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Association mapping of oil content and fatty acid components in soybean

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Abstract

Soybean is a globally important oil crop, and the flavour, stability and nutritional value of soybean oil is dependent on the relative proportions of five primary fatty acids. In this study, association mapping was performed to identify molecular markers associated with QTL regions related to oil traits in soybean. Oil and fatty acid contents were measured in soybean accessions grown under field conditions for 2 years. Based on polymorphisms at 142 SSR loci, 94 soybean accessions were divided into two clusters corresponding to accessions from Asian and American gene pools. Linkage disequilibrium (LD) among the SSR loci suggested a structure across the soybean genome (LD decay) of approximately 12 cM. Pairwise kinship estimates among the accessions showed low values. A mixed linear model (MLM) adjusted using false discovery rate (FDR) and minimum Bayes factor (BFmin) values identified 110 strongly associated marker-traits. Oleic acid content had the highest number of associated SSR loci (33), followed by linoleic acid (26), palmitic acid (24), oil (16) and linolenic acid (14). Specific alleles at eight loci yielded high performing soybeans with respect to fatty acid content, and these are presented in a crossing matrix. Analysis of SSR loci and oil traits confirmed previous findings, and many new markers were also identified that may be useful for quickly improving oil traits in soybean.

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References

  • Abdurakhmonov IY, Saha S, Jenkins JN, Buriev ZT, Shermatov SE, Scheffler BE, Pepper AE, Yu JZ, Kohel RJ, Abdukarimov A (2009) Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm. Genetica 136:401–417

    Article  PubMed  Google Scholar 

  • Abe J, Xu DH, Suzuki Y, Kanazawa A, Shimamoto Y (2003) Soybean germplasm pools in Asia revealed by nuclear SSRs. Theor Appl Genet 106:445–453

    CAS  PubMed  Google Scholar 

  • Agrama HA, Yan WG (2009) Association mapping of straighthead disorder induced by arsenic in Oryza sativa. Plant Breed 128:551–558

    Article  Google Scholar 

  • AOCS (1992) Official methods and recommended practices of the American Oil Chemists’ Society. American Oil Chemists’ Society, Champaign IL

    Google Scholar 

  • Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633–2635

    Article  CAS  PubMed  Google Scholar 

  • Carrão-Panizzi MC (2005) Qualidade da produção de soja no Brasil e as perspectivas para grãos com valor agregado. Workshops. http://www.acsoja.org.ar/images/cms/contenidos/443_b.pdf. Accessed 26 Jun 2014

  • Cui ZL, Carter TE, Burton JW (2000) Genetic diversity patterns in Chinese soybean cultivars based on coefficient of parentage. Crop Sci 40:1780–1793

    Article  Google Scholar 

  • Diers BW, Shoemaker RC (1992) Restriction fragment length polymorphism analysis of soybean fatty-acid content. J Am Oil Chem Soc 69:1242–1244

    Article  CAS  Google Scholar 

  • Diwan N, Cregan PB (1997) Automated sizing of fluorescent-labeled Simple Sequence Repeat (SSR) markers to assay genetic variation in soybean. Theor Appl Genet 95:723–733

    Article  CAS  Google Scholar 

  • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. BRL Focus 12:13–15

    Google Scholar 

  • Duvick DN (2005) The contribution of breeding to yield advances in maize (Zea mays L.). Adv Agron 86:83–145

    Article  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    Article  CAS  PubMed  Google Scholar 

  • Falush D, Stephens M, Pritchard JK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164:1567–1587

    PubMed Central  CAS  PubMed  Google Scholar 

  • Flint-Garcia SA, Thornsberry JM, Buckler ES (2003) Structure of linkage disequilibrium in plants. Annu Rev Plant Biol 54:357–374

    Article  CAS  PubMed  Google Scholar 

  • Goodman SN (2001) Of P-values and Bayes: a modest proposal. Epidemiology 12:295–297

    Article  CAS  PubMed  Google Scholar 

  • Graef G, LaVallee BJ, Tenopir P, Tat M, Schweiger B, Kinney AJ, Van Gerpen JH, Clemente TE (2009) A high-oleic-acid and low-palmitic-acid soybean: agronomic performance and evaluation as a feedstock for biodiesel. Plant Biotechnol J 7:411–421

