{"title":"Genome scans capture key adaptation and historical hybridization signatures in tetraploid wheat.","authors":"Demissew Sertse, Jemanesh K Haile, Ehsan Sari, Valentyna Klymiuk, Amidou N'Diaye, Curtis J Pozniak, Sylvie Cloutier, Sateesh Kagale","doi":"10.1002/tpg2.20410","DOIUrl":"10.1002/tpg2.20410","url":null,"abstract":"<p><p>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 Global Diversity Panel comprising a total of 442 tetraploid wheat and wild progenitor accessions including durum landraces (n = 286), domesticated emmer (T. turgidum ssp. dicoccum (Schrank) Thell.; n = 103) and wild emmer (T. turgidum ssp. dicoccoides (Korn. ex Asch. & Graebn.) Thell.; n = 53) wheats genotyped using the 90K single nucleotide polymorphism (SNP) array, and (2) a second dataset comprising a total 121 accessions of nine T. turgidum subspecies including wild emmer genotyped with >100 M SNPs from whole-genome resequencing. The genome scan on the first dataset detected six outlier loci on chromosomes 1A, 1B, 3A (n = 2), 6A, and 7A. These loci harbored important genes for adaptation to abiotic stresses, phenological responses, such as seed dormancy, circadian clock, flowering time, and key yield-related traits, including pleiotropic genes, such as HAT1, KUODA1, CBL1, and ZFN1. The scan on the second dataset captured a highly differentiated region on chromosome 2B that shows significant differentiation between two groups: one group consists of Georgian (T. turgidum ssp. paleocolchicum A. Love & D. Love) and Persian (T. turgidum ssp. carthlicum (Nevski) A. Love & D. Love) wheat accessions, while the other group comprises all the remaining tetraploids including wild emmer. This is consistent with a previously reported introgression in this genomic region from T. timopheevii Zhuk. which naturally cohabit in the Georgian and neighboring areas. This region harbored several adaptive genes, including the thermomorphogenesis gene PIF4, which confers temperature-resilient disease resistance and regulates other biological processes. Genome scans can be used to fast-track germplasm housed in gene banks and in situ; which helps to identify environmentally resilient accessions for breeding and/or to prioritize them for conservation.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20410"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726425/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136399967","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 : 2025-03-01Epub Date: 2024-11-27DOI: 10.1002/tpg2.20533
Marco Antônio Peixoto, Rodrigo Rampazo Amadeu, Leonardo Lopes Bhering, Luís Felipe V Ferrão, Patrício R Munoz, Márcio F R Resende
{"title":"SimpleMating: R-package for prediction and optimization of breeding crosses using genomic selection.","authors":"Marco Antônio Peixoto, Rodrigo Rampazo Amadeu, Leonardo Lopes Bhering, Luís Felipe V Ferrão, Patrício R Munoz, Márcio F R Resende","doi":"10.1002/tpg2.20533","DOIUrl":"10.1002/tpg2.20533","url":null,"abstract":"<p><p>Selecting parents and crosses is a critical step for a successful breeding program. The ability to design crosses with high means that will maintain genetic variation in the population is the goal for long-term applications. Herein, we describe a new computational package for mate allocation in a breeding program. SimpleMating is a flexible and open-source R package originally designed to predict and optimize breeding crosses in crops with different reproductive systems and breeding designs. Divided into modules, SimpleMating first estimates the cross performance (criterion), such as mid-parental value, cross total genetic value, and/or usefulness of a set of crosses. The second module implements an optimization algorithm to maximize a target criterion while minimizing next-generation inbreeding. The software is flexible, enabling users to specify the desired number of crosses, set maximum and minimum crosses per parent, and define the maximum allowable parent relationship for creating crosses. As an outcome, SimpleMating generates a mating plan from the target parental population using single or multi-trait criteria. For example, we implemented and tested SimpleMating in a simulated maize breeding program obtained through stochastic simulations. The crosses designed via SimpleMating showed a large genetic mean over time (up to 22% more genetic gain than conventional genomic selection programs, with lesser loss of genetic diversity over time), supporting the use of this tool, as well as the use of data-driven decisions in breeding programs.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20533"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726409/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142741056","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 : 2025-03-01Epub Date: 2024-07-23DOI: 10.1002/tpg2.20490
