaron, James Mwololo, Davis M Gimode, David K Okello, Millicent Avosa, Josh Clevenger, Walid Korani, Mildred Ochwo Ssemakula, Thomas L Odong, Damaris A Odeny","doi":"10.1002/tpg2.20515","DOIUrl":"10.1002/tpg2.20515","url":null,"abstract":"<p><p>Groundnut (Arachis hypogaea L.) is one of the most important climate-resilient oil crops in sub-Saharan Africa. There is a significant yield gap for groundnut in Africa because of poor soil fertility, low agricultural inputs, biotic and abiotic stresses. Cross-country evaluations of promising breeding lines can facilitate the varietal development process. The objective of our study was to characterize popular test environments in Uganda (Serere and Nakabango) and Malawi (Chitala and Chitedze) and identify genotypes with stable superior yields for potential future release. Phenotypic data were generated for 192 breeding lines for yield-related traits, while genotypic data were generated using skim-sequencing. We observed significant variation (p < 0.001; p < 0.01; p < 0.05) across genotypes for all yield-related traits: days to flowering (DTF), pod yield (PY), shelling percentage, 100-seed weight, and grain yield within and across locations. Nakabango, Chitedze, and Serere were clustered as one mega-environment with the top five most stable genotypes being ICGV-SM 01709, ICGV-SM 15575, ICGV-SM 90704, ICGV-SM 15576, and ICGV-SM 03710, all Virginia types. Population structure analysis clustered the genotypes in three distinct groups based on market classes. Eight and four marker-trait associations (MTAs) were recorded for DTF and PY, respectively. One of the MTAs for DTF was co-localized within an uncharacterized protein on chromosome 13, while another one (TRv2Chr.11_3476885) was consistent across the two countries. Future studies will need to further characterize the candidate genes as well as confirm the stability of superior genotypes across seasons before recommending them for release.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20515"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628922/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478531","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-12-01Epub Date: 2024-11-21DOI: 10.1002/tpg2.20516
Robert M Stupar, Anna M Locke, Doug K Allen, Minviluz G Stacey, Jianxin Ma, Jackie Weiss, Rex T Nelson, Matthew E Hudson, Trupti Joshi, Zenglu Li, Qijian Song, Joseph R Jedlicka, Gustavo C MacIntosh, David Grant, Wayne A Parrott, Tom E Clemente, Gary Stacey, Yong-Qiang Charles An, Jose Aponte-Rivera, Madan K Bhattacharyya, Ivan Baxter, Kristin D Bilyeu, Jacqueline D Campbell, Steven B Cannon, Steven J Clough, Shaun J Curtin, Brian W Diers, Anne E Dorrance, Jason D Gillman, George L Graef, C Nathan Hancock, Karen A Hudson, David L Hyten, Aardra Kachroo, Jenny Koebernick, Marc Libault, Aaron J Lorenz, Adam L Mahan, Jon M Massman, Michaela McGinn, Khalid Meksem, Jack K Okamuro, Kerry F Pedley, Katy Martin Rainey, Andrew M Scaboo, Jeremy Schmutz, Bao-Hua Song, Adam D Steinbrenner, Benjamin B Stewart-Brown, Katalin Toth, Dechun Wang, Lisa Weaver, Bo Zhang, Michelle A Graham, Jamie A O'Rourke
{"title":"Soybean genomics research community strategic plan: A vision for 2024-2028.","authors":"Robert M Stupar, Anna M Locke, Doug K Allen, Minviluz G Stacey, Jianxin Ma, Jackie Weiss, Rex T Nelson, Matthew E Hudson, Trupti Joshi, Zenglu Li, Qijian Song, Joseph R Jedlicka, Gustavo C MacIntosh, David Grant, Wayne A Parrott, Tom E Clemente, Gary Stacey, Yong-Qiang Charles An, Jose Aponte-Rivera, Madan K Bhattacharyya, Ivan Baxter, Kristin D Bilyeu, Jacqueline D Campbell, Steven B Cannon, Steven J Clough, Shaun J Curtin, Brian W Diers, Anne E Dorrance, Jason D Gillman, George L Graef, C Nathan Hancock, Karen A Hudson, David L Hyten, Aardra Kachroo, Jenny Koebernick, Marc Libault, Aaron J Lorenz, Adam L Mahan, Jon M Massman, Michaela McGinn, Khalid Meksem, Jack K Okamuro, Kerry F Pedley, Katy Martin Rainey, Andrew M Scaboo, Jeremy Schmutz, Bao-Hua Song, Adam D Steinbrenner, Benjamin B Stewart-Brown, Katalin Toth, Dechun Wang, Lisa Weaver, Bo Zhang, Michelle A Graham, Jamie A O'Rourke","doi":"10.1002/tpg2.20516","DOIUrl":"10.1002/tpg2.20516","url":null,"abstract":"<p><p>This