QTL mapping for total grain anthocyanin content and 1 000-kernel weight in barley recombinant inbred lines population

YANG Xiao-Meng1,2 LI Xia1,2 PU Xiao-Ying1,2 DU Juan1,2 Muhammad Kazim Ali3 YANG Jia-Zhen1,2 ZENG Ya-Wen1,2 YANG Tao1,2

(1.Biotechnology and Germplasm Resources Institute, Yunnan Academy of Agricultural Sciences, Kunming, Yunnan, China 650205)
(2.Agricultural Biotechnology Key Laboratory of Yunnan Province, Kunming, Yunnan, China 650205)
(3.Department of Biotechnology, Fedural Urdu University of Arts, Science and Technology, Karachi 75300, Pakistan)
【Knowledge Link】anthocyanin

【Abstract】In this study, 193 recombinant inbred lines (RILs) derived from a cross between Ziguangmangluoerleng (purple barley, endemic to Yunnan, China) and Schooner (yellow barley introduced from Australia), grown at three sites in Yunnan Province of China for three consecutive years (2013–2015), were used to determine total grain anthocyanin content, 1 000-kernel weight and their correlations, and to map QTLs. There was a significantly negative correlation between total grain anthocyanin content and 1 000-kernel weight. Twelve QTLs for total grain anthocyanin content were located on chromosomes 1H, 2H, 4H, 6H, and 7H, which explained 5.06%–23.86% of phenotypic variation. Eight QTLs for 1 000-kernel weight were located on chromosomes 2H, 4H, and 7H, which explained 4.67%–42.32% of phenotypic variation. Ten and five QTLs explained ≥10% and ≥20% of phenotypic variation, respectively, and the highest phenotypic variation explained was 42.32%. In addition, two QTLs for total grain anthocyanin content were repeatedly detected at two sites for two years, which were located in the interval Bmag0125–GBM1309 on 2H and EBmatc0016–Bmag0206 on 7H, explaining 13.66%–17.76% and 13.07%–16.43% of the phenotypic variation, respectively. Two QTLs for 1 000-kernel weight were repeatedly detected at three sites for three years, which were located in the interval scssr03381–scssr07759 on 2H and GBM1297–GBM1303 on 7H , explaining 4.67%–14.55% and 34.51%–42.32% of phenotypic variation, respectively. The common major QTLs for the two agronomic traits were mainly distributed on chromosomes 2H and 7H. These results provide a basis for further fine mapping, cloning and marker-assisted breeding of beneficial genes related to total grain anthocyanin content and 1 000-kernel weight.

【Keywords】 barley RIL; total grain anthocyanin content; 1 000-kernel weight; correlation; QTL mapping;


【Funds】 Yunnan Applied Basic Research Projects of China (2017FD021) China Agriculture Research System (CARS-05-01A-04)

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(Translated by Guo Y)


    [1] Zhu F. Anthocyanins in cereals: composition and health effects. Food Res Internat, 2018, 109: 232–249.

    [2] Hua W, Zhu J H, Shang Y, Jia Q J, Wang J M, Yang J M. Research advances in colored barley. J Plant Genet Resour, 2013, 14: 1020–1024 (in Chinese with English abstract).

    [3] Ma LY, Sun Z H, Zeng Y W, Luo M C, Yang J Z. Molecular mechanism and health role of functional ingredients in blueberry for chronic disease in human beings. Internat J Mol Sci, 2018, 19: 1–19.

    [4] Khlestkina E. The adaptive role of flavonoids: emphasis on cereals. Cereal Res Commun, 2013, 41: 185–198.

    [5] Du L Q, Li R F. Nutritional value and development of black barley. Cereals Oils, 2001, (2): 40–41 (in Chinese with English abstract).

    [6] Martínez M, Motilva M J, de las Hazas M L, Romero M P, Vaculova K, Ludwig I A. Phytochemical composition and β-glucan content of barley genotypes from two different geographic origins for human health food production. Food Chem, 2018, 245: 61–70.

    [7] Deng G F, Xu X R, Zhang Y, Li D, Gan R Y, Li H B. Phenolic compounds and bioactivities of pigmented rice. Critic Rev Food Sci Nutr, 2013, 53: 296–306.

    [8] Cimino F, Ambra R, Canali R, Saija A, Virgili F. Effect of cyanidin-3-O-glucoside on UVB-Induced response in human keratinocytes. J Agric Food Chem, 2006, 54: 4041–4047.

    [9] Li J Y, Wang N, Chen S W, Wu Y Q, Wang R Y, Shen Z H, Mo F. Difference analysis and QTLs detection on three spike traits of different barley varieties (or strains). Mol Plant Breed, 2018, 16: 3973–3979 (in Chinese with English abstract).

    [10] Kim M J, Hyun J N, Kim J A, Park J C, Kim M Y, Kim J G, Lee SJ, Chun S C, Chung I M. Relationship between phenolic compounds, anthocyanins content and antioxidant activity in colored barley germplasm. J Agric Food Chem, 2007, 55: 4802–4809.

    [11] Mayler J I, Stanford E H. Color inheritance in barley. J Am Soc Agric, 1942, 34: 427–436.

