Wu XY, Zhou GC, Chen YX, Wu P, Liu LW, Ma FF, Wu M, Liu CC, Zeng YJ, Chu AE, Hang YY, Chen JQ, Wang B.
Front Plant Sci. 2016 Jul 8;7:998. doi: 10.3389/fpls.2016.00998. eCollection 2016.
Abstract
A major soybean (Forrest cultivar) quantitative trait locus (QTL) gene, Rhg4, which controls resistance to soybean cyst nematodes (SCN), encodes the enzyme serine hydroxylmethyltransferase (SHMT). The resistant allele possesses two critical missense mutations (P130R and N358Y) compared to that of the sensitive allele, rhg4. To understand the evolutionary history of this gene, sequences of 117 SHMT family members from 18 representative plant species were used to reconstruct their phylogeny. According to this phylogeny, the plant SHMT gene family can be divided into two groups and four subgroups (Ia, Ib, IIa, and IIb). Belonging to the Subgroup Ia lineage, the rhg4 gene evolved from a recent duplication event in Glycine sp.. To further explore how the SCN-resistant allele emerged, both the rhg4 gene and its closest homolog, the rhg4h gene, were isolated from 33 cultivated and 68 wild soybean varieties. The results suggested that after gene duplication, the soybean rhg4 gene accumulated a higher number of non-synonymous mutations than rhg4h. Although a higher number of segregating sites and gene haplotypes were detected in wild soybeans than in cultivars, the SCN-resistant Rhg4 allele (represented by haplotype 4) was not found in wild varieties. Instead, a very similar allele, haplotype 3, was observed in wild soybeans at a frequency of 7.4%, although it lacked the two critical non-synonymous substitutions. Taken together, these findings support that the SCN-resistant Rhg4 allele likely emerged via artificial selection during the soybean domestication process, based on a SCN-sensitive allele inherited from wild soybeans.
See http://journal.frontiersin.org/article/10.3389/fpls.2016.00998/full
FIGURE 2. The evolution of legume subgroup Ia SHMT genes. Left, a partial tree cut from Figure 1 showing that three gene duplication events and also one gene loss event had occurred. Middle, gene structural analysis showed that an intron loss event had occurred in the common ancestor of Phavu003G051100 and two soybean genes, Glyma08G108900 (rhg4) and Glyma05G152100 (rhg4h). Right, the amino acids at positions 130 and 389 in each gene are shown.
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