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Multi-environment analysis and improved mapping of a yield-related QTL on chromosome 3B of wheat

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Abstract

Improved mapping, multi-environment quantitative trait loci (QTL) analysis and dissection of allelic effects were used to define a QTL associated with grain yield, thousand grain weight and early vigour on chromosome 3BL of bread wheat (Triticum aestivum L.) under abiotic stresses. The QTL had pleiotropic effects and showed QTL x environment interactions across 21 diverse environments in Australia and Mexico. The occurrence and the severity of water deficit combined with high temperatures during the growing season affected the responsiveness of this QTL, resulting in a reversal in the direction of allelic effects. The influence of this QTL can be substantial, with the allele from one parent (RAC875) increasing grain yield by up to 12.5 % (particularly in environments where both heat and drought stress occurred) and the allele from the other parent (Kukri) increasing grain yield by up to 9 % in favourable environments. With the application of additional markers and the genotyping of additional recombinant inbred lines, the genetic map in the QTL region was refined to provide a basis for future positional cloning.

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References

  • Alexander LM, Kirigwi FM, Fritz AK, Fellers JP (2012) Mapping and quantitative trait loci analysis of drought tolerance in a spring wheat population using amplified fragment length polymorphism and Diversity Array Technology markers. Crop Sci 52:253–261

    Article  Google Scholar 

  • Beales J, Turner A, Griffths S, Snape JW, Laurie DA (2007) A pseudo-response regulator is misexpressed in the photoperiod insensitive Ppd-D1a mutant of wheat (Triticum aestivum L.). Theor Appl Genet 115:721–733

    Article  PubMed  CAS  Google Scholar 

  • Bennett D, Reynolds M, Mullan D, Izanloo A, Kuchel H, Langridge P, Schnurbusch T (2012a) Detection of two major grain yield QTL in bread wheat (Triticum aestivum L.) under heat, drought and high yield potential environments. Theor Appl Genet. doi:10.1007/s00122-012-1927-2

    Google Scholar 

  • Bennett D, Izanloo A, Reynolds M, Kuchel H, Langridge P, Schnurbusch T (2012b) Genetic dissection of grain yield and physical grain quality in bread wheat (Triticum aestivum L.) under water-limited environments. Theor Appl Genet 125:255–271

    Article  PubMed  Google Scholar 

  • Bennett D, Izanloo A, Edwards J, Kuchel H, Chalmers K, Tester M, Reynolds M, Schnurbusch T, Langridge P (2012c) Identification of novel quantitative trait loci for days to ear emergence and flag leaf glaucousness in a bread wheat (Triticum aestivum L.) population adapted to southern Australian conditions. Theor Appl Genet 124:697–711

    Article  PubMed  Google Scholar 

  • Broman K, Wu H with ideas from Gary Churchill SS; Contributions from Brian Yandell (2010) qtl: tools for analysing QTL experiments. R package version 1.15-15

  • Butler D, Cullis B, Gilmour A, Gogel B (2009) ASReml-R, reference manual. Technical report, Queensland Department of Primary Industries

  • Chen G, Krugman T, Fahima T, Chen K, Hu Y, Röder M, Nevo E, Korol A (2010) Chromosomal regions controlling seedling drought resistance in Israeli wild barley Hordeum spontaneum C. Koch. Genet Resour Crop Evol 57:85–99

    Article  Google Scholar 

  • Cone KC, McMullen MD, Bi IV, Davis GL, Yim Y-S, Gardiner JM, Polacco ML, Sanchez-Villeda H, Fang Z, Schroeder SG, Havermann SA, Bowers JE, Paterson AH, Soderlund CA, Engler FW, Wing RA, Coe EH (2002) Genetic, physical, and informatics resources for maize. On the road to an integrated map. Plant Physiol 130:1598–1605

    Article  PubMed  CAS  Google Scholar 

  • Cullis BR, Smith AB, Coombes NE (2006) On the design of early generation variety trials with correlated data. J Agric Biol Environ Stat 11:381–393

    Article  Google Scholar 

  • Deckers J, Verhulst N, Govaerts B (2009) Classification of the soil at CIMMYT’s experimental station in the Yaqui Valley near Ciudad Obregon, Sonora, Mexico. CIMMYT, Mexico, DF

  • Diab AA, Kantety RV, Ozturk NZ, Benscher D, Nachit MM, Sorrells ME (2008) Drought-inducible genes and differentially expressed sequence tags associated with components of drought tolerance in durum wheat. Sci Res Essays 3:9–26

