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Mapping quantitative trait loci associated with stem-related traits in maize (Zea mays L.)

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Abstract

Key message

Mapping QTL for stem-related traits using RIL population with ultra-high density bin map can better dissect pleiotropic QTL controlling stem architecture that can provide valuable information for maize genetic improvement.

Abstract

The maize stem is one of the most important parts of the plant and is also a component of many agronomic traits in maize. This study aimed to advance our understanding of the genetic mechanisms underlying maize stem traits. A recombinant inbred line (RIL) population derived from a cross between Ye478 and Qi319 was used to identify quantitative trait loci (QTL) controlling stem height (SH), ear height (EH), stem node number (SN), ear node (EN), and stem diameter (SD), and two derived traits (ear height coefficient (EHc) and ear node coefficient (ENc)). Using an available ultra-high density bin map, 46 putative QTL for these traits were detected on chromosomes 1, 3, 4, 5, 6, 7, 8, and 10. Individual QTL explained 3.5–17.7% of the phenotypic variance in different environments. Two QTL for SH, three for EH, two for EHc, one for SN, one for EN, and one for SD were detected in more than one environment. QTL with pleiotropic effects or multiple linked QTL were also identified on chromosomes 1, 3, 4, 6, 8, and 10, which are potential target regions for fine-mapping and marker-assisted selection in maize breeding programs. Further, we discussed segregation of bin markers (mk1630 and mk4452) associated with EHc QTL in the RIL population. We had identified two putative WRKY DNA-binding domain proteins, AC209050.3_FG003 and GRMZM5G851490, and a putative auxin response factor, GRMZM2G437460, which might be involved in regulating plant growth and development, as candidate genes for the control of stem architecture.

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Data availability

The raw sequence reads of RILs derived from Ye478 and Qi319 had been public on NCBI (https://www.ncbi.nlm.nih.gov/bioproject/627044, Accession: PRJNA627044).

Abbreviations

SH:

Stem height

EH:

Ear height

EHc:

Ear height coefficient, EH/SH

SN:

Stem node number

EN:

Ear node

ENc:

Ear node coefficient, EN/SN

SD:

Stem diameter

MAS:

Marker-assisted selection

QTL:

Quantitative trait loci

RIL:

Recombinant inbred line

CTK:

Cytokinin

IAA:

Aauxin

GA:

Gibberellin

BR:

Brassinosteroids

References

  • Beavis WD, Smith OS, Grant D, Fincher R (1994) Identification of quantitative trait loci using a small sample of topcrossed and F4 progeny from maize. Crop Sci 34:882–896

    Google Scholar 

  • Bensen RJ, Johal GS, Crane VC, Tossberg JT, Schnable PS, Meeley RB, Briggs SP (1995) Cloning and characterization of the maize An1 gene. Plant Cell 7:75–84

    CAS  PubMed  PubMed Central  Google Scholar 

  • Berke T, Rocheford T (1995) Quantitative trait loci for flowering, plant and ear height, and kernel traits in maize. Crop Sci 35(6):1542–1549

    Google Scholar 

  • Bokore FE, Cuthbert RD, Knox RE, Singh A, Campbell HL, Pozniak CJ, N'Diaye A, Sharpe AG, Ruan Y (2019) Mapping quantitative trait loci associated with common bunt resistance in a spring wheat (Triticum aestivum L.) variety Lillian. Theor Appl Genet 132:3023–3033

    CAS  PubMed  PubMed Central  Google Scholar 

  • Cai Y, Chen X, Xie K, Xing Q, Wu Y, Li J, Du C, Sun Z, Sun Z (2014) Dlf1, a WRKY transcription factor, is involved in the control of flowering time and plant height in rice. PLoS ONE 9:e102529

    PubMed  PubMed Central  Google Scholar 

  • Chen Z, Wang B, Dong X, Liu H, Ren L, Chen J, Hauck A, Song W, Lai J (2014) An ultra-high density bin-map for rapid QTL mapping for tassel and ear architecture in a large F2 maize population. BMC Genomics 15:433

    PubMed  PubMed Central  Google Scholar 

  • Cheng WS, Liu F, Li M, Hu XD, Chen H, Pappoe F (2015) Variation detection based on next-generation sequencing of type Chinese 1 strains of Toxoplasma gondii with different virulence from China. BMC Genomics 16:888

