Springer Nature is making SARS-CoV-2 and COVID-19 research free. View research | View latest news | Sign up for updates

Introgression of novel genetic diversity to improve soybean yield


Key message

Exotic soybean germplasm can be used to increase novel genetic diversity and yield potential of cultivars.


Modern North American soybean (Glycine max [L.] Merr.) cultivars have been derived from only a few ancestors. The objectives of this research were to develop breeding lines with novel genetic diversity that were equivalent to the yield of a commercial cultivar parent and within those lines identify regions of novel genetic diversity that were not present in the Corteva Agriscience elite soybean germplasm pool. Nine lines created from diverse germplasm (USDA-ARS breeding program at the University of Illinois) were crossed to a RM34Elite parent to develop populations and sublines for yield testing. Across yield tests at 30 locations conducted between 2014 and 2016, eleven breeding lines were identified that were equivalent to or significantly higher in yield when compared to the RM34Elite parent. Among the eleven final lines, the introgressed novel haplotypes that were not present in current Corteva Agriscience soybean germplasm occupied an estimated 0.8–10.0% of the genome. JH-2665, the highest yielding line across 3 years of testing, yielded 280 kg/ha more than the RM34Elite parent and had an estimated 8.6% of the genome containing novel diversity haplotypes. JH-2665 had 96 regions of novel diversity introgression ranging from 1 to 12 cM in size, with six regions over 6 cM in length. The methods reported demonstrate how high-yielding lines with novel genetic diversity can be developed. This material will be useful for expanding the genetic diversity needed to improve genetic gain in future soybean cultivar development.

This is a preview of subscription content, log in to check access.

Fig. 1
Fig. 2
Fig. 3


  1. Abney SA, Crochet WD (2004) The uniform soybean tests, northern region 2004. USDA-ARS, Department of Agron, Purdue University, West Lafayette

  2. Abney SA, Crochet WD (2008) The uniform soybean tests, northern region 2008. USDA-ARS, Department of Agron, Purdue University, West Lafayette

  3. Abney SA, Crochet WD (2009) The uniform soybean tests, northern region 2009. USDA-ARS, Department of Agron, Purdue University, West Lafayette

  4. Akpertey A, Belaffif M, Graef GL, Rouf Mian MA, Shannon JG, Cregan PB, Hudson ME, Diers BW, Nelson RL (2014) Effects of selective genetic introgression from wild soybean to soybean. Crop Sci 54:2683–2695

  5. 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

  6. Brown-Guedira GL, Thompson JA, Nelson RL, Warburton ML (2000) Evaluation of genetic diversity of soybean introductions and North American ancestors using RAPD and SSR markers. Crop Sci 40:815–823

  7. Brown-Guedira GL, Warburton ML, Nelson RL (2004) Registration of LG92-1255, LG93-7054, LG93-7654, and LG93-7792 soybean germplasm. Crop Sci 44:356–357

  8. Carter TE, Nelson RL, Sneller CH, Cui Z (2004) Genetic diversity in soybean. In: Boerma HR, Specht JE (eds) Soybeans: improvement, production, and uses, 3rd edn. ASA, CSSA, and SSSA, Madison, pp 301–416

  9. Carter TE, Burton JW, Fountain MO, Rzwenicki PE, Villagarcia MR, Bowman DT (2008) Registration of N8001 soybean. J Plant Regist 2:22–23

  10. Carter TE, Todd SM, Gillen AM (2015a) Registration of N6002 soybean germplasm with enhanced yield derived from Japanese cultivars Fukuyutaka and Nakasennari and elevated seed protein content. J Plant Regist 9:216–221

  11. Carter TE, Todd SM, Gillen AM (2015b) Registration of N6001 soybean germplasm with enhanced yield derived from Japanese cultivar Suzuyutaka. J Plant Regist 9:376–381

  12. Carter TE, Todd SM, Gillen AM (2016) Registration of ‘USDA-N8002’ soybean cultivar with high yield and abiotic stress resistance traits. J Plant Regist 10:238–245

  13. Concibido VC, La Vallee B, McLaird P, Pineda N, Meyer J, Hummel L, Yang J, Wu K, Delannay X (2003) Introgression of a quantitative trait locus for yield from Glycine soja into commercial soybean cultivars. Theor Appl Genet 106(4):575–582

