Yuanyuan Ji , Nadeem Khan , Raju Chaudhary , Sampath Perumal , Zhengping Wang , Pierre Hucl , Bill Biligetu , Andrew G. Sharpe , Lingling Jin
{"title":"小麦草的基因组研究:揭示小麦草属植物的遗传多样性、种群结构和进化动力学。","authors":"Yuanyuan Ji , Nadeem Khan , Raju Chaudhary , Sampath Perumal , Zhengping Wang , Pierre Hucl , Bill Biligetu , Andrew G. Sharpe , Lingling Jin","doi":"10.1016/j.ympev.2025.108397","DOIUrl":null,"url":null,"abstract":"<div><div><em>Pseudoroegneria</em> species are outcrossing perennial grasses with significant ecological and agricultural value due to its resilience in challenging environmental conditions in the temperate regions. Understanding the extent and pattern of genetic diversity and population structure is essential for the breeding improvement and conservation of these species. In the current research, we analyzed genomic variations of 145 genotypes representing seven species (<em>P. spicata, P. tauri, P. geniculata, P. libanotica, P. strigosa, P. stipifolia, and P. cognata</em>) from major global lineages, using genotyping-by-sequencing. Different metrics including nucleotide diversity, observed heterozygosity, and Tajima’s D were used to evaluate genetic diversity among populations revealing significant variation among species, with <em>P. stipifolia</em> exhibiting the highest diversity and <em>P. spicata</em> the lowest. Population structure analyses, including principal component analysis, admixture inference, and phylogenetic reconstruction, identified six distinct genetic clusters, with <em>P. spicata</em> (a North American species) clearly separated from the other six species underscoring its unique genetic identity. In contrast, the Eurasian species exhibit mixed ancestry, indicating intricate genetic relationships and widespread exchange of genetic material. Furthermore, no single species tree fully captures the relationships among them, implying interactions such as hybridization or gene flows between closely related species. To investigate the evolutionary history of Eurasian <em>Pseudoroegneria</em> species, we reconstructed the species tree topology based on the SNV (single nucleotide variants) matrix, and <em>f</em>-branch statistics confirmed close relationships among <em>P. spicata</em>, <em>P. libanotica</em>, and <em>P. tauri</em>, with evidence of unidirectional gene flow between <em>P. stipifolia</em>, <em>P. geniculata</em>, and <em>P. strigosa</em>. These findings highlight the importance of high genetic variation in the <em>P. stipifolia</em> population, suggesting its potential to be a reservoir of valuable alleles for resilient genotypes.</div></div>","PeriodicalId":56109,"journal":{"name":"Molecular Phylogenetics and Evolution","volume":"211 ","pages":"Article 108397"},"PeriodicalIF":3.6000,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Genomic insights into wheatgrass: unravelling genetic diversity, population structure, and evolutionary dynamics in Pseudoroegneria species\",\"authors\":\"Yuanyuan Ji , Nadeem Khan , Raju Chaudhary , Sampath Perumal , Zhengping Wang , Pierre Hucl , Bill Biligetu , Andrew G. Sharpe , Lingling Jin\",\"doi\":\"10.1016/j.ympev.2025.108397\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<div><div><em>Pseudoroegneria</em> species are outcrossing perennial grasses with significant ecological and agricultural value due to its resilience in challenging environmental conditions in the temperate regions. Understanding the extent and pattern of genetic diversity and population structure is essential for the breeding improvement and conservation of these species. In the current research, we analyzed genomic variations of 145 genotypes representing seven species (<em>P. spicata, P. tauri, P. geniculata, P. libanotica, P. strigosa, P. stipifolia, and P. cognata</em>) from major global lineages, using genotyping-by-sequencing. Different metrics including nucleotide diversity, observed heterozygosity, and Tajima’s D were used to evaluate genetic diversity among populations revealing significant variation among species, with <em>P. stipifolia</em> exhibiting the highest diversity and <em>P. spicata</em> the lowest. Population structure analyses, including principal component analysis, admixture inference, and phylogenetic reconstruction, identified six distinct genetic clusters, with <em>P. spicata</em> (a North American species) clearly separated from the other six species underscoring its unique genetic identity. In