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Genome-wide association study of total starch and its components in common wheat

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Abstract

Wheat starch is closely related to yield and quality of wheat-based final products. This genome-wide association study focused on total starch content and its components using single nucleotide polymorphisms (SNPs) in a panel of 205 elite winter wheat accessions. Twenty-nine significant marker-trait associations (MTAs) were detected for total starch (TSC), amylose (AMS) and amylopectin (AMP) contents under four environmental regimes. Nine MTAs were detected for two traits, and eleven MTAs were found for all three traits. These SNPs were distributed across seven chromosomes, explaining 11.26–23.83% of the phenotypic variance (PVE). Furthermore, eighteen MTAs related to the ratio of AMS and AMP under four environmental conditions explained 5.92–17.2% of the phenotypic variance. One important multi-trait MTA on chromosome 3A at the 93 cM position was found for thousand kernel weight, AMP, AMS and TSC. A set of elite alleles was identified, including allele Kukri_c5615_1214-A, which increased AMS and AMP by 5.80% and 15.32%, respectively. The allele Excalibur_c16376_351-T increased AMP by 4.43%, and the T allele of marker BS00022255_51 and T allele of marker D_contig25392_201 had the most significant effects, increasing the ratio of AMS to AMP by 3.77%. Fourteen candidate genes associated with significant markers were identified. For example, TRIAE_CS42_2AL_TGACv1_093900_AA0288950 participated in carbohydrate metabolism and hydrolysed O-glycosyl compounds. The lines that carry these elite alleles could be used as genetic stock for breeding to improve these traits. These results could lay the foundation for molecular marker-assisted selection in improving wheat quality.

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References

  • Araki E, Miura H, Sawada S (1999) Identification of genetic loci affecting amylose content and agronomic traits on chromosome 4A of wheat. Theor Appl Genet 98:977–984

    CAS  Google Scholar 

  • Bandillo N, Jarquin D, Song QJ, Nelson R, Cregan P, Specht J, Specht J, Lorenz A (2015) A population structure and genome-wide association analysis on the USDA soybean germplasm collection. Plant Genome 8:832

    Google Scholar 

  • Batey IL, Hayden MJ, Cai S, Sharp PJ, Cornish GB, Morell MK, Appels R (2002) Genetic mapping of commercially significant starch characteristics in wheat crosses. Aust J Agric Res 52:1287–1296

    Google Scholar 

  • Bradbury PJ, Parker T, Hamblin MT, Jannink JL (2011) Assessment of power and false discovery rate in genome-wide association studies using the barley CAP germplasm. Crop Sci 51:52–59

    Google Scholar 

  • Caballero L, Bancel E, Debiton C, Branlard G (2008) Granule-bound starch synthase (GBSS) diversity of ancient wheat and related species. Plant Breed 127:548–553

    CAS  Google Scholar 

  • Cai CP, Ye WX, Zhang TZ, Guo WZ (2014) Association analysis of fiber quality traits and exploration of elite alleles in upland cotton cultivars/accessions (Gossypium hirsutum L.). J Integr Plant Biol 56:51–62

    CAS  PubMed  Google Scholar 

  • Chen GF, Chen JS, Tian JC (2015) Genome-wide association analysis between SNP markers and plant height related traits in wheat. Acta Agron Sin 41:1500

    CAS  Google Scholar 

  • Chen GF, Zhang H, Deng ZY, Wu RG, Li DM, Wang MY, Tian JC (2016) Genome-wide association study for kernel weight-related traits using SNPs in a Chinese winter wheat population. Euphytica 212:173–185

    CAS  Google Scholar 

  • Chen GF, Wu RG, Li DM, Yu HX, Deng ZY, Tian JC (2017) Genome-wide association study for seedling emergence and tiller number using SNP markers in an elite winter wheat population. J Genet 96:177–186

    PubMed  Google Scholar 

  • Cho YH, Shim JY, Lee HG (2007) Characteristics of wheat flour dough and noodles with amylopectin content and hydrocolloids. Korean J Food Sci Technol 39:138–145

