SoyNAM

Description:

This project identifies the genes and locations that control yield and other important agronomic traits in both domestic and exotic germplasm using association mapping, with a nested association mapping (NAM) population. Please also see the dedicated SoyNAM page, with additional information and plant images.
To request seed, see that section below. Note that a Material Transfer Agreement (MTA) may be required; see details below at "request Parent seed".

BioProject: none

SoyBaseID: SoyBase.C2014.02

Publications:

Citation: Cook DE, Bayless AM, Wang K, Guo X, Song Q, Jiang J, Bent AF. Distinct Copy Number, Coding Sequence, and Locus Methylation Patterns Underlie Rhg1-Mediated Soybean Resistance to Soybean Cyst Nematode. Plant Physiol. 2014 Jun;165(2):630-647. Epub 2014 Apr 14. PMID: 24733883; PMCID: PMC4044848.

Publication link: 10.1104/pp.114.235952

Citation: Xavier A, Muir WM, Rainey KM. 2016. Impact of imputation methods on the amount of genetic variation captured by a single-nucleotide polymorphism panel in soybeans. BMC Bioinformatics 17(55) 2016

Publication link: 10.1186/s12859-016-0899-7

Citation: Xavier A, Muir WM Rainey KM. 2016. Assessing Predictive Properties of Genome-Wide Selection in Soybeans. G3: Genes, Genomes, Genetics 2016 6(8):2611-2616

Publication link: 10.1534/g3.116.032268

Citation: Justin E. Anderson, Jean-Michel Michno, Thomas J. Y. Kono, Adrian O. Stec, Benjamin W. Campbell, Shaun J. Curtin & Robert M. Stupar. 2016. Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants. BMC Biotechnology 2016, 16(41)

Publication link: 10.1186/s12896-016-0271-z

Citation: Song, Q., L. Yan, C. Quigley, B. D. Jordan, E. Fickus, S. Schroeder, B. Song, Y. Charles An, D. Hyten, R. Nelson, K. Rainey, W. D. Beavis, J. Specht, B. Diers, and P. Cregan. Genetic Characterization of the Soybean Nested Association Mapping Population. Plant Genome 10 (2017).

Publication link: 10.3835/plantgenome2016.10.0109

Citation: Alencar Xavier, Benjamin Hall, Shaun Casteel, William Muir, Katy Martin Rainey. 2017. Using unsupervised learning techniques to assess interactions among complex traits in soybeans. Euphytica 2017 213:200.

Publication link: 10.1007/s10681-017-1975-4

Citation: Alencar Xavier, Benjamin Hall, Anthony A. Hearst, Keith A. Cherkauer and Katy M. Rainey. 2017. Genetic Architecture of Phenomic-Enabled Canopy Coverage in Glycine max. Genetics 2017 206(2):1081-1089.

Publication link: 10.1534/genetics.116.198713

Citation: Brian W. Diers, Jim Specht, Katy Martin Rainey, Perry Cregan, Qijian Song, Vishnu Ramasubramanian, George Graef, Randall Nelson, William Schapaugh, Dechun Wang, Grover Shannon, Leah McHale, Stella K. Kantartzi, Alencar Xavier, Rouf Mian, Robert M. Stupar, Jean-Michel Michno, Yong-Qiang Charles An, Wolfgang Goettel, Russell Ward, Carolyn Fox, Alexander E. Lipka, David Hyten, Troy Cary and William D. Beavis. 2018. Genetic Architecture of Soybean Yield and Agronomic Traits. G3: Genes, Genomes, Genetics October 1, 2018 vol. 8 no. 10 3367-3375.

Publication link: 10.1534/g3.118.200332

Citation: Jarquin D, Howard R, Xavier A, Choudhury SD. 2018. Increasing Predictive Ability by Modeling Interactions between Environments, Genotype and Canopy Coverage Image Data for Soybeans. Agronomy 2018, 8(4), 51

Publication link: 10.3390/agronomy8040051

Citation: Xavier A, Jarquin D, Howard R, Ramasubramanian V, Specht JE, Graef GL, Beavis WD, Diers BW, Song Q, Cregan PB, Nelson R, Mian R, Shannon JG, McHale L, Wang D, Schapaugh W, Lorenz AJ, Xu S, Muir WM, Rainey KM. Genome-Wide Analysis of Grain Yield Stability and Environmental Interactions in a Multiparental Soybean Population. G3 (Bethesda). 2018 Feb 2;8(2):519-529. PMID: 29217731; PMCID: PMC5919731.

Publication link: 10.1534/g3.117.300300

Citation: Lopez MA, Xavier A, Rainey KM. Phenotypic Variation and Genetic Architecture for Photosynthesis and Water Use Efficiency in Soybean (Glycine max L. Merr). Front Plant Sci. 2019 May 24;10:680. PMID: 31178887; PMCID: PMC6543851.

Publication link: 10.3389/fpls.2019.00680

Citation: Scott K, Balk C, Veney D, McHale LK, Dorrance AE. 2019. Quantitative Disease Resistance Loci towards Phytophthora sojae and Three Species of Pythium in Six Soybean Nested Association Mapping Populations. Crop Science 2019, 59(2):605-623

Publication link: 10.2135/cropsci2018.09.0573

Data Links:

request seed

• Click here to request Parent seed.
• Click here to request RIL seed.
• Material Transfer Agreement (MTA) for seed requests.

code

• R Package SoyNAM, by Xavier, Beavis, Specht et al.

visualization

• Descriptions and images of recombinant inbred lines from the cross between the NAM parents and IA3023.
• View the distribution in the soybean genome of the SoyNAM SNPs.
• See copy number estimates for gene models in the SoyNAM population.

map

• See SoyNAM QTL in SoyBase genetic maps

browser

• See SoyNAM QTL in SoyBase sequence browser

data

• Get field and collaborator information for the SoyNAM trials.
• Phenotypic data for all SoyNAM Populations.
• SNP haplotypes for all SoyNAM parents using Wm82.a1 coordinates
• SNP alleles for all SoyNAM parents using Wm82.a1 coordinates
• SNP haplotypes for all SoyNAM parents using Wm82.a2 coordinates
• SNP alleles for all SoyNAM parents using Wm82.a2 coordinates
• SNP haplotypes for the parents and progeny for all SoyNAM families using Wm82.a1 coordinates
• SNP alleles for the parents and progeny for all SoyNAM families using Wm82.a1 coordinates
• SNP haplotypes for the parents and progeny for all SoyNAM families using Wm82.a2 coordinates
• SNP alleles for the parents and progeny for all SoyNAM families using Wm82.a2 coordinates
• Supplemental Table S1: 103 Marker Trait Associations that were signficant for yield, maturity, height, lodging, or seed mass in the soybean NAM population.
• Soy50K imputed haplotypes for the parents and progeny for all SoyNAM families, genotyped using the SoySNP50K and SoyNAM6K assays
• Soy50K imputed haplotypes for the parents and progeny for all SoyNAM families, genotyped with WGS and the SoySNP50K and SoyNAM6K assays

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