Yichen Kang, Samir Alahmad, Shanice V Haeften, Oluwaseun Akinlade, Jingyang Tong, Eric Dinglasan, Kai P Voss-Fels, Andries B Potgieter, Andrew K Borrell, Manar Makhoul, Christian Obermeier, Rod Snowdon, Emma Mace, David R Jordan, Lee T Hickey
{"title":"Mapping quantitative trait loci for seminal root angle in a selected durum wheat population.","authors":"Yichen Kang, Samir Alahmad, Shanice V Haeften, Oluwaseun Akinlade, Jingyang Tong, Eric Dinglasan, Kai P Voss-Fels, Andries B Potgieter, Andrew K Borrell, Manar Makhoul, Christian Obermeier, Rod Snowdon, Emma Mace, David R Jordan, Lee T Hickey","doi":"10.1002/tpg2.20490","DOIUrl":"10.1002/tpg2.20490","url":null,"abstract":"<p><p>Seminal root angle (SRA) is an important root architectural trait associated with drought adaptation in cereal crops. To date, all attempts to dissect the genetic architecture of SRA in durum wheat (Triticum durum Desf.) have used large association panels or structured mapping populations. Identifying changes in allele frequency generated by selection provides an alternative genetic mapping approach that can increase the power and precision of QTL detection. This study aimed to map quantitative trait loci (QTL) for SRA by genotyping durum lines created through divergent selection using a combination of marker-assisted selection (MAS) for the major SRA QTL (qSRA-6A) and phenotypic selection for SRA over multiple generations. The created 11 lines (BC<sub>1</sub>F<sub>2:5</sub>) were genotyped with genome-wide single-nucleotide polymorphism (SNP) markers to map QTL by identifying markers that displayed segregation distortion significantly different from the Mendelian expectation. QTL regions were further assessed in an independent validation population to confirm their associations with SRA. The experiment revealed 14 genomic regions under selection, 12 of which have not previously been reported for SRA. Five regions, including qSRA-6A, were confirmed in the validation population. The genomic regions identified in this study indicate that the genetic control of SRA is more complex than previously anticipated. Our study demonstrates that selection mapping is a powerful approach to complement genome-wide association studies for QTL detection. Moreover, the verification of qSRA-6A in an elite genetic background highlights the potential for MAS, although it is necessary to combine additional QTL to develop new cultivars with extreme SRA phenotypes.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20490"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11733660/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141753188","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 : 2025-03-01Epub Date: 2024-10-02DOI: 10.1002/tpg2.20520
Adedayo O Adeyanju, Patrick J Rich, Gebisa Ejeta
{"title":"A powerful molecular marker to detect mutations at sorghum LOW GERMINATION STIMULANT 1.","authors":"Adedayo O Adeyanju, Patrick J Rich, Gebisa Ejeta","doi":"10.1002/tpg2.20520","DOIUrl":"10.1002/tpg2.20520","url":null,"abstract":"<p><p>The parasitic weed Striga (Striga hermonthica) limits productivity of sorghum (Sorghum bicolor) and other cereals in sub-Saharan Africa and elsewhere. Improved host plant genetics is an effective control method but verified loci contributing to Striga resistance are limited. LOW GERMINATION STIMULANT 1 remains the only known sorghum locus affecting resistance to Striga. Functional loss (lgs1) alleles at this locus result in low Striga germination stimulant activity. We developed a robust polymerase chain reaction (PCR)-based LGS1 marker that detects all known natural lgs1 alleles. We have successfully used this marker to improve Striga resistance in our sorghum breeding program. To check its utility among diverse sets of germplasm, we genotyped 406 lines of the sorghum association panel (SAP) with the marker and phenotyped them for Striga germination stimulant activity. The SAP contains 23 lines (6%) with lgs1 mutations that involve a complete loss of this gene. Three previously described deletion alleles (lgs1-1, lgs1-2, and lgs1-3) ranging from 28.5 to 34 kbp are present among SAP members with a new one, lgs1-6, missing nearly 50 kbp relative to the reference genome. All 23 members of the SAP carrying lgs1 alleles had low Striga germination stimulant activity. The smaller previously described intragenic deletion mutations lgs1-4 and lgs1-5 are not present in the SAP. The LGS1 marker is useful for both detecting sources of lgs1 and introgressing Striga resistance into new genetic backgrounds.