Skip to main content
SpringerLink
Log in

Multi-environment QTL analysis of grain morphology traits and fine mapping of a kernel-width QTL in Zheng58 × SK maize population

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

Abstract

Key message

Sixteen major QTLs regulating maize kernel traits were mapped in multiple environments and one of them, qKW - 9.2 , was restricted to 630 Kb, harboring 28 putative gene models.

Abstract

To elucidate the genetic basis of kernel traits, a quantitative trait locus (QTL) analysis was conducted in a maize recombinant inbred line population derived from a cross between two diverse parents Zheng58 and SK, evaluated across eight environments. Construction of a high-density linkage map was based on 13,703 single-nucleotide polymorphism markers, covering 1860.9 cM of the whole genome. In total, 18, 26, 23, and 19 QTLs for kernel length, width, thickness, and 100-kernel weight, respectively, were detected on the basis of a single-environment analysis, and each QTL explained 3.2–23.7 % of the phenotypic variance. Sixteen major QTLs, which could explain greater than 10 % of the phenotypic variation, were mapped in multiple environments, implying that kernel traits might be controlled by many minor and multiple major QTLs. The major QTL qKW-9.2 with physical confidence interval of 1.68 Mbp, affecting kernel width, was then selected for fine mapping using heterogeneous inbred families. At final, the location of the underlying gene was narrowed down to 630 Kb, harboring 28 putative candidate-gene models. This information will enhance molecular breeding for kernel traits and simultaneously assist the gene cloning underlying this QTL, helping to reveal the genetic basis of kernel development in maize.

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
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Alonso-Blanco C, Koornneef M (2000) Naturally occurring variation in Arabidopsis: an underexploited resource for plant genetics. Trends Plant Sci 5:22–29

    Article  CAS  PubMed  Google Scholar 

  • Austin D, Lee M (1996) Comparative mapping in F2:3 and F6:7 generations of quantitative trait loci for grain yield and yield components in maize. Theor Appl Genet 92:817–826

    Article  CAS  PubMed  Google Scholar 

  • Bai X, Luo L, Yan W, Kovi MR, Zhan W, Xing Y (2010) Genetic dissection of rice grain shape using a recombinant inbred line population derived from two contrasting parents and fine mapping a pleiotropic quantitative trait locus qGL7. BMC Genet 11:16

    Article  PubMed  PubMed Central  Google Scholar 

  • Bao J (2014) Genes and QTLs for rice grain quality improvement. In: Yan WG, Bao JS (ed) Rice-germplasm genetics and improvement, chap 9. InTech, pp 239–278

  • Blummel M, Grings E, Erenstein O (2013) Potential for dual-purpose maize varieties to meet changing maize demands: synthesis. Field Crop Res 153:107–112

    Article  Google Scholar 

  • Borrás L, Gambín BL (2010) Trait dissection of maize kernel weight: towards integrating hierarchical scales using a plant growth approach. Field Crop Res 118:1–12

    Article  Google Scholar 

  • Brown TA, Jones MK, Powell W, Allaby RG (2009) The complex origins of domesticated crops in the Fertile Crescent. Trends Ecol Evol 24:103–109

    Article  PubMed  Google Scholar 

  • Coles ND (2009) The genetic architecture of maize photoperiod sensitivity revealed by recombinant inbred line, backcross, and heterogeneous inbred family populations. Ph.D. thesis, Department of Crop Science, North Carolina State University, Raleigh. http://www.lib.ncsu.edu/resolver/1840.16/4750

  • Doerge RW, Churchill GA (1996) Permutation tests for multiple loci affecting a quantitative character. Genetics 142:285–294

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164–1171

    Article  CAS  PubMed  Google Scholar 

  • Guo J, Su G, Zhang J, Wang G (2008) Genetic analysis and QTL mapping of maize yield and associate agronomic traits under semi-arid land condition. Afr J Biotechnol 7:12

    Google Scholar 

  • Gupta PK, Rustgi S, Kumar N (2006) Genetic and molecular basis of grain size and grain number and its relevance to grain productivity in higher plants. Genome 49:565–571

    Article  PubMed  Google Scholar 

  • Hong Y, Chen L, Du LP, Su Z, Wang J, Ye X, Qi L, Zhang Z (2014) Transcript suppression of TaGW2 increased grain width and weight in bread wheat. Funct Integr Genomics 14:341–349

