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Identification of genetic loci and a candidate gene related to flag leaf traits in common wheat by genome-wide association study and linkage mapping

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Abstract

Flag leaf traits influence wheat yield by affecting photosynthetic capacity and plant architecture. In this study, flag leaf traits over 4 years in Chinese common wheat were investigated for genome-wide association study (GWAS) analysis using the wheat 90 K SNP array. A total of 618 significant SNPs were identified in 9 environments and 36 of them are significant in at least three environments and BLUP (best linear unbiased prediction). Linkage mapping indicated that 23 QTL regulating flag leaf traits were detected in a bi-parental population with 5.8 to 28.7% phenotypic variation explained, respectively. Further analysis of multi-environmentally significant SNP revealed a candidate gene TaFLL-5B1 (TraesCS5B02G390300) related to flag leaf length (FLL). Sequencing results indicated that a 40-bp InDel (insertion/deletion) was identified in TaFLL-5B1 gene of different wheat cultivars. Association analysis showed that cultivars with TaFLL-5B1a (with a 40-bp InDel) showed significantly longer FLL than those with TaFLL-5B1b (without a 40-bp InDel). EMS-mutagenized tetraploid wheat line Kronos2282 with premature stop codon of TaFLL-5B1 gene showed significantly shorter FLL than wild type. It suggests that TaFLL-5B1 possibly plays a key role in modulating wheat flag leaf traits. This research increases our understanding of the genetic basis of flag leaf traits and provides genetic loci potentially useful in breeding programs focused on improving wheat architecture and yield.

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References

  • Cavanagh CR, Chao S, Wang S, Huang BE, Stephen S, Kiani S, Forrest K, Saintenac C, Brown-Guedira GL, Akhunova A, See D, Bai G, Pumphrey M, Tomar L, Wong D, Kong S, Reynolds M, Silva ML, Bockelman H, Talbert L, Anderson JA, Dreisigacker S, Baenziger S, Carter A, Korzun V, Morrell PL, Dubcovsky J, Morell MK, Sorrells ME, Hayden MJ, Akhunov E (2013) Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars. Proc Natl Acad Sci U S A 110(20):8057–8062

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen JH, Zhang FY, Zhao CJ, Lv GG, Sun CW, Pan YB, Guo XY, Chen F (2019) Genome-wide association study of six quality traits reveals the association of the TaRPP13L1 gene with flour color in Chinese bread wheat. Plant Biotechnol J 17:2106–2122

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen ML, Luo J, Shao GN, Wei XJ, Tang SQ, Sheng ZH, Song J, Hu PS (2012) Fine mapping of a major QTL for flag leaf width in rice, qFLW4, which might be caused by alternative splicing of NAL1. Plant Cell Rep 31(5):863–872

    Article  CAS  PubMed  Google Scholar 

  • Colasuonno P, Gadaleta A, Giancaspro A, Nigro D, Giove S, Incerti O, Signorile A, Simeone R, Blanco A (2014) Development of a high-density SNP-based linkage map and detection of yellow pigment content QTLs in durum wheat. Mol Breed 34:1563–1578

    Article  CAS  Google Scholar 

  • Edae EA, Byrne PF, Haley SD, Lopes MS, Reynolds MP (2014) Genome-wide association mapping of yield and yield components of spring wheat under contrasting moisture regimes. Theor Appl Genet 127(4):791–807

    Article  CAS  PubMed  Google Scholar 

  • Fan XL, Cui F, Zhao CH, Zhang W, Yang LJ, Zhao XQ, Han J, Su QN, Ji J, Zhao ZW, Tong YP, Li JM (2015) QTLs for flag leaf size and their influence on yield-related traits in wheat (Triticum aestivum L.). Mol Breed 35:24

    Article  Google Scholar 

  • Fujino K, Matsuda Y, Ozawa K, Nishimura T, Koshiba T, Fraaije MW, Sekiguchi H (2008) Narrow LEAF 7 controls leaf shape mediated by auxin in rice. Mol Gen Genomics 279(5):499–507

    Article  CAS  Google Scholar 

  • Gao FM, Wen WE, Liu JD, Rasheed A, Yin GH, Xia XC, Wu XX, He ZH (2015) Genome-wide linkage mapping of QTL for yield components, plant height and yield-related physiological traits in the Chinese wheat cross Zhou 8425B/Chinese spring. Front Plant Sci 6:1099

