Skip to main content


Log in

Genetic and epistatic effects for grain quality and yield of three grain-size QTLs identified in brewing rice (Oryza sativa L.).

  • Published:
Molecular Breeding Aims and scope Submit manuscript


Rice (Oryza sativa L.) in Japan is not only a food staple but also an important material for the Japanese alcoholic beverage, sake. The grain used in sake brewing has different characters from the cooking rice grain, including a large grain size and high white-core expression rate (WCE). Because large-sized grains often have a heavy grain weight and higher yield, this trait is also important for cooking rice. Chalky grains, such as white-core or white-belly grains, are not ideal as cooking rice. Here, we report that three grain-size quantitative trait loci (QTLs; qGL4-2, qGWh5, qGWh10), derived from the brewing cultivar, Yamadanishiki, affect grain shape, chalky grain rate, and yield, using near isogenic and pyramiding lines in the genetic background of the cooking cultivar, Koshihikari. First, these QTLs influenced multiple components of grain shape, where epistatic effects were detected between qGL4-2 and qGWh5, for grain width and thickness, and between qGL4-2 and qGWh10, for grain length. Therefore, these QTLs may coordinate to control grain shape. Second, lines harboring qGWh5 or qGWh10 at the Yamadanishiki allele exhibited increased WCE, whereas lines with qGL4-2 and qGWh10 exhibited decreased white-belly grain rate (WBR). Thus, grain shape is associated with the occurrence of chalky grain, where the chalky type depends on the QTL. Finally, we used total panicle weight of plants as a simplified rice yield index, and a promising line pyramiding qGL4-2 and qGWh5 emerged. In conclusion, qGL4-2 would be useful for the breeding of cooking rice, to decrease WBR, while qGWh5 and qGWh10 were definitely more beneficial for that of brewing rice, to increase grain weight and WCE.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1

Similar content being viewed by others



Analyses of variance


Basal-white grain rate


Days to heading


Grain length


Grain thickness


Grain width


Milky white grain rate


Near isogenic line


Panicle number


Pyramiding line


Quantitative trait locus


Spikelet number per panicle


1000-grain weight


Total panicle weight per plant


White-core expression rate


White-belly grain rate


  • Aramaki I, Ogawa K, Yamamoto K, Suzuki J, Kanno M, Kizaki Y, Okazaki N (1995) Polishing properties of white-core and non-white-core grains fractionated from the same variety of rice. Seibutsu-kogaku 73:381–386

    CAS  Google Scholar 

  • Chen L, Gao W, Chen S, Wang L, Zou J, Liu Y, Wang H, Chen Z, Guo T (2016) High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice. Rice 9:48

    Article  PubMed  PubMed Central  Google Scholar 

  • Dang X, Thi TGT, Edzesi WM, Liang L, Liu Q, Liu E, Wang Y, Qiang S, Liu L, Hong D (2015) Population genetic structure of Oryza sativa in east and Southeast Asia and the discovery of elite alleles for grain traits. Sci Rep 5:11254

    Article  PubMed  PubMed Central  Google Scholar 

  • De-yong M, Yu-jun Z, Yong-hong YU, Ye-yang F, De-run H, Jie-yun Z (2013) Quantitative trait loci for grain chalkiness and endosperm transparency detected in three recombinant inbred line populations of indica rice. J Integr Agric 12:1–11

    Article  Google Scholar 

  • Duan P, Rao Y, Zeng D, Yang Y, Xu R, Zhang B, Dong G, Qian Q, Li Y (2014) SMALL GRAIN 1, which encodes a mitogen-activated protein kinase kinase 4, influences grain size in rice. Plant J 77:547–557

    Article  PubMed  Google Scholar 

  • Fan Y, Li Y (2019) Molecular, cellular and yin-Yang regulation of grain size and number in rice. Mol Breed 39:163