    Article  CAS  PubMed  Google Scholar 

  • Hu Z, He H, Zhang S, Sun F, Xin X, Wang W, Qian X, Yang J, Luo X (2012) A Kelch motif-containing serine/threonine protein phosphatase determines the large grain QTL trait in rice. J Integr Plant Biol 54:979–990

    Article  CAS  PubMed  Google Scholar 

  • Huang R, Jiang L, Zheng J, Wang T, Wang H, Huang Y, Hong Z (2013) Genetic bases of rice grain shape: so many genes, so little known. Trends Plant Sci 18:218–226

    Article  CAS  PubMed  Google Scholar 

  • Lai J, Li R, Xu X, Jin W, Xu M, Zhao H, Xiang Z, Song W, Ying K, Zhang M (2010) Genome-wide patterns of genetic variation among elite maize inbred lines. Nat Genet 42:1027–1030

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Wang Y, Shi Y, Song Y, Wand T, Li Y (2009) Correlation analysis and QTL mapping for traits of kernel structure and yield components in maize. Sci Agric Sin 42:408–418

    CAS  Google Scholar 

  • Li M, Guo X, Zhang M, Wang X, Zhang G, Tian Y, Wang Z (2010a) Mapping QTLs for grain yield and yield components under high and low phosphorus treatments in maize (Zea mays L.). Plant Sci 178:454–462

    Article  CAS  Google Scholar 

  • Li Q, Li L, Yang X, Warburton ML, Bai G, Dai J, Li J, Yan J (2010b) Relationship, evolutionary fate and function of two maize co-orthologs of rice GW2 associated with kernel size and weight. BMC Plant Biol 10:143

    Article  PubMed  PubMed Central  Google Scholar 

  • Li Q, Yang X, Bai G, Warburton ML, Mahuku G, Gore M, Dai J, Li J, Yan J (2010c) Cloning and characterization of a putative GS3 ortholog involved in maize kernel development. Theor Appl Genet 120:753–763

    Article  CAS  PubMed  Google Scholar 

  • Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, Li X, Xiao J (2011) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43:1266–1269

    Article  CAS  PubMed  Google Scholar 

  • Lid SE, Gruis D, Jung R, Lorentzen JA, Ananiev E, Chamberlin M, Niu X, Meeley R, Nichols S, Olsen OA (2002) The defective kernel 1 (dek1) gene required for aleurone cell development in the endosperm of maize grains encodes a membrane protein of the calpain gene superfamily. Proc Natl Acad Sci 99:5460–5465

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu XH, Zheng P, Tan ZB, Li Z, He C (2010) Quantitative trait locus (QTL) mapping for 100-kernel weight of maize (Zea mays L.) under different nitrogen regimes. Afr J Biotechnol 49:8283–8289

    Google Scholar 

  • Liu Z, Ji H, Cui Z, Wu X, Duan L, Feng X, Tang J (2011) QTL detected for grain-filling rate in maize using a RIL population. Mol Breed 27:25–36

    Article  Google Scholar 

  • Liu Y, Wang L, Sun C, Zhang Z, Zheng Y, Qiu F (2014) Genetic analysis and major QTL detection for maize kernel size and weight in multi-environments. Theor Appl Genet 127:1019–1037

    Article  CAS  PubMed  Google Scholar 

  • Liu J, Deng M, Guo H, Raihan S, Luo J, Xu Y, Dong X, Yan J (2015) Maize orthologs of rice GS5 and their trans-regulator are associated with kernel development. J Integr Plant Biol. doi:10.1111/jipb.12421

    PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  • Maitz M, Santandrea G, Zhang Z, Lal S, Hannah LC, Salamini F, Thompson RD (2000) rgf1, a mutation reducing grain filling in maize through effects on basal endosperm and pedicel development. Plant J 23:29–42

    Article  CAS  PubMed  Google Scholar 

  • Messmer R, Fracheboud Y, Bänziger M, Vargas M, Stamp P, Ribaut JM (2009) Drought stress and tropical maize: QTL-by-environment interactions and stability of QTLs across environments for yield components and secondary traits. Theorl Appl Genet 119:913–930

    Article  Google Scholar 

  • Monaco MK, Sen TZ, Dharmawardhana PD, Ren L, Schaeffer M, Naithani S, Amarasinghe V, Thomason J, Harper L, Gardiner J, Cannon EK (2013) Maize metabolic network construction and transcriptome analysis. Plant Genome 6:1–12