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20520"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726417/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142367054","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 : 2025-03-01Epub Date: 2024-12-04DOI: 10.1002/tpg2.20541
Anthony Piot, Yousry A El-Kassaby, Ilga Porth
{"title":"Exon disruptive variants in Populus trichocarpa associated with wood properties exhibit distinct gene expression patterns.","authors":"Anthony Piot, Yousry A El-Kassaby, Ilga Porth","doi":"10.1002/tpg2.20541","DOIUrl":"10.1002/tpg2.20541","url":null,"abstract":"<p><p>Forest trees may harbor naturally occurring exon disruptive variants (DVs) in their gene sequences, which potentially impact important ecological and economic phenotypic traits. However, the abundance and molecular regulation of these variants remain largely unexplored. Here, 24,420 DVs were identified by screening 1014 Populus trichocarpa full genomes. The identified DVs were predominantly heterozygous with allelic frequencies below 5% (only 26% of DVs had frequencies greater than 5%). Using common garden-grown trees, DVs were assessed for gene expression variation in the developing xylem, revealing that their gene expression can be significantly altered, particularly for homozygous DVs (in the range of 27%-38% of cases depending on the studied common garden). DVs were further investigated for their correlations with 13 wood quality traits, revealing that, among the 148 discovered DV associations, 15 correlated with more than one wood property and six genes had more than one DV in their coding sequences associated with wood traits. Approximately one-third of DVs correlated with wood property variation also showed significant gene expression variation, confirming their non-spurious impact. These findings offer potential avenues for targeted introduction of homozygous mutations using tree biotechnology, and while the exact mechanisms by which DVs may directly influence wood formation remain to be unraveled, this study lays the groundwork for further investigation.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20541"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726415/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142780906","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 : 2025-03-01DOI: 10.1002/tpg2.70005
Jingyi Zhu, Qinghua Liu, Shu Diao, Zhichun Zhou, Yangdong Wang, Xianyin Ding, Mingyue Cao, Dinghui Luo
{"title":"Development of a 101.6K liquid-phased probe for GWAS and genomic selection in pine wilt disease-resistance breeding in Masson pine.","authors":"Jingyi Zhu, Qinghua Liu, Shu Diao, Zhichun Zhou, Yangdong Wang, Xianyin Ding, Mingyue Cao, Dinghui Luo","doi":"10.1002/tpg2.70005","DOIUrl":"10.1002/tpg2.70005","url":null,"abstract":"<p><p>Masson pine (Pinus massoniana Lamb.), indigenous to southern China, faces serious threats from pine wilt disease (PWD). Several natural genotypes have survived PWD outbreaks. Conducting genetic breeding with these resistant genotypes holds promise for enhancing resistance to PWD in Masson pine at its source. We conducted a genome-wide association study (GWAS) and genomic selection (GS) on 1013 Masson pine seedlings from 72 half-sib families to advance disease-resistance breeding. A set of efficient 101.6K liquid-phased probes was developed for single-nucleotide polymorphisms (SNPs) genotyping through target sequencing. PWD inoculation experiments were then performed to obtain phenotypic data for these populations. Our analysis reveals that the targeted sequencing data successfully divided the experimental population into three subpopulations consistent with the provenance, verifying the reliability of the liquid-phased probe. A total of 548 SNPs were considerably associated with disease-resistance traits using four GWAS algorithms. Among them, 283 were located on or linked to 169 genes, including common plant disease resistance-related protein families such as NBS-LRR and AP2/ERF. The DNNGP (deep neural network-based method for genomic prediction) model demonstrated superior performance in GS, achieving a maximum predictive accuracy of 0.71. The accuracy of disease resistance predictions reached 90% for the top 20% of the testing population ordered by resistance genomic estimated breeding value. This study establishes a foundational framework for advancing research on disease-resistant genes in P. massoniana and offers preliminary evidence supporting the feasibility of utilizing GS for the early identification of disease-resistant individuals.