Genomic analysis of a major seed protein/oil QTL region on soybean linkage group I

The economic and nutritional value of soybeans is determined by its seed protein and oil contents. The genetic control of seed protein/oil is quantitative and many genomic regions associated with the regulation of these traits have been identified in soybean. The protein/oil quantitative trait locus (QTL) mapped to LG I (chromosome 20) is ubiquitous among high protein soybean lines. Identification of the candidate gene(s) underlying this major QTL would help us understand the genetic and molecular mechanisms regulating seed protein/oil accumulation in soybean. Map based cloning to identify the candidate genes for the LG I QTL was undertaken. A BAC based physical map of the region was developed by chromosome walking. Utilizing the genome sequence of soybean and the fine genetic mapping, the QTL region was delineated to an approximately 8.4 Mbp pericentromeric region on chromosome 20. Thirteen genes exhibiting differential expression in developing seeds of near isogenic-lines (NILs) contrasting in protein/oil contents, were identified as potential candidates for the QTL. The homoeologous region corresponding to the QTL region was identified on chromosome 10, spanning a 7.3 Mbp pericentromeric region. Evidence suggests these regions were products of the recent soybean genome duplication 10-14 million years ago (MYA). Comparative analysis of the two regions indicated that both regions are hot spots for retrotransposon accumulation. However, the chromosome 20 region showed preferential accumulation of retrotransposons. The extent of synteny was poor in the retrotransposon rich (gene poor) regions while the adjacent retrotransposon poor (gene rich) regions showed high levels of synteny and colinearity. The genes conserved across the regions showed evidence of sub-funtionalization. The conserved genes were evolving under purifying selection and were enriched for genes involved in stress responses and transcription regulation. The abundance of retrotransposons in these regions points to the likely role of retrotransposons in the evolution of these regions. A detailed study of the retrotransposon insertions in BAC-sized regions around the QTL indicated intergenic and intragenic insertions. The majority of retrotransposon accumulations in the regions studied, happened in the past two million years. Retrotransposon insertions and selection against the insertions could be the predominant forces driving the evolution of this major protein/oil QTL region in soybean.