    PubMed  PubMed Central  Google Scholar 

  • Collard B, Jahufer M, Brouwer J, Pang E (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 142:169–196

    CAS  Google Scholar 

  • Feng G, Huang C, Xing J (2008) The research progress in lodging resistance of maize. Crops 4:12–14

    Google Scholar 

  • Feng G, Jing X, Li Y, Wang L, Huang C (2010) Correlation and path analysis of lodging resistance with maize stem characters. Acta Agric Boreali-Sin 25:72–74

    Google Scholar 

  • Fu Z, Shao K, Chen D, Wang B, Xu Z, Ding D (2011) Correlation analysis of the internode number above ear and lodging resistance in maize. J Henan Agric Univ 145:149–154

    Google Scholar 

  • Fujioka S, Yamane H, Spray CR, Gaskin P, Macmillan J, Phinney BO, Takahashi N (1988) Qualitative and quantitative analyses of gibberellins in vegetative shoots of normal, dwarf-1, dwarf-2, dwarf-3, and dwarf-5 seedlings of Zea mays L. Plant Physiol 88:1367–1372

    CAS  PubMed  PubMed Central  Google Scholar 

  • Guo D, Wang X, Han X, Wei B, Wang J, Li B, Yu H, Huang Q, Gu H, Qu L, Qin G (2015) The WRKY transcription factor WRKY71/EXB1 controls shoot branching by transcriptionally regulating RAX genes in Arabidopsis. Plant Cell 27:3112–3127

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hackenberg D, Asare-Bediako E, Baker A, Walley P, Jenner C, Greer S, Bramham L, Batley A, Edwards D, Delourme R, Barker G, Teakle G, Walsh J (2019) Identifcation and QTL mapping of resistance to Turnip yellows virus (TuYV) in oilseed rape, Brassica napus. Theor Appl Genet 133:383–393

    PubMed  PubMed Central  Google Scholar 

  • Hittalmani S, Shashidhar H, Bagali P, Huang N, Sidhu J, Singh V, Khush G (2002) Molecular mapping of quantitative trait loci for plant growth, yield and yield related traits across three diverse locations in a doubled haploid rice population. Euphytica 125:207–214

    CAS  Google Scholar 

  • Huang X, Ding F, Peng H-X, Pan J, He X, Xu J, Li L (2019) Research progress on family of plant WRKY transcription factors. Biotechnol Bull 35(12):129–143

    Google Scholar 

  • Koester RP, Sisco PH, Stuber CW (1993) Identification of quantitative trait loci controlling days to flowering and plant height in two near isogenic lines of maize. Crop Sci 33:1209–1216

    Google Scholar 

  • Li A, Dong H, Li H (2007) The study on combining ability of 6 exotic maize populations based on different heterotic backgrounds. J Hebei Agric Univ 30:13–18

    CAS  Google Scholar 

  • Li D, Mao L, Yang J, Liu J, Zhang Y (2005) Breeding process and utilization of excellent maize inbred line 478. J Laiyang Agric Coll 22:159–164

    Google Scholar 

  • Li Z, Zhang H, Wu X, Sun Y, Liu X (2014) Quantitative trait locus analysis for ear height in maize based on a recombinant inbred line population. Gene Mol Res 13:450–456

    CAS  Google Scholar 

  • Lima M, Souza C, Bento D, Souza A, Garcia L (2006) Mapping QTL for grain yield and plant traits in a tropical maize population. Mol Breed 17:227–239

    Google Scholar 

  • Liu K, Xu H, Liu G, Guan P, Zhou X, Peng H, Yao Y, Ni Z, Sun Q, Du J (2018) QTL mapping of flag leaf-related traits in wheat (Triticum aestivum L.). Theor Appl Genet 131:839–849

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu T, Zhang J, Wang M, Wang Z, Li G, Qu L, Wang G (2007) Expression and functional analysis of ZmDWF4, an ortholog of Arabidopsis DWF4 from maize (Zea mays L.). Plant Cell Rep 26:2091–2099

    CAS  PubMed  Google Scholar 

  • Ma Y, Wang Q (2012) Research progress on the relationship between corn stalk traits and lodging resistance. Crops 2:10–15

