title: Molecular insights into the genetic diversity of Hemarthria compressa germplasm collections native to southwest China.
abstract: Start codon targeted polymorphism (SCoT) analysis was employed to distinguish 37 whipgrass (Hemarthria compressa L.) clones and assess the genetic diversity and population structure among these genotypes. The informativeness of markers was also estimated using various parameters. Using 25 highly reproducible primer sets, 368 discernible fragments were generated. Of these, 282 (77.21%) were polymorphic. The number of alleles per locus ranged from five to 21, and the genetic variation indices varied. The polymorphism information content (PIC) was 0.358, the Shannon diversity index (H) was 0.534, the marker index (MI) was 4.040, the resolving power (RP) was 6.108, and the genotype index (GI) was 0.782. Genetic similarity coefficients (GS) between the accessions ranged from 0.563 to 0.872, with a mean of 0.685. Their patterns observed in a dendrogram constructed using the unweighted pair group method with arithmetic mean analysis (UPGMA) based on GS largely confirmed the results of principal coordinate analysis (PCoA). PCoA was further confirmed by Bayesian model-based STRUCTURE analysis, which revealed no direct association between genetic relationship and geographical origins as validated by Mantel's test (r = 0.2268, p = 0.9999). In addition, high-level genetic variation within geographical groups was significantly greater than that between groups, as determined by Shannon diversity analysis, analysis of molecular variance (AMOVA) and Bayesian analysis. Overall, SCoT analysis is a simple, effective and reliable technique for characterizing and maintaining germplasm collections of whipgrass and related species.
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an 625014, China. guozhihui-2008@163.com.
authors.forename: Zhi-Hui
authors.initials: ZH
authors.lastname: Guo
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an 625014, China. linzhuyan@126.com.
authors.forename: Kai-Xin
authors.initials: KX
authors.lastname: Fu
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an 625014, China. zhangxq@sicau.edu.cn.
authors.forename: Xin-Quan
authors.initials: XQ
authors.lastname: Zhang
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an 625014, China. baishiqie@yeah.net.
authors.forename: Shi-Qie
authors.initials: SQ
authors.lastname: Bai
authors.affiliation: Chongqing Municipal Institute of Animal Husbandry, Chongqing 400039, China. cq_fy001@163.com.
authors.forename: Yan
authors.initials: Y
authors.lastname: Fan
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an 625014, China. pengyanlee@163.com.
authors.forename: Yan
authors.initials: Y
authors.lastname: Peng
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an 625014, China. huanglinkai@sicau.edu.cn.
authors.forename: Lin-Kai
authors.initials: LK
authors.lastname: Huang
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an 625014, China. yanyanhong3588284@126.com.
authors.forename: Yan-Hong
authors.initials: YH
authors.lastname: Yan
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an 625014, China. lwgrass@126.com.
authors.forename: Wei
authors.initials: W
authors.lastname: Liu
authors.affiliation: Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an 625014, China. maroar@126.com.
authors.forename: Xiao
authors.initials: X
authors.lastname: Ma
mesh_terms: D001483:Base Sequence; D001499:Bayes Theorem; D002681:China; D016000:Cluster Analysis; D018387:Codon, Initiator / Q000235:genetics; D017931:DNA Primers / Q000235:genetics; D017343:Genes, Plant; D005819:Genetic Markers; D006239:Haplotypes; D008957:Models, Genetic; D010802:Phylogeny; D058974:Phylogeography; D006109:Poaceae / Q000235:genetics*; D011110:Polymorphism, Genetic
chemical_list: D018387:Codon, Initiator; D017931:DNA Primers; D005819:Genetic Markers