Skip to main content

Advertisement

SpringerLink
Log in

Confirmation of delayed canopy wilting QTLs from multiple soybean mapping populations

  • Original Article
  • Published:
Theoretical and Applied Genetics Aims and scope Submit manuscript

Abstract

Key message

QTLs for delayed canopy wilting from five soybean populations were projected onto the consensus map to identify eight QTL clusters that had QTLs from at least two independent populations.

Abstract

Quantitative trait loci (QTLs) for canopy wilting were identified in five recombinant inbred line (RIL) populations, 93705 KS4895 × Jackson, 08705 KS4895 × Jackson, KS4895 × PI 424140, A5959 × PI 416937, and Benning × PI 416937 in a total of 15 site-years. For most environments, heritability of canopy wilting ranged from 0.65 to 0.85 but was somewhat lower when averaged over environments. Putative QTLs were identified with composite interval mapping and/or multiple interval mapping methods in each population and positioned on the consensus map along with their 95 % confidence intervals (CIs). We initially found nine QTL clusters with overlapping CIs on Gm02, Gm05, Gm11, Gm14, Gm17, and Gm19 identified from at least two different populations, but a simulation study indicated that the QTLs on Gm14 could be false positives. A QTL on Gm08 in the 93705 KS4895 × Jackson population co-segregated with a QTL for wilting published previously in a Kefeng1 × Nannong 1138-2 population, indicating that this may be an additional QTL cluster. Excluding the QTL cluster on Gm14, results of the simulation study indicated that the eight remaining QTL clusters and the QTL on Gm08 appeared to be authentic QTLs. QTL × year interactions indicated that QTLs were stable over years except for major QTLs on Gm11 and Gm19. The stability of QTLs located on seven clusters indicates that they are possible candidates for use in marker-assisted selection.

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

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  • Abdel-Haleem H, Lee G, Boerma HR (2011) Identification of QTL for increased fibrous roots in soybean. Theor Appl Genet 122:935–946

    Article  PubMed  Google Scholar 

  • Abdel-Haleem H, Carter TE Jr, Purcell LC, King CA, Ries LL, Chen PC, Schapaugh W Jr, Sinclair TR, Boerma HR (2012) Mapping of quantitative trait loci for canopy-wilting trait in soybean [Glycine max (L) Merr]. Theor Appl Genet 125:837–846

    Article  CAS  PubMed  Google Scholar 

  • Abdel-Haleem H, Pengsheng J, Boerma HR, Li Z (2013) An R Package for SNP marker based parent-offspring tests. Plant Methods 9:44

    Article  PubMed Central  PubMed  Google Scholar 

  • Boerma H, Hussey R, Phillips D, Wood E, Rowan G, Finnerty S (1997) Registration of ‘Benning’ soybean. Crop Sci 37:1982

    Article  Google Scholar 

  • Brim CA (1966) A modified pedigree method of selection in soybeans. Crop Sci 6:220

    Article  Google Scholar 

  • Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19:889–890

    Article  CAS  PubMed  Google Scholar 

  • Carpentieri-Pipolo V, Pipolo A, Abdel-Haleem H, Boerma HR, Sinclair T (2011) Identification of QTLs associated with limited leaf hydraulic conductance in soybean. Euphytica 186:679–686

    Article  Google Scholar 

  • Carter TE Jr, DeSouza RI, Purcell LC (1999) Recent advances in breeding for drought and aluminum resistance in soybean. In: Kauffman HE (ed) Proc. World Soybean Res. Conf. VI, Chicago, IL. 4–7 Aug 1999. Superior Print., Champaign, pp 106–125

  • Carter TE Jr, Nelson RL, Sneller C, Cui Z (2004) Genetic diversity in soybean. In: Boerma HR, Specht JE (eds) Soybean monograph, 3rd edn. American Society of Agronomy, Madison, pp 303–416

    Google Scholar 

  • Charlson DV, Bhatnagar S, King CA, Ray JD, Sneller CH, Carter TE Jr, Purcell LC (2009) Polygenic inheritance of canopy wilting in soybean [Glycine max (L) Merr]. Theor Appl Genet 119:587–594

    Article  PubMed  Google Scholar 

  • Chung J, Babka HL, Graef GL, Staswick PE, Lee DJ, Cregan PB, Shoemaker RC, Specht JE (2003) The seed protein, oil, and yield QTL on soybean linkage group 1. Crop Sci 43:1053–1067

