International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
University of Georgia (UGA), Tifton, USA.
Sci Rep. 2017 Jan 16;7:40577. doi: 10.1038/srep40577.
Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array 'Axiom_Arachis' with 58 K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogaea), fair representation was kept for other diploids (A. duranensis, A. stenosperma, A. cardenasii, A. magna and A. batizocoi). Genotyping of the groundnut 'Reference Set' containing 300 genotypes identified 44,424 polymorphic SNPs and genetic diversity analysis provided in-depth insights into the genetic architecture of this material. The availability of the high-density SNP array 'Axiom_Arachis' with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut.
单核苷酸多态性（SNPs）是基因组中最丰富的 DNA 序列变异，可用于将基因型变异与表型相关联。因此，具有均匀基因组覆盖的高密度 SNP 阵列的可用性可以推进遗传研究和育种应用。在这里，我们报告了高密度 SNP 阵列“Axiom_Arachis”的开发，该阵列具有 58,000 个 SNPs，可用于研究落花生的遗传多样性。在这种情况下，从 41 个落花生品种和野生二倍体祖先的 DNA 重测序和 RNA 测序中总共获得了 163782 个 SNPs，从中总共选择了 58233 个独特的、信息丰富的 SNPs 来开发该阵列。除了栽培落花生（Arachis hypogaea）外，还为其他二倍体（A. duranensis、A. stenosperma、A. cardenasii、A. magna 和 A. batizocoi）保持了公平的代表。对包含 300 个基因型的落花生“参考集”进行的基因分型确定了 44424 个多态性 SNPs，遗传多样性分析深入了解了该材料的遗传结构。具有 58000 个 SNPs 的高密度 SNP 阵列“Axiom_Arachis”的可用性将加速栽培落花生的高分辨率性状遗传学和分子育种进程。
