Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250131, China.
BMC Genomics. 2018 Aug 29;19(1):641. doi: 10.1186/s12864-018-5035-9.
Soybean is not only an important oil crop, but also an important source of edible protein and industrial raw material. Yield-traits and quality-traits are increasingly attracting the attention of breeders. Therefore, fine mapping the QTLs associated with yield-traits and quality-traits of soybean would be helpful for soybean breeders. In the present study, a high-density linkage map was constructed to identify the QTLs for the yield-traits and quality-traits, using specific length amplified fragment sequencing (SLAF-seq).
SLAF-seq was performed to screen SLAF markers with 149 F individuals from a cross between a semi wild soybean, 'Huapidou', and a cultivated soybean, 'Qihuang26', which generated 400.91 M paired-end reads. In total, 53,132 polymorphic SLAF markers were obtained. The genetic linkage map was constructed by 5111 SLAF markers with segregation type of aa×bb. The final map, containing 20 linkage groups (LGs), was 2909.46 cM in length with an average distance of 0.57 cM between adjacent markers. The average coverage for each SLAF marker on the map was 81.26-fold in the male parent, 45.79-fold in the female parent, and 19.84-fold average in each F individual. According to the high-density map, 35 QTLs for plant height (PH), 100-seeds weight (SW), oil content in seeds (Oil) and protein content in seeds (Protein) were found to be distributed on 17 chromosomes, and 14 novel QTLs were identified for the first time. The physical distance of 11 QTLs was shorter than 100 Kb, suggesting a direct opportunity to find candidate genes. Furthermore, three pairs of epistatic QTLs associated with Protein involving 6 loci on 5 chromosomes were identified. Moreover, 13, 14, 7 and 9 genes, which showed tissue-specific expression patterns, might be associated with PH, SW, Oil and Protein, respectively.
With SLAF-sequencing, some novel QTLs and important QTLs for both yield-related and quality traits were identified based on a new, high-density linkage map. Moreover, 43 genes with tissue-specific expression patterns were regarded as potential genes in further study. Our findings might be beneficial to molecular marker-assisted breeding, and could provide detailed information for accurate QTL localization.
大豆不仅是一种重要的油料作物，也是食用蛋白和工业原料的重要来源。产量性状和品质性状越来越受到育种者的关注。因此，精细定位与大豆产量性状和品质性状相关的 QTL 有助于大豆育种者。本研究利用特定长度扩增片段测序（SLAF-seq）构建了一张高密度连锁图谱，用于鉴定产量性状和品质性状的 QTL。
对来自半野生大豆‘Huapidou’和栽培大豆‘Qihuang26’杂交后代的 149 个个体进行 SLAF-seq 筛选，共获得 400.91M 配对末端reads，共筛选到 53132 个多态性 SLAF 标记。采用分离类型为 aa×bb 的 5111 个 SLAF 标记构建了遗传连锁图谱。最终图谱包含 20 个连锁群（LG），总长度为 2909.46cM，相邻标记之间的平均距离为 0.57cM。图谱上每个 SLAF 标记在雄性亲本中的平均覆盖度为 81.26 倍，在雌性亲本中的平均覆盖度为 45.79 倍，在每个 F1 个体中的平均覆盖度为 19.84 倍。根据高密度图谱，共检测到 35 个与株高（PH）、百粒重（SW）、种子含油量（Oil）和种子蛋白质含量（Protein）相关的 QTL 分布在 17 条染色体上，首次鉴定到 14 个新的 QTL。11 个 QTL 的物理距离小于 100Kb，提示有直接机会找到候选基因。此外，还鉴定到与蛋白质相关的涉及 5 条染色体上 6 个位点的三对上位性 QTL。此外，13、14、7 和 9 个基因的组织特异性表达模式可能分别与 PH、SW、Oil 和 Protein 相关。
利用 SLAF 测序技术，在一张新的高密度连锁图谱的基础上，鉴定到一些与产量相关和品质性状相关的新的和重要的 QTL，同时还鉴定到 43 个具有组织特异性表达模式的基因，这些基因可能是进一步研究的潜在候选基因。本研究结果可能有助于分子标记辅助育种，并为准确的 QTL 定位提供详细信息。
