Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean.
Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean.
复制标题
DOI：
10.1038/srep19199
复制
发表时间：
2016-01-19
影响因子：
4.6
通讯作者：
Nguyen HT
中科院分区：
文献类型：
--
作者：
Patil G;Do T;Vuong TD;Valliyodan B;Lee JD;Chaudhary J;Shannon JG;Nguyen HT
土壤盐分是作物产量的限制因素。大豆对土壤盐分敏感，其中显性基因Glyma03g32900主要负责耐盐性。鉴定高通量、高鲁棒性的标记和选育耐盐品种是减少盐碱条件下产量损失的有效途径。利用高质量（15x）全基因组重测序（WGRS）对106个大豆品系进行分析，鉴定出GmCHX1基因启动子和基因区域的3个主要结构变异和等位基因变异。与结构变异相关的单核苷酸多态性（snp）的发现促进了六种KASPar试验的设计。此外，利用公开的WGRS数据集对93个美国祖先系进行了单倍型分析和系谱追踪。利用来自PI483463 × Hutcheson的104个大豆品系和种间双亲本群体（F8），对鉴定的SNP标记进行了验证，并观察到基因型与盐处理表型（叶片焦烧、叶绿素含量和Na+积累）之间存在很强的相关性。这些标记精确地鉴定出耐盐/敏感基因型（>91%）和不同的结构变异（>98%）。这些SNP分析，在准确的表型分析、单倍型分析和谱系跟踪信息的支持下，将加速标记辅助选择计划，以加强耐盐大豆品种的开发。
Soil salinity is a limiting factor of crop yield. The soybean is sensitive to soil salinity, and a dominant gene, Glyma03g32900 is primarily responsible for salt-tolerance. The identification of high throughput and robust markers as well as the deployment of salt-tolerant cultivars are effective approaches to minimize yield loss under saline conditions. We utilized high quality (15x) whole-genome resequencing (WGRS) on 106 diverse soybean lines and identified three major structural variants and allelic variation in the promoter and genic regions of the GmCHX1 gene. The discovery of single nucleotide polymorphisms (SNPs) associated with structural variants facilitated the design of six KASPar assays. Additionally, haplotype analysis and pedigree tracking of 93 U.S. ancestral lines were performed using publically available WGRS datasets. Identified SNP markers were validated, and a strong correlation was observed between the genotype and salt treatment phenotype (leaf scorch, chlorophyll content and Na+ accumulation) using a panel of 104 soybean lines and, an interspecific bi-parental population (F8) from PI483463 x Hutcheson. These markers precisely identified salt-tolerant/sensitive genotypes (>91%), and different structural-variants (>98%). These SNP assays, supported by accurate phenotyping, haplotype analyses and pedigree tracking information, will accelerate marker-assisted selection programs to enhance the development of salt-tolerant soybean cultivars.