    Google Scholar 

  • Ma Y, Xue H, Zhang L, Zhang F, Ou C, Wang F, Zhang Z (2016) Involvement of auxin and brassinosteroid in dwarfism of autotetraploid apple (Malus × domestica). Sci Rep 6:26719

    CAS  PubMed  PubMed Central  Google Scholar 

  • Melchinger AE, Utz HF, Schön CC (1998) Quantitative trait locus (QTL) mapping using different testers and independent population samples in maize reveals low power of QTL detection and large bias in estimates of QTL effects. Genetics 149:383–403

    CAS  PubMed  PubMed Central  Google Scholar 

  • Michalczuk L (2002) Indole-3-acetic acid level in wood, bark and cambial sap of apple rootstocks differing in growth vigour. Acta Physiol Plant 24:131–136

    CAS  Google Scholar 

  • Ribaut J, Betrán J (1999) Single large-scale marker-assisted selection (SLS-MAS). Mol Breed 5:531–541

    Google Scholar 

  • Sakamoto T (2006) Phytohormones and rice crop yield: strategies and opportunities for genetic improvement. Transgenic Res 15:399–404

    CAS  PubMed  Google Scholar 

  • Sakamoto T, Miura K, Itoh H, Tatsumi T, Ueguchi-Tanaka M, Ishiyama K, Kobayashi M, Agrawal GK, Takeda S, Abe K, Miyao A, Hirochika H, Kitano H, Ashikari M, Matsuoka M (2004) An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiol 134:1642–1653

    CAS  PubMed  PubMed Central  Google Scholar 

  • SAS Institute Inc (1999) SAS/STAT user’s guide, version 8. SAS Institute Inc, Cary, NC

    Google Scholar 

  • Shang Q, Zhang D, Wang K, Wang G, Pan J, Li X, Shi L (2020) Diversity analysis of stalk traits in maize inbred lines in China. J Plant Genet Res 21:321–329

    Google Scholar 

  • Soumelidou K, Morris DA, Battey NH, Barnett JR, John P (1994) Auxin transport capacity in relation to the dwarfing effect of apple rootstocks. J Horticult Sci 69:719–725

    CAS  Google Scholar 

  • Spray CR, Kobayashi M, Suzuki Y (1996) The dwarf-1 (d1) mutant of Zea mays blocks three steps in the gibberellin-biosynthetic pathway. P Natl Acad Sci USA 93:10515–10518

    CAS  Google Scholar 

  • Tanksley S (1993) Mapping polygenes. Annu Rev Genet 27:205–233

    CAS  PubMed  Google Scholar 

  • Teng F, Zhai L, Liu R, Bai W, Wang L, Huo D, Tao Y, Zheng Y, Zhang Z (2013) ZmGA3ox2, a candidate gene for a major QTL, qPH3.1, for plant height in maize. Plant J 73:405–416

    CAS  PubMed  Google Scholar 

  • van Ooijen J (2004) MapQTL® 5: software for the mapping of quantitative trait loci in experimental populations. Kyazma BV, Wageningen

    Google Scholar 

  • Veldboom LR, Lee M (1994) Molecular-marker-facilitated studies of morphological traits in maize. 2: determination of QTLs for grain yield and yield components. Theor Appl Genet 894:451–458

    Google Scholar 

  • Veldboom LR, Lee M (1996a) Genetic mapping of quantitative trait loci in maize in stress and nonstress environments. 1. Grain yield and yield components. Crop Sci 36:1310–1319

    CAS  Google Scholar 

  • Veldboom LR, Lee M (1996b) Genetic mapping of quantitative trait loci in maize in stress and nonstress environments. 2. Plant Height Flower Crop Sci 36:1320–1327

    CAS  Google Scholar 

  • Veldboom LR, Lee M, Woodman WL (1994) Molecular marker-facilitated studies in an elite maize population: 1. Linkage analysis and determination of QTL for morphological traits. Theor Appl Genet 88:7–16

    CAS  PubMed  Google Scholar 

  • VSN International Ltd (2008) GENSTAT for windows, 11th edn. VSN International, Hemel Hempstead

    Google Scholar 

  • Wang T, Wang M, Hu S, Xiao Y, Tong H, Pan Q, Xue J, Yan J, Li J, Yang X (2015) Genetic basis of maize kernel starch content revealed by high-density single nucleotide polymorphism markers in a recombinant inbred line population. BMC Plant Biol 288:1–12