    PubMed  PubMed Central  Google Scholar 

  • Guo J, Hao CY, Zhang Y, Zhang BQ, Cheng XM, Qin L, Li T, Shi WP, Chang XP, Jing RL, Yang WY, Hu WJ, Zhang XY, Cheng SH (2015) Association and validation of yield-favored alleles in Chinese cultivars of common wheat (Triticum aestivum L.). PLos One 10(6):e0130029

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Guo Z, Chen D, Alqudah AM, Röder MS, Ganal MW, Schnurbusch T (2017) Genome-wide association analyses of 54 traits identified multiple loci for the determination of floret fertility in wheat. New Phytol 214(1):257–270

    Article  CAS  PubMed  Google Scholar 

  • Hussain W, Baenziger PS, Belamkar V, Guttieri MJ, Venegas JP, Easterly A, Sallam A, Poland J (2017) Genotyping-by-sequencing derived high-density linkage map and its application to QTL mapping of flag leaf traits in bread wheat. Sci Rep 7(1):16394

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Jia HY, Wan HS, Yang SH, Zhang ZZ, Kong ZX, Xue SL, Zhang LX, Ma ZQ (2013) Genetic dissection of yield-related traits in a recombinant inbred line population created using a key breeding parent in china's wheat breeding. Theor Appl Genet 126(8):2123–2139

    Article  CAS  PubMed  Google Scholar 

  • Khaliq I, Irshad A, Ahsan M (2008) Awns and flag leaf contribution towards grain yield in spring wheat (Triticum aestivum L.). Cereal Res Commun 36(1):65–76

    Article  Google Scholar 

  • Lehnert H, Serfling A, Enders M, Friedt W, Ordon F (2017) Genetics of mycorrhizal symbiosis in winter wheat (Triticum aestivum L). New Phytol 215(2):779–791

    Article  CAS  PubMed  Google Scholar 

  • Li HH, Ye GY, Wang JK (2007) A modified algorithm for the improvement of composite interval mapping. Genetics 175(1):361–374

    Article  PubMed  PubMed Central  Google Scholar 

  • Li MX, Yeung JM, Cherny SS, Sham PC (2012) Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets. Hum Genet 131(5):747–756

    Article  CAS  PubMed  Google Scholar 

  • Lipka AE, Tian F, Wang QS, Peiffer J, Li M, Bradbury PJ, Gore MA, Buckler ES, Zhang ZW (2012) GAPIT: genome association and prediction integrated tool. Bioinformatics 28(18):2397–2399

    Article  CAS  PubMed  Google Scholar 

  • Liu KY, Xu H, Liu G, Guan PF, Zhou XY, Peng HR, Yao YY, Ni ZF, Sun QX, Du JK (2018b) QTL mapping of flag leaf-related traits in wheat (Triticum aestivum L.). Theor Appl Genet 131(4):839–849

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu LP, Sun GL, Ren XF, Li CD, Sun DF (2015) Identification of QTL underlying physiological and morphological traits of flag leaf in barley. BMC Genet 16:29

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Liu YX, Tao Y, Wang ZQ, Guo QL, Wu FK, Yang XL, Deng M, Ma J, Chen GD, Wei YM, Zheng YL (2018a) Identification of QTL for flag leaf length in common wheat and their pleiotropic effects. Mol Breed 38(1):11

    Article  CAS  Google Scholar 

  • Lv GG, Dong ZD, Wang Y, Geng JY, Li J, Lv XL, Sun CW, Ren Y, Zhang J, Chen F (2020) Identification of genetic loci of black point in Chinese common wheat by genome-wide association study and linkage mapping. Plant Dis. https://doi.org/10.1094/PDIS-12-19-2733-RE

  • Meng L, Li HH, Zhang LY, Wang JK (2015) QTL IciMapping: integrated software for genetic linkage map construction and quantitative trait locus mapping in bi-parental populations. Crop J 3(3):169–173

    Article  Google Scholar 

  • Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC (2007) Plink: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559–575

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Qi J, Qian Q, Bu QY, Li SY, Chen Q, Sun JQ, Liang WX, Zhou YH, Chu CC, Li XG, Ren FG, Palme K, Zhao BR, Chen JF, Chen MS, Li CY (2008) Mutation of the rice narrow leaf1 gene, which encodes a novel protein, affects vein patterning and polar auxin transport. Plant Physiol 147(4):1947–1959

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quarrie SA, Quarrie SP, Radosevic R, Rancic D, Kaminska A, Barnes JD, Leverington M, Ceoloni C, Dodig D (2006) Dissecting a wheat QTL for yield present in a range of environments: from the QTL to candidate genes. J Exp Bot 57(11):2627–2637

