{"title":"基因组扫描捕获了四倍体小麦的关键适应和历史杂交特征。","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":null,"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":3.9000,"publicationDate":"2025-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726425/pdf/","citationCount":"0","resultStr":"{\"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\":null,\"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\":3.9000,\"publicationDate\":\"2025-03-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11726425/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Plant Genome\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1002/tpg2.20410\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2023/11/16 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q1\",\"JCRName\":\"GENETICS & HEREDITY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Plant Genome","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1002/tpg2.20410","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2023/11/16 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0
摘要
四倍体小麦(Triticum turgidum L.),包括硬粒小麦(T. turgidum ssp.)。硬质(Desf)。是具有高营养和文化价值的重要作物。然而,它们的生产受到对环境条件的敏感性的限制。为了寻找追踪历史选择和杂交事件的适应性遗传特征,我们对两个数据集进行了基因组扫描:(1)硬粒小麦全球多样性小组,包括442个四倍体小麦和野生祖先,包括硬粒小麦地方品种(n = 286)、驯化二粒小麦(T. turgidum ssp);dicoccum(名词);n = 103)和野生二聚体(T. turgidum ssp.)。dicoccoides(科恩。Asch交货。& Graebn)。Thell。n = 53)小麦,使用90K单核苷酸多态性(SNP)阵列进行基因分型;(2)第二个数据集包括9个T. turgidum亚种共121个,包括野生emmer,通过全基因组重测序获得bbb100 M SNP基因分型。对第一个数据集进行基因组扫描,在1A、1B、3A (n = 2)、6A和7A染色体上检测到6个异常位点。这些基因座包含了适应非生物胁迫、物候反应(如种子休眠、生物钟、开花时间)和关键产量相关性状的重要基因,包括多效基因(如HAT1、KUODA1、CBL1和ZFN1)。对第二个数据集的扫描捕获了2B染色体上高度分化的区域,显示了两组之间的显著分化:一组由格鲁吉亚(T. turgidum ssp)组成。古冷chicum A. Love和D. Love)和波斯语(T. turgidum ssp.)。carthlicum (Nevski) A. Love & D. Love)小麦品种,而另一组包括所有剩余的四倍体,包括野生二倍体。这与先前报道的timopheevi Zhuk在该基因组区域的渐渗一致。它们自然地生活在格鲁吉亚和邻近地区。该区域包含几个适应性基因,包括温度形态发生基因PIF4,该基因赋予温度抗逆性疾病抗性并调节其他生物过程。基因组扫描可用于快速追踪基因库和原位保存的种质;这有助于确定环境适应性强的物种进行繁殖和/或优先保护。
Genome scans capture key adaptation and historical hybridization signatures in tetraploid wheat.
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.
期刊介绍:
The Plant Genome publishes original research investigating all aspects of plant genomics. Technical breakthroughs reporting improvements in the efficiency and speed of acquiring and interpreting plant genomics data are welcome. The editorial board gives preference to novel reports that use innovative genomic applications that advance our understanding of plant biology that may have applications to crop improvement. The journal also publishes invited review articles and perspectives that offer insight and commentary on recent advances in genomics and their potential for agronomic improvement.