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70005"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11873169/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143537979","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 : 2025-03-01DOI: 10.1002/tpg2.70011
Jeffrey B Endelman, Moctar Kante, Hannele Lindqvist-Kreuze, Andrzej Kilian, Laura M Shannon, Maria V Caraza-Harter, Brieanne Vaillancourt, Kathrine Mailloux, John P Hamilton, C Robin Buell
{"title":"Erratum to: Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR.","authors":"Jeffrey B Endelman, Moctar Kante, Hannele Lindqvist-Kreuze, Andrzej Kilian, Laura M Shannon, Maria V Caraza-Harter, Brieanne Vaillancourt, Kathrine Mailloux, John P Hamilton, C Robin Buell","doi":"10.1002/tpg2.70011","DOIUrl":"10.1002/tpg2.70011","url":null,"abstract":"","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":"18 1","pages":"e70011"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11915481/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143659442","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":"Mapping resistance to Sclerotinia white mold in two pinto bean recombinant inbred line populations.","authors":"Alvaro Soler-Garzón, Fernanda Souza Lopes, Jayanta Roy, Josh Clevenger, Zachary Myers, Walid Korani, Welison Andrade Pereira, Qijian Song, Timothy Porch, Phillip E McClean, Phillip N Miklas","doi":"10.1002/tpg2.20538","DOIUrl":"10.1002/tpg2.20538","url":null,"abstract":"<p><p>White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a devastating disease affecting common bean (Phaseolus vulgaris L.) production worldwide. Breeding for resistance to white mold is challenging due to its quantitative inheritance and intricate genetic mechanisms. This research aimed to validate and characterize physiological resistance in the pinto dry bean market class through greenhouse straw tests under controlled conditions and field assessments under natural environments. Classical quantitative trait locus (QTL) mapping and Khufu de novo QTL-seq were employed to detect and narrow QTL intervals and identify candidate genes associated with white mold resistance in two pinto bean recombinant inbred line populations, PT9-5-6/USPT-WM-12 (P2) and PT12-37/VCP-13 (P3). Eleven QTL, five in P2 and six in P3, conditioning white mold resistance were identified. New QTL were discovered including WM1.4 and WM11.5 in P2, and WM1.5 and WM7.7 in P3. Existing major-effect QTL were validated: WM5.4 (34%-phenotypic variation explained) and WM7.4 (20%) in straw tests, and WM2.2 (15%) and WM3.1 (27%) under field conditions. QTL for avoidance traits such as resistance to lodging and late maturity overlapped WM2.2 in P2 and WM1.5, WM3.1, WM5.4, and WM7.7 in P3. WM5.4 (Pv05: 7.0-38.7 Mb) was associated with a large Phaseolus coccineus L. genome introgression in the resistant parent VCP-13. These findings offer narrowed genomic intervals and putative candidate genes for marker-assisted selection targeting white mold resistance improvement in pinto beans.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20538"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726412/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142802886","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 : 2025-03-01Epub Date: 2024-07-31DOI: 10.1002/tpg2.20485
Renan Uhdre, Clarice J Coyne, Britton Bourland, Julia Piaskowski, Ping Zheng, Girish M Ganjyal, Zhiwu Zhang, Rebecca J McGee, Dorrie Main, Nonoy Bandillo, Mario Morales, Yu Ma, Chengci Chen, William Franck, Adam Thrash, Marilyn L Warburton