    Google Scholar 

  • Fleury D, Jefferies S, Kuchel H, Langridge P (2010) Genetic and genomic tools to improve drought tolerance in wheat. J Exp Bot 61:3211–3222

    Article  PubMed  CAS  Google Scholar 

  • Hayden MJ, Nguyen TM, Waterman A, Chalmers KJ (2008) Multiplex-ready PCR: a new method for multiplexed SSR and SNP genotyping. BMC Genomics 9:80

    Article  PubMed  Google Scholar 

  • Holland JB (2007) Genetic architecture of complex traits in plants. Curr Opin Plant Biol 10:156–161

    Article  PubMed  CAS  Google Scholar 

  • Hunt JR, Kirkegaard JA (2011) Re-evaluating the contribution of summer fallow rain to wheat yield in southern Australia. Crop Pasture Sci 62:915–929

    Article  Google Scholar 

  • Jongdee B, Fukai S, Cooper M (2002) Leaf water potential and osmotic adjustment as physiological traits to improve drought tolerance in rice. Field Crop Res 76:153–163

    Article  Google Scholar 

  • Kenward MG, Roger JH (1997) Small sample inference for fixed effects from restricted maximum likelihood. Biometrics 53:983–997

    Article  PubMed  CAS  Google Scholar 

  • Kosina P, Reynolds M, Dixon J, Joshi A (2007) Stakeholder perception of wheat production constraints, capacity building needs, and research partnerships in developing countries. Euphytica 157:475–483

    Article  Google Scholar 

  • Krattinger S, Wicker T, Keller B (2009) Map-based cloning of genes in Triticeae (wheat and barley). In: Muehlbauer GJ, Feuillet C (eds) Genetics and genomics of the Triticeae. Springer US, pp 337–357

  • Lander ES, Green P (1987) Construction of multilocus genetic-linkage maps in humans. Proc Natl Acad Sci USA 84:2363–2367

    Article  PubMed  CAS  Google Scholar 

  • Li J, Ji L (2005) Adjusting multiple testing in multilocus analyses using the eigenvalues of a correlation matrix. Heredity 95:221–227

    Article  PubMed  CAS  Google Scholar 

  • Liao M, Palta JA, Fillery IRP (2006) Root characteristics of vigorous wheat improve early nitrogen uptake. Aust J Agric Res 57:1097–1107

    Article  Google Scholar 

  • Ludwig F, Asseng S (2010) Potential benefits of early vigor and changes in phenology in wheat to adapt to warmer and drier climates. Agr Syst 103:127–136

    Article  Google Scholar 

  • Maccaferri M, Sanguineti MC, Corneti S, Ortega JL, Salem MB, Bort J, DeAmbrogio E, del Moral LF, Demontis A, El-Ahmed A, Maalouf F, Machlab H, Martos V, Moragues M, Motawaj J, Nachit M, Nserallah N, Ouabbou H, Royo C, Slama A, Tuberosa R (2008) Quantitative trait loci for grain yield and adaptation of durum wheat (Triticum durum Desf.) across a wide range of water availability. Genetics 178:489–511

    Article  PubMed  Google Scholar 

  • Malosetti M, Ribaut J, Vargas M, Crossa J, van Eeuwijk F (2008) A multi-trait multi-environment QTL mixed model with an application to drought and nitrogen stress trials in maize (Zea mays L.). Euphytica 161:241–257

    Article  Google Scholar 

  • Manly KF, Cudmore RH, Meer JM (2001) Map Manager QTX, cross-platform software for genetic mapping. Mamm Genome 12:930–932

    Article  PubMed  CAS  Google Scholar 

  • Martinez O, Curnow RN (1992) Estimating the locations and the sizes of the effects of quantitative trait loci using flanking markers. Theor Appl Genet 85:480–488

    Article  Google Scholar 

  • Mason RE, Mondal S, Beecher FW, Pacheco A, Jampala B, Ibrahim AMH, Hays DB (2010) QTL associated with heat susceptibility index in wheat (Triticum aestivum L.) under short-term reproductive stage heat stress. Euphytica 174:423–436

    Article  Google Scholar 

  • Mathews KL, Malosetti M, Chapman S, McIntyre L, Reynolds M, Shorter R, van Eeuwijk F (2008) Multi-environment QTL mixed models for drought stress adaptation in wheat. Theor Appl Genet 117:1077–1091

