Genetic characterization of the soybean Nested Association Mapping (NAM) population

Authors: Song, Qijian; YAN, LONG - Hebei Academy Of Agriculture; Quigley, Charles - Chuck; JORDAN, BRANDON - University Of Illinois; Fickus, Edward; Schroeder, Steven - Steve; SONG, BAO-HUA - University Of North Carolina; An, Yong-Qiang - Charles; HYTEN, DAVID - University Of Nebraska; Nelson, Randall; RAINEY, KATY - Purdue University; BEAVIS, WILLIAM - Iowa State University; SPECHT, JAMES - University Of Nebraska; DIERS, BRIAN - University Of Illinois; CREGAN, PERRY - Retired ARS Employee

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/23/2017
Publication Date: 4/27/2017
Citation: Song, Q., Yan, L., Quigley, C.V., Jordan, B.D., Fickus, E.W., Schroeder, S.G., Song, B., An, Y., Hyten, D., Nelson, R.L., Rainey, K., Beavis, W.D., Specht, J., Diers, B., Cregan, P. 2017. Genetic characterization of the soybean Nested Association Mapping (NAM) population. The Plant Genome. 10(2). doi: 10.3835/plantgenome2016.10.0109.

Interpretive Summary: Many important traits related to seed yield, yield components, seed quality, and stress resistance in crops are controlled by multiple loci (QTL) in the genome. The performance of these complex traits is affected by the environment and interaction between the environment and loci. Two types of the populations, family-based population derived from a cross between two parents and nature population from existing accessions, were used to position these loci. Nested association mapping (NAM) was proposed to increase the resolution of QTL mapping via nature population and increase power of the analysis via family-based population. Unlike traditional family-based population which only uses two parental individuals, we developed a NAM population by crossing 40 diverse cultivars to a common parent followed by the development of progenies in each family, a total of 5,600 progenies were then genotyped with 6,000 markers while the parents were sequenced and resulted in millions of markers. The markers of the parents were then used to impute the progenies. Thus, the association of the imputed genotypic data with the phenotypic data of the progenies can be analyzed to identify genes or loci associated with the traits. This is the first largest mapping population that has been developed and characterized in the soybean so far. The information will be a valuable community resource for dissecting complex traits in soybean coupled with the availability of the seeds from each line.

Technical Abstract: A population of nested association mapping (NAM) families can be a valuable resource to a research community. A set of NAM families were developed by crossing 40 diverse soybean genotypes to the common hub cultivar IA 3023. The 41 parents were sequenced with next generation sequencing for single nucleotide polymorphism (SNP) discovery. Among the 5,232,558 SNPs identified, 30,174 were polymorphic in more than 12 of the 40 families and passed a number of selection criteria for Illumina BeadChip design. From these, a set of 6000 SNPs was selected to be included in the SoyNAM6K BeadChip for genotyping the parents and 5600 recombinant inbred lines (RILs) from the families. Successful genotypic data were obtained for 4,312 SNPs. Analysis of the SNP profiles of the RILs showed an average of 58 recombination events per RIL with a range of 43 to 77 among the 40 families. The genetic linkage maps varied from 981 cM to 1780 cM among families. The total length of the composite linkage map based on RILs across the NAM families was 1736 cM. Of the SNPs obtained from sequencing the parents or use of the SoySNP50K BeadChip assay, a total of 525,772 high confidence SNPs could be used to impute the SNP alleles in the RILs of the NAM families. The genotypic datasets for the RILs and parents are publically available and are anticipated to be useful to fine map genes or quantitative trait loci controlling important traits in soybean.