    Article  CAS  Google Scholar 

  • Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138:967–971

    Google Scholar 

  • Darvasi A, Vinreb A, Minke V, Weller JI, Soller M (1993) Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map. Genetics 134:943–951

    PubMed Central  CAS  PubMed  Google Scholar 

  • Du W, Yu D, Fu S (2009) Detection of quantitative trait loci for yield and drought tolerance traits in soybean using a recombinant inbred line population. J Integr Plant Biol 51:868–878

    Article  CAS  PubMed  Google Scholar 

  • Fehr WR, Caviness CE (1977) Stages of soybean development. Iowa Cooperative Extension Service, Iowa Agricultural and Home Economics Experiment Station: Special Report 80

  • Fletcher AL, Sinclair TR, Allen LH Jr (2007) Transpiration responses to vapor pressure deficit in well watered ‘slow-wilting’ and commercial soybean. Environ Exp Bot 61:145–151

    Article  CAS  Google Scholar 

  • Fox CM, Cary TR, Colgrove AL, Nafziger ED, Haudenshield JS, Hartman GL, Specht JE, Diers BW (2013) Estimating soybean genetic gain for yield in the northern United States-Influence of cropping history. Crop Sci 53:2473–2482

    Article  Google Scholar 

  • 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

    Article  Google Scholar 

  • Gizlice Z, Carter TE Jr, Burton JW (1993) Genetic diversity in North American Soybean: I. Multivariate analysis of founding stock and relation to coefficient of parentage. Crop Sci 33:614–620

    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 

  • Hudak C, Patterson R (1995) Vegetative growth analysis of a drought-resistant soybean plant introduction. Crop Sci 35:464–471

    Article  Google Scholar 

  • Hufstetler EV, Boerma HR, Carter TE Jr, Earl HJ (2007) Genotypic variation for three physiological traits affecting drought tolerance in soybean. Crop Sci 47:25–35

    Article  Google Scholar 

  • Hwang S, King CA, Davies MK, Ray JD, Cregan PB, Purcell LC (2013) QTL analysis of shoot ureide and nitrogen concentrations in soybean [Glycine max (L) Merr]. Crop Sci 53:1–13

    Article  Google Scholar 

  • Hwang S, King CA, Davies MK, Charlson DV, Ray JD, Cregan PB, Sneller CH, Chen P, Carter TE Jr, Purcell LC (2014a) Registration of the KS4895 × Jackson mapping population (AR93705). J Plant Regist 9:266–271

  • Hwang S, Ray JD, Cregan PB, King CA, Davies MK, Purcell LC (2014b) Genetics and mapping of quantitative traits for nodule number, weight, and size in soybean (Glycine max L [Merr]). Euphytica 195:419–434

    Article  CAS  Google Scholar 

  • Hyten DL, Song Q, Zhu Y, Choi IY, Nelson RL, Costa JM, Specht JE, Shoemaker RC, Cregan PB (2006) Impacts of genetic bottlenecks on soybean genome diversity. P Natl Acad Sci USA 103:16617–16618

    Article  Google Scholar 

  • Hyten DL, Choi IY, Song Q, Specht JE, Carter TE Jr, Shoemaker RC, Hwang EY, Atukumalli LK, Cregan PB (2010) A high density integrated genetic linkage map of soybean and the development of a 1536 universal soy linkage panel for quantitative trait locus mapping. Crop Sci 50:1–9

    Article  Google Scholar 

  • Jiang C, Zeng ZB (1995) Multiple trait analysis and genetic mapping for quantitative trait loci. Genetics 140:1111–1127

    PubMed Central  CAS  PubMed  Google Scholar 

  • Johnson HW (1958) Registration of soybean varieties. VI Agron J 11:690–691

    Article  Google Scholar 

  • Kao CH, Zeng ZB, Teasdale RD (1999) Multiple interval mapping for quantitative trait loci. Genetics 152:1203–1216

    PubMed Central  CAS  PubMed  Google Scholar 

  • Kearsey MJ, Hyne V (1994) QTL analysis: a simple marker regression approach. Theor Appl Genet 89:698–702

