Soybean BARCSoySNP6K - An assay for soybean genetics and breeding research

Authors: Song, Qijian; YAN, LONG - Hebei Academy Of Agriculture & Forestry; Quigley, Charles - Chuck; Fickus, Edward; WEI, HE - Henan Agricultural University; CHEN, LINFENG - Nanjing Agricultural University; DONG, FAMING - Huazhong Agricultural University; ARYA, SUSAN - Oak Ridge Institute For Science And Education (ORISE); LIU, JINLONG - Nanchang University; HYTEN, DAVID - University Of Nebraska; PANTALONE, VINCE - University Of Tennessee; Nelson, Randall

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/30/2020
Publication Date: 8/9/2020
Citation: Song, Q., Yan, L., Quigley, C.V., Fickus, E.W., Wei, H., Chen, L., Dong, F., Arya, S., Liu, J., Hyten, D., Pantalone, V., Nelson, R.L. 2020. Soybean BARCSoySNP6K - An assay for soybean genetics and breeding research. Plant Journal. https://doi.org/10.1111/tpj.14960.
DOI: https://doi.org/10.1111/tpj.14960

Interpretive Summary: When two soybean parents are crossed to produce new seed, the DNA naturally recombines. The recombinations create DNA marker signatures that can be used to characterize progeny from two crossed parents and to map and identify genetic traits and genes that are important to soybean cultivation. In soybean, the recombinations of DNA between the chromosomes are lower than what occurs in some other plants. Consequently, breeders do not need many markers to characterize the progeny from a bi-parental soybean cross. So, we developed a breeder's assay, BARCSoySNP6K, containing 6,000 DNA markers for soybean genome evaluation. These markers were carefully selected based on their position in the genome, variation among >18,000 different types of soybean in the USDA Germplasm Collection, and trait mapping quality. Analysis of progeny from two large families studied with a larger assay containing 50,000 DNA markers vs. the BARCSoySNP6K assay showed that position of the markers along maps was consistent. The rate of redundant markers, however, was dramatically reduced with the BARCSoySNP6K. We also observed that BARCSoySNP6K has the same efficiency and resolution to identify genes controlling traits as that of a whole genome sequencing approach. The assay is an excellent resource for detecting quantitative trait loci controlling soybean traits in the families derived from bi-parents and for selecting lines with desired performance. This assay is expected to accelerate trait mapping and breeding in soybean and will be useful to scientists and breeders working in industry, academics and the government who wish to improve soybean.

Technical Abstract: The limited number of recombinant events in recombinant inbred lines suggests that for a biparental population, with a limited number of recombinant inbred lines, it is unnecessary to genotype the lines with many markers. For genomic prediction and genomic selection, previous studies have demonstrated that only 1,000~2,000 genome-wide markers across all lines/accessions are needed to reach maximum efficiency of genomic prediction in populations. Evaluation of too many markers will not only increase the cost but also generate redundant information. Therefore, we developed a new soybean assay -BARCSoySNP6K containing 6,000 markers which were carefully chosen from the SoySNP50K assay containing >50,000 SNPs based on their position in the soybean genome and haplotype blocks, polymorphism among accessions and genotyping quality. The assay includes 5000 SNPs from euchromatic and 1000 from heterochromatic regions. The average minor allele frequency of the SNPs was 0.34 in the euchromatic and 0.30 in the heterochromatic regions. The percentage of SNPs with minor allele frequency >0.10 was 95% and 91% in the euchromatic and heterochromatic regions, respectively. Analysis of progeny from two large families genotyped with SoySNP50K vs. the BARCSoySNP6K showed that the position of the common markers and number of unique bins along linkage maps were consistent based on the SNPs genotyped with the two assays, however, the rate of redundant markers was dramatically reduced with the BARCSoySNP6K. The BARCSoySNP6K assay is proven an excellent tool for the detection of quantitative trait loci, genomic selection and for assessing genetic relationship and pedigree. The beadchip assay is commercialized by Illumina Inc and being widely used by soybean breeders and geneticists in private and public sectors. The list of SNPs in the assay is also an ideal resource for SNP genotyping by targeted sequencing.