Protein and Fat Content QTL Mapping and Gene Annotation Based on High-density Soybean SNP Genetic Map

In order to construct a high-density genetic map of soybean with significant differences in fat and protein content, and carry out QTL mapping based on SNP markers and gene annotation within the mapping interval to find new loci, this study was based on the F₂ segregation population obtained by crossing Jinong 45 as female parent and Suinong 76 as male parent, SNP markers were obtained by targeted sequencing genotyping technique to construct a high-density genetic map. Combined with seed fat and protein content, composite interval mapping（CIM） method and inclusive composite interval mapping（ICIM） method were used to map QTL, and the physical interval of QTL was determined according to the chromosome physical location information provided by SNP markers. Soybase and Phytozome databases were used to mine, annotate and screen genes in the interval. A total of 2 399 polymorphic molecular markers were obtained, and the genetic maps with 1 020.5 cM of a total map distance and 0.61 cM of average distance between markers were constructed. A total of 4 QTL were detected by CIM method, of which 2 protein content loci were qPro-11-1 and qPro-11-2, and 2 fat content loci were qOil-7-1 and qOil-19-1, with a contribution rate of 1.31%-21.69%. A total of 3 QTL were detected by ICIM method, of which two protein content loci were qPro-11-3 and qPro-14-1, and one fat content locus was qOil-16-1, with a contribution rate of 8.41%-17.83%. Through gene annotation, 26, 29, 6, 1, 124 and 36 genes related to fat and protein storage, oil biosynthesis, oil metabolism, fatty acid biosynthesis, seed development and seed germination were screened in 6 physical intervals, respectively. Among the 6 different loci, adipose QTL was located on chromosomes 7, 16 and 19, and protein QTL was located on chromosomes 11 and 14, respectively. qPro-11-2 and qPro-11-3 were the same loci located by the two methods. Four loci were similar to the results of previous loci, and qPro-11-2 and qPro-14-1 were new loci.