Genome-wide patterns of population structure and association mapping of nut-related traits in Persian walnut populations from Iran using the Axiom J. regia 700K SNP array
Genome-wide patterns of population structure and association mapping of nut-related traits in Persian walnut populations from Iran using the Axiom J. regia 700K SNP array
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DOI：
10.1038/s41598-019-42940-1
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发表时间：
2019-04-23
影响因子：
4.6
通讯作者：
Vahdati, Kourosh
中科院分区：
文献类型：
--
作者：
Arab, Mohammad Mehdi;Marrano, Annarita;Vahdati, Kourosh
波斯高原（包括伊朗）被认为是核桃的主要起源中心之一。从这个竞技场采集核桃树样本，并利用下一代测序（NGS）的能力，可以为核桃基因组的遗传变异程度提供新的见解。本研究旨在探讨伊朗波斯核桃（Juglans regia L.）的群体结构和基因组变异。并使用新的Axiom J. regia 700 K SNP基因分型阵列鉴定坚果和仁相关性状变异的潜在基因座。我们对一个多样性小组进行了基因分型，该小组包括来自伊朗八个省的95种核桃基因型，这些省具有各种气候带。大多数SNPs（323，273，53.03%）属于“Poly High Resolution”多态性类别，其中包括最高质量的变体。遗传结构评估，使用几种方法，伊朗核桃面板分为四个主要的集群，反映其地理分区。我们在所有群体中观察到高遗传变异（H-o = 0.34和H-E = 0.38）。种群间遗传分化总体水平为中等（F-ST = 0.07）。然而，塞姆南人群表现出很高的分歧，从其他伊朗人口（平均F-ST = 0.12），最有可能是由于其地理隔离。基于亲子关系分析，相关性水平是非常低的伊朗核桃检查，反映了我们的研究中考虑的伊朗各省之间的地理距离。最后，我们进行了全基因组关联研究（GWAS），确定了55个与坚果和仁相关性状显著相关的SNP。总之，通过应用新的Axiom J. regia 700 K SNP阵列，我们发现了新的未探索的遗传多样性，并确定了波斯核桃坚果相关性状的重要标记-性状关联，这将对伊朗和其他国家的未来育种计划有用。
Persian plateau (including Iran) is considered as one of the primary centers of origin of walnut. Sampling walnut trees originating from this arena and exploiting the capabilities of next-generation sequencing (NGS) can provide new insights into the degree of genetic variation across the walnut genome. The present study aimed to explore the population structure and genomic variation of an Iranian collection of Persian walnut (Juglans regia L.) and identify loci underlying the variation in nut and kernel related traits using the new Axiom J. regia 700K SNP genotyping array. We genotyped a diversity panel including 95 walnut genotypes from eight Iranian provinces with a variety of climate zones. A majority of the SNPs (323,273, 53.03%) fell into the "Poly High Resolution" class of polymorphisms, which includes the highest quality variants. Genetic structure assessment, using several approaches, divided the Iranian walnut panel into four principal clusters, reflecting their geographic partitioning. We observed high genetic variation across all of the populations (H-o = 0.34 and H-E = 0.38). The overall level of genetic differentiation among populations was moderate (F-ST = 0.07). However, the Semnan population showed high divergence from the other Iranian populations (on average F-ST = 0.12), most likely due to its geographical isolation. Based on parentage analysis, the level of relatedness was very low among the Iranian walnuts examined, reflecting the geographical distance between the Iranian provinces considered in our study. Finally, we performed a genome-wide association study (GWAS), identifying 55 SNPs significantly associated with nut and kernel-related traits. In conclusion, by applying the novel Axiom J. regia 700K SNP array we uncovered new unexplored genetic diversity and identified significant marker-trait associations for nut-related traits in Persian walnut that will be useful for future breeding programs in Iran and other countries.