Objective  Genetic variations in the southern high-protein soybeans were revealed by re-sequencing the whole genome.

  Method   High-throughput sequencing was conducted on the whole genome of the southern high-protein soybean Fudou 234 to detect genetic variations.

  Result  In the 64757037 clean reads, the sequencing depth was 17× with genome coverage of 98.08% (1×) and 96.25% (5×). There were 1478393 single nucleotide polymorphisms (SNPs) and 356739 small insertion-deletions (Small InDels) identified. Among them, 14323 non-synonymous SNP mutations and 4186Small InDel mutated genes were found in the coding sequence (CDS). Analysis by COG (Clusters of orthologous groups of proteins) revealed that signal transduction mechanisms, transcription, carbohydrate translocation and metabolism and KEGG(Kyoto encyclopedia of genes and genomes) analyses revealed that the pathways of carbon metabolism, starch and sucrose metabolism, amino acid biosynthesis, phytohormone signalling, and endoplasmic reticulum protein processing were associated with genetic variation in Fudou 234. In addition, by studying the candidate genes in two major segments of soybean kernel protein quantitative trait locus (QTL), 10 SNP and 7 Small InDel type variations were discovered in 65 genes.

  Conclusion  The genetic variations in the southern high-protein soybeans deviated from the regular varieties were unveiled to provide new venue for breeding and developing molecular markers in studying soybeans.