    Google Scholar 

  • Cockram J, White J, Zuluaga DL, Smith D, Comadran J, Macaulay M, Luo ZW, Kearsey MJ, Werner P, Harrap D, Tapsell C, Liu H, Hedley PE, Stein N, Schulte D, Steuernagel B, Marshall DF, Thomas WTB, Ramsay L, Mackay I, Balding DJ, Waugh R, O’Sullivan DM, Booer C, Pike S, Hamilton G, Jellis G, Davies N, Ross A, Bury P, Habgood R, Klose S, Vequaud D, Christerson T, Brosnan J, Newton A, Russell J, Shaw P, Bayles R, Wang MH (2010) Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome. Proc Natl Acad Sci U S A 107:21611–21616

    CAS  PubMed  PubMed Central  Google Scholar 

  • Crofts N, Nakamura Y, Fujita N (2017) Critical and speculative review of the roles of multi-protein complexes in starch biosynthesis in cereals. Plant Sci 262:1–8

    CAS  PubMed  Google Scholar 

  • Cui F, Fan XL, Zhao CH, Zhang W, Chen M, Ji J, Li JM (2014) A novel genetic map of wheat: utility for mapping QTL for yield under different nitrogen treatments. BMC Genet 15:57

    PubMed  PubMed Central  Google Scholar 

  • Deng ZY, Hu SN, Chen F, Li WJ, Chen JS, Sun CL, Zhang YX, Wang SY, Song XJ, Tian JC (2015) Genetic dissection of interaction between wheat protein and starch using three mapping populations. Mol Breed 35:12

    Google Scholar 

  • Deng ZY, Cui Y, Han QD, Fang WQ, Li JF, Tian JC (2017) Discovery of consistent QTLs of wheat spike-related traits under nitrogen treatment at different development stages. Front Plant Sci 8:2120

    PubMed  PubMed Central  Google Scholar 

  • Deng ZY, Fang WQ, Guo X, Zhao XY, Guo H, Hu SN, Tian JC (2018) Genetic dissection of interactions between wheat flour starch and its components in two populations using two QTL mapping methods. Mol Breed 38:41

    Google Scholar 

  • Gupta PK, Mir RR, Mohan A, Kumar J (2008) Wheat genomics: present status and future prospects. Int J Plant Genom 2008:896451

    CAS  Google Scholar 

  • Huang XH, Zhao Y, Wei XH, Li CY, Wang AH, Zhao Q, Li WJ, Guo YL, Deng LW, Zhu CR, Fan DL, Lu YQ, Weng QJ, Liu KY, Zhou TY, Jing YF, Si LZ, Dong GJ, Huang T, Lu TT, Feng Q, Qian Q, Li JY, Han B (2011) Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet 44:32–39

    CAS  PubMed  Google Scholar 

  • Hurkman WJ, McCue KF, Altenbach S, Korn A, Tanaka CK, Kothari KM, Johnson EL, Bechtel DB, Wilson JD, Anderson OD, DuPont FM (2003) Effect of temperature on expression of genes encoding enzymes for starch biosynthesis in developing wheat endosperm. Plant Sci 164:873–881

    CAS  Google Scholar 

  • Jin YH, Zhang KL, Zhang XC, Du JH (2009) Determination of amylose and amylopectin in wheat and wheat malt by dual -wavelength spectrophotometry. J Chin Cereals Oils Assoc 24:137–140

    CAS  Google Scholar 

  • Li ZY, Chu XS, Mouille G, Yan LL, Kosar-Hashemi B, Hey S, Napier J, Shewry P, Clarke B, Appels R, Morell MK, Rahman S (1999) The localization and expression of the class ii starch synthases of wheat. Plant Physiol 120:1147–1155

    CAS  PubMed  PubMed Central  Google Scholar 

  • Li ZY, Sun F, Xu SM, Chu XS, Mukai Y, Yamamoto M, Ali S, Rampling L, Kosar-Hashemi B, Rahman S, Morell M (2003) The structural organization of the gene encoding class II starch synthase of wheat and barley and the evolution of the genes encoding starch synthases in plants. Funct Integr Genom 3:76–85

    CAS  Google Scholar 

  • Li WY, Yin YZ, Shi XQ, Yan SH, Wang ZL (2011) Comparison of starch composition and pasting properties between A and B type starch granule in wheat grain. Acta Agric Boreali Sin 26:136–139