    Article  Google Scholar 

  • Fang N, Xu R, Huang L, Zhang B, Duan P, Li N, Luo Y, Li Y (2016) SMALL GRAIN 11 controls grian size, grain number and grain yield in rice. Rice 9(64)

  • Fitzgerald MA, McCouch SR, Hall RD (2009) Not just a grain of rice: the quest for quality. Trends Plant Sci 14:133–139

    Article  PubMed  Google Scholar 

  • Gong J, Miao J, Zhao Y, Zhao Q, Feng Q, Zhan Q, Cheng B, Zia J, Huang X, Yang S, Han B (2017) Dissecting the genetic basis of grain shape and chalkiness traits in hybrid rice using multiple collaborative populations. Mol Plant 10:1353–1356

    Article  PubMed  Google Scholar 

  • Guo T, Chen K, Dong NQ, Shi CL, Ye WW, Gao JP, Shan JX, Lin HX (2018) GRAIN SIZE AND NUMBER1 negatively regulates the OsMKKK10-OsMKK4-OsMPK6 cascade to coordinate the trade-off between grain NUMBER per panicle and grain size in rice. Plant Cell 30:871–888

    Article  PubMed  PubMed Central  Google Scholar 

  • He P, Li SG, Qian Q, Ma YQ, Li JZ, Wang WM, Chen Y, Zhu LH (1999) Genetic analysis of rice grain quality. Theor Appl Genet 98:502–508

    Article  Google Scholar 

  • Horigane AK, Suzuki K, Yoshida M (2014) Moisture distribution in rice grains used for sake brewing analyzed by magnetic resonance imaging. J Cereal Sci 60:193–201

    Article  Google Scholar 

  • Hu J, Wang Y, Fang Y, Zeng L, Xu J, Yu H, Shi Z, Pan J, Zhang D, Kang S, Zhu L, Dong G, Guo L, Zeng D, Zhang G, Xie L, Xiong G, Li J, Qian Q (2015) A rare allele of GS2 enhances grain size and grain yield in rice. Mol Plant 8:1455–1465

    Article  PubMed  Google Scholar 

  • Hu Z, Lu SJ, Wang MJ, Hr H, Sun L, Wang H, Liu XH, Jiang L, Sun JL, Xin X, Kong W, Chu C, Xue HW, Yang J, Luo X, Liu JX (2018) A novel QTL qTGW3 encodes the GSK3/SHAGGY-like kinase OsGSK5/OsSK41 that interacts with OsARF4 to negatively regulate grain size and weight in rice. Mol Plant 11:736–749

    Article  PubMed  Google Scholar 

  • Huang N, Parco A, Mew T, Magpantay G, McCouch S, Guiderdoni E, Xu J, Subudhi P, Angeles ER, Khush GS (1997) RFLP mapping of isozymes, RAPD and QTLs for grain shape, brown planthopper resistance in a doubled haploid rice population. Mol Breed 3:105–113

    Article  Google Scholar 

  • Huang R, Jiang L, Zheng J, Wang T, Wang H, Huang Y, Hong Z (2013) Genetic bases of rice grain shape: so many genes, so little known. Trends Plant Sci 18:218–226

    Article  PubMed  Google Scholar 

  • Ishii K, Oba K, Maruyama A, Katano M (2008) Effect of high temperature at grain filling period in TGC on grain texture of brewers’ rice “Yamada-nishiki”. Rep Kyushu Br Crop Sci Soc Japan 74:24–26

    Google Scholar 

  • Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, Onodera H, Kashiwagi T, Ujiie K, Shimizu B, Onichi A, Miyagawa H, Katoh E (2013) Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield. Nat Genet 45:707–711

    Article  PubMed  Google Scholar 

  • Li N, Li Y (2016) Signaling pathways of seed size control in plants. Cur Opin Plany Bio 33:23–32

    Article  Google Scholar 

  • Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, Li X, Xiao J, He Y, Zhang Q (2011) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43:1266–1269

