Genome-Wide Association Studies Of Seed Size And Shape Traits In Soybean And Development Of Distortedmap Software

Soybean (Glycine max L. Merr.) is one of the most important grain and oil crops in the world. Soybean is attached much attention as its abundance of protein and oil, its ability to fix nitrogen and wide utilization on agricultural production. Both seed size and shape traits play a critical role in appearance quality and yield. Therefore, it is not only on theory but also on practice valuable to elucidate the genetic mechanism of seed size and shape traits.Previous studies on seed size and shape traits in soybean are derived from bi-parental segregation populations with a small number of markers. However, these results were limited to the two parents, and novel alleles can not be fully mined. Therefore, it is necessary to carry out genome-wide association studies (GWAS) with high throughput SNP markers. In this study, the information of 32,916 SNP markers, along with the observations of seed size and seed shape traits, in 286 soybean cultivars was used to carry out the GWAS. We would identify the candidate genes by the associated SNPs. Further, we would deduce the molecular mechanisms of the above traits using GO enrichment and comparative genomic analysis. In addition, the construction of genetic linkage map is affected by marker segregation distortion in bi-parental segregation population. To correct the genetic distance between distorted markers, software packages named DistortedMap V1.0 was developed based on the proposed approach in our lab. The mian results are as follows:1. At the significant threshold of-log10 P≥5.82 in GWAS, a total of 33,86 and 69 SNP markers were simultaneously detected for seed length, width and thickness during 2008-2013, respectively; and 147 SNP markers were simultaneously detected for 100-seed weight during 2011-2013. Among these associated markers,90 SNP were related to at least two traits.335 elite alleles and typical soybean cultivars were further mined.2. Using the above 193 SNPs associated with the above traits,162 candidate genes were predicted. Among these genes,23 included 25 SNP markers,34 were near to at least two SNPs detected. Using GO enrichment and comparative genomic analysis,7 genes were identified:Glyma04g37760, Glymallg15480, Glyma11g15490, Glyma17g34330, Glyma04g25590, Glyma17g18040 and Glyma14g24660.3. A software packages of DistortedMap V1.0 were developed. The DistortedMap V1.0 had five main functions:simulating distorted segregation populations, analyzing data of molecular markers, correcting linkage map, comparing maps from various programs and mapping QTL in segregation distortion populations.