    [12] Woodward R W, Thieret J W. A genetic study of complementary genes for purple lemma, palea and pericarp in barley (Hordeum vulgare L.). Agron J, 1953, 45: 182–185.

    [13] Choo T M, Vigier B, Ho K M, Ceccarelli S, Grando S, Franckowiak J D. Comparison of black, purple and yellow barleys. Genet Resour Crop Evol, 2005, 52: 121–126.

    [14] Finch R A, Simpson E. New colours and complementary colour genes in barley. Zeitschrift Fuer Pflanzenzuechtung, 1978, 81: 40–53.

    [15] Strygina K V, Börner A, Khlestkina E K. Identification and characterization of regulatory network components for anthocyanin synthesis in barley aleurone. BMC Plant Biol, 2017, 17: 109–117.

    [16] Lundqvist U, Franckowiak J D, Konishi T. New and revised descriptions of barley genes. Barley Genet Newslett, 1997, 26: 22–516.

    [17] Jia Q J, Zhu J H, Wang J M, Yang J M, Zhang G P. Genetic mapping and molecular marker development for the gene Pre2 controlling purple grains in barley. Euphytica, 2016, 208: 215–223.

    [18] Shoeva O Y, Mock H P, Kukoeva T V, Börner A, Khlestkina E K. Regulation of the flavonoid biosynthesis pathway genes in purple and black grains of hordeum vulgare. PLoS One, 2016, 11: 1–16.

    [19] Du H, Zhang Y, Xue M Y, Jing J J, Bai Z Y, Li C D. Difference and correlation analysis of grain traits in the near-isogenic line of plant height of barley. Acta Agric Boreali-Sin, 2015, 30 (5): 97–103 (in Chinese with English abstract).

    [20] Zhang X Y, Zhang Y J, Pan G F. Study on germplasm resource among different rowed barley. J Triticeae Crops, 2006, 26 (6): 39–41 (in Chinese with English abstract).

    [21] Li X H, Chang W S, Zhang C Y, Li B Y, Ma Z Y. The evaluation on growing stages and yield traits of seven introduced malting beer barley varieties. J Agric Univ Hebei, 2007, 30 (3): 22–25 (in Chinese with English abstract).

    [22] Lyu Y. QTL Analysis of Some Agronomic Traits in Qing-Tibetan Plateau Annual Wild Barley. MS Thesis of Huazhong Agricultural University, Wuhan, Hubei, China, 2007. pp 18–25 (in Chinese with English abstract).

    [23] Wang J L, Feng X B, Fu G, Hou W H, Wang G H, Dacizhuoga, Zhong Z M. Relationship between spatial distribution pattern and factors affecting weight per 1 000-seeds of cultivated barley in Qinghai-Tibet Plateau. Acta Ecol Sin, 2018, 38: 1114–1123 (in Chinese with English abstract).

    [24] Chen G D, Li H B, Zheng Z, Wei Y M, Zheng Y L, Mclntyre C L, Zhou M X, Liu C J. Characterization of a QTL affecting spike morphology on the long arm of chromosome 3H in barley (Hordeum vulgare L.) based on near isogenic lines and a NIL-derived population. Theor Appl Genet, 2012, 125: 1385–1392.

    [25] Hori K, Kobayashi T, Shimizu A, Sato K, Takeda K, Kawasaki S. Efficient construction of high-density linkage map and its application to QTL analysis in barley. Theor Appl Genet, 2003, 107: 806–813.

    [26] Baghizadeh A, Taleei A, Naghavi M. QTL analysis for some agronomic traits in barley (Hordeum vulgare L.). Internat J Agric Biol, 2007, 9: 372–374.

    [27] Wang J, Sun G, Ren X, Li C, Liu L, Wang Q, Du B, Sun D. QTL underlying some agronomic traits in barley detected by SNP markers. BMC Genet, 2016, 17: 1–13.

    [28] Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles E R, Qian Q, Kitano H, Matsuoka M. Cytokinin oxidase regulates rice grain production. Science, 2005, 309: 741–745.

    [29] Qin H N, Yan M, Wang Z H, Guo Y, Wang H, Sun H Y, Liu Z Z, Cai Y L. QTL mapping for anthocyanin and melanin contents in maize kernel. Acta Agron Sin, 2012, 38: 275–284 (in Chinese with English abstract).

    [30] Hosseinian F S, Li W, Beta T. Measurement of anthocyanins and other phytochemicals in purple wheat. Food Chem, 2008, 109: 916–924.

    [31] Zeng Y W, Du J, Yang X M, Pu X Y, Wang L X, Yang J Z, Du L J, Yang T, Yang S M, Sun Z H. Identification of quantitative trait loci for mineral elements in grains and grass powder of barley. Genet Mol Res, 2016, 15 (4): 1–13.

    [32] Li H H, Ribaut J M, Li Z L, Wang J K. Inclusive composite interval mapping (ICIM) for digenic epistasis of quantitative traits in biparental populations. Theor Appl Genet, 2008, 116: 243–260.

    [33] Wang J K. Inclusive composite interval mapping of quantitative trait genes. Acta Agron Sin, 2009, 35: 239–245 (in Chinese with English abstract).

    [34] Sun M M, Han L Z. Variation and correlation analyses of total anthocyanin content of brown rice (Oryza sativa) in F5 lines from japonica rice cross Longjin 1/Xiangruanmi 1578. J Plant Genet Resour, 2017, 18: 186–192 (in Chinese with English abstract).

    [35] Huang Y Y. QTL Identification Underlying Anthocyanin and Mineral Elements Content Related Traits in Rice. MS Thesis of Northeast Agricultural University, Harbin, Heilongjiang, China, 2013. pp 1–41 (in Chinese with English abstract).

    [36] Wang N, Wang J X, Xie W Y, Chen S W, Yang Y B, Wang L. Difference of the anthocyanin components and their contents of 25 local barley variety grains. J Yunnan Agric Univ, 2015, 30: 829–835 (in Chinese with English abstract).

    [37] Hu J K, Xie W Y, Chen S W, Wang N, Yang Y B, Wang L. The content difference of total flavonoids and anthocyanin from the grains of 25 local barley varieties. J Yunnan Agric Univ, 2015, 30: 522–527 (in Chinese with English abstract).

    [38] Zheng G Z. Effects of Blackish Purple Colored Seed Coat on Grain Quality and Yield Associated Characters in Rice (Oryza sativa L.). MS Thesis of Seoul University, Seoul, Republic of Korea, 2000. pp 1–41.

    [39] Chang H L. QTL Analysis of Anthocyanin and Proanthocyanidin Content and Research on Relationship between Yield Traits in Rice. MS Thesis of Northeast Agricultural University, Harbin, Heilongjiang, China, 2015. pp 1–55 (in Chinese with English abstract).

    [40] Du H, Ma T T, Hou X M, Zhang Y, Bai Z Y, Li C D. Difference and correlation analysis of agronomic and yield characters in twenty pairs near-isogenic line of plant height of barley. Acta Agric Boreali-Sin, 2016, 31 (5): 114–121 (in Chinese with English abstract).

    [41] Zhang Y, Si E J, Meng Y X, Ma X L, Li B C, Wang H J. Analysis on agronomic traits, grain protein content and population structure of barley germplasm from different geographical origins. J Triticeae Crops, 2015, 35: 940–947 (in Chinese with English abstract).

    [42] Bauer A M, Hoti F, Korff M V, Pillen K, Léon J, Sillanpä M J. Advanced backcross: QTL analysis in spring barley (H. vulgare ssp. spontaneum) comparing a REML versus a Bayesian model in multi-environmental field trials. Theor Appl Genet, 2009, 119: 105–123.

    [43] Lai Y, Jia J L, Wang J M, Ren L, Lyu Z Y, Zhu H Q, Ma H, Yang L N, Li Z R. Analysis of genetic diversity and association with agronomic traits in barley (Hordeum vulgare L.) introduced from abroad using SSR markers. J Triticeae Crops, 2017, 37: 197–204 (in Chinese with English abstract).

    [44] Marquez-Cedillo L A, Hayes P M, Kleinhofs A, Legge W G, Jones B L, Rossnagel B G, Sato K, Ullrich S E, Wesenberg D M. QTL analysis of agronomic traits in barley based on the doubled-haploid progeny of two elite North American varieties representing different germplasm groups. Theor Appl Genet, 2001, 103: 625–637.

    [45] Zhang X W, Jiang Q T, Wei Y M, Liu C. Inheritance analysis and mapping of quantitative trait loci (QTL) controlling individual anthocyanin compounds in purple barley (Hordeum vulgare L.) grains. PLoS One, 2017, 12 (8): e0183704.

    [46] Himi E, Taketa S. Isolation of candidate genes for the barley Ant1 and wheat Rc genes controlling anthocyanin pigmentation in different vegetative tissues. Mol Genet Genom, 2015, 290: 1287–1298.

    [47] Guan W W. QTL Analysis of Main Agronomic Traits and Inheritance of Isozymes Peroxidase, Esterase and Cytochrome Oxidase in Barley. MS Thesis of Huazhong Agricultural University, Wuhan, Hubei, China, 2011. pp 25–31 (in Chinese with English abstract).

    [48] Pillen K, Zacharias A, Léon J. Advanced backcross QTL analysis in barley (Hordeum vulgare L.). Theor Appl Genet, 2003, 107: 340–352.

    [49] Beheshtizadeh H, Fakheri B A, Aghnoum R, Mahdinezhad N, Pourdad S S, Masoudi B. QTL mapping of grain yield and its components under normal and drought stress conditions in barley (Hordeum vulgare L.). Ind J Genet, 2018, 78: 69–80.

    [50] Si E J, Zhang Y, Wang J C, Meng Y X, Li B C, Ma X L, Shang X W, Wang H J. Association analysis between SSR marker and agronomic traits in barley. Acta Agron Sin, 2015, 41: 1064–1072 (in Chinese with English abstract).

This Article



Vol 46, No. 01, Pages 52-61

January 2020


Article Outline



  • 1 Materials and methods
  • 2 Results
  • 3 Discussion
  • 4 Conclusion
  • References