    Google Scholar 

  • Li WY, Zhang B, Zhang JN, Cheng XP, Li RZ, Jing RL (2012) Exploring elite alleles for chlorophyll content of flag leaf in natural population of wheat by association analysis. Theor Appl Genet 38:962–970

    CAS  Google Scholar 

  • Li GQ, Bai GH, Carver BF, Elliott NC, Bennett RS, Wu YQ, Hunger R, Bonman JM, Xu XY (2017a) Genome-wide association study reveals genetic architecture of coleoptile length in wheat. Theor Appl Genet 130:391–401

    CAS  PubMed  Google Scholar 

  • Li JY, Rasheed A, Guo Q, Dong Y, Liu JD, Xia XC, Zhang Y, He ZH (2017b) Genome-wide association mapping of starch granule size distribution in common wheat. J Cereal Sci 77:211–218

    CAS  Google Scholar 

  • Liu JJ, He ZH, Zhao ZD, Pena RJ, Rajaram S (2003) Wheat quality and quality parameters of cooked dry white Chinese noodles. Euphytica 131:147–154

    CAS  Google Scholar 

  • Liu N, Xue YD, Guo ZY, Li WH, Tang JH (2016) Genome-wide association study identifies candidate genes for starch content regulation in maize kernels. Front Plant Sci 7:1046

    PubMed  PubMed Central  Google Scholar 

  • Martin C, Smith AM (1995) Starch biosynthesis. Plant Cell 7:971–985

    CAS  PubMed  PubMed Central  Google Scholar 

  • Martin JM, Talbert LE, Habernicht DK, Lanning SP, Sherman JD, Carlson G, Giroux MJ (2004) Reduced amylose effects on bread and white salted noodle quality. Cereal Chem 81:188–193

    CAS  Google Scholar 

  • Mccartney CA, Somers DJ, Lukow O, Ames N, Noll J, Cloutier S (2006) QTL analysis of quality traits in the spring wheat cross RL4452 × ‘AC Domain’. Plant Breed 125:565–575

    CAS  Google Scholar 

  • Mick E, McGough JJ, Middleton FA, Neale B, Faraone VS (2011) Genome-wide association study of blood pressure response to methylphenidate treatment of attention-deficit/hyperactivity disorder. Prog Neuro-Psychopharmacol Biol Psychiatry 35:466–472

    CAS  Google Scholar 

  • Murai J, Taira T, Ohta D (1999) Isolation and characterization of the three waxy genes granule-bound starch synthase in hexaploid wheat. Gene 234:71–79

    CAS  PubMed  Google Scholar 

  • Nakamura T, Yamamori M, Hirano H, Hidaka S (1993) Identification of three Wx proteins in wheat (Triticum aestivum L.). Biochem Genet 31:75–86

    CAS  PubMed  Google Scholar 

  • Nakamura Y, Ono M, Sawada T, Crofts N, Fujita N, Steup M (2017) Characterization of the functional interactions of plastidial starch phosphorylase and starch branching enzymes from rice endosperm during reserve starch biosynthesis. Plant Sci 2017:83–95

    Google Scholar 

  • Newell MA, Asoro FG, Scott MP, White PJ, Beavis WD, Jannink JL (2012) Genome-wide association study for oat (Avena sativa L.) beta-glucan concentration using germplasm of worldwide origin. Theor Appl Genet 125:1687–1696

    CAS  PubMed  Google Scholar 

  • Ovenden B, Milgate A, Wade LJ, Rebetzke GJ, Holland JB (2017) Genome-wide associations for water-soluble carbohydrate concentration and relative maturity in wheat using SNP and DArT marker arrays. G3 (Bethesda, Md) 7:2821–2830

    CAS  PubMed Central  Google Scholar 

  • Park SH, Wilson JD, Chung OK, Seib PA (2004) Size distribution and properties of wheat starch granules in relation to crumb grain score of pup-loaf bread. Cereal Chem 81:699–704

    CAS  Google Scholar 

  • Peterson DG, Fulcher RG (2001) Variation in Minnesota HRS wheat: starch granule size distribution. Food Res Int 34:357–363

