冀北坝上大豆结瘤相关性状全基因组关联分析

Genome-Wide Association Analysis of Soybean Nodulation-Related Traits in the Northern Hebei

【目的】挖掘适应坝上生态条件的高效结瘤大豆种质,鉴定调控大豆-根瘤菌共生结瘤的遗传位点和候选基因,提高大豆共生固氮效率。【方法】以包含260份大豆种质的自然群体为研究对象,在河北坝上室外盆栽条件下接种根瘤菌菌株USDA110。以单株根瘤数量、单株根瘤干重数值作为表型数据,结合大豆260份种质基因型数据,对其进行全基因组关联分析,挖掘大豆共生结瘤相关基因。【结果】共检测到18个与大豆根瘤数量显著关联的SNP,分别位于第2、7、8、13、18和19染色体上。其中,位于第2染色体上的显著关联位点BARC_2.01_Chr02_43161654_A_G是控制大豆根瘤数量的主效位点(LOD=3.89),对该位点上下游共200 kb区间进行连锁不平衡分析,在包含BARC_2.01_Chr02_43161654_A_G的连锁区间内,共获得10个调控大豆根瘤数量候选基因,通过单倍型分析发现,Glyma.02G243200不同单倍型所对应的材料之间的根瘤数量具有显著差异(P<0.05),在SoyBase数据库中查询该基因的表达模式发现,Glyma.02G243200在根毛中表达。该基因可能是影响大豆根瘤数量的关键基因。共检测到6个与大豆根瘤干重显著关联的SNP,分别位于第6、18和20染色体上。其中,位于第6染色体上的显著关联位点BARC_2.01_Chr06_6069381_G_A和BARC_2.01_Chr06_6192925_T_C是控制大豆根瘤干重的主效位点(LOD=3.49和LOD=3.35),对BARC_2.01_Chr06_6069381_G_A上游100 kb和BARC_2.01_Chr06_6192925_T_C下游100 kb区间进行连锁不平衡分析,获得14个调控大豆根瘤干重候选基因,并进行单倍型分析。其中,Glyma.06G079600和Glyma.06G079900不同单倍型所对应的材料之间的根瘤干重具有显著差异(P<0.01,P<0.001),在SoyBase数据库中查询这两个基因的表达模式发现,Glyma.06G079600和Glyma.06G079900在根中表达。这两个基因可能是影响大豆根瘤干重的关键基因。【结论】在第2染色体上发现一个与根瘤数量显著相关的候选基因,在第6染色体上发现2个与根瘤干重显著相关的候选基因。

【Objective】Exploring efficient nodulation soybean germplasm adapted to the ecological conditions of the Bashang area,identifying genetic loci and candidate genes regulating soybean-rhizobium symbiotic nodulation,and improving soybean symbiotic nitrogen fixation efficiency.【Method】This study utilized a natural population of 260 soybean germplasms as the research object,rhizobium strain USDA110 was inoculated under outdoor potted conditions in the Bashang of Hebei Province.The single plant nodule number and single plant nodule dry weight data were used as phenotypic values.Combined with genotype data of the 260 germplasms,a genome-wide association analysis was conducted to explore genes related to soybean-rhizobium symbiotic nodulation.【Result】A total of 18 SNPs significantly associated with soybean nodule number were detected,located on chromosomes 2,7,8,13,18,and 19.Among them,the significant associated locus BARC_2.01_Chr02_43161654_A_G on chromosome 2 was identified as the main locus controlling soybean nodule number(LOD=3.89).Linkage disequilibrium analysis within the 200 kb interval upstream and downstream of this locus containing BARC_2.01_Chr02_43161654_A_G identified 10 candidate genes regulating soybean nodule number.There was a significant difference in the number of nodules among the materials corresponding to different haplotypes of Glyma.02G243200(P<0.05),the expression pattern of this gene was queried in the SoyBase database,and it was expressed in root hairs,indicating that Glyma.02G243200 may be a key gene influencing soybean nodule number.Additionally,six SNPs significantly associated with soybean nodule dry weight were identified,located on chromosomes 6,18,and 20.Among them,the significant associated loci BARC_2.01_Chr06_6069381_G_A and BARC_2.01_Chr06_6192925_T_C on chromosome 6 were identified as the main loci controlling soybean nodule dry weight(LOD=3.49 and LOD=3.35,respectively).Linkage disequilibrium analysis within the 100 kb interval upstream of BARC_2.01_Chr06_6069381_G_A and downstream of BARC_2.01_Chr06_6192925_T_C identified 14 candidate genes regulating soybean nodule dry weight.Haplotype analysis revealed significant differences in nodule dry weight for the genes Glyma.06G079600 and Glyma.06G079900 between different haplotype materials(P<0.01,P<0.001),the expression pattern of this gene was queried in the SoyBase database,and they were expressed in roots,indicating that these two genes may be key genes influencing soybean nodule dry weight.【Conclusion】This study identified a candidate gene significantly associated with nodule number on chromosome 2 and two candidate genes significantly associated with nodule dry weight on chromosome 6,providing new genetic resources and references for genetic improvement of soybean nodulation traits.