    Article  PubMed  Google Scholar 

  • Li N, Xu R, Duan P, Li Y (2018) Control of grain size in rice. Plant Reproduction 31:237–251

    Article  PubMed  Google Scholar 

  • Liu X, Wang Y, Wang SW (2012) QTL analysis of percentage of grains with chalkiness in Japonica rice (Oryza sativa). Genet Mol Res 11:717–724

    Article  PubMed  Google Scholar 

  • Liu S, Hua L, Dong S, Chen H, Zhu X, Jiang J, Zhang F, Li Y, Fang X, Chen F (2015) OsMAPK6, a mitogen-activated protein kinase, influences rice grain size and biomass production. Plant J 84:672–681

    Article  PubMed  Google Scholar 

  • Lu B, Yang C, Xie K, Zhang L, Wu T, Li L, Liu X, Jiang L, Wan J (2013) Quantitative trait loci for grain-quality traits across a rice F2 population and backcross inbred lines. Euphytica 192:25–35

    Article  Google Scholar 

  • Mackay TFC (2014) Epistasis and quantitative traits: using model organisms to study gene-gene interactions. Nat Rev Genet 15:22–33

    Article  PubMed  Google Scholar 

  • Morita S (2000) Effects of high air temperature on ripening in rice plants. Jpn J Crop Sci 69:391–399

    Article  Google Scholar 

  • Nagata K, Ando T, Nonoue Y, Mizubayashi T, Kirazawa N, Shomura A, Matsubara K, Ono N, Mizobuchi R, Shibaya T, Ogiso-Tanaka E, Hori K, Yano M, Fukuoka S (2015) Advanced backcross QTL analysis reveals complicated genetic control of rice grain shape in a japonica × indica cross. Breed Sci 65:308–318

    Article  PubMed  PubMed Central  Google Scholar 

  • Nagato K, Ebata M (1959) Studies on white-core rice kernel. II. On the physical properties of the kernel. Jpn J Crop Sci 28:46–50

    Article  Google Scholar 

  • Nagato K, Ebata M (1965) Effects of high temperature during ripening period on the development and the quality of rice kernels. Jpn J Crop Sci

  • Nelson JC, McClung AM, Fjellstrom RG, Moldenhauer KAK, Boza E, Jodari F, Oard JH, Linscombe S, Scheffler BE, Yeater KM (2011) Mapping QTL main and interaction influences on milling quality in elite US rice germplasm. Theor Appl Genet 122:291–309

    Article  PubMed  Google Scholar 

  • Okada S, Yamasaki M (2019) Validation of a quantitative trait locus for the white-core expression rate of grain on chromosome 6 in a brewing rice cultivar and development of DNA markers for marker-assisted selection. Breed Sci 69:401–409

    Article  PubMed  PubMed Central  Google Scholar 

  • Okada S, Suehiro M, Ebana K, Hori K, Onogi A, Iwata H, Yamasaki M (2017) Genetic dissection of grain traits in Yamadanishiki, an excellent sake-brewing rice cultivar. Theor Appl Genet 130:2567–2585

    Article  PubMed  Google Scholar 

  • Okada S, Onogi A, Iijima K, hori K, Iwata H, Yokoyama W, Suehiro M, Yamasaki M (2018a) Identification of QTLs for grain size using a novel set of chromosomal segment substitution lines derived from Yamadanishiki in the genetic background of Koshihikari. Breed Sci 68:210–218

    Article  PubMed  Google Scholar 

  • Okada S, Sasaki M, Yamasaki M (2018b) A novel rice QTL qOPW11 associated with panicle weight affects panicle and plant architecture. Rice 11:53

    Article  PubMed  PubMed Central  Google Scholar 

  • Peng B, Wang L, Fan C, Jiang G, Luo L, Li Y, He Y (2014) Comparative mapping of chalkiness components in rice using five populations across two environments. BMC Genet 15:49