strategic plan summarizes the major accomplishments achieved in the last quinquennial by the soybean [Glycine max (L.) Merr.] genetics and genomics research community and outlines key priorities for the next 5 years (2024-2028). This work is the result of deliberations among over 50 soybean researchers during a 2-day workshop in St Louis, MO, USA, at the end of 2022. The plan is divided into seven traditional areas/disciplines: Breeding, Biotic Interactions, Physiology and Abiotic Stress, Functional Genomics, Biotechnology, Genomic Resources and Datasets, and Computational Resources. One additional section was added, Training the Next Generation of Soybean Researchers, when it was identified as a pressing issue during the workshop. This installment of the soybean genomics strategic plan provides a snapshot of recent progress while looking at future goals that will improve resources and enable innovation among the community of basic and applied soybean researchers. We hope that this work will inform our community and increase support for soybean research.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20516"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628913/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142689369","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-12-01Epub Date: 2024-11-07DOI: 10.1002/tpg2.20528
Shameela Mohamedikbal, Hawlader A Al-Mamun, Jacob I Marsh, Shriprabha Upadhyaya, Monica F Danilevicz, Henry T Nguyen, Babu Valliyodan, Adam Mahan, Jacqueline Batley, David Edwards
{"title":"Local haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean.","authors":"Shameela Mohamedikbal, Hawlader A Al-Mamun, Jacob I Marsh, Shriprabha Upadhyaya, Monica F Danilevicz, Henry T Nguyen, Babu Valliyodan, Adam Mahan, Jacqueline Batley, David Edwards","doi":"10.1002/tpg2.20528","DOIUrl":"10.1002/tpg2.20528","url":null,"abstract":"<p><p>The timing of flowering in soybean [Glycine max (L.) Merr.], a key legume crop, is influenced by many factors, including daylight length or photoperiodic sensitivity, that affect crop yield, productivity, and geographical adaptation. Despite its importance, a comprehensive understanding of the local linkage landscape and allelic diversity within regions of the genome influencing flowering and contributing to phenotypic variation in subpopulations has been limited. This study addresses these gaps by conducting an in-depth trait association and linkage analysis coupled with local haplotyping using advanced bioinformatics tools, including crosshap, to characterize genomic variation using a pangenome dataset representing 915 domesticated and wild-type individuals. The association analysis identified eight significant loci on seven chromosomes. Moving beyond traditional association analysis, local haplotyping of targeted regions on chromosomes 6 and 20 identified distinct haplotype structures, variation patterns, and genomic candidates influencing flowering in subpopulations. These results suggest the action of a network of genomic candidates influencing flowering time and an untapped reservoir of genomic variation for this trait in wild germplasm. Notably, GlymaLee.20G147200 on chromosome 20 was identified as a candidate gene that may cause delayed flowering in soybean, potentially through histone modifications of floral repressor loci as seen in Arabidopsis thaliana (L.) Heynh. These findings support future functional validation of haplotype-based alleles for marker-assisted breeding and genomic selection to enhance latitude adaptability of soybean without compromising yield.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20528"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628924/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-12-01Epub Date: 2024-09-25DOI: 10.1002/tpg2.20513
Sajal R Sthapit, Travis M Ruff, Marcus A Hooker, Bosen Zhang, Xianran Li, Deven R See
