Nested association mapping of important agronomic traits in three interspecific soybean populations

Authors: BECHE, EDUARDO - University Of Missouri; Gillman, Jason; Song, Qijian; Nelson, Randall; BEISSINGER, TIM - Georg August University; DECKER, JARED - University Of Missouri; SHANNON, GROVER - University Of Missouri; SCABOO, ANDREW - University Of Missouri

Submitted to: Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/30/2019
Publication Date: 1/23/2020
Citation: Beche, E., Gillman, J.D., Song, Q., Nelson, R.L., Beissinger, T., Decker, J., Shannon, G., Scaboo, A.M. 2020. Nested association mapping of important agronomic traits in three interspecific soybean populations. Theoretical and Applied Genetics. 133:1039-1054. https://doi.org/10.1007/s00122-019-03529-4.
DOI: https://doi.org/10.1007/s00122-019-03529-4

Interpretive Summary: The primary aim of modern soybean breeding programs is to improve productivity. However, future gains in soybean productivity could be limited due to the very low genetic diversity present in domesticated soybean germplasm pools. This problem is only exacerbated by the common practice of only crossing elite x elite germplasm. Wild soybean gene pools have demonstrably greater genetic diversity, but have only very rarely been used as parents in soybean breeding programs. We utilized a relatively new method, Nested Association Mapping (NAM), to evaluate the potential of genes from three wild soybean accessions to affect and improve four critical agronomic traits, including seed yield. Numerous genetic loci controlling these traits were identified, and the impact of wild soybean alleles was compared with domesticated soybean alleles. Of particular note was one QTL from wild soybean which had a strong positive effect on grain yield; lines that inherited this QTL averaged +6% over those that had inherited alleles from the domesticated soybean. Our results demonstrate the substantial gains may be possible by introgressing alleles from wild soybean.

Technical Abstract: Given the demonstrated narrow genetic base of the US soybean production, it is essential to identify beneficial alleles from exotic germplasm, such as wild soybean, to enhance genetic gain for favorable traits. Nested association mapping (NAM) is an approach to population development that permits the comparison of allelic effects of the same QTL in multiple parents. Seed yield, plant maturity, plant height and plant lodging were evaluated in a NAM panel consisting of 392 recombinant inbred lines derived from three biparental interspecific soybean populations in eight environments during 2016 and 2017. Nested association mapping, combined with linkage mapping, identified three major QTL for plant maturity in chromosomes 6, 11 and 12 associated with alleles from wild soybean resulting in significant increases in days to maturity. A significant QTL for plant height was identified on chromosome 13 with the allele increasing plant height derived from wild soybean. A significant grain yield QTL was detected on chromosome 17, and the allele from Glycine soja had a positive effect of 166 kg ha-1; RIL’s with the wild soybean allele yielded on average 6% more than the lines carrying the Glycine max allele. These findings demonstrate the usefulness and potential of alleles from wild soybean germplasm to enhance important agronomic traits in a soybean breeding program.