  14. Diers BW, Specht J, Martin Rainey K, Cregan P, Song Q, Ramasubramanian V, Graef G, Nelson R, Schapaugh W, Wang D, Shannon G, McHale L, Kantartzi SK, Xavier A, Mian R, Stupar RM, Michno J-M, An Y-QC, Goettel W, Ward R, Fox C, Lipka AE, Hyten D, Cary T, Beavis WD (2018) Genetic architecture of soybean yield and agronomic traits. G3 Genes Genomes Genet 8:3367–3375

  15. Eskandari M, Cober ER, Rajcan I (2013) Genetic control of soybean seed oil: II. QTL and genes that increase oil concentration without decreasing protein or with increased seed yield. Theor Appl Genet 126:1677–1687

  16. Fox CM, Cary TR, Nelson RL, Diers BW (2015) Confirmation of a seed yield QTL in soybean. Crop Sci 55:992–998

  17. 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

  18. Gilmour AR, Gogel BJ, Cullis BR, Thompson R (2009) ASReml user guide release 30. VSN International, Hemel Hempstead

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

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

  21. Hyten DL, Song Q, Zhu Y, Ik-Young C, Nelson R, Costa JM, Specht JE, Shoemaker RC, Cregan PB (2006) Impacts of genetic bottlenecks on soybean genome diversity. PNAS 45:16666–16671

  22. Jarquin D, Specht JE, Lorenz A (2016) Prospects of genomic prediction in the USDA soybean germplasm collection: historical data creates robust models for enhancing selection of accessions. G3 Genes Genom Genet 6:2329–2341

  23. Jun TH, Van K, Kim MY, Kwak M, Lee SH (2011) Uncovering signatures of selection in the soybean genome using SSR diversity near QTLs of agronomic importance. Genes Genomics 33:391–397

  24. 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

  25. Kim K-S, Diers BW, Hyten DL, Rouf Mian MA, Shannon JG, Nelson RL (2012) Identification of positive yield QTL alleles from exotic soybean germplasm in two backcross populations. Theor Appl Genet 125:1353–1369

  26. Lander Eric S, Green Philip (1987) Construction of multilocus genetic linkage maps in humans. PNAS 84(8):2363–2367

  27. Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10(3):R25. https://doi.org/10.1186/gb-2009-10-3-r25

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

  29. Li Y, Zhao S, Ma J, Li D, Yan L, Li J, Qi X, Guo X, Zhang L, He W, Chang R, Liang Q, Guo Y, Ye C, Wang X, Tao Y, Guan R, Wang J, Liu Y, Jin L, Zhang X, Liu Z, Zhang L, Chen J, Wang K, Nielsen R, Li R, Chen P, Li W, Reif J, Purugganan M, Wang J, Zhang M, Wang J, Qiu L (2013) Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genom 14:579

  30. Mikel MA, Diers BW, Nelson RL, Smith HH (2010) Genetic diversity and agronomic improvement of North American soybean germplasm. Crop Sci 50:1219–1229

  31. Nelson RL (2018) Ensuring and exploiting the genetic diversity of soybeans. In: Nguyen H (ed) Achieving sustainable cultivation of soybeans. Burleigh Dodds Science Publishing Limited, Cambridge

  32. Nelson RL, Johnson EOC (2006a) Registration of LG96-1797 soybean germplasm. Crop Sci 46:1403

  33. Nelson RL, Johnson EOC (2006b) Registration of soybean germplasm lines LG97-7012, LG98-1445, and LG98-1605. Crop Sci 46:1822–1824

  34. Nelson RL, Johnson EOC (2011a) Registration of soybean germplasm line LG00-6313. J Plant Regist 5:406–409

  35. Nelson RL, Johnson EOC (2011b) Registration of soybean germplasm line LG00-3372. J Plant Regist 5:403–405

  36. Nelson RL, Johnson EOC (2012) Registration high-yielding soybean germplasm line LG04-6000. J Plant Regist 6:1–4

  37. Nelson RL, Johnson EOC, Shannon JG, Mian MAR, Diers BW (2014) Registration of high-yielding soybean germplasm line LG06-5798. J Plant Regist 8:102–105

  38. Nichols DM, Glover KD, Carlson SR, Specht JE, Diers BW (2006) Fine mapping of a seed protein QTL on soybean linkage group I and its correlated effects on agronomic traits. Crop Sci 46:834–839