{"title":"Candidate selective sweeps in US wheat populations.","authors":"Sajal R Sthapit, Travis M Ruff, Marcus A Hooker, Bosen Zhang, Xianran Li, Deven R See","doi":"10.1002/tpg2.20513","DOIUrl":"10.1002/tpg2.20513","url":null,"abstract":"<p><p>Exploration of novel alleles from ex situ collection is still limited in modern plant breeding as these alleles exist in genetic backgrounds of landraces that are not adapted to modern production environments. The practice of backcross breeding results in preservation of the adapted background of elite parents but leaves little room for novel alleles from landraces to be incorporated. Selection of adaptation-associated linkage blocks instead of the entire adapted background may allow breeders to incorporate more of the landrace's genetic background and to observe and evaluate novel alleles. Important adaptation-associated linkage blocks would have been selected over multiple cycles of breeding and hence are likely to exhibit signatures of positive selection or selective sweeps. We conducted genome-wide scan for candidate selective sweeps (CSS) using F<sub>st</sub>, Rsb, and xpEHH in state, regional, spring, winter, and market-class population pairs and reported 446 CSS in 19 population pairs over time and 1033 CSS in 44 population pairs across geography and class. Further validation of these CSS in specific breeding programs may lead to identification of sets of loci that can be selected to restore population-specific adaptation in pre-breeding germplasms.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20513"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628914/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142330654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Functional analysis of PagERF021 gene in salt stress tolerance in Populus alba × P. glandulosa.","authors":"Gaofeng Fan, Yuan Gao, Xinyue Wu, Yingying Yu, Wenjing Yao, Jiahui Jiang, Huanzhen Liu, Tingbo Jiang","doi":"10.1002/tpg2.20521","DOIUrl":"10.1002/tpg2.20521","url":null,"abstract":"<p><p>Poplar trees are crucial for timber and greening, but high levels of salt in the soil have severely limited the yield of poplar. Ethylene response factor (ERF) transcription factors play an important role in growth, development, and stress response in eukaryotes. Our study focused on the PagERF021 gene from Populus alba × P. glandulosa, which was significantly upregulated in various tissues under salt stress [Correction added on October 4, 2024, after first online publication: \"ETS2 reporter factor\" is changed to \"Ethylene response factor\".]. Both the tissue-specific expression pattern and β-glucuronidase (GUS) staining of proPagERF021-GUS plants indicated that this gene was predominantly expressed in the roots and stems. The subcellular localization showed that the protein was only localized in the nucleus. The yeast assay demonstrated that this protein had transcriptional activation activity at its C-terminal and could specifically binding to the MYB-core cis-element. The overexpression of PagERF021 gene could scavenge the accumulation of reactive oxygen species and reduce the degree of cellular membrane damage, indicating that this gene enhanced the salt tolerance of poplars. This finding will provide a feasible insight for future research into the regulatory mechanisms of ERF genes in resisting to abiotic stress and the development of new stress-resistant varieties in plants.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20521"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628909/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478517","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-12-01Epub Date: 2024-10-24DOI: 10.1002/tpg2.20518
Inés Medina-Lozano, Juan Ramón Bertolín, Jörg Plieske, Martin Ganal, Heike Gnad, Aurora Díaz
{"title":"Studies of genetic diversity and genome-wide association for vitamin C content in lettuce (Lactuca sativa L.) using high-throughput SNP arrays.","authors":"Inés Medina-Lozano, Juan Ramón Bertolín, Jörg Plieske, Martin Ganal, Heike Gnad, Aurora Díaz","doi":"10.1002/tpg2.20518","DOIUrl":"10.1002/tpg2.20518","url":null,"abstract":"<p><p>Lettuce (Lactuca sativa L.) is a source of beneficial compounds though they are generally present in low quantities. We used 40K Axiom and 9K Infinium SNP (single nucleotide polymorphism) arrays to (i) explore the genetic variability in 21 varieties and (ii) carry out genome-wide association studies (GWAS) of vitamin C content in21 varieties and