    Article  PubMed  PubMed Central  Google Scholar 

  • Qiu X, Chen K, Lv W, Ou X, Zhu Y, Xing D, Yang L, Fan F, Yang J, Xu J, Zheng T, Li Z (2017) Examining two sets introgression lines reveals background-independent and stably expressed QTL that improve grain appearance quality in rice (Oryza sativa L.). Theor Appl Genet 130:951–967

    Article  PubMed  PubMed Central  Google Scholar 

  • R Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna URL

    Google Scholar 

  • Redona ED, Mackill DJ (1998) Quantitative trait locus analysis for rice panicle and grian characteristics. Theor Appl Genet 96:957–963

    Article  Google Scholar 

  • Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M (2008) Deletion in a gene associated with grain size increased yield during rice domestication. Nat Genet 40:1023–1028

    Article  PubMed  Google Scholar 

  • Si L, Chen J, Huang X, Gong H, Luo J, Hou Q, Zhou T, Lu T, Zhu J, Shangguan Y, Chen E, Gong C, Zhao Q, Jing Y, Zhao Y, Li Y, Cui L, Fan D, Lu Y, Weng Q, Wang Y, Zhan Q, Liu K, Wei X, An K, An G, Han B (2016) OsSPL13 controls grain size in cultivated rice. Nat Genet 48:447–456

    Article  PubMed  Google Scholar 

  • Song XJ, Huang W, Shi M, Zhu MZ, Lin HX (2007) A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nat Genet 39:623–630

    Article  PubMed  Google Scholar 

  • Sun Z, Zhu Y, Chen J, Zhang H, Zhang Z, Niu X, Fan Y, Zhuang J (2018) Minor-effect QTL for heading date detected in crosses between indica rice cultivar Teqing and near isogenic lines of IR24. The Crop J 6:291–298

    Article  Google Scholar 

  • Tan YF, Xing YZ, Li JX, Yu SB, Xu CG, Zhang Q (2000) Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid. Theor Appl Genet 101:823–829

    Article  Google Scholar 

  • Tanabata T, Shibaya T, Hori K, Ebana K, Yano M (2012) SmartGrain: high-throughput phenotyping software for measuring seed shape through image analysis. Plant Physiol 160:1871–1880

    Article  PubMed  PubMed Central  Google Scholar 

  • Tsukaguchi T, Yamamura T, Inoue H, Nakagawa H, Murakami K, Kita E (2012) The response of the occurrence of milky white kernels with different cross-sectional patterns of chalkiness in the endosperm to grain-filling temperature and to assimilate supply in Koshihikari. Jpn J Crop Sci 81:267–274

    Article  Google Scholar 

  • Wada H, Matsumoto-Kubo C, Gholipour Y, Nonami H, Tanaka F, Erra-Balsells R, Tsutsumi K, Hiraoka K, Morita S (2014) Rice chalky ring formation caused by temporal reduction in starch biosynthesis during osmotic adjustment under foehn-induced dry wind. PLoS One 9:e110374

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang S, Wu K, Tuan Q, Liu X, Liu Z, Lin X, Zeng R, Zhu H, Dong G, Qian Q, Zhang G, Fu X (2012) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44:950–954

    Article  PubMed  Google Scholar 

  • Wang S, Li S, Liu Q, Wu K, Zhang J, Wang S, Wang Y, Chen X, Zhang Y, Gao C, Wang F, Huang H, Fu X (2015a) The OsSPL16-GW7 regulatory module determines grain shape and simultaneously improves rice yield and grain quality. Nat Genet 47:949–954

    Article  PubMed  Google Scholar 

  • Wang Y, Xiong G, Hu J, Jiang L, Yu H, Xu J, Fang Y, Zeng L, Xu J, Ye W, Meng X, Liu R, Chen H, jing Y, Wang Y, Zhu X, Li J, Qian Q (2015b) Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet 47:944–948

