Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA
Prairie cordgrass (<i>Spartina pectinata</i> Link) is a native perennial warm-season (C4) grass common in North American prairies. With its high biomass yield and abiotic stress tolerance, there is a high potential of developing prairie cordgrass for conservation practices and as a dedic...
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MDPI AG
2021-08-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/8/1240 |
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| author | Jia Guo Patrick J. Brown Albert L. Rayburn Carolyn J. Butts-Wilmsmeyer Arvid Boe DoKyoung Lee |
| author_facet | Jia Guo Patrick J. Brown Albert L. Rayburn Carolyn J. Butts-Wilmsmeyer Arvid Boe DoKyoung Lee |
| author_sort | Jia Guo |
| collection | DOAJ |
| description | Prairie cordgrass (<i>Spartina pectinata</i> Link) is a native perennial warm-season (C4) grass common in North American prairies. With its high biomass yield and abiotic stress tolerance, there is a high potential of developing prairie cordgrass for conservation practices and as a dedicated bioenergy crop for sustainable cellulosic biofuel production. However, as with many other undomesticated grass species, little information is known about the genetic diversity or population structure of prairie cordgrass natural populations as compared to their ecotypic and geographic adaptation in North America. In this study, we sampled and characterized a total of 96 prairie cordgrass natural populations with 9315 high quality SNPs from a genotyping-by-sequencing (GBS) approach. The natural populations were collected from putative remnant prairie sites throughout the Midwest and Eastern USA, which are the major habitats for prairie cordgrass. Partitioning of genetic variance using SNP marker data revealed significant variance among and within populations. Two potential gene pools were identified as being associated with ploidy levels, geographical separation, and climatic separation. Geographical factors such as longitude and altitude, and environmental factors such as annual temperature, annual precipitation, temperature of the warmest month, precipitation of the wettest month, precipitation of Spring, and precipitation of the wettest month are important in affecting the intraspecific distribution of prairie cordgrass. The divergence of prairie cordgrass natural populations also provides opportunities to increase breeding value of prairie cordgrass as a bioenergy and conservation crop. |
| first_indexed | 2024-03-10T08:47:43Z |
| format | Article |
| id | doaj.art-5f1c7b1f1c0844eda1dc1348d8593a13 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T08:47:43Z |
| publishDate | 2021-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-5f1c7b1f1c0844eda1dc1348d8593a132023-11-22T07:46:34ZengMDPI AGGenes2073-44252021-08-01128124010.3390/genes12081240Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USAJia Guo0Patrick J. Brown1Albert L. Rayburn2Carolyn J. Butts-Wilmsmeyer3Arvid Boe4DoKyoung Lee5Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USADepartment of Plant Sciences, University of California at Davis, Davis, CA 95616, USADepartment of Crop Sciences, University of Illinois, Urbana, IL 61801, USADepartment of Crop Sciences, University of Illinois, Urbana, IL 61801, USADepartment of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57007, USADepartment of Crop Sciences, University of Illinois, Urbana, IL 61801, USAPrairie cordgrass (<i>Spartina pectinata</i> Link) is a native perennial warm-season (C4) grass common in North American prairies. With its high biomass yield and abiotic stress tolerance, there is a high potential of developing prairie cordgrass for conservation practices and as a dedicated bioenergy crop for sustainable cellulosic biofuel production. However, as with many other undomesticated grass species, little information is known about the genetic diversity or population structure of prairie cordgrass natural populations as compared to their ecotypic and geographic adaptation in North America. In this study, we sampled and characterized a total of 96 prairie cordgrass natural populations with 9315 high quality SNPs from a genotyping-by-sequencing (GBS) approach. The natural populations were collected from putative remnant prairie sites throughout the Midwest and Eastern USA, which are the major habitats for prairie cordgrass. Partitioning of genetic variance using SNP marker data revealed significant variance among and within populations. Two potential gene pools were identified as being associated with ploidy levels, geographical separation, and climatic separation. Geographical factors such as longitude and altitude, and environmental factors such as annual temperature, annual precipitation, temperature of the warmest month, precipitation of the wettest month, precipitation of Spring, and precipitation of the wettest month are important in affecting the intraspecific distribution of prairie cordgrass. The divergence of prairie cordgrass natural populations also provides opportunities to increase breeding value of prairie cordgrass as a bioenergy and conservation crop.https://www.mdpi.com/2073-4425/12/8/1240prairie cordgrasspopulationsdiversityvariationSNPgenomics |
| spellingShingle | Jia Guo Patrick J. Brown Albert L. Rayburn Carolyn J. Butts-Wilmsmeyer Arvid Boe DoKyoung Lee Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA Genes prairie cordgrass populations diversity variation SNP genomics |
| title | Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA |
| title_full | Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA |
| title_fullStr | Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA |
| title_full_unstemmed | Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA |
| title_short | Genomic Variation Shaped by Environmental and Geographical Factors in Prairie Cordgrass Natural Populations Collected across Its Native Range in the USA |
| title_sort | genomic variation shaped by environmental and geographical factors in prairie cordgrass natural populations collected across its native range in the usa |
| topic | prairie cordgrass populations diversity variation SNP genomics |
| url | https://www.mdpi.com/2073-4425/12/8/1240 |
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