    Article  CAS  PubMed  Google Scholar 

  • Guan RX, Chang RZ, Li YH, Wang LX, Liu ZX, Qiu LJ (2010) Genetic diversity comparison between Chinese and Japanese soybeans (Glycine max (L.) Merr.) revealed by nuclear SSRs. Genet Resour Crop Evol 57:229–242

    Article  CAS  Google Scholar 

  • Gupta PK, Rustgi S, Kulwal PL (2005) Linkage disequilibrium and association studies in higher plants: present status and future prospects. Plant Mol Biol 57:461–485

    Article  CAS  PubMed  Google Scholar 

  • Hao D, Chao M, Yin Z, Yu D (2012) Genome-wide association analysis detecting significant single nucleotide polymorphisms for chlorophyll and chlorophyll fluorescence parameters in soybean (Glycine max) landraces. Euphytica 186:919–931

    Article  CAS  Google Scholar 

  • Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyse spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620

    Article  Google Scholar 

  • Hiromoto DM, Vello NA (1986) The genetic base of Brazilian soybean (Glycine max (L) Merr.) cultivars. Braz J Genet 9:295–306

    Google Scholar 

  • Hou JF, Wang CL, Hong XJ, Zhao JM, Xue CC, Guo N, Gai JY, Xing H (2011) Association analysis of vegetable soybean quality traits with SSR markers. Plant Breed 130:444–449

    Article  CAS  Google Scholar 

  • Hu FB, Manson JE, Willett WC (2001) Types of dietary fat and risk of coronary heart disease: a critical review. J Am Coll Nutr 20:5–19

    Article  PubMed  Google Scholar 

  • Hwang EY, Song Q, Jia G, Specht JE, Hyten DL, Costa J, Cregan PB (2014) A genome-wide association study of seed protein and oil content in soybean. BMC Genom 15:1–12

    Article  Google Scholar 

  • Hyten DL, Pantalone VR, Saxton AM, Schmidt ME, Sams CE (2004) Molecular mapping and identification of soybean fatty acid modifier quantitative trait loci. J Am Oil Chem Soc 81:1115–1118

    Article  CAS  Google Scholar 

  • Jun TH, Van K, Kim MY, Lee SH, Walker DR (2008) Association analysis using SSR markers to find QTL for seed protein content in soybean. Euphytica 162:179–191

    Article  CAS  Google Scholar 

  • Katan MB, Zock PL, Mensink RP (1995) Trans fatty acids and their effects on lipoproteins in humans. Annu Rev Nutr 15:473–493

    Article  CAS  PubMed  Google Scholar 

  • Katki HA (2008) Invited commentary: evidence-based evaluation of p values and Bayes factors. Am J Epidemiol 168:384–388

    Article  Google Scholar 

  • Korir PC, Zhang J, Wu KJ, Zhao TJ, Gai JY (2013) Association mapping combined with linkage analysis for aluminum tolerance among soybean cultivars released in Yellow and Changjiang River Valleys in China. Theor Appl Genet 126:1659–1675

    Article  CAS  PubMed  Google Scholar 

  • Li ZL, Qiu LJ, Thompson JA, Welsh MM, Nelson RL (2001) Molecular genetic analysis of US and Chinese soybean ancestral lines. Crop Sci 41:1330–1336

    Article  CAS  Google Scholar 

  • Li ZL, Wilson RF, Rayford WE, Boerma HR (2002) Molecular mapping genes conditioning reduced palmitic acid content in N87-2122-4 soybean. Crop Sci 42:373–378

    Article  CAS  Google Scholar 

  • Li YH, Guan RX, Liu ZX, Ma YS, Wang LX, Li LH, Lin FY, Luan WJ, Chen PY, Yan Z, Guan Y, Zhu L, Ning XC, Smulders MJM, Li W, Piao RH, Cui YH, Yu ZM, Guan M, Chang RZ, Hou AF, Shi AN, Zhang B, Zhu SL, Qiu LJ (2008) Genetic structure and diversity of cultivated soybean (Glycine max (L.) Merr.) landraces in China. Theor Appl Genet 117:857–871

    Article  CAS  PubMed  Google Scholar 

  • Li HW, Zhao TJ, Wang YF, Yu DY, Chen SY, Zhou RB, Gai JY (2011a) Genetic structure composed of additive QTL, epistatic QTL pairs and collective unmapped minor QTL conferring oil content and fatty acid components of soybeans. Euphytica 182:117–132

