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Identification of positive yield QTL alleles from exotic soybean germplasm in two backcross populations

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Abstract

Increasing seed yield is an important breeding goal of soybean [Glycine max (L.) Merr.] improvement efforts. Due to the small number of ancestors and subsequent breeding and selection, the genetic base of current soybean cultivars in North America is narrow. The objective of this study was to map quantitative trait loci (QTL) in two backcross populations developed using soybean plant introductions as donor parents. The first population included 116 BC2F3-derived lines developed using “Elgin” as the recurrent parent and PI 436684 as the donor parent (E population). The second population included 93 BC3F3-derived lines developed with “Williams 82” as the recurrent parent and PI 90566-1 as the donor parent (W population). The two populations were evaluated with 1,536 SNP markers and during 2 years for seed yield and other agronomic traits. Genotypic and phenotypic data were analyzed using the programs MapQTL and QTLNetwork to identify major QTL and epistatic QTL. In the E population, two yield QTL were identified by both MapQTL and QTLNetwork, and the PI 436684 alleles were associated with yield increases. In the W population, a QTL allele from PI 90566-1 accounted for 30 % of the yield variation; however, the PI region was also associated with later maturity and shorter plant height. No epistasis for seed yield was identified in either population. No yield QTL was previously reported at the regions where these QTL map indicating that exotic germplasm can be a source of new alleles that can improve soybean yield.

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Abbreviations

PI:

Plant introduction

MAS:

Marker-assisted selection

SNP:

Single nucleotide polymorphism

QTL:

Quantitative trait loci

CIM:

Composite interval mapping

MCIM:

Mixed-model-based composite interval mapping

References

  • Abe J, Xu D, Miyano A, Komatsu K, Kanazawa A, Shimamoto Y (2003) Photoperiod-insensitive Japanese soybean landraces differ at two maturity loci. Crop Sci 43:1300–1304

    Article  Google Scholar 

  • Ablett GR, Beversdorf WD, Dirks VA (1989) Performance and stability of indeterminate and determinate soybean in short-season environments. Crop Sci 29:1428–1433

    Article  Google Scholar 

  • Bernard RL, Cremeens CR (1988) Registration of Williams 82 soybean. Crop Sci 28:1027–1028

    Google Scholar 

  • Bernard RL, Cremeens CR, Cooper RL, Collins FI, Krober OA, Athow KL, Laviolette FA, Coble CJ, and Nelson RL (1998) Evaluation of the USDA Soybean Germplasm Collection: Maturity Groups 000 to IV (FC 01.547 to PI 266.807). US Department of Agriculture Technical Bulletin No. 1844

  • Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li HH, Mitchell SE, Pressoir G, Peiffer JA, Rosas MO, Rocheford TR, Romay MC, Romero S, Salvo S, Villeda HS, da Silva HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu JM, Zhang ZW, Kresovich S, McMullen MD (2009) The genetic architecture of maize flowering time. Science 325:714–718

    Article  CAS  PubMed  Google Scholar 

  • Carter TE Jr, Nelson RL, Sneller CH, Zhanglin C (2004) Genetic diversity in soybean. In: Boerma HR, Specht JE (eds) Soybeans: improvement, production, and uses, 3rd edn. American Society of Agronomy, Madison, pp 303–416

    Google Scholar 

  • Chakraborty N, Curley J, Frederick RD, Hyten DL, Nelson RL, Hartman GL, Diers BW (2009) Mapping and confirmation of a new allele at Rpp 1 from soybean PI 594538A conferring RB lesion type resistance to soybean rust. Crop Sci 49:783–790

    Article  CAS  Google Scholar 

  • Choi IY, Hyten DL, Matukumalli LK, Song Q, Chaky JM, Quigley CV, Chase K, Lark KG, Reiter RS, Yoon MS, Hwang EY, Yi SI, Young ND, Shoemaker RC, van Tassell CP, Specht JE, Cregan PB (2007) A soybean transcript map: gene distribution, haplotype and single-nucleotide polymorphism analysis. Genetics 176:685–696

    Article  CAS  PubMed  Google Scholar 

  • Cober ER, Morrison MJ (2010) Regulation of seed yield and agronomic characters by photoperiod sensitivity and growth habit genes in soybean. Theor Appl Genet 120:1005–1012

    Article  CAS  PubMed  Google Scholar 

  • Cui, Z, Carter TE Jr, Gai J, Qui J, Nelson RL (1999) Origin, description, and pedigree of Chinese soybean cultivars released from 1923 to 1995. US Department of Agriculture Technical Bulletin No. 1871

  • Diers BW, Kim KS (2008) Improving soybean using exotic germplasm. Proceedings of the 12th International Lupin Conference. pp 222–225

  • Fehr WR, Bahrenfus JB (1984) Registration of Elgin soybean. Crop Sci 24:385–386

