Fingerprinting Soybean Germplasm and Its Utility in Genomic Research

Abstract

The United States Department of Agriculture, Soybean Germplasm Collection includes 18,480 domesticated soybean and 1168 wild soybean accessions introduced from 84 countries or developed in the United States. This collection was genotyped with the SoySNP50K BeadChip containing greater than 50K single-nucleotide polymorphisms. Redundant accessions were identified in the collection, and distinct genetic backgrounds of soybean from different geographic origins were observed that could be a unique resource for soybean genetic improvement. We detected a dramatic reduction of genetic diversity based on linkage disequilibrium and haplotype structure analyses of the wild, landrace, and North American cultivar populations and identified candidate regions associated with domestication and selection imposed by North American breeding. We constructed the first soybean haplotype block maps in the wild, landrace, and North American cultivar populations and observed that most recombination events occurred in the regions between haplotype blocks. These haplotype maps are crucial for association mapping aimed at the identification of genes controlling traits of economic importance. A case-control association test delimited potential genomic regions along seven chromosomes that most likely contain genes controlling seed weight in domesticated soybean. The resulting dataset will facilitate germplasm utilization, identification of genes controlling important traits, and will accelerate the creation of soybean varieties with improved seed yield and quality.

Shown for reading. Its publisher allows quoting it, not republishing it.

References 35

1. 1.

   Alexander D. H. Novembre J. Lange K., 2009 Fast model-based estimation of ancestry in unrelated individuals. Genome Res. 19: 1655–1664.

   Not in our library10.1101/gr.094052.109

2. 2.

   Bailey M. A. Mian M. A. R. Carter T. E. Ashley D. A. Boerma H. R., 1997 Pod dehiscence of soybean: identification of quantitative trait loci. J. Hered. 88: 152–154.

   Not in our library

3. 3.

   Cardon L. R. Abecasis G. R., 2003 Using haplotype blocks to map human complex trait loci. Trends Genet. 19: 135–140.

   Not in our library10.1016/s0168-9525(03)00022-2

4. 4.

   Carter T. E. Nelson R. L. Sneller C. H. Cui Z., 2004 Genetic diversity in soybean, pp. 303–416 in Soybeans: Improvement, Production, and Uses. Ed. 3. (American Society of Agronomy Monograph Series, Agronomy Monograph No. 16), edited by Boerma H. R. Specht J. E. American Society of Agronomy-Crop Science Society of America-Soil Science Society of America, Madison, WI.

   Not in our library

5. 5.

   Chen Q. Zhang Z. Liu C. Xin D. Qiu H., 2007 QTL analysis of major agronomic traits in soybean Ag. Sci. China 6: 399–405.

   Not in our library

6. 6.

   Chien Y.-L. Hwu H.-G. Fann C. S. J. Chang C.-C. Tsuang M.-T., 2013 DRD2 haplotype associated with negative symptoms and sustained attention deficits in Han Chinese with schizophrenia in Taiwan. J. Hum. Genet. 58: 229–232.

   Not in our library10.1038/jhg.2012.157

7. 7.

   Daly M. J. Rioux J. D. Schaffner S. F. Hudson T. J. Lander E. S., 2001 High-resolution haplotype structure in the human genome. Nat. Genet. 29: 229–232.

   Not in our library10.1038/ng1001-229

8. 8.
   Arlequin (version 3.0): An integrated software package for population genetics data analysis · 2005

   No notice
9. 9.

   Gabriel S. B. Schaffner S. F. Nguyen H. Moore J. M. Roy J., 2002 The structure of haplotype blocks in the human genome. Science 296: 2225–2229.

   Not in our library10.1126/science.1069424

10. 10.

    Gai J. Wang Y. Wu X. Chen S., 2007 A comparative study on segregation analysis and QTL mapping of quantitative traits in plants-with a case in soybean. Front. Agric. China 1: 1–7.

    Not in our library

11. 11.

    Gizlice Z. Carter T. Burton J., 1994 Genetic base for North American public soybean cultivars released between 1947 and 1988. Crop Sci. 34: 1143–1151.

    Not in our library

12. 12.

    Hoeck J. A. Fehr W. R. Shoemaker R. C. Welke G. A. Johnson S. L., 2003 Molecular marker analysis of seed size in soybean. Crop Sci. 43: 68–74.

    Not in our library

13. 13.
    A genome-wide association study of seed protein and oil content in soybean · 2014

    No notice
14. 14.

    Hymowitz T. Harlan J. R., 1983 Introduction of soybean to North America by Samuel Bowen in 1765. Econ. Bot. 37: 371–379.

    Not in our library

15. 15.

    Hyten D. L. Pantalone V. R. Sams C. E. Saxton A. M. Landau-Ellis D., 2004 Seed quality QTL in a prominent soybean population. Theor. Appl. Genet. 109: 552–561.

    Not in our library10.1007/s00122-004-1661-5

16. 16.

    Hyten D. L. Song Q. Zhu Y. Choi I. Y. Nelson R. L., 2006 Impacts of genetic bottlenecks on soybean genome diversity. Proc. Natl. Acad. Sci. USA 103: 16666–16671.

    Not in our library10.1073/pnas.0604379103

17. 17.

    Hyten D. L. Choi I.-Y. Song Q. Shoemaker R. C. Nelson R. L., 2007 Highly variable patterns of linkage disequilibrium in multiple soybean populations. Genetics 175: 1937–1944.