    Google Scholar 

  • Risch N, Merikangas K (1996) The future of genetic studies of complex human diseases. Science 273:1516–1517

    CAS  PubMed  Google Scholar 

  • Sajjad M, Khan SH, Kazi AM (2012) The low down on association mapping in hexaploid wheat (Triticum aestivum L.). J Crop Sci Biotechnol 15:147–158

    Google Scholar 

  • Shu XL, Backes G, Rasmussen SK (2012) Genome-wide association study of resistant starch (RS) phenotypes in a barley variety collection. J Agric Food Chem 60:10302–10311

    CAS  PubMed  Google Scholar 

  • Song JM, Liu AF, Li HS, Dai S, Liu JJ, Zhao ZD, Liu GT (2008) Relationship between starch physiochemical properties of wheat grain and noodle quality. Sci Agric Sin 41:272–279

    CAS  Google Scholar 

  • Sukumaran S, Yu J (2014) Association mapping of genetic resources: achievements and future perspectives. In: Roberto T, Andreas G, Emile F (eds) Genomics of plant genetic resources. Springer, Netherlands, pp 207–235

    Google Scholar 

  • Sun HY, Lv JH, Fan YD, Zhao Y, Kong FM, Wang HG, Li SS (2008) QTL analysis of wheat protein and starch quality. Prog Nat Sci 5:505–513

    Google Scholar 

  • Tetlow IJ, Morell MK, Emes MJ (2004) Recent developments in understanding the regulation of starch metabolism in higher plants. J Exp Bot 55:2131–2145

    CAS  PubMed  Google Scholar 

  • Tian B, Deng ZY, Xie QF, Tian JC (2015) Genetic dissection of the developmental behaviour of total starch content and its components in wheat grain. Crop Pasture Sci 66:445–455

    CAS  Google Scholar 

  • Wang XZ, Li H, Gou HJ, Zhang L (1998) The relativity between processing characteristics of wheat and quality characteristics of steamed bread. J Chin Cereals Oils Assoc 6:6–8

    Google Scholar 

  • Wang SC, 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, 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 90000 single nucleotide polymorphism array. Plant Biotechnol J 12:787–796

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wilson LM, Whitt SR, Ibanez AM, Rocheford TR, Goodman MM, Buckler ES IV (2004) Dissection of maize kernel composition and starch production by candidate gene associations. Plant Cell 16:2719–2733

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yan SH, Wang ZL, Dai ZM, Li WY, Fu GZ, He MR, Yin YP (2007) Comparison of starch synthase activity and starch accumulation in two different wheat varieties with different amylose contents. Acta Agron Sin 33:84–89

    CAS  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Zhou ZM (2012) Effect of wheat starch on the quality of steamed bread. Farm Prod Process 3:7

    Google Scholar 

  • Zhu CS, Gore M, Buckler ES, Yu JM (2008) Status and prospects of association mapping in plants. Plant Genome 1:5–20

    CAS  Google Scholar 

Download references

Acknowledgements

We are grateful for grants from the Natural Science Foundation of China (No. 31871613), the key research and development plan of Shandong Province (2017GNC10102), the University of Science and Technology of Shandong Province (J17KA148), and the Shandong “Double Tops” Program.

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Author notes

  1. Xiaoying Chen and Wenqi Fang contributed equally to this work.

Authors and Affiliations

  1. State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai’an, 271000, Shandong, People’s Republic of China

    Xiaoying Chen, Wenqi Fang, Mengqi Ji, Shuai Xu, Yanxin Jiang, Shu Song, Jichun Tian & Zhiying Deng

  2. College of Ecology and Garden Architecture, Dezhou University, Dezhou, 253023, China

    Guangfeng Chen

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  1. Xiaoying Chen
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Contributions

ZD designed and revised this paper; XC wrote the manuscript; WF analysed the data; XC, SX, YJ and SS investigated the phenotypic data; GC constructed the map; and JT reviewed the manuscript. All authors have read and approved the paper.

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Correspondence to Zhiying Deng.

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Chen, X., Fang, W., Ji, M. et al. Genome-wide association study of total starch and its components in common wheat. Euphytica 215, 201 (2019). https://doi.org/10.1007/s10681-019-2517-z

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