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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Publications at this Location » Publication #320056
Title: SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance

Author
item SHI, ZI - University Of Georgia
item LIU, SHIMING - Southern Illinois University
item NOE, JAMES - University Of Georgia
item Arelli, Prakash
item MEKSEM, KHALID - Southern Illinois University
item LI, ZENGLU - University Of Georgia

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/18/2015
Publication Date: 4/18/2015
Citation: Shi, Z., Liu, S., Noe, J., Arelli, P.R., Meksem, K., Li, Z. 2015. SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance. BMC Genomics. 10.1186/s/2864-015-1531-3.

Interpretive Summary: Soybean yields worldwide are limited by the Soybean cyst nematode (SCN), a microscopic size roundworm attaching the roots of the plant and absorbing the nutrition from the soybean plant. Resistant cultivars have been the most effective means of controlling the pest. Nematode populations are variable and over time will adapt to reproduce on resistant cultivars rendering once resistant cultivar a susceptible one. Therefore, breeding is a constant challenge for developing more durable resistance. Selection for resistance is a time consuming process. Usually, progenies of soybean crosses are evaluated in the greenhouse following standard protocols. Nematode populations are collected from infested soybean fields and for several generations are increased on susceptible soybean cultivars. This method allows to produce selected nematode populations that can be used in greenhouse tests with stable reactions on soybean plants. To confirm the validity of these greenhouse tests, more improved methods with DNA markers tagged to resistance genes in soybean plants are currently used in marker assisted selection. The research results that are presented include more robust and improved method using refined DNA markers for better accuracy to identify resistant soybean plants. This new method is called KASP that has identified SNP markers tagged to resistance genes. The bottom line is developing soybean cultivars with nematode resistance becomes more accurate and amount of time required to breed them will be reduced by 1/3. More resistant varieties can be available to choose for planting in infested fields. Soybean growers will be the ultimate beneficiaries with more profit and lower yield losses.

Technical Abstract: Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) remains to be the most economically devastating pathogen of soybean [Glycine max L. (Merr.)]. Two resistance Rhg1 and Rhg4 primarily contribute resistance to a major nematode population, 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 Rhg1 allele. Simple sequence repeat (SSR) markers have been reported for both loci, but they are linked markers and are not user friendly to be applied in breeding programs. The objectives of this research were to develop robust functional marker assays for high-throughput selection of SCN resistance and also to differentiate the sources of resistance. Based on the genomic DNA sequences of 27 soybeans lines with known reaction to SCN phenotypes, we have developed KASP assays for two SNPs from Glyma08ag11490 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. Sequenced alignment revealed seven SNPs/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 Rhg1 resistance allele and another SNP that can be employed to differentiate Peking and PI 88788-type resistance. A strong correlation was observed between these SNP haplotypes and reactions to SCN race 3 based on a panel of 153 soybean lines, as well as a bi-parental population: F5-derived recombinant inbred lines (RILs) from G00-3213 x LG04-6000. Three SNP markers (two for Rhg1 locus and one for Rhg4 locus) were identified that could provide haplotype information for the selection of SCN resistance from Peking or PI 88788 sources for most germplasm lines. The SNP marker assays perform well and could be applied for the high throughput marker-assisted selection.