Genomic variation among dwarf and normal soybean F6 lines obtained from the cross of G.max and G soja

Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. Thus, we studied DNA variations in dwarf mutants derived from F5 RILs with 96.8% homozygous genotypes. Here, we report DNA variations between the normal and dwarf members of 4 lines containing dwarf mutants among the seeds harvested from a single seed parent in an F6 RIL population derived from a cross between Glycine max var. Peking and Glycine soja IT182936. The dwarf mutants displayed reduced plant height and shortened internodes. We discovered 2 dwarf mutant lines and 2 semi dwarf mutant lines among the normal F6 RIL plants. Whole genome sequencing was carried out, and the DNA variations in the whole genome were compared between the normal and dwarf samples in triplicate. We found a large number of DNA variations in both the dwarf and semi dwarf lines, with 1 SNP per at least 3.68 kb in the dwarf lines and 1 SNP per 11.13 kb of the whole genome. This value is 2.18 times higher than the expected DNA variation in the F6 population. A total of 186 SNPs and 241 SNPs were discovered in the coding regions of the dwarf lines 1282 and 1303, respectively, and we discovered a total of 33 homogeneous nonsynonymous SNPs that occurred at the same loci in each set of dwarf and normal soybean plants derived from normal soybean ancestors. Of them, 5 SNPs were discovered in the same positions between lines 1282 and 1303. Two of them were in the transcription factor jumonji (jmjC) domain, and one was in each of the matrixin family protein, TTF-type zinc finger protein and cytochrome P450 families. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding. These polymorphisms could be useful genetic resources for plant breeders, geneticists and biologists for future molecular biology and breeding projects.