利用超级集群分离分析法鉴别大豆增变基因

Identification of mutators in soybean genome by super bulked segregant analysis

【目的】利用大豆基因组Wm82.a2.v1及HapMap数据来鉴别大豆中可能存在的增变基因。【方法】将大豆HapMap数据（包含19 652份大豆种质在52 041个位点上的分型结果）预处理后,利用改进的超级集群分离分析法,选取滑动窗口大小、步长及阈值大小为参数,对预处理后的大豆种质数据进行分析,测算大豆点突变比率及突变热点区数目,并将点突变比率及突变热点区数目与分子标记进行关联性分析,从强关联区内挖掘候选增变基因,用大豆基因组Wm82.a2.v1对其功能进行初步推测。【结果】大豆HapMap数据预处理后,15 391份大豆种质点突变比率为0.089~0.531,平均变异率为0.261;突变热点区数目为5~1 324个,平均每份种质包含347.8个突变热点区。超级集群分离分析结果表明,Gm16上的29 153 474-30 604 603bp和Gm17上的12 133 293-12 147 725bp片段为与点突变比率和突变热点区数目2个表型同时存在强关联的区域;其中Gm16上的Glyma16g26440.1和Gm17上的Glyma17g15420.1同属于nudix水解酶基因家族,推测其与基因组突变有关。【结论】Glyma16g26440.1和Glyma17g15420.1 2个nudix水解酶基因家族成员都与点突变比率和突变热点区数目存在强关联,可作为大豆基因组候选增变基因。

【Objective】In this study,the soybean genome Wm82.a2.v1 and HapMap were used to identify the potential mutators.【Method】After pretreatment,the soybean HapMap data（comprising 52 041 genotype from 19 652 soybean germplasm）were used for association loci mining by improved Super-BSA method with selected size of the sliding window,step size and threshold parameters.The candidate genes associated with both point mutation rate and the number of mutation hotspots were considered as soybean mutators.All these genes are used for functional prediction by the soybean genome Wm82.a2.v1.【Result】After the pretrtatment of HapMap data,15 391 individuals were retained.Among these,the range of mutation rate was 0.089-0.531 with an average mutation rate of 0.261,and the range of number of mutation hotspots was 5-1 324 with a mean of 347.8.Super bulked segregant analysis also showed that the intervals 29 153 474-30 604 603 bp on Gm16 and 12 133 293-12 147 725 bp on Gm17 were two regions with strong associations with both phenotypes.Glyma16g26440.1on Gm16 and Glyma17g15420.1on Gm17 belonged to the nudix hydrolase superfamily involving in genome mutations.【Conclusion】The two membersof nudix hydrolase（Glyma16g26440.1and Glyma17g15420.1）were associated with mutation rate and the number of mutation hotspots,and could be considered as candidate soybean mutators for further studies.