    Article  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Nikolić A, Anđelković V, Dodig D, Mladenović-Drinić S, Kravić N, Ignjatović-Micić D (2013) Identification of QTL-s for drought tolerance in maize, II: yield and yield components. Genetika 45:341–350

    Article  Google Scholar 

  • Pan Q, Li L, Yang X, Tong H, Xu S, Li Z, Li W, Muehlbauer GJ, Li J, Yan J (2015) Genome wide recombination dynamics are associated with phenotypic variation in maize. New Phytol. doi:10.1111/nph.13810

    PubMed Central  Google Scholar 

  • Paterson AH, De Verna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124:735–742

    CAS  PubMed  PubMed Central  Google Scholar 

  • Paterson AH, Lin YR, Li Z, Schertz KF, Doebley JF, Pinson SR, Liu SC, Stansel JW, Irvine JE (1995) Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269:1714–1718

    Article  CAS  PubMed  Google Scholar 

  • Peng B, Li Y, Wang Y, Liu C, Liu Z, Tan W, Zhang Y, Wang D, Shi Y, Sun B (2011) QTL analysis for yield components and kernel-related traits in maize across multi-environments. Theor Appl Genet 122:1305–1320

    Article  PubMed  Google Scholar 

  • Poehlman JM, Sleper DA (1995) Breeding soybean. In: Breeding field crops, 4th edn. Iowa State University Press, Ames, pp 300–318

  • Pozzi C, Rossini L, Vecchietti A, Salamini F (2004) Gene and genome changes during domestication of cereals. In: Gupta PK, Varshney RK et al (eds) Cereal genomics. Springer, pp 165–198

  • Prado SA, César G, López M, Senior L, Borrás L (2014) The genetic architecture of maize (Zea mays L.) kernel weight determination. G3 (Bethesda) 4:1611–1621

    Article  Google Scholar 

  • Qi X, Zhao Y, Jiang L, Cui Y, Wang Y, Liu B (2009) QTL analysis of kernel soluble sugar content in super sweet corn. Afr J Biotechnol 8:6913–6917

    CAS  Google Scholar 

  • Qi P, Lin YS, Song XJ, Shen JB, Huang W, Shan JX, Zhu MZ, Jiang L, Gao JP, Lin HX (2012) The novel quantitative trait locus GL3. 1 controls rice grain size and yield by regulating Cyclin-T1; 3. Cell Res 22:1666–1680

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ramya P, Chaubal A, Kulkarni K, Gupta L, Kadoo N, Dhaliwal H, Chhuneja P, Lagu M, Gupt V (2010) QTL mapping of 1000-kernel weight, kernel length, and kernel width in bread wheat (Triticum aestivum L.). J Appl Genet 51:421–429

    Article  CAS  PubMed  Google Scholar 

  • Revilla P, Butrón A, Malvar R, Ordás R (1999) Relationship among kernel weight, early vigor, and growth in maize. Crop Sci 39:654–658

    Article  Google Scholar 

  • Ross AJ, Hallauer AR, Lee M (2006) Genetic analysis of traits correlated with maize ear length. Maydica 151(2):301

    Google Scholar 

  • Sanguinetti CJ, Dias Neto E, Simpson AJG (1994) Rapid silver staining and recovery of PCR products separated on polyacrylamide gels. Biotechniques 17:915–919

    Google Scholar 

  • Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yields during rice domestication. Nat Genet 40:1023–1028

    Article  CAS  PubMed  Google Scholar 

  • Song XJ, Ashikari M (2008) Toward an optimum return from crop plants. Rice 1:135–143

    Article  Google Scholar 

  • Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630

    Article  CAS  PubMed  Google Scholar 

  • SPSS Inc. (1999) SPSS base 10.0 for Windows user’s guide. SPSS Inc., Chicago

    Google Scholar 

  • Statista (2014) Worldwide production of grain in 2013, by type. http://www.statista.com/statistics/263977/world-grain-production-by-type/. Accessed 20 Aug 2015

  • Tang J, Yan J, Ma X, Teng W, Wu W, Dai J, Dhillon BS, Melchinger AE, Li J (2010) Dissection of the genetic basis of heterosis in an elite maize hybrid by QTL mapping in an immortalized F2 population. Theor Appl Genet 120:333–340

    Article  PubMed  Google Scholar 

  • Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335:6170

    Google Scholar 

  • Team RC (2014) A language and environment for statistical computing 2012. R Foundation for Statistical Computing, Vienna. ISBN 3-900051-07-0