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

  40. Orf JH, Chase K, Adler FR, Mansur LM, Lark KG (1999b) Genetics of soybean agronomic traits: II. Interactions between yield quantitative trait loci in soybean. Crop Sci 39:1652–1657

  41. Palomeque L, Li-Jun L, Li W, Hedges B, Cober ER, Rajcan I (2009) QTL in mega-environments: I. Universal and specific seed yield QTL detected in a population derived from a cross of high-yielding adapted × high-yielding exotic soybean lines. Theor Appl Genet 119:417–427

  42. Panthee DR, Pantalone VR, Saxton AM, West DR, Sams CE (2007) Quantitative trait loci for agronomic traits in soybean. Plant Breeding 126:51–57

  43. Reinprecht Y, Poysa VW, Yu K, Rajcan I, Ablett GR, Pauls KP (2006) Seed and agronomic QTL in low linolenic acid, lipoxygenase-free soybean (Glycine max (L.) Merrill) germplasm. Genome 49:1510–1527

  44. Reyna N, Sneller CH (2001) Evaluation of marker-assisted introgression of yield QTL alleles into adapted soybean. Crop Sci 41:1317–1321

  45. Rossi ME, Orf JH, Liu L, Dong Z, Rajcan I (2013) Genetic basis of soybean adaptation to North American vs. Asian mega-environments in two independent populations from Canadian × Chinese crosses. Theor Appl Genet 126:1809–1823

  46. Sebastian SA, Streit LG, Stephens PA, Thompson JA, Hedges BA, Fabrizius MA, Soper JF, Schmidt DH, Kallem RL, Hinds MA, Feng L, Hoeck JA (2010) Context specific MAS for improved seed yield in Elite soybean populations. Crop Sci 50:1196–1206

  47. Shannon JG, Nelson RL, Wrather JA (2005) Registration of S99-11509 and S99-11986 improved soybean germplasm with diverse pedigree. Crop Sci 45:1672–1673

  48. Shannon JG, Nelson RL, Lee JD, Wrather JA (2010) Registration of LG04-6863 soybean germplasm line with diverse pedigree. J Plant Regist 4:70–72

  49. 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

  50. Song Q, Hyten DL, Jia G, Quigley CV, Fickus EW, Nelson RL, Cregan PB (2013) Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS ONE 8:e54985

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

  52. Thompson JA, Nelson RL (1998) Utilization of diverse germ-plasm for soybean yield improvement. Crop Sci 38:1362–1368

  53. Thompson JA, Amdor PJ, Nelson RL (1999) Registration of LG90-2550 and LG91-7350R soybean germplasm. Crop Sci 39:302–303

  54. Van K, Kim MY, Shin JH, Kim KD, Lee YH, Lee SH (2014) Molecular evidence for soybean domestication. Gen Plant Genet Resour 1:465–481

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

  56. Wang X, Jiang G-L, Green M, Scott RA, Song Q, Hyten DL, Cregan PB (2014) Identification and validation of quantitative trait loci for seed yield, oil and protein contents in two recombinant inbred line populations of soybean. Mol Genet Genomics 289:935–949

  57. Webb DM (1995) Soybean cyst nematode resistant soybeans and methods of breeding and identifying resistant plants. US Patent 5491081

  58. Webb DM (1997) Brown stem rot resistance in soybean. US Patent 5689035

  59. 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

  60. Zhang W-K, Wang Y-J, Luo G-Z, Zhang J-S, He C-Y, Wu X-L, Gai J-Y, Chen S-Y (2004) 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

Download references

Author information

JMH designed the populations and performed the field research; SR-B designed and performed the molecular and bioinformatics analysis; JMH, RLN, SR-B, and LF analyzed the data; JMH wrote the manuscript with input from RLN, SR-B, LF, and JMC.

Correspondence to J. M. Hegstad.

Ethics declarations

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

R. L. Nelson: Retired from Department of Crop Sciences, University of Illinois, USDA-Agricultural Research Service, 1101 W. Peabody Dr., Urbana, IL, 61801, USA.

Communicated by Brian Diers.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Hegstad, J.M., Nelson, R.L., Renny-Byfield, S. et al. Introgression of novel genetic diversity to improve soybean yield. Theor Appl Genet 132, 2541–2552 (2019). https://doi.org/10.1007/s00122-019-03369-2

Download citation


  • Breeding
  • Exotic germplasm
  • Native diversity
  • Plant introductions
  • Soybean
  • Yield