    Article  CAS  PubMed  Google Scholar 

  • King CA, Purcell LC, Brye KR (2009) Differential wilting among soybean genotypes in response to water deficit. Crop Sci 49:290–298

    Article  Google Scholar 

  • Knapp SJ, Stroup WW, Ross WM (1985) Exact confidence intervals for heritability on a progeny mean basis. Crop Sci 25:192–194

    Article  Google Scholar 

  • Kosambi DD (1944) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Article  Google Scholar 

  • Lande R, Thompson R (1990) Efficiency of marker-assisted selection in the improvement of quantitative traits. Genetics 124:743–756

    PubMed Central  CAS  PubMed  Google Scholar 

  • Lander E, Kruglyak L (1995) Genetic dissection of complex traits: guidelines for interpreting and reporting linkage results. Nat Genet 11:241–247

    Article  CAS  PubMed  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) Mapmaker an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  CAS  PubMed  Google Scholar 

  • Manjarrez P, Carter TE Jr, Webb DM, Burton JW (1997) RFLP genetic similarity estimates and coefficient of parentage as genetic variance predictors for soybean yield. Crop Sci 37:698–703

    Article  Google Scholar 

  • Meng XL, Rubin DB (1993) Maximum likelihood estimation via the ECM algorithm: a general framework. Biometrika 80:267–278

    Article  Google Scholar 

  • Molnar SJ, Rai S, Charette M, Cober ER (2003) Simple sequence repeat markers linked to E1, E2, E3, and E7 maturity genes in soybean. Genome 46:1024–1036

    Article  CAS  PubMed  Google Scholar 

  • Piepho HP, Gauch HG (2001) Marker pair selection for mapping quantitative trait loci. Genetics 157:433–444

    PubMed Central  CAS  PubMed  Google Scholar 

  • Purcell LC, Specht JE (2004) Physiological traits for ameliorating drought stress. In: Boerma HR, Specht JE (ed) Soybeans: Improvements, production, and uses, 3rd ed. Agron Monogr 16 ASA, CSSA, SSSA, Madison, pp 520–569

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

    Article  Google Scholar 

  • Ries LL, Purcell LC, Carter TE Jr, Edwards JT, King CA (2012) Physiological traits contributing to differential canopy wilting in soybean under drought. Crop Sci 52:272–281

    Article  Google Scholar 

  • Sadok W, Sinclair TR (2010) Genetic variability of transpiration response of soybean [Glycine max (L) Merr] shoots to leaf hydraulic conductance inhibitor AgNO3. Crop Sci 50:1423–1430

    Article  CAS  Google Scholar 

  • Schapaugh WT, Dille RE (1998) Registration of ‘KS4895’ soybean. Crop Sci 38:892

    Google Scholar 

  • Sen S, Satagopan JM, Broman KW, Churchill GA (2007) R/qtldesign: inbred line cross experimental design. Mamm Genome 18:87–93

    Article  PubMed Central  PubMed  Google Scholar 

  • Sinclair TR, Messina CD, Beatty A, Samples M (2010) Assessment across the United States of the benefits of altered soybean drought traits. Agron J 102:475–482

    Article  Google Scholar 

  • Sloane RJ, Patterson RP, Carter TE Jr (1990) Field drought tolerance of a soybean plant introduction. Crop Sci 30:118–123

    Article  Google Scholar 

  • Specht JE, Hume DJ, Kumudini SV (1999) Soybean yield potential-A genetic and physiological perspective. Crop Sci 39:1560–1570

    Article  Google Scholar 

  • 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

    Article  CAS  Google Scholar 

  • USDA-ARS National Genetic Resources Program (2014a) PI 424140 Glycine max (L) Merr FABACEAE. National Germplasm Resources Laboratory, Beltsville. http://www.arsgrin.gov/cgibin/npgs/acc/display.pl?1319411. Accessed 17 July 2014

  • USDA-ARS National Genetic Resources Program (2014b) PI 416937 Glycine max (L.) Merr FABACEAE. National Germplasm Resources Laboratory, Beltsville. http://www.arsgrin.gov/cgibin/npgs/acc/display.pl?1314868. Accessed 17 July 2014

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. Hered J 93:77–78

    Article  CAS  Google Scholar 

  • Wang CS (1994) Bayesian analysis of mixed linear models via Gibbs sampling with an application to litter size in Iberian pigs. Genet Sel Evol 26:91–115