    Google Scholar 

  • Wei L, Zhang X, Zhang Z, Liu H, Lin Z (2018) A new allele of the Brachytic2 gene in maize can efficiently modify plant architecture. Heredity 121:75–86

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wu J, Liu C, Shi Y, Song Y, Zhang G, Ma Z, Wang T, Li Y (2005) QTL analysis of plant height and ear height in maize under different water regimes. J Plant Genet Res 6:266–271

    Google Scholar 

  • Xing A, Gao Y, Ye L, Zhang W, Cai L, Ching A, Llaca V, Johnson B, Liu L, Yang X, Kang D, Yan J, Li J (2015) A rare SNP mutation in Brachytic2 moderately reduces plant height and increases yield potential in maize. J Exp Bot 66:3791–3802

    CAS  PubMed  PubMed Central  Google Scholar 

  • Xu T, Zhou F, Huang L, Xie P, Guan Y, Lan C, Liu P (2019) Research advances in maize lodging resistance. Anhui Agric Sci Bull 25:29–32

    Google Scholar 

  • Ye J (2000) The first inbred lines Qi319 immune to maize southern rust bred in China. Agric Sci China 33:110

    Google Scholar 

  • Zhang Y (2010) Mapping of quantitative trait loci (QTL) and genetic basis for plant height and ear height in maize. Dissertation, Chinese Academy of Agricultural Sciences

  • Zhao B, Li J (2012) Regulation of brassinosteroid biosynthesis and inactivation. J Integr Plant Biol 54:746–759

    CAS  PubMed  Google Scholar 

  • Zhao J, Wang R (2009) Factors promoting the steady increase of American maize production and their enlightenments for China. J Maize Sci 17(156–159):163

    Google Scholar 

  • Zheng L (2016) Construction of chromosome segment substitution line and QTL mapping of plant height in maize. Dissertation, Northeast Agricultural University

  • Zheng X, Zhao Y, Shan D, Shi K, Wang L, Li Q, Wang N, Zhou J, Yao J, Xue Y, Fang S, Chu J, Guo Y, Kong J (2018) MdWRKY9 overexpression confers intensive dwarfing in the M26 rootstock of apple by directly inhibiting brassinosteroid synthetase MdDWF4 expression. New Phytol 217:1086–1098

    CAS  PubMed  Google Scholar 

  • Zheng ZP, Liu XH (2013) Genetic analysis of agronomic traits associated with plant architecture by QTL mapping in maize. Gene Mol Res 12:1243–1253

    CAS  Google Scholar 

  • Zhou Z, Zhang C, Lu X, Wang L, Hao Z, Li M, Zhang D, Yong H, Weng J, Li X (2018) Dissecting the genetic basis underlying combining ability of plant height related traits in maize. Front Plant Sci 9:1117

    PubMed  PubMed Central  Google Scholar 

  • Zhou Z, Zhang C, Zhou Y, Hao Z, Wang Z, Zeng X, Di H, Li M, Zhang D, Yong H, Zhang S, Weng J, Li X (2016) Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines. BMC Genomics 17:178

    PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This research was jointly supported by the National Natural Science Foundation of China (31671706) and the Beijing Education Commission-General Project (KM201810020005).

Funding

This research was jointly supported by the National Natural Science Foundation of China (31671706) and the Beijing Education Commission-General Project (KM201810020005).

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Author notes

  1. Qiqi Shang, Degui Zhang and Rong Li have contributed equally to this work.

Authors and Affiliations

  1. College of Plant Science and Technology, Beijing University of Agriculture, 7 Beinong Road, Changping District, Beijing, 102206, China

    Qiqi Shang, Rong Li, Kaixin Wang, Zimeng Cheng, Jinbao Pan & Liyu Shi

  2. Institute of Crop Science, The National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China

    Degui Zhang, Zhiqiang Zhou, Zhuanfang Hao & Xinhai Li

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  1. Qiqi Shang
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Correspondence to Xinhai Li or Liyu Shi.

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Shang, Q., Zhang, D., Li, R. et al. Mapping quantitative trait loci associated with stem-related traits in maize (Zea mays L.). Plant Mol Biol 104, 583–595 (2020). https://doi.org/10.1007/s11103-020-01062-3

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