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Identification of molecular markers for starch content in barley (Hordeum vulgare L.) by genome-wide association studies based on bulked samples

Published online by Cambridge University Press:  16 July 2020

Yinghu Zhang
Affiliation:
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
Haiye Luan
Affiliation:
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
Hui Zang
Affiliation:
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
Hongyan Yang
Affiliation:
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
Xiao Xu
Affiliation:
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
He Chen
Affiliation:
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
Hailong Qiao*
Affiliation:
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
Huiquan Shen*
Affiliation:
Jiangsu Coastal Area Institute of Agricultural Sciences, Kai fang North Avenue 9, Yancheng City, Jiangsu Province224002, People's Republic of China
*
*Corresponding authors. E-mail: jsycshq@163.com, hlqiao80@163.com
*Corresponding authors. E-mail: jsycshq@163.com, hlqiao80@163.com

Abstract

Starch content is an important trait in barley. To evaluate the genetic diversity and identify molecular markers of starch content in barley, 40 cultivated barley genotypes collected from different regions, including genotypes whose starch content is at either the high or low end of the spectrum (15), were used in this study. All the genotypes were re-sequenced by the double-digest-restriction associated DNA sequencing method, and a total of 299,103 single-nucleotide polymorphism (SNP) markers were obtained. The genotypes were divided into four sub-populations based on FASTSTRUCTURE, principal component analysis and neighbour-joining tree analysis. All four sub-populations had a high linkage disequilibrium, especially group 3, whose members were recently bred for malting in the Jiangsu coastal area. The starch content of the barley lines was evaluated during three growing seasons (2014–2017), and the average values of starch content across the three growing seasons at the low and high ends were 51.5 and 55.0%, respectively. The starch content was affected by population structure, the barley in group 2 had a low starch content, while the barley in group 4 had a high starch content. Twenty-six SNP markers were identified as being significantly associated with starch content (P ⩽ 0.001) based on the average values across the three growing seasons using the mixed linear model method. These SNP markers were located on chromosomes 1H and 4H, and were considered loci of qSC1-1 and qSC4-1, respectively. The major identified QTLs for starch content are helpful for further research on carbohydrates and for barley breeding.