a population of 205 plants from the richest variety in vitamin C ('Lechuga del Pirineo'). Structure and phylogenetic analyses showed that the group formed mainly by traditional varieties was the most diverse, whereas the red commercial varieties clustered together and very distinguishably apart from the rest. GWAS consistently detected, in a region of chromosome 2, several SNPs related to dehydroascorbic acid (a form of vitamin C) content using three different methods to assess population structure, subpopulation membership coefficients, multidimensional scaling, and principal component analysis. The latter detected the highest number of SNPs (17) and the most significantly associated, 12 of them showing a high linkage disequilibrium with the lead SNP. Among the 84 genes in the region, some have been reported to be related to vitamin C content or antioxidant status in other crops either directly, like those encoding long non-coding RNA, several F-box proteins, and a pectinesterase/pectinesterase inhibitor, or indirectly, like extensin-1-like protein and endoglucanase 2 genes. The involvement of other genes identified within the region in vitamin C levels needs to be further studied. Understanding the genetic control of such an important quality trait in lettuce becomes very relevant from a breeding perspective.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20518"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142511141","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Characterization of a new barley greenbug resistance gene Rsg4 in the Chinese landrace CI 2458.","authors":"Xiangyang Xu, Dolores Mornhinweg, Guihua Bai, Genqiao Li, Ruolin Bian, Amy Bernardo","doi":"10.1002/tpg2.20527","DOIUrl":"10.1002/tpg2.20527","url":null,"abstract":"<p><p>Barley (Hordeum vulgare) is a climate-resilient crop widely cultivated in both highly productive and suboptimal agricultural systems, and its ability to adapt to multiple biotic and abiotic stresses has contributed significantly to food security. Greenbug is a destructive insect pest for global barley production, and new greenbug resistance genes are needed to overcome the challenges posed by diverse greenbug biotypes in fields. CI 2458 is a Chinese landrace exhibiting a unique resistance profile to a set of 14 greenbug biotypes, which suggests the presence of a new greenbug resistance gene in CI 2458. A recombinant inbred line population from the cross Weskan × CI 2458 was developed, evaluated for responses to greenbug biotype F, and genotyped using single nucleotide polymorphism (SNP) markers generated by genotyping-by-sequencing. Linkage analysis revealed a single gene, designated Rsg4, conditioning greenbug resistance in CI 2458. Rsg4 was delimited to a 1.14 Mb interval between SNP markers S3H_666512114 and S3H_667651446 in the terminal region of chromosome arm 3HL, with genetic distances of 1.2 cM proximal to S3H_667651446 and 1.1 cM distal to S3H_666512114. Allelism tests confirmed that Rsg4 is a new greenbug resistance gene independent of Rsg1 and Rsg3, which reside in the same chromosome arm. Rsg4 differs from Rsg1 alleles and Rsg3 in its resistance to greenbug biotype TX1, one of the most widely virulent biotypes. The introgression of Rsg4 into locally adapted barley cultivars is of agronomic importance, and kompetitive allele-specific polymerase chain reaction (KASP) markers flanking Rsg4, KASP-Rsg336-1 and KASP-Rsg336-2, enable rapid pyramiding of Rsg4 with other resistance genes to develop durable greenbug-resistant cultivars.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20527"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628878/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142606409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-12-01Epub Date: 2024-10-13DOI: 10.1002/tpg2.20523
Andrew T Wiersma, John P Hamilton, Brieanne Vaillancourt, Julia Brose, Halima E Awale, Evan M Wright, James D Kelly, C Robin Buell