    Article  PubMed  Google Scholar 

  • Wang X, Pang Y, Wang C, Chen K, Zhu Y, Shen C, Ali J, Xu J, Li Z (2017) New candidate genes affecting rice grain appearance and milling quality detected by genome-wide and gene-based association analyses. Front Plant Sci 7:1998

    PubMed  PubMed Central  Google Scholar 

  • Weng J, Gu S, Wan X, Gao H, Guo T, Su N, Lei C, Zhang X, Cheng Z, Guo X, Wang J, Jiang L, Zhai H, Wan J (2008) Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight. Cell Res 18:1199–1209

    Article  PubMed  Google Scholar 

  • Yanagiuchi T, Yamamoto H, Miyazaki N, Nagano T, Mizuma T, Wakai Y (1997) Influence of grain type on suitability of rice for sake brewing. Seibutsu-kogaku 75:169–176

    CAS  Google Scholar 

  • Yoshida S, Ikegami M, Kuze J, Sawada K, Hashimoto Z, Ishii T, Nakamura C, Kamijima O (2002) QTL analysis for plant and grain characters of Sake-brewing rice using a doubled haploid population. Breed Sci 52:309–317

    Article  Google Scholar 

  • Yun P, Zhu Y, Wu B, Gao G, Sun P, Zhang Q, He Y (2016) Genetic mapping and confirmation of quantitative trait loci for grain chalkiness in rice. Mol Breed 36:162

    Article  Google Scholar 

  • Zeng Y, Ji Z, Wen Z, Liang Y, Yang C (2016) Combination of eight alleles at four quantitative trait loci determines grain length in rice. PLoS One 11:e0150832

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhao X, Daygon VD, Mcnally KL, Hamilton RS, Xie F, Reinke RF, Fitzgerald MA (2016) Identification of stable QTLs causing chalk in rice grains in nine environments. Theor Appl Genet 129:141–153

    Article  PubMed  Google Scholar 

  • Zhao DS, Li QF, Zhang CQ, Zhang C, Yang QQ, Pan LX, Ren XY, Lu J, Gu MH, Liu QQ (2018) GS9 acts as a transcriptional activator to regulate rice grain shape and appearance quality. Nat Commun 9:1240

    Article  PubMed  PubMed Central  Google Scholar 

  • Zhen W, Jun-yu C, Yu-jun Z, Ye-yang F, Jie-yun Z (2017) Validation of qGS10, a quantitative trait locus for grain size on the long arm of chromosome 10 in rice (Oryza sativa L.). J Integr Agric 16:16–26

    Article  Google Scholar 

  • Zheng L, Zhang W, Liu S, Chen L, Liu X, Chen X, Ma J, Chen W, Zhao Z, Jiang L, Wan J (2012) Genetic relationship between grain chalkiness, protein content, and paste viscosity properties in a backcross inbred population of rice. J Cereal Sci 56:153–160

    Article  Google Scholar 

  • Zhu H, Li Y, Liang J, Luan X, Xu P, Wang S, Zhang G, Liu G (2018) Analysis of QTLs on heading date based on single segment substitution lines in rice (Oryza sativa L.). Sci Rep 8:13232

    Article  PubMed  PubMed Central  Google Scholar 

Download references


We would like to thank Miki Suehiro and Wakana Yokoyama for their help with sampling.


This work was supported by JSPS KAKENHI Grant Number 17J01082 and the Japan Science and Technology Agency (JST) CREST Grant Number JPMJCR17O3.

Author information

Authors and Affiliations



SO and MY designed experiments; SO, KI, and KH performed genotyping; SO conducted phenotyping and data analysis; and SO and MY wrote the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Masanori Yamasaki.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material


(PPTX 2368 kb)


(XLSX 10 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Okada, S., Iijima, K., Hori, K. et al. Genetic and epistatic effects for grain quality and yield of three grain-size QTLs identified in brewing rice (Oryza sativa L.).. Mol Breeding 40, 88 (2020).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: