Soybean mosaic virus (SMV) disease is one of the most serious and broadly distributed soybean (Glycine max (L.) Merr.) diseases. Here, we combine the advantages of association and linkage analysis to identify and fine-map the soybean genes associated with resistance to SMV strain SC7. A set of 191 soybean accessions from different geographic origins and 184 recombinant inbred lines (RILs) derived from Kefeng No.1 (resistant) × Nannong 1138-2 (susceptible) were used in this study. The SC7 resistance genes were previously mapped to a 2.65 Mb region on chromosome 2 and a 380 kb region on chromosome 13. Among 19 single nucleotide polymorphisms (SNPs) detected via association analysis in the study, the SNP BARC-021625-04157 was located in the 2.65 Mb region, and the SNP BARC-041671-08065 was located near the 380 kb region; three genes harboring the SNPs were probably related to SC7 resistance. The resistance gene associated with BARC-021625-04157 was then fine-mapped to a region of approximately 158 kb on chromosome 2 using 184 RILs. Among the 15 genes within this region, one NBS-LRR type gene, one HSP40 gene and one serine carboxypeptidase-type gene might be candidate SC7 resistance genes. These results will be useful for map-based cloning and marker-assisted selection in soybean breeding programs.

Soybean isoflavone synthase (IFS) and flavanone 3-hydroxylase (F3H) are two key enzymes catalyzing the biosynthesis of isoflavonoids and flavonoids, both of which play diverse roles in stress responses. However, little is known about the evolutionary pattern of these genes in cultivated soybean and its wild progenitors. Herein, we investigated the nucleotide polymorphisms in Isoflavone synthase (IFS1, IFS2) and Flavanone 3-hydroxylase (F3H2) genes from 33 soybean accessions, including 17 cultivars (Glycine max) and 16 their wild progenitors (Glycine soja). Our data showed that the target genes shared the levels of nucleotide polymorphism with three reference genes involved in plant-microbe interactions, but possessed a much higher nucleotide polymorphism than other reference genes. Moreover, no significant genetic differentiation was found between cultivated soybean and its wild relatives in three target genes, despite of considering bottleneck and founder effect during domestication. These results indicate that IFS and F3H genes could have experienced gene introgressions or diversifying selection events during domestication process. Especially, F3H2 gene appears to evolve under positive selection and enjoy a faster evolutionary rate than IFS1 and IFS2 genes.

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Resistance and tolerance are different plant defense mechanisms against herbivores. In this study, four compensatory growth (tolerance) indexes-the ratios of treatment to control for plant height (RPH), branching number of the stem (RBN), seed number per plant (RSN), and seed weight per plant (RSW)-and three resistance indexes-larval weight (LW), pupal weight (PW), and larva-consumed leaf weight (LCL)-were used to evaluate soybean (Glycine max (L.) Merr) defense against common cutworm (CCW; Spodoptera litura Fabricius). The phenotypic variations of seven traits among 170 accessions were significant (ANOVA, P \ 0.01). Five of the seven traits had a large variation ([20 %) in this population. The decay distance of linkage disequilibrium was approximately 639 kb on average in intrachromosomal regions. Approximately 80 % of the intervals between two neighboring single-nucleotide polymorphisms were less than 600 kb. The natural population was divided into two subpopulations with little population structure. The genetic relationship among the accessions was distant. Fifty-one quantitative trait loci (QTLs) were significantly associated with the seven traits: six for RPH, nine for RBN, seven for RSN/RSW, one for RBN/RSN/RSW, six for LW, nineteen for LCL, and three for PW (-Log P C 2.00, P B 0.01). Single QTLs contributed 2.8-11 % of the phenotypic variance. Three QTLs were co-associated with soybean resistance and compensatory growth at the 0.05 significant level. Of these three QTLs, the qSCCW18-3 located in the promoter sequence of the soybean Rubisco activase b subunit gene (GmRCAb) and its resistance allele reduced LW and increased plant height.

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