    Not in our library10.1534/genetics.106.069740

18. 18.

    Kabelka E. A. Diers B. W. Fehr W. R. LeRoy A. R. Baianu I. C., 2004 Putative alleles for increased yield from soybean plant introductions. Crop Sci. 44: 784–791.

    Not in our library

19. 19.

    Kang S.-T. Kwak M. Kim H.-K. Choung M.-G. Han W.-Y., 2009 Population-specific QTLs and their different epistatic interactions for pod dehiscence in soybean [Glycine max (L.) Merr.] Euphytica 166: 15–24.

    Not in our library

20. 20.

    Keim P. Olson T. C. Shoemaker R. C., 1988 A rapid protocol for isolating soybean DNA. Soybean Genet. Newsl. 15: 150–152.

    Not in our library

21. 21.

    Lam H. M. Xu X. Liu X. Chen W. Yang G., 2010 Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection. Nat. Genet. 42: 1053–1059.

    Not in our library10.1038/ng.715

22. 22.

    Li Y. Guan R. Liu Z. Ma Y. Wang L., 2008 Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor. Appl. Genet. 117: 857–871.

    Not in our library10.1007/s00122-008-0825-0

23. 23.

    Mian M. A. R. Bailey M. A. Tamulonis J. P. Shipe E. R. Carter T. E., 1996 Molecular markers associated with seed weight in two soybean populations. Theor. Appl. Genet. 93: 1011–1016.

    Not in our library10.1007/bf00230118

24. 24.

    Panthee D. R. Pantalone V. R. West D. R. Saxton A. M. Sams C. E., 2005 Quantitative trait loci for seed protein and oil concentration, and seed size in soybean. Crop Sci. 45: 2015–2022.

    Not in our library

25. 25.

    Phillips M. S. Lawrence R. Sachidanandam R. Morris A. P. Balding D. J., 2003 Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots. Nat. Genet. 33: 382–387.

    Not in our library10.1038/ng1100

26. 26.

    Purcell S. Neale B. Todd-Brown K. Thomas L. Ferreira M. A., 2007 PLINK: a tool set for whole-genome association and population-based linkage analyses. Am. J. Hum. Genet. 81: 559–575.

    Not in our library10.1086/519795

27. 27.

    Raj A. Stephens M. Pritchard J. K., 2014 fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197: 573–589.

    Not in our library10.1534/genetics.114.164350

28. 28.
    Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean · 2013

    No notice
29. 29.

    Specht J. E. Chase K. Macrander M. Graef G. L. Chung J., 2001 Soybean response to water: a QTL analysis of drought tolerance. Crop Sci. 4: 493–509.

    Not in our library

30. 30.

    Tamura K. Peterson D. Peterson N. Stecher G. Nei M., 2011 MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28: 2731–2739.

    Not in our library10.1093/molbev/msr121

31. 31.

    Tian Z. Wang X. Lee R. Li Y. Specht J. E., 2010 Artificial selection for determinate growth habit in soybean. Proc. Natl. Acad. Sci. USA 107: 8563–8568.

    Not in our library10.1073/pnas.1000088107

32. 32.

    Zhang D. Cheng H. Wang H. Hengyou Z. Liu C., 2007 Identification of genomic regions determining flower and pod numbers development in soybean (Glycine max L). J. Genet. Genomics 37: 545–556.

    Not in our library10.1016/s1673-8527(09)60074-6

33. 33.

    Zhang K. Qin Z. S. Liu J. S. Chen T. Waterman M. S., 2004 a Haplotype block partitioning and tag SNP selection using genotype data and their applications to association studies. Genome Res. 14: 908–916.

    Not in our library10.1101/gr.1837404

34. 34.

    Zhang W. K. Wang Y. J. Luo G. Z. Zhang J. S. He C. Y., 2004 b QTL mapping of ten agronomic traits on the soybean (Glycine max L. Merr.) genetic map and their association with EST markers. Theor. Appl. Genet. 108: 1131–1139.

    Not in our library10.1007/s00122-003-1527-2

35. 35.

    Zhu Y. L. Song Q. J. Hyten D. L. Van Tassell C. P. Matukumalli L. K., 2003 Single-nucleotide polymorphisms in soybean. Genetics 163: 1123–1134.

    Not in our library10.1093/genetics/163.3.1123

Cited by papers we hold 9

• Identification of Candidate Genes for a Major Quantitative Disease Resistance Locus From Soybean PI 427105B for Resistance to Phytophthora sojae · 2022
  Not checked
• Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing · 2021
  Not checked
• The patterns of deleterious mutations during the domestication of soybean · 2021
  Not checked
• Progress in soybean functional genomics over the past decade · 2021
  No notice
• Comparing Different Statistical Models and Multiple Testing Corrections for Association Mapping in Soybean and Maize · 2020
  No notice
• Genomic introgression through interspecific hybridization counteracts genetic bottleneck during soybean domestication · 2019
  Not checked
• Identification of QTL with large effect on seed weight in a selective population of soybean with genome-wide association and fixation index analyses · 2017
  Not checked
• Molecular mapping and genomics of soybean seed protein: a review and perspective for the future · 2017
  No notice
• Back into the wild—Apply untapped genetic diversity of wild relatives for crop improvement · 2016
  No notice

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.