单核苷酸多态性 (SNP) 标记用于研究埃塞俄比亚大麦 (Hordeum vulgare L.) 种质的遗传多样性和群体结构。

Single nucleotide polymorphism (SNP) markers for genetic diversity and population structure study in Ethiopian barley (Hordeum vulgare L.) germplasm.

机构信息

Department of Applied Biology, School of Applied Natural Science, Adama Science and Technology University, P.O.Box 1888, Adama, Ethiopia.

Department of Plant Science, College of Agriculture and Natural Resource, Madda Walabu University, P.O.Box 247, Robe, Oromia, Ethiopia.

出版信息

BMC Genom Data. 2023 Feb 14;24(1):7. doi: 10.1186/s12863-023-01109-6.

BACKGROUND

High-density single nucleotide polymorphisms (SNPs) are the most abundant and robust form of genetic variants and hence make highly favorable markers to determine the genetic diversity and relationship, enhancing the selection of breeding materials and the discovery of novel genes associated with economically important traits. In this study, a total of 105 barley genotypes were sampled from various agro-ecologies of Ethiopia and genotyped using 10 K single nucleotide polymorphism (SNP) markers. The refined dataset was used to assess genetic diversity and population structure.

RESULTS

The average gene diversity was 0.253, polymorphism information content (PIC) of 0.216, and minor allelic frequency (MAF) of 0.118 this revealed a high genetic variation in barley genotypes. The genetic differentiation also showed the existence of variations, ranging from 0.019 to 0.117, indicating moderate genetic differentiation between barley populations. Analysis of molecular variance (AMOVA) revealed that 46.43% and 52.85% of the total genetic variation occurred within the accessions and populations, respectively. The heat map, principal components and population structure analysis further confirm the presence of four distinct clusters.

CONCLUSIONS

This study confirmed that there is substantial genetic variation among the different barley genotypes. This information is useful in genomics, genetics and barley breeding.

背景

高密度单核苷酸多态性（SNPs）是最丰富和最稳健的遗传变异形式，因此是确定遗传多样性和关系的高度有利标记，增强了对育种材料的选择和与经济重要性状相关的新基因的发现。在这项研究中，从埃塞俄比亚的各种农业生态区共采集了 105 个大麦基因型，并用 10K 单核苷酸多态性（SNP）标记进行了基因分型。使用细化数据集评估遗传多样性和种群结构。

结果

平均基因多样性为 0.253，多态信息含量（PIC）为 0.216，次要等位基因频率（MAF）为 0.118，这表明大麦基因型具有较高的遗传变异。遗传分化也显示出存在差异，范围从 0.019 到 0.117，表明大麦群体之间存在中等遗传分化。分子方差分析（AMOVA）表明，46.43%和 52.85%的总遗传变异分别发生在个体内和群体内。热图、主成分和种群结构分析进一步证实了存在四个不同的聚类。