    Google Scholar 

  • Thévenot C, Simond-Côte E, Reyss A, Manicacci D, Trouverie J, Le Guilloux M, Ginhoux V, Sidicina F, Prioul J-L (2005) QTLs for enzyme activities and soluble carbohydrates involved in starch accumulation during grain filling in maize. J Exp Bot 56:945–958

    Article  PubMed  Google Scholar 

  • Tuinstra M, Ejeta G, Goldsbrough P (1997) Heterogeneous inbred family (HIF) analysis: a method for developing near-isogenic lines that differ at quantitative trait loci. Theor Appl Genet 95:1005–1011

    Article  CAS  Google Scholar 

  • Wan X, Weng J, Zhai H, Wang J, Lei C, Liu X, Guo T, Jiang L, Su N, Wan J (2008) Quantitative trait loci (QTL) analysis for rice grain width and fine mapping of an identified QTL allele gw-5 in a recombination hotspot region on chromosome 5. Genetics 179:2239–2252

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang S, Basten CJ, Zeng ZB (2010) Windows QTL cartographer 2.5. Department of statistics. North Carolina State University, Raleigh. http://www.statgen.ncsu.edu/qtlcart/WQTLCart.htm

  • Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Zeng R, Zhu H, Dong G, Qian Q (2012) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44:950–954

    Article  CAS  PubMed  Google Scholar 

  • Weng J, Gu S, Wan X, Gao H, Guo T, Su N, Lei C, Zhang X, Cheng Z, Guo X (2008) Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res 18:1199–1209

    Article  CAS  PubMed  Google Scholar 

  • Xing Y, Zhang Q (2010) Genetic and molecular bases of rice yield. Annu Rev Plant Biol 61:421–442

    Article  CAS  PubMed  Google Scholar 

  • Xu Y (2010) Molecular plant breeding. CAB International, Wallingford

    Book  Google Scholar 

  • Yan B, Liu R, Li Y, Wang Y, Gao G, Zhang Q, Liu X, Jiang G, He Y (2014) QTL analysis on rice grain appearance quality, as exemplifying the typical events of transgenic or backcrossing breeding. Breed Sci 64:231

    Article  PubMed  PubMed Central  Google Scholar 

  • Yang X, Gao S, Xu S, Zhang Z, Prasanna BM, Li L, Li J, Yan J (2011) Characterization of a global germplasm collection and its potential utilization for analysis of complex quantitative traits in maize. Mol Breed 28:511–526

    Article  Google Scholar 

  • Yang W, Guo Z, Huang C, Duan L, Chen G, Jiang N, Fang W, Feng H, Xie W, Lian X, Wang G (2014) Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Nat Commun 5:5087

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160

    Article  CAS  PubMed  Google Scholar 

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

    CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang X, Wang J, Huang J, Lan H, Wang C, Yin C, Wu Y, Tang H, Qian Q, Li J (2012) Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proc Natl Acad Sci 109:21534–21539

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang W, Sun P, He Q, Shu F, Wang J, Deng H (2013) Fine mapping of GS2, a dominant gene for big grain rice. Crop J 1:160–165

    Article  Google Scholar 

  • Zhang Z, Liu Z, Hu Y, Li W, Fu Z, Ding D, Li H, Qiao M, Tang J (2014) QTL analysis of kernel-related traits in maize using an immortalized F2 population. PLoS One 9:e89645

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

We thankfully acknowledge and greatly appreciate Mr. Xiongbing Yan for his admirable field work. This research was supported by the Genetically Modified Organisms Breeding Major Projects (2014ZX0800944B) and the National Natural Science Foundation of China (31222041).

Author information

Authors and Affiliations

  1. National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China

    Mohammad Sharif Raihan, Jie Liu, Juan Huang, Huan Guo, Qingchun Pan & Jianbing Yan

Authors
  1. Mohammad Sharif Raihan
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jie Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Juan Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Huan Guo
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Qingchun Pan
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Jianbing Yan
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jianbing Yan.

Ethics declarations

Conflict of interest

The authors declare that they have no conflicts of interest.

Additional information

Communicated by N. de Leon.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (DOCX 222 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Raihan, M.S., Liu, J., Huang, J. et al. Multi-environment QTL analysis of grain morphology traits and fine mapping of a kernel-width QTL in Zheng58 × SK maize population. Theor Appl Genet 129, 1465–1477 (2016). https://doi.org/10.1007/s00122-016-2717-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00122-016-2717-z

Keywords

Search

Navigation