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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Soybean Genomics & Improvement Laboratory » Research » Publications at this Location » Publication #394351

Research Project: Characterization of Genetic Diversity in Soybean and Common Bean, and Its Application toward Improving Crop Traits and Sustainable Production

Location: Soybean Genomics & Improvement Laboratory

Title: Development of molecular inversion probes for soybean progeny genomic selection genotyping

item WANG, HAICHUAN - University Of Nebraska
item CAMPBELL, BENJAMIN - University Of Minnesota
item HAPP, MARY - University Of Nebraska
item MCCONAUGHY, SAMANTHA - University Of Nebraska
item LORENZ, AARON - University Of Minnesota
item AMUNDSEN, KEENAN - University Of Nebraska
item Song, Qijian
item PANTALONE, VINCENT - University Of Tennessee
item HYTEN, DAVID - University Of Nebraska

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/25/2022
Publication Date: 11/21/2022
Citation: Wang, H., Campbell, B., Happ, M., McConaughy, S., Lorenz, A., Amundsen, K., Song, Q., Pantalone, V., Hyten, D. 2022. Development of molecular inversion probes for soybean progeny genomic selection genotyping. The Plant Genome. Article e20270.

Interpretive Summary: Early-generation breeding and selection of desirable progeny can be performed with molecular markers instead of selecting for physical plant attributes which are usually affected by environment. Because thousands of breeding lines are to be evaluated during this process, breeders need a system with low cost for marker analysis. Researchers at USDA and University of Nebraska selected a set of 1,000 molecular markers from the pre-existing USDA marker set called ‘BARCSoySNP6K’ and developed a method to target these markers in a high-throughput instrument to detect presence of the markers. They demonstrated that the system could be used for low density marker analysis in soybean breeding programs in the North Central and Mid-South regions of the United States. The accuracy and low per sample cost make this new method a powerful tool for use by soybean breeders.

Technical Abstract: Increasing rate of genetic gain for key agronomic traits through genomic selection requires the development of new molecular methods to run genome-wide single nucleotide polymorphisms (SNPs). The main limitation of current methods is the cost is too high to screen breeding populations. Molecular inversion probes (MIPs) is a targeted genotyping-by-sequencing method that could be used for soybeans that is both cost effective, high-throughput, and provides high data quality to screen breeder’s germplasm for genomic selection. A 1K MIP SNP set was developed for soybean with uniformly distributed markers across the genome. The SNPs were selected to maximize the number of informative markers in germplasm being tested in soybean breeding programs located in the North and South-Central regions of the United States. The 1K SNP MIP set was tested on diverse germplasm and a recombinant inbred line population. Targeted sequencing with MIPs obtained an 85% enrichment for the targeted SNPs. MIP’s genotyping accuracy was 93% overall while homozoygous call accuracy was 98% with less than 10% missing data. The accuracy of MIPs combined with its low per sample cost makes it a powerful tool to enable genomic selection within soybean breeding programs.