Nested Association Mapping (NAM) of Genes Controlling Soybean Yield and Other Key Traits

Our goal is to improve the yield potential of soybean varieties. To this end we have mapped the chromosomal locations of genes that control yield and other important agronomic traits in both domestic and exotic germplasm using a Nested Association Panel composed of 40 important soybean varieties and cultivars crossed to a common hub parent. Further details about the SoyNAM Project are avaliable. Funding was provided by the North Central Soybean research Program (NCSRP) and the United Soybean Board (USB).

NAM Parents

140 Recombinant Inbred Lines (RILs) were developed from each cross between the NAM parents and IA3023.

Click on a NAM Parent for details about that Population.
High Yielding Lines	Lines With Diverse Ancestry	PIs With High Yields in Drought	Hub Parent
4J105-3-4	LG03-2979	PI 398881	IA3023
5M20-2-5-2	LG03-3191	PI 427136
CL0J095-4-6	LG00-3372	PI 437169B
CL0J173-6-8	LG04-4717	PI 518751
HS6-3976	LG04-6000	PI 561370
LD00-3309	LG05-4292	PI 404188A
LD01-5907	LG05-4317	PI 574486
LD02-4485	LG05-4464	PI 507681B*
LD02-9050	LG05-4832	*Analysis of the progeny of SoyNAM population 46 (PI 507681B x IA3023) showed that the cross was not as described. No phenotypic data for SoyNAM 46 are available.
Magellan	LG90-2550
Maverick	LG92-1255
NE3001	LG94-1128
Prohio	LG94-1906
S06-13640	LG97-7012
Skylla	LG98-1605
TN05-3027
U03-100612

You can also browse through images of the populations with our image browser.

Publications

Distinct Copy Number, Coding Sequence, and Locus Methylation Patterns Underlie Rhg1-Mediated Soybean Resistance to Soybean Cyst Nematode
David E. Cook, Adam M. Bayless, Kai Wang, Xiaoli Guo, Qijian Song, Jiming Jiang, Andrew F. Bent
Plant Physiol. 2014, 165:630-647 DOI:/10.1104/pp.114.235952

Impact of imputation methods on the amount of genetic variation captured by a single-nucleotide polymorphism panel in soybeans
A. Xavier, William M. Muir & Katy M. Rainey
BMC Bioinformatics 17(55) 2016 DOI:10.1186/s12859-016-0899-7

Assessing Predictive Properties of Genome-Wide Selection in Soybeans
Alencar Xavier, William M. Muir and Katy Martin Rainey
G3: Genes, Genomes, Genetics 2016 6(8):2611-2616; DOI:/10.1534/g3.116.032268

Genomic variation and DNA repair associated with soybean transgenesis: a comparison to cultivars and mutagenized plants
Justin E. Anderson, Jean-Michel Michno, Thomas J. Y. Kono, Adrian O. Stec, Benjamin W. Campbell, Shaun J. Curtin & Robert M. Stupar
BMC Biotechnology 2016, 16(41) DOI:/10.1186/s12896-016-0271-z

Genetic Characterization of the Soybean Nested Association Mapping Population
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
Plant Genome 10 (2017). doi:10.3835/plantgenome2016.10.0109

Using unsupervised learning techniques to assess interactions among complex traits in soybeans
Alencar Xavier, Benjamin Hall, Shaun Casteel, William Muir, Katy Martin Rainey
Euphytica 2017 213:200. DOI:/10.1007

Genetic Architecture of Phenomic-Enabled Canopy Coverage in Glycine max
Alencar Xavier, Benjamin Hall, Anthony A. Hearst, Keith A. Cherkauer and Katy M. Rainey
Genetics 2017 206(2):1081-1089; DOI:/10.1534/genetics.116.198713

Genetic Architecture of Soybean Yield and Agronomic Traits
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
G3: Genes, Genomes, Genetics October 1, 2018 vol. 8 no. 10 3367-3375. doi:10.1534/g3.118.200332

Increasing Predictive Ability by Modeling Interactions between Environments, Genotype and Canopy Coverage Image Data for Soybeans
Diego Jarquin, Reka Howard, Alencar Xavier and Sruti Das Choudhury
Agronomy 2018, 8(4), 51 DOI:/10.3390/agronomy8040051

Genome-Wide Analysis of Grain Yield Stability and Environmental Interactions in a Multiparental Soybean Population
Alencar Xavier, Diego Jarquin, Reka Howard, Vishnu Ramasubramanian, James E. Specht, George L. Graef, William D. Beavis, Brian W. Diers, Qijian Song, Perry B. Cregan, Randall Nelson, Rouf Mian, J. Grover Shannon, Leah McHale, Dechun Wang, William Schapaugh, Aaron J. Lorenz, Shizhong Xu, William M. Muir and Katy M. Rainey
G3: Genes, Genomes, Genetics 2018 8(2):519-529; DOI:/10.1534/g3.117.300300

Phenotypic Variation and Genetic Architecture for Photosynthesis and Water Use Efficiency in Soybean (Glycine max L. Merr)
Miguel Angel Lopez1, Alencar Xavier2 and Katy Martin Rainey
Front. Plant Sci. 2019 DOI:/10.3389/fpls.2019.00680

Quantitative Disease Resistance Loci towards Phytophthora sojae and Three Species of Pythium in Six Soybean Nested Association Mapping Populations
Kelsey Scotta, Christine Balkb, Deloris Veneya, Leah K. McHalecd and Anne E. Dorrance
Crop Science 2019, 59(2):605-623 DOI:/10.2135/cropsci2018.09.0573

R Package 'SoyNAM'
Alencar Xavier, William Beavis, James Specht, Brian Diers, Rouf Mian, Reka Howard,George Graef, Randall Nelson, William Schapaugh, Dechun Wang, Grover Shan-non, Leah McHale,Perry Cregan, Qijian Song, Miguel Lopez, William Muir, Katy Rainey.
CRAN

View Results of Analyses

Download Data

• Click here to see the distribution in the soybean genome of the SoyNAM SNPs.
• 
  
• Click here to download the phenotypic data for all SoyNAM Populations.
• 
  
• Click here to get field and collaborator information for the SoyNAM trails.
• 
  
• Click here to see copy number estimates for gene models in the SoyNAM population.
• 
  
• Click here to download the SNP haplotypes for all SoyNAM parents using Wm82.a1 coordinates
• Click here to download the SNP alleles for all SoyNAM parents using Wm82.a1 coordinates
• Click here to download the SNP haplotypes for all SoyNAM parents using Wm82.a2 coordinates
• Click here to download the SNP alleles for all SoyNAM parents using Wm82.a2 coordinates
• 
  
• Click here to download the SNP haplotypes for the parents and progeny for all SoyNAM families using Wm82.a1 coordinates
• Click here to download the SNP alleles for the parents and progeny for all SoyNAM families using Wm82.a1 coordinates
• Click here to download the SNP haplotypes for the parents and progeny for all SoyNAM families using Wm82.a2 coordinates
• Click here to download the SNP alleles for the parents and progeny for all SoyNAM families using Wm82.a2 coordinates
• 
  
• Click here to download Supplemental Table S1: 103 Marker Trait Associations that were signficant for yield, maturity, height, lodging, or seed mass in the soybean NAM population.
• 
  
• Click here to download Soy50K imputed haplotypes for the parents and progeny for all SoyNAM families using Wm82.a1 coordinates
• Click here to download Soy50K imputed haplotypes for the parents and progeny for all SoyNAM families using Wm82.a2 coordinates

Request Seed

Click here to request Parent seed.
Click here to request RIL seed.