    Article  PubMed Central  Google Scholar 

  • Weller JI (1986) Maximum likelihood techniques for the mapping and analysis of quantitative trait loci with the aid of genetic markers. Biometrics 42:627–640

    Article  CAS  PubMed  Google Scholar 

  • Xu Z, Zou F, Vision TJ (2005) Improving quantitative trait loci mapping resolution in experimental crosses by the use of genotypically selected samples. Genetics 170:401–408

    Article  PubMed Central  CAS  PubMed  Google Scholar 

  • Yamanaka N, Ninomiya S, Hoshi M, Tsubokura Y, Yano M, Nagamura Y, Sasaki T, Harada K (2001) An informative linkage map of soybean reveals QTLs for flowering time, leaflet morphology and regions of segregation distortion. DNA Res 8:61–72

    Article  CAS  PubMed  Google Scholar 

  • Yang J, Zhu J, Williams RW (2007) Mapping the genetic architecture of complex traits in experimental populations. Bioinformatics 23:1527–1536

    Article  CAS  PubMed  Google Scholar 

  • Yang J, Hu C, Hu H, Yu R, Xia Z, Ye X, Zhu J (2008) QTL Network: mapping and visualizing genetic architecture of complex traits in experimental populations. Bioinformatics 24:721–723

    Article  PubMed  Google Scholar 

  • Zeng ZB (1994) Precise mapping of quantitative trait loci. Genetics 136:1457–1468

    PubMed Central  CAS  PubMed  Google Scholar 

  • Zhang W, Wang Y, Luo G, Zhang J, He C, Wu X, Gai J, Chen S (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

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgments

The authors gratefully acknowledge financial support for this research from the United Soybean Board. This work was also supported in part by the United States Department of Agriculture–Agriculture Research Service (USDA-ARS) project number 6066-21220-012-00D.

Conflict of interest

The authors declare that they have no conflict of interest.

Author information

Authors and Affiliations

  1. Department of Crop, Soil, and Environmental Sciences, University of Arkansas, 1366 Altheimer Drive, Fayetteville, AR, 72704, USA

    Sadal Hwang, C. Andy King, Pengyin Chen & Larry C. Purcell

  2. Crop Genetics and Production Research Unit, USDA-ARS, Stoneville, MS, 38776, USA

    Jeffery D. Ray

  3. Soybean Genomics and Improvement Laboratory, USDA-ARR, BARC-West, Beltsville, MD, 20705-2350, USA

    Perry B. Cregan

  4. Department of Crop Science, North Carolina State University, USDA-ARS, Raleigh, NC, 27695, USA

    Thomas E. Carter Jr.

  5. Department of Crop and Soil Sciences and Center for Applied Genetic Technologies, The University of Georgia, 111 Riverbend Rd., Athens, GA, 30602-6810, USA

    Zenglu Li

  6. US Arid-Land Agricultural Research Center, USDA-ARS, 21881 North Cardon Lane, Maricopa, AZ, 85138, USA

    Hussein Abdel-Haleem

  7. Global Soybean Breeding, Monsanto Company, St. Louis, MO, 63167, USA

    Kevin W. Matson

  8. Department of Agronomy, Kansas State University, 2004C Throckmorton Hall, Manhattan, KS, 6506-5501, USA

    William Schapaugh Jr.

Authors
  1. Sadal Hwang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. C. Andy King
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Jeffery D. Ray
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Perry B. Cregan
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Pengyin Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Thomas E. Carter Jr.
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Zenglu Li
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Hussein Abdel-Haleem
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Kevin W. Matson
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. William Schapaugh Jr.
    View author publications

    You can also search for this author in PubMed Google Scholar

  11. Larry C. Purcell
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Larry C. Purcell.

Additional information

Communicated by I. Rajcan.

Mention of a trademark or proprietary product does not constitute a guarantee or warranty of the product by the U.S. Department of Agriculture and does not imply approval or the exclusion of other products that may also be suitable.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Hwang, S., King, C.A., Ray, J.D. et al. Confirmation of delayed canopy wilting QTLs from multiple soybean mapping populations. Theor Appl Genet 128, 2047–2065 (2015). https://doi.org/10.1007/s00122-015-2566-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-015-2566-1

Keywords

Search

Navigation