    Article  Google Scholar 

  • Fehr WR, Caviness CE, Burmood DT, Pennington JS (1971) Stage of development descriptions for soybeans, Glycine max (L.) Merrill. Crop Sci 11:929–931

    Article  Google Scholar 

  • Gizlice Z, Carter TE Jr, Burton JW (1994) Genetic base for North American public soybean cultivars released between 1947 and 1988. Crop Sci 34:1143–1151

    Article  Google Scholar 

  • Gutierrez-Gonzalez JJ, Guttikonda SK, Tran LS, Aldrich DL, Zhong R, Yu O, Nguyen HT, Sleper DA (2010) Differential expression of isoflavone biosynthetic genes in soybean during water deficits. Plant Cell Physiol 51:936–948

    Article  CAS  PubMed  Google Scholar 

  • Gutierrez-Gonzalez JJ, Vuong TD, Zhong R, Yu O, Lee JD, Shannon G, Ellersieck M, Nguyen HT, Sleper DA (2011) Major locus and other novel additive and epistatic loci involved in modulation of isoflavone concentration in soybean seeds. Theor Appl Genet 123:1375–1385

    Article  CAS  PubMed  Google Scholar 

  • Guzman PS, Diers BW, Neece DJ, Martin SKS, Leroy AR, Grau CR, Hughes TJ, Nelson RL (2007) QTL associated with yield in three backcross-derived populations of soybean. Crop Sci 47:111–122

    Article  CAS  Google Scholar 

  • Han Y, Xie D, Teng W, Zhang S, Chang S, Li W (2011) Dynamic QTL analysis of linolenic acid content in different developmental stages of soybean seed. Theor Appl Genet 122:1481–1488

    Article  CAS  PubMed  Google Scholar 

  • Hill J, Becker HC, Tigerstedt PMA (1998) Quantitative and ecological aspects of plant breeding. Chapman & Hall, London

    Google Scholar 

  • Hyten D, Song Q, Choi I, Yoon M, Specht J, Matukumalli L, Nelson R, Shoemaker R, Young N, Cregan P (2008) High-throughput genotyping with the GoldenGate assay in the complex genome of soybean. Theor Appl Genet 116:945–952

    Article  CAS  PubMed  Google Scholar 

  • Hyten DL, Smith J, Frederick RD, Tucker ML, Song Q, Cregan PB (2009) Bulked segregant analysis using the GoldenGate assay to locate the Rpp 3 locus that confers resistance to soybean rust in soybean. Crop Sci 49:265–271

    Article  CAS  Google Scholar 

  • Hyten DL, Choi IY, Song Q, Specht JE, Carter TE, Shoemaker RC, Hwang EY, Matukumalli LK, Cregan PB (2010) A high density integrated genetic linkage map of soybean and the development of a 1,536 universal soy linkage panel for QTL mapping. Crop Sci 50:960–968

    Article  CAS  Google Scholar 

  • Jun TH, Mian MAR, Michel AP (2012) Genetic mapping revealed two loci for soybean aphid resistance in PI 567301B. Theor Appl Genet 124:13–22

    Article  CAS  PubMed  Google Scholar 

  • Kabelka EA, Diers BW, Fehr WR, LeRoy AR, Baianu IC, You T, Neece DJ, Nelson RL (2004) Putative alleles for increased yield from soybean plant introductions. Crop Sci 44:784–791

    Article  Google Scholar 

  • Kabelka EA, Carlson SR, Diers BW (2006) Glycine soja PI 468916 SCN resistance loci associated effects on soybean yield and other agronomic traits. Crop Sci 46:622–629

    Article  Google Scholar 

  • Kassem MA, Shultz J, Meksem K, Wood AJ, Iqbal MJ, Lightfoot DA (2006) An updated ‘Essex’ by ‘Forrest’ linkage map and first composite interval map of QTL underlying six soybean traits. Theor Appl Genet 113:1015–1026

    Article  CAS  PubMed  Google Scholar 

  • Keim P, Diers BW, Olson TC, Shoemaker RC (1990) RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics 126:735–742

    CAS  PubMed  Google Scholar 

  • Kim KS, Diers BW (2009) The associated effects of the soybean aphid resistance locus Rag1 on soybean yield and other agronomic traits. Crop Sci 49:1726–1732

    Article  CAS  Google Scholar 

  • Kim M, Hyten DL, Niblack TL, Diers BW (2011) Stacking resistance alleles from wild and domestic soybean sources improves soybean cyst nematode resistance. Crop Sci 51:934–943

    Article  Google Scholar 

  • Kulwal PL, Kumar N, Kumar A, Gupta RK, Balyan HS, Gupta PK (2005) Gene networks in hexaploid wheat: interacting quantitative trait loci for grain protein content. Funct Integr Genomics 5:254–259