Type
Research Article
Copyright
Copyright © NIAB 2020

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References

Abdel-Haleem, H, Bowman, J, Giroux, M, Kanazin, V, Talbert, H, Surber, L and Blake, T (2010) Quantitative trait loci of acid detergent fiber and grain chemical composition in hulled × hull-less barley population. Euphytica 172: 405418.CrossRefGoogle Scholar
Abdel-Haleem, H, Bowman, JGP, Surber, L and Blake, T (2012) Variation in feed quality traits for beef cattle in Steptoe × Morex barley population. Molecular Breeding 29: 503514.CrossRefGoogle Scholar
Amezrou, R, Gyawali, S, Belqadi, L, Chao, S, Arbaoui, M, Mamidi, S, Rehman, S, Sreedasyam, A and Verma, RPS (2018) Molecular and phenotypic diversity of ICARDA spring barley (Hordeum vulgare L.) collection. Genetic Resources and Crop Evolution 65: 255269.CrossRefGoogle Scholar
Andrews, KR, Good, JM, Miller, MR, Luikart, G and Hohenlohe, PA (2016) Harnessing the power of RADseq for ecological and evolutionary genomics. Nature Reviews Genetics 17: 8192.CrossRefGoogle ScholarPubMed
Badr, A, Muller, K, Sch, R, Rabey, HE, Effgen, S, Ibrahim, HH, Pozzi, C, Rohde, W and Salamini, F (2000) On the origin and domestication history of barley (Hordeum vulgare). Molecular Biology and Evolution 17: 499510.CrossRefGoogle Scholar
Barrett, JC, Fry, B, Maller, JB and Daly, MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics (Oxford, England) 21: 263265.CrossRefGoogle ScholarPubMed
Bengtsson, T, Manninen, O, Jahoor, A and Orabi, J (2017) Genetic diversity, population structure and linkage disequilibrium in Nordic spring barley (Hordeum vulgare L. subsp. vulgare). Genetic Resources and Crop Evolution 64: 20212033.CrossRefGoogle Scholar
Bowman, JGP, Blake, T, Surber, L, Habernicht, DK and Bockelman, HE (2001) Feed-quality variation in the barley core collection of the USDA National Small Grains Collection. Crop Science 41: 863870.CrossRefGoogle Scholar
Bradbury, PJ, Zhang, Z, Kroon, DE, Casstevens, TM, Ramdoss, Y and Buckler, ES (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics (Oxford, England) 23: 26332635.CrossRefGoogle ScholarPubMed
Cheng, Z, Wang, P and Xu, Y (2016) Bulked sample analysis in genetics, genomics and crop improvement. Plant Biotechnology Journal 14: 19411955.Google Scholar
DePristo, MA, Banks, E, Poplin, RE, Garimella, KV, Maguire, JR, Hartl, C, Philippakis, AA, del Angel, G, Rivas, MA, Hanna, M, McKenna, A, Fennell, TJ, Kernytsky, AM, Sivachenko, AY, Cibulskis, K, Gabriel, SB, Altshuler, D and Daly, MJ (2011) A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics 43: 491498.CrossRefGoogle ScholarPubMed
De Wouw, MV, Kik, C, Van Hintum, T, Van Treuren, R and Visser, B (2010) Genetic erosion in crops: concept, research results and challenges. Plant Genetic Resources 8: 115.CrossRefGoogle Scholar
Du, H, Zhu, J, Su, H, Huang, M, Wang, H, Ding, S, Zhang, B, Luo, A, Wei, S, Tian, X and Xu, Y (2017) Bulked segregant RNA-seq reveals differential expression and SNPs of candidate genes associated with waterlogging tolerance in maize. Frontiers in Plant Science 8: 1022.CrossRefGoogle ScholarPubMed
Elakhdar, A, Kumamaru, T, Qualset, CO, Brueggeman, RS, Amer, K and Capochichi, LJA (2018) Assessment of genetic diversity in Egyptian barley (Hordeum vulgare L.) genotypes using SSR and SNP markers. Genetic Resources and Crop Evolution 65: 19371951.CrossRefGoogle Scholar
Ganal, MW, Altmann, T and Roder, MS (2009) SNP Identification in crop plants. Current Opinion in Plant Biology 12: 211217.CrossRefGoogle ScholarPubMed
Haseneyer, G, Stracke, S, Paul, C, Einfeldt, C, Broda, A, Piepho, HP, Graner, A and Geiger, HH (2010) Population structure and phenotypic variation of a spring barley world collection set up for association studies. Plant Breeding 129: 271279.CrossRefGoogle Scholar
Kesawat, MS and Kumar, BD (2009) Molecular markers: it's application in crop improvement. Journal of Crop Science and Biotechnology 12: 169181.CrossRefGoogle Scholar
Kumar, S, Banks, TW and Cloutier, S (2012) SNP discovery through next-generation sequencing and its applications. International Journal of Plant Genomics 2012: 831460831460.CrossRefGoogle ScholarPubMed
Li, H and Durbin, R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics (Oxford, England) 25: 17541760.10.1093/bioinformatics/btp324CrossRefGoogle ScholarPubMed
Li, H, Handsaker, B, Wysoker, A, Fennell, T, Ruan, J, Homer, N, Marth, GT, Abecasis, GR and Durbin, R (2009) The sequence alignment/map format and SAMtools. Bioinformatics (Oxford, England) 25: 20782079.CrossRefGoogle ScholarPubMed
Malysheva-Otto, LV, Ganal, MW and Roder, MS (2006) Analysis of molecular diversity, population structure and linkage disequilibrium in a worldwide survey of cultivated barley germplasm (Hordeum vulgare L.). BMC Genetics 7: 6.CrossRefGoogle Scholar
Mascher, M, Gundlach, H, Himmelbach, A, Beier, S, Twardziok, SO, Wicker, T, Radchuk, V, Dockter, C, Hedley, PE, Russell, J, Bayer, M, Ramsay, L, Liu, H, Haberer, G, Zhang, X, Zhang, Q, Barrero, RA, Li, L, Taudien, S, Groth, M, Felder, M, Hastie, A, Šimková, H, Staňková, H, Vrána, J, Chan, S, Muñoz-Amatriaín, M, Ounit, R, Wanamaker, S, Bolser, D, Colmsee, C, Schmutzer, T, Aliyeva-Schnorr, L, Grasso, S, Tanskanen, J, Chailyan, A, Sampath, D, Heavens, D, Clissold, L, Cao, S, Chapman, B, Dai, F, Han, Y, Li, H, Li, X, Lin, C, McCooke, JK, Tan, C, Wang, P, Wang, S, Yin, S, Zhou, G, Poland, JA, Bellgard, MI, Borisjuk, L, Houben, A, Doležel, J, Ayling, S, Lonardi, S, Kersey, P, Langridge, P, Muehlbauer, GJ, Clark, MD, Caccamo, M, Schulman, AH, Mayer, KFX, Platzer, M, Close, TJ, Scholz, U, Hansson, M, Zhang, G, Braumann, I, Spannagl, M, Li, C, Waugh, R and Stein, N (2017) A chromosome conformation capture ordered sequence of the barley genome. Nature 544: 427433.CrossRefGoogle ScholarPubMed
Milner, SG, Jost, M, Taketa, S, Mazón, ER, Himmelbach, A, Oppermann, M, Weise, S, Knüpffer, H, Basterrechea, M, König, P, Schüler, D, Sharma, R, Pasam, RK, Rutten, T, Guo, G, Xu, D, Zhang, J, Herren, G, Müller, T, Krattinger, SG, Keller, B, Jiang, Y, González, MY, Zhao, Y, Habekuß, A, Färber, S, Ordon, F, Lange, M, Börner, A, Graner, A, Reif, JC, Scholz, U, Mascher, M and Stein, N (2019) Genebank genomics highlights the diversity of a global barley collection. Nature Genetics 51: 319326.CrossRefGoogle ScholarPubMed
Munozamatriain, M, Cuestamarcos, A, Endelman, JB, Comadran, J, Bonman, JM, Bockelman, HE, Chao, S, Russell, J, Waugh, R, Hayes, PM and Muehlbauer, GJ (2014) The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS ONE 9: 4.Google Scholar
Newman, CW and Newman, RK (2006) A brief history of barley foods. Cereal Foods World 51: 47.Google Scholar
Ordon, F, Ahlemeyer, J, Werner, K, Kohler, W and Friedt, W (2005) Molecular assessment of genetic diversity in winter barley and its use in breeding. Euphytica 146: 2128.CrossRefGoogle Scholar
Pankin, A, Altmuller, J, Becker, C and Von Korff, M (2018) Targeted resequencing reveals genomic signatures of barley domestication. New Phytologist 218: 12471259.CrossRefGoogle ScholarPubMed
Pasam, RK, Sharma, R, Malosetti, M, Van Eeuwijk, FA, Haseneyer, G, Kilian, B and Graner, A (2012) Genome-wide association studies for agronomical traits in a world wide spring barley collection. BMC Plant Biology 12: 16.10.1186/1471-2229-12-16CrossRefGoogle Scholar
Peterson, BK, Weber, JN, Kay, EH, Fisher, HS and Hoekstra, HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS ONE 7: 5.CrossRefGoogle Scholar
Qi, J, Chen, J, Wang, J, Wu, F, Cao, L and Zhang, G (2005) Protein and hordein fraction content in barley seeds as affected by sowing date and their relations to malting quality. Journal of Zhejiang University Science B 6: 10691075.10.1631/jzus.2005.B1069CrossRefGoogle ScholarPubMed
Raj, A, Stephens, M and Pritchard, JK (2014) fastSTRUCTURE: variational inference of population structure in large SNP data sets. Genetics 197: 573589.CrossRefGoogle ScholarPubMed
Shu, X and Rasmussen, SRK (2014) Quantification of amylose, amylopectin, and β-glucan in search for genes controlling the three major quality traits in barley by genome-wide association studies. Frontiers in Plant Science 5: 197197.CrossRefGoogle ScholarPubMed
Usubaliev, B, Brantestam, AK, Salomon, B, Garkavagustavson, L and Von Bothmer, R (2013) Genetic diversity in farmer grown spring barley material from Kyrgyzstan. Genetic Resources and Crop Evolution 60: 18431858.CrossRefGoogle Scholar
Wang, K, Li, M and Hakonarson, H (2010) ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research 38: e164.CrossRefGoogle ScholarPubMed
Watterson, GA (1975) On the number of segregating sites in genetical models without recombination. Theoretical Population Biology 7: 256276.CrossRefGoogle ScholarPubMed
Wu, K, Yao, X, Yao, Y, Chi, D and Feng, Z (2017) Analysis of the relationship between Wx gene polymorphisms and amylose content in Hulless Barley. Czech Journal of Genetics and Plant Breeding 53: 144152.10.17221/105/2016-CJGPBCrossRefGoogle Scholar
Zeng, X, Guo, Y, Xu, Q, Mascher, M, Guo, G, Li, SC, Mao, L, Liu, Q, Xia, Z, Zhou, J, Yuan, H, Tai, S, Wang, Y, Wei, Z, Song, L, Zha, S, Li, S, Tang, Y, Bai, L, Zhuang, Z, He, W, Zhao, S, Fang, X, Gao, Q, Yin, Y, Wang, J, Yang, H, Zhang, J, Henry, RJ, Stein, N and Tashi, N (2018) Origin and evolution of qingke barley in Tibet. Nature Communications 9: 5433.10.1038/s41467-018-07920-5CrossRefGoogle ScholarPubMed
Zhang, Z, Ersoz, ES, Lai, C, Todhunter, RJ, Tiwari, HK, Gore, MA, Bradbury, PJ, Yu, J, Arnett, DK, Ordovas, JM and Buckler, ES (2010) Mixed linear model approach adapted for genome-wide association studies. Nature Genetics 42: 355360.CrossRefGoogle ScholarPubMed
Zhu, F (2017) Barley starch: composition, structure, properties, and modifications. Comprehensive Reviews in Food Science and Food Safety 16: 558579.CrossRefGoogle ScholarPubMed
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