{"title":"Association study of crude seed protein and fat concentration in a USDA pea diversity panel.","authors":"Renan Uhdre, Clarice J Coyne, Britton Bourland, Julia Piaskowski, Ping Zheng, Girish M Ganjyal, Zhiwu Zhang, Rebecca J McGee, Dorrie Main, Nonoy Bandillo, Mario Morales, Yu Ma, Chengci Chen, William Franck, Adam Thrash, Marilyn L Warburton","doi":"10.1002/tpg2.20485","DOIUrl":"10.1002/tpg2.20485","url":null,"abstract":"<p><p>Pea (Pisum sativum L.) is a key rotational crop and is increasingly important in the food processing sector for its protein. This study focused on identifying diverse high seed protein concentration (SPC) lines in pea plant genetic resources. Objectives included identifying high-protein pea lines, exploring genetic architecture across environments, pinpointing genes and metabolic pathways associated with high protein, and documenting information for single nucleotide polymorphism (SNP)-based marker-assisted selection. From 2019 to 2021, a 487-accession pea diversity panel, More protein, More pea, More profit, was evaluated in a randomized complete block design. DNA was extracted for genomic analysis via genotype-by-sequencing. Phenotypic analysis included protein and fat measurements in seeds and flower color. Genome-wide association study (GWAS) used multiple models, and the Pathways Association Study Tool was used for metabolic pathway analysis. Significant associations were found between SNPs and pea seed protein and fat concentration. Gene Psat7g216440 on chromosome 7, which targets proteins to cellular destinations, including seed storage proteins, was identified as associated with SPC. Genes Psat4g009200, Psat1g199800, Psat1g199960, and Psat1g033960, all involved in lipid metabolism, were associated with fat concentration. GWAS also identified genes annotated for storage proteins associated with fat concentration, indicating a complex relationship between fat and protein. Metabolic pathway analysis identified 20 pathways related to fat and seven to protein concentration, involving fatty acids, amino acid and protein metabolism, and the tricarboxylic acid cycle. These findings will assist in breeding of high-protein, diverse pea cultivars, and SNPs that can be converted to breeder-friendly molecular marker assays are identified for genes associated with high protein.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20485"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726435/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141861363","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 : 2025-03-01Epub Date: 2024-08-28DOI: 10.1002/tpg2.20498
Prabin Bajgain, Hannah Stoll, James A Anderson
{"title":"Improving complex agronomic and domestication traits in the perennial grain crop intermediate wheatgrass with genetic mapping and genomic prediction.","authors":"Prabin Bajgain, Hannah Stoll, James A Anderson","doi":"10.1002/tpg2.20498","DOIUrl":"10.1002/tpg2.20498","url":null,"abstract":"<p><p>The perennial grass Thinopyrum intermedium (intermediate wheatgrass [IWG]) is being domesticated as a food crop. With a deep root system and high biomass, IWG can help reduce soil and water erosion and limit nutrient runoff. As a novel grain crop undergoing domestication, IWG lags in yield, seed size, and other agronomic traits compared to annual grains. Better characterization of trait variation and identification of genetic markers associated with loci controlling the traits could help in further improving this crop. The University of Minnesota's Cycle 5 IWG breeding population of 595 spaced plants was evaluated at two locations in 2021 and 2022 for agronomic traits plant height, grain yield, and spike weight, and domestication traits shatter resistance, free grain threshing, and seed size. Pairwise trait correlations were weak to moderate with the highest correlation observed between seed size and height (0.41). Broad-sense trait heritabilities were high (0.68-0.77) except for spike weight (0.49) and yield (0.44). Association mapping using 24,284 genome-wide single nucleotide polymorphism markers identified 30 main quantitative trait loci (QTLs) across all environments and 32 QTL-by-environment interactions (QTE) at each environment. The genomic prediction model significantly improved predictions when parents were used in the training set and significant QTLs and QTEs used as covariates. Seed size was the best predicted trait with model predictive ability (r) of 0.72; yield was predicted moderately well (r = 0.45). We expect this discovery of significant genomic loci and mostly high trait predictions from genomic prediction models to help improve future IWG breeding populations.</p>","PeriodicalId":49002,"journal":{"name":"Plant Genome","volume":" ","pages":"e20498"},"PeriodicalIF":3.9,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726416/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142094008","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}