    Article  CAS  PubMed  Google Scholar 

  • Lark KG, Chase K, Adler F, Mansur LM, Orf JH (1995) Interactions between quantitative trait loci in soybean in which trait variation at one locus is conditional upon a specific allele at another. Proc Natl Acad Sci USA 92:4656–4660

    Article  CAS  PubMed  Google Scholar 

  • Lee SH, Bailey MA, Mian MAR, Carter TE, Ashley DA Jr, Hussey RS, Parrott WA, Boerma HR (1996) Molecular markers associated with soybean plant height, lodging, and maturity across locations. Crop Sci 36:728–735

    Article  CAS  Google Scholar 

  • Li Z, Pinson SRM, Park WD, Paterson AH, Stansel JW (1997) Epistasis for three grain yield components in rice (Oryza sativa L.). Genetics 145:453–465

    CAS  PubMed  Google Scholar 

  • Li D, Pfeiffer TW, Cornelius PL (2008) Soybean QTL for yield and yield components associated with Glycine soja alleles. Crop Sci 48:571–581

    Article  Google Scholar 

  • Lukens LN, Doebley J (1999) Epistatic and environmental interactions for quantitative trait loci involved in maize evolution. Genet Res 74:291–302

    Article  CAS  Google Scholar 

  • Ma XQ, Tang JH, Teng WT, Yan JB, Meng YJ, Li JS (2007) Epistatic interaction is an important genetic basis of grain yield and its components in maize. Mol Breed 20:41–51

    Article  Google Scholar 

  • Mackay I, Powell W (2007) Methods for linkage disequilibrium mapping in crops. Trends Plant Sci 12:57–63

    Article  CAS  PubMed  Google Scholar 

  • Mansur LM, Orf JH, Chase K, Jarvik T, Cregan PB, Lark KG (1996) Genetic mapping of agronomic traits using recombinant inbred lines of soybean. Crop Sci 36:1327–1336

    Article  CAS  Google Scholar 

  • McElroy JP, Zhang W, Koehler KJ, Lamont SJ, Dekkers JC (2006) Comparison of methods for analysis of selective genotyping survival data. Genet Sel Evol 38:637–655

    CAS  PubMed  Google Scholar 

  • Molnar SJ, Rai S, Charette M, Cober ER (2003) Simple sequence repeat (SSR) markers linked to E1, E3, E4, and E7 maturity genes in soybean. Genome 46:1024–1036

    Article  CAS  PubMed  Google Scholar 

  • Montooth KL, Marden GH, Clark AG (2003) Mapping determinants of variation in energy metabolism, respiration and flight in Drosophila. Genetics 165:623–635

    CAS  PubMed  Google Scholar 

  • Nelson RL, Johnson EOC (2012) Registration of the High-Yielding Soybean Germplasm Line LG04-6000. J Plant Reg 6:1–4

    Article  Google Scholar 

  • Nelson RL, Amdor PJ, Orf JH, Cavins JF (1988) Evaluation of the USDA Soybean Germplasm Collection: Maturity Groups 000 to IV (PI 427.136 to PI 445.845). US Department of Agriculture Technical Bulletin No. 1726

  • Orf JH, Chase K, Jarvik T, Mansur LM, Cregan PB, Adler FR, Lark KG (1999) Genetics of soybean agronomic traits. I. Comparison of three related recombinant inbred populations. Crop Sci 39:1642–1651

    Article  Google Scholar 

  • Ravi K, Vadez V, Isobe S, Mir RR, Guo Y, Nigam SN, Gowda MVC, Radhakrishnan T, Bertioli DJ, Knapp SJ, Varshney RK (2011) Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.). Theor Appl Genet 122:1119–1132

    Article  CAS  PubMed  Google Scholar 

  • Reif JC, Maurer HP, Korzun V, Ebmeyer E, Miedaner T, Würschum T (2011) Mapping QTLs with main and epistatic effects underlying grain yield and heading time in soft winter wheat. Theor Appl Genet 123:283–292

    Article  PubMed  Google Scholar 

  • Saghai Maroof MA, Soliman KM, Jorgensen RA, Allard RW (1984) Ribosomal DNA spacer length polymorphisms in barley: mendelian inheritance, chromosomal location, and population dynamics. Proc Natl Acad Sci USA 81:8014–8018

    Article  CAS  PubMed  Google Scholar 

  • SAS Institute (2002) The SAS system for Windows. Release 9.2. SAS Institute, Cary

  • Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, Xu D, Hellsten U, May GD, Yu Y, Sakurai T, Umezawa T, Bhattacharyya MK, Sandhu D, Valliyodan B, Lindquist E, Peto M, Grant D, Shu S, Goodstein D, Barry K, Futrell-Griggs M, Abernathy B, Du J, Tian Z, Zhu L, Gill N, Joshi T, Libault M, Sethuraman A, Zhang XC, Shinozaki K, Nguyen HT, Wing RA, Cregan P, Specht J, Grimwood J, Rokhsar D, Stacey G, Shoemaker RC, Jackson SA (2010) Genome sequence of the palaeopolyploid soybean. Nature 463:178–183

    Google Scholar 

  • Schön CC, Melchinger AE, Boppenmaier J, Brunklaus-Jung E, Herrmann RG, Seitzer JF (1994) RFLP mapping in maize: quantitative trait loci affecting testcross performance of elite European flint lines. Crop Sci 34:378–389

    Article  Google Scholar 

  • Sebastian S, Streit L, Stephens P, Thompson J, Hedges B, Fabrizius M, Soper J, Schmidt D, Kallem R, Hinds M (2010) Context-specific marker-assisted selection for improved grain yield in elite soybean populations. Crop Sci 50:1196–1206

    Article  Google Scholar 

  • Smalley MD, Fehr WR, Cianzio SR, Han F, Sebastian SA, Streit LG (2004) Quantitative trait loci for soybean seed yield in elite and plant introduction germplasm. Crop Sci 44:436–442

    CAS  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 

  • Specht JE, Chase K, Macrander M, Graef GL, Chung JU, Markwell JP, Germann M, Orf JH, Lark KG (2001) Soybean response to water: a QTL analysis of drought tolerance. Crop Sci 41:493–509

    Article  CAS  Google Scholar 

  • Van Ooijen JW, Voorrips RW (2001) Joinmap 3.0. Software for the calculation of genetic linkage maps. Plant Research International, Wageningen

  • Van Ooijen JW, Boer MP, Jansen RC, Maliepaard C (2002) MapQTL 4.0. Software for the calculation of QTL positions on genetic maps. Plant Research International, Wageningen

  • Vuong TD, Sleper DA, Shannon JG, Nguyen HT (2010) Novel quantitative trait loci for broad-based resistance to soybean cyst nematode (Heterodera glycines Ichinohe) in soybean PI 567516C. Theor Appl Genet 121:1253–1266

    Article  CAS  PubMed  Google Scholar 

  • Wang D, Graef GL, Procopiuk AM, Diers BW (2004) Identification of putative QTL that underline yield in interspecific soybean backcross populations. Theor Appl Genet 108:458–467

    Article  CAS  PubMed  Google Scholar 

  • Yang J, Hu CC, Hu H, Yu RD, Xia Z, Ye XZ, Zhu J (2008) QTLNetwork: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics 24:721–723

    Article  PubMed  Google Scholar 

  • Yuan J, Njiti VN, Meksem K, Iqbal MJ, Triwitayakorn K, Kassem MA, Davis GT, Schmidt ME, Lightfoot DA (2002) Quantitative trait loci in two soybean recombinant inbred line populations segregating for yield and disease resistance. Crop Sci 42:271–277

    Article  CAS  PubMed  Google Scholar 

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Acknowledgments

This research was funded through support from the Illinois Soybean Association.

Author information

Author notes

  1. D. L. Hyten

    Present address: Pioneer Hi-Bred International Inc., 8305 NW 62nd Avenue, P.O. Box 7060, Johnston, IA, 50131, USA

Authors and Affiliations

  1. Department of Crop Science, University of Illinois, 1101 W. Peabody Drive, Urbana, IL, 61801, USA

    K.-S. Kim & B. W. Diers

  2. Soybean Genomics and Improvement Laboratory, USDA-Agricultural Research Service, 10300 Baltimore Avenue, Beltsville, MD, 20705, USA

    D. L. Hyten

  3. Corn and Soybean Research Unit, Department of Horticulture and Crop Science, USDA-Agricultural Research Service, Ohio State University, 1680 Madison Avenue, Wooster, OH, 44691, USA

    M. A. Rouf Mian

  4. Division of Plant Sciences, University of Missouri-Delta Center, P.O. Box 160, Portageville, MO, 63873, USA

    J. G. Shannon

  5. USDA-Agricultural Research Service, Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, Department of Crop Sciences, University of Illinois, 1101 W. Peabody Drive, Urbana, IL, 61801, USA

    R. L. Nelson

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  1. K.-S. Kim
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Correspondence to R. L. Nelson.

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Communicated by I. Rajcan.

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Kim, KS., Diers, B.W., Hyten, D.L. et al. Identification of positive yield QTL alleles from exotic soybean germplasm in two backcross populations. Theor Appl Genet 125, 1353–1369 (2012). https://doi.org/10.1007/s00122-012-1944-1

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  • DOI: https://doi.org/10.1007/s00122-012-1944-1

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