Genetic relationships of soybean cyst nematode resistance originated in Gedenshirazu and PI84751 on Rhg1 and Rhg4 loci

Mapping soybean rhg2 locus, which confers resistance to soybean cyst nematode race 1 in combination with rhg1 and Rhg4 derived from PI 84751

The soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is a devastating pest of soybean (Glycine max (L.) Merr.) in the world. Three soybean QTLs for resistance to SCN race 1 were detected through QTL analyses using recombinant inbred lines (RILs) derived from a cross between 'Tokei 758' (susceptible) and 'To-8E' (resistant to races 1 and 3, derived from 'PI 84751' and 'Gedenshirazu'). Two of the three QTLs appear to be rhg1 and Rhg4 from their locations on the linkage map. The third QTL, detected around Satt359 on chromosome 11, was tentatively identified as rhg2. All RILs resistant to race 1 had all three QTLs. We developed lines carrying the three loci in various combinations, including all and none, from descendants of a cross between 'NIL-SCN' (with resistance derived from 'PI 84751' in the 'Natto-shoryu' background) and 'Natto-shoryu'. Evaluating these lines in a race 1-infected field in Mito, Ibaraki, showed that resistance to race 1 required all three loci. Through field evaluation of 10 recombinant fixed pairs that we developed, we located the rhg2 locus to an 821 kb-region between SSR markers Sat_123 (=WGSP11_0140) and BARCSOYSSR11_1420 on chromosome 11.

Impacts of genomic research on soybean improvement in East Asia

It has been commonly accepted that soybean domestication originated in East Asia. Although East Asia has the historical merit in soybean production, the USA has become the top soybean producer in the world since 1950s. Following that, Brazil and Argentina have been the major soybean producers since 1970s and 1990s, respectively. China has once been the exporter of soybean to Japan before 1990s, yet she became a net soybean importer as Japan and the Republic of Korea do. Furthermore, the soybean yield per unit area in East Asia has stagnated during the past decade. To improve soybean production and enhance food security in these East Asian countries, much investment has been made, especially in the breeding of better performing soybean germplasms. As a result, China, Japan, and the Republic of Korea have become three important centers for soybean genomic research. With new technologies, the rate and precision of the identification of important genomic loci associated with desired traits from germplasm collections or mutants have increased significantly. Genome editing on soybean is also becoming more established. The year 2019 marked a new era for crop genome editing in the commercialization of the first genome-edited plant product, which is a high-oleic-acid soybean oil. In this review, we have summarized the latest developments in soybean breeding technologies and the remarkable progress in soybean breeding-related research in China, Japan, and the Republic of Korea.

SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance

BACKGROUND

Soybean cyst nematode (SCN) is the most economically devastating pathogen of soybean. Two resistance loci, Rhg1 and Rhg4 primarily contribute resistance to SCN race 3 in soybean. Peking and PI 88788 are the two major sources of SCN resistance with Peking requiring both Rhg1 and Rhg4 alleles and PI 88788 only the Rhg1 allele. Although simple sequence repeat (SSR) markers have been reported for both loci, they are linked markers and limited to be applied in breeding programs due to accuracy, throughput and cost of detection methods. The objectives of this study were to develop robust functional marker assays for high-throughput selection of SCN resistance and to differentiate the sources of resistance.

RESULTS

Based on the genomic DNA sequences of 27 soybean lines with known SCN phenotypes, we have developed Kompetitive Allele Specific PCR (KASP) assays for two Single nucleotide polymorphisms (SNPs) from Glyma08g11490 for the selection of the Rhg4 resistance allele. Moreover, the genomic DNA of Glyma18g02590 at the Rhg1 locus from 11 soybean lines and cDNA of Forrest, Essex, Williams 82 and PI 88788 were fully sequenced. Pairwise sequence alignment revealed seven SNPs/insertion/deletions (InDels), five in the 6th exon and two in the last exon. Using the same 27 soybean lines, we identified one SNP that can be used to select the Rhg1 resistance allele and another SNP that can be employed to differentiate Peking and PI 88788-type resistance. These SNP markers have been validated and a strong correlation was observed between the SNP genotypes and reactions to SCN race 3 using a panel of 153 soybean lines, as well as a bi-parental population, F5-derived recombinant inbred lines (RILs) from G00-3213xLG04-6000.

CONCLUSIONS

Three functional SNP markers (two for Rhg1 locus and one for Rhg4 locus) were identified that could provide genotype information for the selection of SCN resistance and differentiate Peking from PI 88788 source for most germplasm lines. The robust KASP SNP marker assays were developed. In most contexts, use of one or two of these markers is sufficient for high-throughput marker-assisted selection of plants that will exhibit SCN resistance.