Song Jian, Li Zhen, Liu Zhangxiong, Guo Yong, Qiu Li-Juan
The National Key Facility for Crop Gene Resources and Genetic Improvement/MOA Key Labs of Crop Germplasm and Soybean Biology, Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China.
Front Plant Sci. 2017 May 31;8:919. doi: 10.3389/fpls.2017.00919. eCollection 2017.
Next-generation sequencing (NGS)-based bulked-segregant analysis (BSA) approaches have been proven successful for rapidly mapping genes in plant species. However, most such methods are based on mutants and usually only one gene controlling the mutant phenotype is identified. In this study, NGS-based BSA was employed to map simultaneously two qualitative genes controlling cotyledon color of seed in soybean. Yellow-cotyledon (YC) and green-cotyledon (GC) bulks from progenies of a biparental population (Zhonghuang 30 × Jiyu 102) were sequenced. The SNP-index of each SNP locus in YC and GC bulks was calculated and two genomic regions on chromosomes 1 and 11 harboring, respectively, loci and were identified by Δ(SNP-index) analysis. These two BSA-seq-derived loci were further validated with SSR markers and fine-mapped. was mapped to a 30.7-kb region containing four annotated genes and was mapped to a 67.7-kb region with nine genes. These two regions contained, respectively, genes and , which had previously been identified by homology-based cloning as being associated with cotyledon color. Sequence analysis of the NGS data also identified a frameshift deletion in the coding region of . These results suggested that BSA-seq could accelerate the mapping of loci controlling qualitative traits, even if a trait is controlled by more than one locus.
基于新一代测序（NGS）的混合分组分析法（BSA）已被证明在快速定位植物物种中的基因方面是成功的。然而，大多数此类方法基于突变体，通常只能鉴定出一个控制突变体表型的基因。在本研究中，采用基于NGS的BSA同时定位控制大豆种子子叶颜色的两个质量性状基因。对一个双亲群体（中黄30×吉育102）后代的黄子叶（YC）和绿子叶（GC）混合群体进行测序。计算YC和GC混合群体中每个SNP位点的SNP指数，并通过Δ（SNP指数）分析确定1号和11号染色体上分别含有位点 和 的两个基因组区域。这两个基于BSA-seq获得的位点进一步用SSR标记进行验证并精细定位。 被定位到一个包含四个注释基因的30.7 kb区域， 被定位到一个包含九个基因的67.7 kb区域。这两个区域分别包含基因 和 ，它们先前已通过基于同源性的克隆被鉴定为与子叶颜色相关。对NGS数据的序列分析还在 的编码区鉴定出一个移码缺失。这些结果表明，即使一个性状由多个位点控制，BSA-seq也可以加速控制质量性状的位点的定位。