{"title":"k-mer genome-wide association study for anthracnose and BCMV resistance in a Phaseolus vulgaris Andean Diversity Panel.","authors":"Andrew T Wiersma, John P Hamilton, Brieanne Vaillancourt, Julia Brose, Halima E Awale, Evan M Wright, James D Kelly, C Robin Buell","doi":"10.1002/tpg2.20523","DOIUrl":"10.1002/tpg2.20523","url":null,"abstract":"<p><p>Access to broad genomic resources and closely linked marker-trait associations for common beans (Phaseolus vulgaris L.) can facilitate development of improved varieties with increased yield, improved market quality traits, and enhanced disease resistance. The emergence of virulent races of anthracnose (caused by Colletotrichum lindemuthianum) and bean common mosaic virus (BCMV) highlight the need for improved methods to identify and incorporate pan-genomic variation in breeding for disease resistance. We sequenced the P. vulgaris Andean Diversity Panel (ADP) and performed a genome-wide association study (GWAS) to identify associations for resistance to BCMV and eight races of anthracnose. Historical single nucleotide polymorphism (SNP)-chip and phenotypic data enabled a three-way comparison between SNP-chip, reference-based whole genome shotgun sequence (WGS)-SNP, and reference-free k-mer (short nucleotide subsequence) GWAS. Across all traits, there was excellent concordance between SNP-chip, WGS-SNP, and k-mer GWAS results-albeit at a much higher marker resolution for the WGS data sets. Significant k-mer haplotype variation revealed selection of the linked I-gene and Co-u traits in North American breeding lines and cultivars. Due to structural variation, only 9.1 to 47.3% of the significantly associated k-mers could be mapped to the reference genome. Thus, to determine the genetic context of cis-associated k-mers, we generated draft whole genome assemblies of four ADP accessions and identified an expanded local repertoire of disease resistance genes associated with resistance to anthracnose and BCMV. With access to variant data in the context of a pan-genome, high resolution mapping of agronomic traits for common bean is now feasible.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20523"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628888/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478528","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Plant GenomePub Date : 2024-12-01Epub Date: 2024-10-15DOI: 10.1002/tpg2.20524
Peri A Tobias, Jacob Downs, Peter Epaina, Gurpreet Singh, Robert F Park, Richard J Edwards, Eirene Brugman, Andi Zulkifli, Junaid Muhammad, Agus Purwantara, David I Guest
{"title":"Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback.","authors":"Peri A Tobias, Jacob Downs, Peter Epaina, Gurpreet Singh, Robert F Park, Richard J Edwards, Eirene Brugman, Andi Zulkifli, Junaid Muhammad, Agus Purwantara, David I Guest","doi":"10.1002/tpg2.20524","DOIUrl":"10.1002/tpg2.20524","url":null,"abstract":"<p><p>Diseases of Theobroma cacao L. (Malvaceae) disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by Ceratobasidium theobromae, is a new encounter disease of cacao currently contained to southeast Asia and Melanesia. Resistance to VSD has been tested with large progeny trials in Sulawesi, Indonesia, and in Papua New Guinea with the identification of informative quantitative trait loci (QTLs). Using a VSD susceptible progeny tree (clone 26), derived from a resistant and susceptible parental cross, we assembled the genome to chromosome-level and discriminated alleles inherited from either resistant or susceptible parents. The parentally phased genomes were annotated for all predicted genes and then specifically for resistance genes of the nucleotide-binding site leucine-rich repeat class (NLR). On investigation, we determined the presence of NLR clusters and other potential disease response gene candidates in proximity to informative QTLs. We identified structural variants within NLRs inherited from parentals. We present the first diploid, fully scaffolded, and parentally phased genome resource for T. cacao L. and provide insights into the genetics underlying resistance and susceptibility to VSD.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20524"},"PeriodicalIF":3.9,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11628906/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142478529","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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