    Article  CAS  PubMed  Google Scholar 

  • Russo MA, Ficco DBM, Laidò G, Marone D, Papa R, Blanco A, Gadaleta A, Vita PD, Mastrangelo AM (2014) A dense durum wheat × T. dicoccum linkage map based on SNP markers for the study of seed morphology. Mol Breed 34:1579–1597

    Article  Google Scholar 

  • Shi CN, Zheng YT, Geng JY, Liu CY, Pei H, Ren Y, Dong Z, Zhao L, Zhang N, Chen F (2020) Identification of herbicide resistance loci using a genome-wide association study and linkage mapping in Chinese common wheat. Crop J. https://doi.org/10.1016/j.cj.2020.02.004

  • Shi WP, Hao CY, Zhang Y, Cheng JY, Zhang Z, Liu J, Yi X, Cheng XM, Sun DZ, Xu YH, Zhang XY, Cheng SH, Guo PY, Guo J (2017) A combined association mapping and linkage analysis of kernel number per spike in common wheat (Triticum aestivum L.). Front Plant Sci 8:1412

    Article  PubMed  PubMed Central  Google Scholar 

  • Sukumaran S, Dreisigacker S, Lopes M, Chavez P, Reynolds MP (2015) Genome-wide association study for grain yield and related traits in an elite spring wheat population grown in temperate irrigated environments. Theor Appl Genet 128(2):353–363

    Article  CAS  PubMed  Google Scholar 

  • Sun CW, Dong ZD, Zhao L, Ren Y, Zhang N, Chen F (2020) The Wheat 660K SNP array demonstrates great potential for marker-assisted selection in polyploid wheat. Plant Biotechnol J 18:1354–1360

  • Sun CW, Zhang FY, Yan XF, Zhang XF, Dong ZD, Cui DQ, Chen F (2017) Genome-wide association study for 13 agronomic traits reveals distribution of superior alleles in bread wheat from the Yellow and Huai Valley of China. Plant Biotechnol J 15(8):953–969

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Su ZQ, Hao CY, Wang LF, Dong YC, Zhang XY (2011) Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theor Appl Genet 122(1):211–223

    Article  CAS  PubMed  Google Scholar 

  • Tian ZW, Jing Q, Dai TB, Jiang D, Cao WX (2011) Effects of genetic improvements on grain yield and agronomic traits of winter wheat in the Yangtze River Basin of China. Field Crop Res 124(3):417–425

    Article  Google Scholar 

  • Valluru R, Reynolds MP, Davies WJ, Sukumaran S (2017) Phenotypic and genome-wide association analysis of spike ethylene in diverse wheat genotypes under heat stress. New Phytol 214(1):271–283

    Article  CAS  PubMed  Google Scholar 

  • Wang F, Song Y, Yang W, Sun J, Li X, Liu D, Zhang A (2016) Cloning and functional analysis of flag leaf width-related gene TaNAL1-5 in common wheat (Triticum aestivum L.). Mol Plant Breed 14(5):1037–1048

    CAS  Google Scholar 

  • Wang JK (2009) Inclusive composite interval mapping of quantitative trait genes. Acta Agron Sin 35(2):239–245

    Article  CAS  Google Scholar 

  • Wang P, Zhou GL, Yu HH, Yu SB (2011) Fine mapping a major QTL for flag leaf size and yield-related traits in rice. Theor Appl Genet 123(8):1319–1330

    Article  CAS  PubMed  Google Scholar 

  • Wang S, Wong D, Forrest K, Allen A, Chao S, Huang BE, Maccaferri M, Salvi S, Milner SG, Cattivelli L, Mastrangelo AM, Whan A, Stephen S, Barker G, Wieseke R, Plieske J, International Wheat Genome Sequencing Consortium, Lillemo M, Mather D, Appels R, Dolferus R, Brown-Guedira G, Korol A, Akhunova AR, Feuillet C, Salse J, Morgante M, Pozniak C, Luo MC, Dvorak J, Morell M, Dubcovsky J, Ganal M, Tuberosa R, Lawley C, Mikoulitch I, Cavanagh C, Edwards KJ, Hayden M, Akhunov E (2014) Characterization of polyploid wheat genomic diversity using a high-density 90,000 single nucleotide polymorphism array. Plant Biotechnol J 12(6):787–796

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang SS, Zhang XF, Chen F, Cui DQ (2015) A single-nucleotide polymorphism of TaGS5 gene revealed its association with kernel weight in Chinese bread wheat. Front Plant Sci 6:1166