    Article  Google Scholar 

  • Li YH, Smulders MJM, Chang RZ, Qiu LJ (2011b) Genetic diversity and association mapping in a collection of selected Chinese soybean accessions based on SSR marker analysis. Conserv Genet 12:1145–1157

    Article  Google Scholar 

  • Mackay TFC, Stone EA, Ayroles JF (2009) The genetics of quantitative traits: challenges and prospects. Nat Rev Genet 10:565–577

    Article  CAS  PubMed  Google Scholar 

  • Miller JF, Zimmerman DC, Vick BA (1987) Genetic-control of high oleic-acid content in sunflower oil. Crop Sci 27:923–926

    Article  CAS  Google Scholar 

  • Monteros MJ, Burton JW, Boerma HR (2008) Molecular mapping and confirmation of QTLs associated with oleic acid content in N00-3350 soybean. Crop Sci 48:2223–2234

    Article  Google Scholar 

  • Narvel JM, Fehr WR, Chu WC, Grant D, Shoemaker RC (2000) Simple sequence repeat diversity among soybean plant introductions and elite genotypes. Crop Sci 40:1452–1458

    Article  CAS  Google Scholar 

  • Niu Y, Xu Y, Liu XF, Yang SX, Wei SP, Xie FT, Zhang YM (2013) Association mapping for seed size and shape traits in soybean cultivars. Mol Breed 31:785–794

    Article  CAS  Google Scholar 

  • Panthee DR, Pantalone VR, Saxton AM (2006) Modifier QTL for fatty acid composition in soybean oil. Euphytica 152:67–73

    Article  CAS  Google Scholar 

  • Priolli RHG, Wysmierski PT, da Cunha CP, Pinheiro JB, Vello NA (2013) Genetic structure and a selected core set of Brazilian soybean cultivars. Genet Mol Biol 36:382–390

    Article  PubMed Central  PubMed  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed Central  CAS  PubMed  Google Scholar 

  • Raymond M, Rousset F (1995) Genepop (version-1.2): population-genetics software for exact tests and ecumenicism. J Heredity 86:248–249

    Google Scholar 

  • Ritland K (1996) Estimators for pairwise relatedness and individual inbreeding coefficients. Genet Res 67:175–185

    Article  Google Scholar 

  • Shi A, Chen P, Zhang B, Hou A (2010) Genetic diversity and association analysis of protein and oil content in food-grade soybeans from Asia and the United States. Plant Breed 129:250–256

    Article  CAS  Google Scholar 

  • Singh RK, Bhat KV, Bhatia VS, Mohapatra T, Singh NK (2008) Association mapping for photoperiod insensitivity trait in soybean. Natl Acad Sci Lett India 31:281–283

    Google Scholar 

  • Snedecor GW, Cochran WG (1989) Statistical Methods, 8th edn. Iowa State University Press, Ames

    Google Scholar 

  • Song QJ, Marek LF, Shoemaker RC, Lark KG, Concibido VC, Delannay X, Specht JE, Cregan PB (2004) A new integrated genetic linkage map of the soybean. Theor Appl Genet 109:122–128

    Article  CAS  PubMed  Google Scholar 

  • Sorkheh K, Malysheva-Otto LV, Wirthensohn MG, Tarkesh-Esfahani S, Martinez-Gomez P (2008) Linkage disequilibrium, genetic association mapping and gene localization in crop plants. Genet Mol Biol 31:805–814

    Article  Google Scholar 

  • Spencer MM, Pantalone VR, Meyer EJ, Landau-Ellis D, Hyten DL (2003) Mapping the Fas locus controlling stearic acid content in soybean. Theor Appl Genet 106:615–619

    CAS  PubMed  Google Scholar 

  • Storey JD, Tibshirani R (2003) Statistical significance for genomewide studies. Proc Natl Acad Sci USA 100:9440–9445

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Tavaud-Pirra M, Sartre P, Nelson R, Santoni S, Texier N, Roumet P (2009) Genetic diversity in a soybean collection. Crop Sci 49:895–902

