Sequence divergence of recently duplicate genes in soybean (Glycine max L. Merr.)

Sequence divergence of duplicate genes was investigated in soybean, a diploldized paleopolyploid. To examine gene duplication, a total of seven primers designed from expressed sequence tags (ESTs) were selected for this study because they produced (1) a single band but showed poor sequencing quality and (2) double bands on an agarose gel. After PCR amplification with genomic DNA duplicate genes were identified by clonnig and subsequent sequencing of twenty randomly-selected clones. Based on their alignment, two or three classes were identified in each amplicon. Linkage analysis confirmed that two duplicate loci were located on different chromosomes. The exon/intron structure was conserved between duplicate gene pairs. A detailed examination of the variation between duplicate pairs showed that the coding regions are highly conserved while many substitutions and insertion/deletions (indels) were identified in non-coding regions. In particular, non-homologs fragments were numerous and, on average, 82 bp in length within the non-coding region. Quantitative trait loci (QTL) for some major agronomic characters, such as seed protein and oil, seed Yield, plant height, and corn earworm resistance, were positioned across duplicate loci of TC225246 and TC224550, suggesting that the gene families appear to have retained similar functions throughout genome duplication and evolution events.