    PubMed  PubMed Central  Google Scholar 

  • Wu QH, Chen YX, Fu L, Zhou SH, Chen JJ, Zhao XJ, Zhang D, Ouyang SH, Wang ZZ, Li D, Wang GX, Zhang DY, Yuan CG, Wang LX, You MS, Han J, Liu ZY (2016) QTL mapping of flag leaf traits in common wheat using an integrated high-density SSR and SNP genetic linkage map. Euphytica 208:337–351

    Article  CAS  Google Scholar 

  • Xue DW, Chen MC, Zhou MX, Chen S, Mao Y, Zhang GP (2008) QTL analysis of flag leaf in barley (Hordeum vulgare L.) for morphological traits and chlorophyll content. J Zhejiang Univ Sci B 9(12):938–943

    Article  PubMed  PubMed Central  Google Scholar 

  • Xue SL, Xu F, Li GQ, Zhou Y, Lin MS, Gao ZX, Su XH, Xu XW, Jiang G, Zhang S, Jia HY, Kong ZX, Zhang LX, Ma ZQ (2013) Fine mapping Taflw1, a major QTL controlling flag leaf width in bread wheat (Triticum aestivum L.). Theor Appl Genet 126(8):1941–1949

    Article  CAS  PubMed  Google Scholar 

  • Yan XF, Zhao L, Ren Y, Dong ZD, Cui DQ, Chen F (2019) Genome-wide association study revealed that the TaGW8 gene was associated with kernel size in Chinese bread wheat. Sci Rep 9:2702

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Yang X, Pan YB, Singh PK, He XY, Ren Y, Zhao L, Zhang N, Cheng SH, Chen F (2019) Investigation and genome-wide association study for Fusarium crown rot resistance in Chinese common wheat. BMC Plant Biol 19:153

    Article  PubMed  PubMed Central  Google Scholar 

  • Yin CB, Li HH, Zhao ZG, Wang ZQ, Liu SJ, Chen LM, Liu X, Tian YL, Ma J, Xu LD, Zhang DS, Zhu SS, Li DT, Wan JM, Wang JK (2017) Genetic dissection of top three leaf traits in rice using progenies from a japonica × indica cross. J Integr Plant Biol 59(12):866–880

    Article  CAS  PubMed  Google Scholar 

  • Yue B, Xue WY, Luo LJ, Xing YZ (2006) QTL analysis for flag leaf characteristics and their relationships with yield and yield traits in rice. J Genet Genomics 33(9):824–832

    CAS  Google Scholar 

  • Yu JM, Pressoir G, Briggs WH, Vroh BI, Yamasaki M, Doebley JF, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38(2):203–208

    Article  CAS  PubMed  Google Scholar 

  • Zhang B, Ye WJ, Ren DY, Peng T, Peng YL, Gao Y, Ruan BP, Wang L, Zhang GH, Guo LB, Qian Q, Gao ZY (2015) Genetic analysis of flag leaf size and candidate genes determination of a major QTL for flag leaf width in rice. Rice 8(1):39

    Article  PubMed  Google Scholar 

  • Zhang XF, Chen JH, Yan Y, Yan XF, Shi CN, Zhao L, Chen F (2018) Genome-wide association study of heading and flowering dates and construction of its prediction equation in Chinese common wheat. Theor Appl Genet 131:2271–2285

    Article  CAS  PubMed  Google Scholar 

  • Zhang ZW, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, Gore MA, Bradbury PJ, Yu J, Arnett DK, Ordovas JM, Buckler ES (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42(2):355–360

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Funding

This project was funded by the National Key Research and Development Program (2016YFD0101802), National Natural Science Foundation (31971947 and 182102110120), Henan Major Science and Technology Projects (181100110200), Ten-Thousand Talents Plan (Z04295) of China.

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  1. Xuefang Yan and Lei Zhao contributed equally to this work.

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  1. Agronomy College/National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 15 Longzihu College District, Zhengzhou, 450046, People’s Republic of China

    Xuefang Yan, Lei Zhao, Yan Ren, Ning Zhang, Zhongdong Dong & Feng Chen

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  1. Xuefang Yan
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Correspondence to Feng Chen.

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Yan, X., Zhao, L., Ren, Y. et al. Identification of genetic loci and a candidate gene related to flag leaf traits in common wheat by genome-wide association study and linkage mapping. Mol Breeding 40, 58 (2020). https://doi.org/10.1007/s11032-020-01135-7

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