Genetic diversity, SNP-trait associations and genomic selection accuracy in a west African collection of Kersting's groundnut [Macrotyloma geocarpum(Harms) Marechal & Baudet]
Genetic diversity, SNP-trait associations and genomic selection accuracy in a west African collection of Kersting's groundnut [Macrotyloma geocarpum(Harms) Marechal & Baudet]
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DOI：
10.1371/journal.pone.0234769
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发表时间：
2020-06-30
期刊：
影响因子：
3.7
通讯作者：
Sibiya, Julia
中科院分区：
文献类型：
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作者：
Akohoue, Felicien;Achigan-Dako, Enoch Gbenato;Sibiya, Julia
了解复杂性状变异的机制是高效作物改良的必要条件。本研究对281份Kersting花生种质资源进行了分子鉴定、标记-性状关联分析和基因组选择的可能性研究。多样性小组使用阿尔法点阵设计在两个对比环境中进行两次重复的表型分型。使用通过测序技术的基因分型对登记进行基因分型。全基因组关联分析之间的单核苷酸多态性标记和产量相关性状在测试环境。SNP标记被用来计算观察到的（Ho）和预期的杂合性（He），和总的基因多样性（Ht）。分析了不同生态起源地区种质资源的遗传分化。我们的结果显示493个高质量的SNPs，其中113个的次要等位基因频率>0.05，总基因多样性为0.43，平均Ho和He值分别为0.04和0.22。四个集群，高度分化的种皮颜色（Fst = 0.79），进行了鉴定。种群结构分析表明，两个亚种群在不同生态区具有高度分化（Fst = 0.37）。GWAS揭示了10个显著的标记-性状关联，其中6个SNP在不同环境中是一致的。通过交叉验证的基因组选择显示出对小叶长度、种子尺寸性状、100粒种子重量、50%开花天数和成熟天数的中等至高的预测精度。这证明了Kersting花生内存在遗传变异，并显示了该物种改进的潜力。这些发现还提供了第一个洞察到的表型基因型的关系，在克斯汀的花生，使用SNP标记。
Understanding the mechanisms governing complex traits variation is a requirement for efficient crop improvement. In this study, the molecular characterization, marker-trait associations and the possibility for genomic selection in a collection of 281 Kersting's groundnut accessions were carried out. The diversity panel was phenotyped using an Alpha lattice design with two replicates in two contrasting environments. Accessions were genotyped using genotyping by sequencing technology. Genome-wide association analyses were performed between single nucleotide polymorphism markers and yield-related traits across tested environments. SNP markers were used to calculate the observed (Ho) and expected heterozygosity (He), and the total gene diversity (Ht). Genetic differentiation among accessions across ecological regions of origin was analysed. Our results revealed 493 quality SNPs of which 113 had a minor allele frequency>0.05, a total gene diversity of 0.43 and average Ho and He values of 0.04 and 0.22, respectively. Four clusters, highly differentiated by seed coat colour (Fst = 0.79), were identified. The population structure analysis showed two subpopulations with high differentiation across ecological regions (Fst = 0.37). The GWAS revealed 10 significant marker-trait associations, of which six SNPs were consistent across environments. The genomic selection through cross-validation showed moderate to high prediction accuracies for leaflet length, seed dimension traits, 100 seed weight, days to 50% flowering and days to maturity. This demonstrates the existence of genetic variability within Kersting's groundnut and shows the potential for the improvement of the species. The findings also provide a first insight into the phenotype-to-genotype relationships in Kersting's groundnut, using SNP markers.