Abstract
Cultivated soybean (Glycine max) carrying the Rj2 allele restricts nodulation with specific Bradyrhizobium strains via host immunity, mediated by rhizobial type III secretory protein NopP and the host resistance protein Rj2. Here we found that the single isoleucine residue I490 in Rj2 is required for induction of symbiotic incompatibility. Furthermore, we investigated the geographical distribution of the Rj2-genotype soybean in a large set of germplasm by single nucleotide polymorphism (SNP) genotyping using a SNP marker for I490. By allelic comparison of 79 accessions in the Japanese soybean mini-core collection, we suggest substitution of a single amino acid residue (R490 to I490) in Rj2 induces symbiotic incompatibility with Bradyrhizobium diazoefficiens USDA 122. The importance of I490 was verified by complementation of rj2-soybean by the dominant allele encoding the Rj2 protein containing I490 residue. The Rj2 allele was also found in Glycine soja, the wild progenitor of G. max, and their single amino acid polymorphisms were associated with the Rj2-nodulation phenotype. By SNP genotyping against 1583 soybean accessions, we detected the Rj2-genotype in 5.4% of G. max and 7.7% of G. soja accessions. Distribution of the Rj2-genotype soybean plants was relatively concentrated in the temperate Asian region. These results provide important information about the mechanism of host genotype-specific symbiotic incompatibility mediated by host immunity and suggest that the Rj2 gene has been maintained by environmental conditions during the process of soybean domestication.
Highlights
Cultivated soybean (Glycine max [L.] Merr.) is an important leguminous crop and source of nutrition for humans and livestock worldwide
Four accessions of Rj2-genotype G. soja inoculated with 122nopP110 formed significantly more nodules on the roots than did wild-type USDA 122 and the leaves of 122nopP110 were green, indicating nitrogen-fixing activity of the nodules (S1 Fig). These results suggest that induction of symbiotic incompatibility between USDA 122 and G. soja is mediated by NopP, as seen in G. max
Based on allelic comparisons using the soybean mini-core collection [7], we demonstrated that the single amino acid residue I490 in the Rj2 protein is the host determinant that induces symbiotic incompatibility with B. diazoefficiens USDA 122 (Figs 1–3)
Summary
Cultivated soybean (Glycine max [L.] Merr.) is an important leguminous crop and source of nutrition for humans and livestock worldwide. Zucc.) is an important genetic resource for soybean breeding. It has been suggested that G. max was domesticated from G. soja in East Asia 6000–9000 years ago [1,2]. Single amino acid determinant in soybean Rj2 protein for symbiotic incompatibility with Bradyrhizobium from the Ministry of Education, Culture, Sports, Science and Technology of Japan, and the Ministry of Agriculture, Forestry and Fisheries of Japan (Genomics-Based Technology for Agricultural Improvement, SFC2003 to KM). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript
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