contrast, the Eurasian species exhibit mixed ancestry, indicating intricate genetic relationships and widespread exchange of genetic material. Furthermore, no single species tree fully captures the relationships among them, implying interactions such as hybridization or gene flows between closely related species. To investigate the evolutionary history of Eurasian <em>Pseudoroegneria</em> species, we reconstructed the species tree topology based on the SNV (single nucleotide variants) matrix, and <em>f</em>-branch statistics confirmed close relationships among <em>P. spicata</em>, <em>P. libanotica</em>, and <em>P. tauri</em>, with evidence of unidirectional gene flow between <em>P. stipifolia</em>, <em>P. geniculata</em>, and <em>P. strigosa</em>. These findings highlight the importance of high genetic variation in the <em>P. stipifolia</em> population, suggesting its potential to be a reservoir of valuable alleles for resilient genotypes.</div></div>\",\"PeriodicalId\":56109,\"journal\":{\"name\":\"Molecular Phylogenetics and Evolution\",\"volume\":\"211 \",\"pages\":\"Article 108397\"},\"PeriodicalIF\":3.6000,\"publicationDate\":\"2025-06-22\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Molecular Phylogenetics and Evolution\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://www.sciencedirect.com/science/article/pii/S1055790325001149\",\"RegionNum\":1,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOCHEMISTRY & MOLECULAR BIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Phylogenetics and Evolution","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1055790325001149","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
Genomic insights into wheatgrass: unravelling genetic diversity, population structure, and evolutionary dynamics in Pseudoroegneria species
Pseudoroegneria species are outcrossing perennial grasses with significant ecological and agricultural value due to its resilience in challenging environmental conditions in the temperate regions. Understanding the extent and pattern of genetic diversity and population structure is essential for the breeding improvement and conservation of these species. In the current research, we analyzed genomic variations of 145 genotypes representing seven species (P. spicata, P. tauri, P. geniculata, P. libanotica, P. strigosa, P. stipifolia, and P. cognata) from major global lineages, using genotyping-by-sequencing. Different metrics including nucleotide diversity, observed heterozygosity, and Tajima’s D were used to evaluate genetic diversity among populations revealing significant variation among species, with P. stipifolia exhibiting the highest diversity and P. spicata the lowest. Population structure analyses, including principal component analysis, admixture inference, and phylogenetic reconstruction, identified six distinct genetic clusters, with P. spicata (a North American species) clearly separated from the other six species underscoring its unique genetic identity. In contrast, the Eurasian species exhibit mixed ancestry, indicating intricate genetic relationships and widespread exchange of genetic material. Furthermore, no single species tree fully captures the relationships among them, implying interactions such as hybridization or gene flows between closely related species. To investigate the evolutionary history of Eurasian Pseudoroegneria species, we reconstructed the species tree topology based on the SNV (single nucleotide variants) matrix, and f-branch statistics confirmed close relationships among P. spicata, P. libanotica, and P. tauri, with evidence of unidirectional gene flow between P. stipifolia, P. geniculata, and P. strigosa. These findings highlight the importance of high genetic variation in the P. stipifolia population, suggesting its potential to be a reservoir of valuable alleles for resilient genotypes.
期刊介绍:
Molecular Phylogenetics and Evolution is dedicated to bringing Darwin''s dream within grasp - to "have fairly true genealogical trees of each great kingdom of Nature." The journal provides a forum for molecular studies that advance our understanding of phylogeny and evolution, further the development of phylogenetically more accurate taxonomic classifications, and ultimately bring a unified classification for all the ramifying lines of life. Phylogeographic studies will be considered for publication if they offer EXCEPTIONAL theoretical or empirical advances.