    Article  PubMed  Google Scholar 

  • McCord AK, Payne RA (2004) Report on the condition of agricultural land in South Australia. Department of Water Land and Biodiversity Conservation, Adelaide

    Google Scholar 

  • McIntyre C, Mathews K, Rattey A, Chapman S, Drenth J, Ghaderi M, Reynolds M, Shorter R (2010) Molecular detection of genomic regions associated with grain yield and yield-related components in an elite bread wheat cross evaluated under irrigated and rainfed conditions. Theor Appl Genet 120:527–541

    Article  PubMed  CAS  Google Scholar 

  • Oakey H, Verbyla A, Pitchford W, Cullis B, Kuchel H (2006) Joint modeling of additive and non-additive genetic line effects in single field trials. Theor Appl Genet 113:809–819

    Article  PubMed  Google Scholar 

  • Olivares-Villegas JJ, Reynolds MP, McDonald GK (2007) Drought-adaptive attributes in the Seri/Babax hexaploid wheat population. Funct Plant Biol 34:189–203

    Article  Google Scholar 

  • Palta JA, Chen X, Milroy SP, Rebetzke GJ, Dreccer MF, Watt M (2011) Large root systems: are they useful in adapting wheat to dry environments? Funct Plant Biol 38:347–354

    Article  Google Scholar 

  • Patterson HD, Thompson R (1971) Recovery of inter-block information when block sizes are unequal. Biometrika 58:545–554

    Article  Google Scholar 

  • Paux E, Sourdille P, Salse J, Saintenac C, Choulet F, Leroy P, Korol A, Michalak M, Kianian S, Spielmeyer W, Lagudah E, Somers D, Kilian A, Alaux M, Vautrin S, Berges H, Eversole K, Appels R, Safar J, Simkova H, Dolezel J, Bernard M, Feuillet C (2008) A physical map of the 1-gigabase bread wheat chromosome 3B. Science 322:101–104

    Article  PubMed  CAS  Google Scholar 

  • Paux E, Faure S, Choulet F, Roger D, Gauthier V, Martinant JP, Sourdille P, Balfourier F, Le Paslier MC, Chauveau A, Cakir M, Gandon B, Feuillet C (2010) Insertion site-based polymorphism markers open new perspectives for genome saturation and marker-assisted selection in wheat. Plant Biotechnol J 8:196–210

    Article  PubMed  CAS  Google Scholar 

  • Paux E, Sourdille P, Mackay I, Feuillet C (2011) Sequence-based marker development in wheat: advances and applications to breeding. Biotechnol Adv 30:1071–1088

    Article  PubMed  Google Scholar 

  • Peleg ZVI, Fahima T, Krugman T, Abbo S, Yakir DAN, Korol AB, Saranga Y (2009) Genomic dissection of drought resistance in durum wheat × wild emmer wheat recombinant inbreed line population. Plant Cell Environ 32:758–779

    Article  PubMed  CAS  Google Scholar 

  • Pinto RS, Reynolds MP, Mathews KL, McIntyre CL, Olivares-Villegas JJ, Chapman SC (2010) Heat and drought adaptive QTL in a wheat population designed to minimize confounding agronomic effects. Theor Appl Genet 121:1001–1021

    Article  PubMed  Google Scholar 

  • Qu Y–Y, Mu P, Li X-Q, Tian Y-X, Wen F, Zhang H-L, Li Z-C (2008) QTL mapping and correlations between leaf water potential and drought resistance in rice under upland and lowland environments. Acta Agron Sin 34:198–206

    Article  CAS  Google Scholar 

  • Rebetzke GJ, Bonnett DG, Ellis MH (2012) Combining gibberellic acid-sensitive and insensitive dwarfing genes in breeding of higher-yielding, sesqui-dwarf wheats. Field Crops Res 127:17–25

    Article  Google Scholar 

  • Reynolds M, Manes Y, Izanloo A, Langridge P (2009a) Phenotyping approaches for physiological breeding and gene discovery in wheat. An Appl Biol 155:309–320

    Article  Google Scholar 

  • Reynolds M, Foulkes MJ, Slafer GA, Berry P, Parry MAJ, Snape JW, Angus WJ (2009b) Raising yield potential in wheat. J Exp Bot 60:1899–1918