    Article  CAS  Google Scholar 

  • Ude GN, Kenworthy WJ, Costa JM, Cregan PB, Alvernaz J (2003) Genetic diversity of soybean cultivars from China, Japan, North America, and North American ancestral lines determined by amplified fragment length polymorphism. Crop Sci 43:1858–1867

    Article  CAS  Google Scholar 

  • Wang LX, Guan Y, Guan RX, Li YH, Ma YS, Dong ZM, Liu X, Zhang HY, Zhang YQ, Liu ZX, Chang RZ, Xu HM, Li LH, Lin FY, Luan WJ, Yan Z, Ning XC, Zhu L, Cui YH, Piao R, Liu Y, Chen PY, Qiu LJ (2006) Establishment of Chinese soybean Glycine max core collections with agronomic traits and SSR markers. Euphytica 151:215–223

    Article  Google Scholar 

  • Wang J, McClean PE, Lee R, Goos RJ, Helms T (2008) Association mapping of iron deficiency chlorosis loci in soybean (Glycine max L. Merr.) advanced breeding lines. Theor Appl Genet 116:777–787

    Article  CAS  PubMed  Google Scholar 

  • Wilson RF (2004) Seed composition. In: Boerma HR, Specht JE (eds) Soybeans: improvement, production, and uses. ASA-CSSA-SSSA, Madison, pp 621–669

    Google Scholar 

  • Wysmierski PT, Vello NA (2013) The genetic base of Brazilian soybean cultivars: evolution over time and breeding implications. Genet Mol Biol 36:547–555

    Article  PubMed Central  PubMed  Google Scholar 

  • Yang Q, Cui J, Chazaro I, Cupples LA, Demissie S (2005) Power and type I error rate of false discovery rate approaches in genome-wide association studies. BMC Genet 6:S134. doi:10.1186/1471-2156-6-s1-s134

    Article  PubMed Central  PubMed  Google Scholar 

  • Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nature Genet 38:203–208

    Article  CAS  PubMed  Google Scholar 

  • Yu XG, Bai GH, Luo N, Chen ZB, Liu SW, Liu JX, Warnke SE, Jiang YW (2011) Association of simple sequence repeat (SSR) markers with submergence tolerance in diverse populations of perennial ryegrass. Plant Sci 180:391–398

    Article  CAS  PubMed  Google Scholar 

  • Zhao KY, Aranzana MJ, Kim S, Lister C, Shindo C, Tang CL, Toomajian C, Zheng HG, Dean C, Marjoram P, Nordborg M (2007) An Arabidopsis example of association mapping in structured samples. PLoS Genet 3:e4. doi:10.1371/journal.pgen.0030004

    Article  PubMed Central  PubMed  Google Scholar 

  • Zhu CS, Gore M, Buckler ES, Yu JM (2008) Status and prospects of association mapping in plants. Plant Genome 1:5–20

    Article  CAS  Google Scholar 

  • Zuo QM, Hou JF, Zhou B, Wen ZX, Zhang SY, Gai JY, Xing H (2013) Identification of QTLs for growth period traits in soybean using association analysis and linkage mapping. Plant Breed 132:317–323

    Article  CAS  Google Scholar 

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Acknowledgments

This work was supported by the São Paulo Research Foundation (project FAPESP/BIOEN, 2008/56249-9). We thank Marcelo Fernandes de Oliveira (Embrapa soybean) for the seeds. We also thank the National Council for Scientific and Technological Development (CNPq) and Coordination for the Improvement of Higher Education Personnel (CAPES) for scholarships.

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Authors and Affiliations

  1. Department of Genetics, ESALQ, USP, Av. Padua Dias 11, Piracicaba, SP, 13400-970, Brazil

    R. H. G. Priolli, J. B. Campos, N. S. Stabellini, J. B. Pinheiro & N. A. Vello

  2. ECOMAR, UNISANTA, R. Oswaldo Cruz 266, Santos, SP, 11045-970, Brazil

    R. H. G. Priolli

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  1. R. H. G. Priolli
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  2. J. B. Campos
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  3. N. S. Stabellini
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Correspondence to R. H. G. Priolli.

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Priolli, R.H.G., Campos, J.B., Stabellini, N.S. et al. Association mapping of oil content and fatty acid components in soybean. Euphytica 203, 83–96 (2015). https://doi.org/10.1007/s10681-014-1264-4

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