    Article  PubMed  CAS  Google Scholar 

  • Richards RA, Watt M, Rebetzke GJ (2007) Physiological traits and cereal germplasm for sustainable agricultural systems. Euphytica 154:409–425

    Article  Google Scholar 

  • Scholander PF, Hammel HT, Hemmingsen EA, Bradstreet ED (1964) Hydrostatic pressure and osmotic potential in leaves of mangroves and some other plants. Proc Natl Acad Sci USA 52:119–125

    Article  PubMed  CAS  Google Scholar 

  • Schwarz G (1978) Estimating the dimension of a model. Ann Stat 6:461–464

    Article  Google Scholar 

  • Shi J, Li R, Qiu D, Jiang C, Long Y, Morgan C, Bancroft I, Zhao J, Meng J (2009) Unraveling the complex trait of crop yield with quantitative trait loci mapping in Brassica napus. Genetics 182:851–861

    Article  PubMed  CAS  Google Scholar 

  • Smith A, Cullis B, Thompson R (2001) Analyzing variety by environment data using multiplicative mixed models and adjustments for spatial field trend. Biometrics 57:1138–1147

    Article  PubMed  CAS  Google Scholar 

  • Smith AB, Cullis BR, Thompson R (2005) The analysis of crop cultivar breeding and evaluation trials: an overview of current mixed model approaches. J Agric Sci 143:449–462

    Article  Google Scholar 

  • Tardieu F, Davies WJ (1993) Integration of hydraulic and chemical signalling in the control of stomatal conductance and water status of droughted plants. Plant Cell Environ 16:341–349

    Article  CAS  Google Scholar 

  • Van Os H, Stam P, Visser RGF, Van Eck HJ (2005) RECORD: a novel method for ordering loci on a genetic linkage map. Theor Appl Genet 112:30–40

    Article  PubMed  CAS  Google Scholar 

  • von Korff M, Grando S, Del Greco A, This D, Baum M, Ceccarelli S (2008) Quantitative trait loci associated with adaptation to Mediterranean dryland conditions in barley. Theor Appl Genet 117:653–669

    Article  Google Scholar 

  • Watt M, Kirkegaard JA, Rebetzke GJ (2005) A wheat genotype developed for rapid leaf growth copes well with the physical and biological constraints of unploughed soil. Funct Plant Biol 32:695–706

    Article  Google Scholar 

  • Wilhelm EP, Turner AS, Laurie DA (2009) Photoperiod insensitive Ppd-A1a mutations in tetraploid wheat (Triticum durum Desf.). Theor Appl Genet 118:285–294

    Article  PubMed  CAS  Google Scholar 

  • Wu X, Chang X, Jing R (2012) Genetic insight into yield-associated traits of wheat grown in multiple rain-fed environments. PLoS ONE 7:e31249

    Article  PubMed  CAS  Google Scholar 

  • Yoshida T, Nishida H, Zhu J, Nitcher R, Distelfeld A, Akashi Y, Kato K, Dubcovsky J (2010) Vrn-D4 is a vernalization gene located on the centromeric region of chromosome 5D in hexaploid wheat. Theor Appl Genet 120:543–552

    Article  PubMed  CAS  Google Scholar 

  • Zhang XK, Xiao YG, Zhang Y, Xia XC, Dubcovsky J, He ZH (2008) Allelic variation at the vernalization genes Vrn-A1, Vrn-B1, Vrn-D1, and Vrn-B3 in Chinese wheat cultivars and their association with growth habit. Crop Sci 48:458–470

    Article  CAS  Google Scholar 

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Acknowledgments

The authors thank Ali Izanloo for field data; Eugenio Perez, Araceli Torres and other members of the CIMMYT physiology group for data collection; Delphine Fleury and other members of the ACPFG for advice and technical support; and Pierre Sourdille (INRA Clermont-Ferrand) for marker sequences. The work was supported through funding from the Grain Research and Development Corporation, the Australian Research Council, the Government of South Australia and the University of Adelaide.

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Correspondence to Julien Bonneau.

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Communicated by J. Dubcovsky.

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Bonneau, J., Taylor, J., Parent, B. et al. Multi-environment analysis and improved mapping of a yield-related QTL on chromosome 3B of wheat. Theor Appl Genet 126, 747–761 (2013). https://doi.org/10.1007/s00122-012-2015-3

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  • DOI: https://doi.org/10.1007/s00122-012-2015-3

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