Temperature-dependent QTLs in indica alleles for improving grain quality in rice: increased prominence of QTLs responsible for reduced chalkiness under high-temperature conditions
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Quantitative trait loci (QTLs) for the apparent quality of brown rice under high temperatures during ripening were analyzed using chromosomal segment substitution lines. Segments from the indica cultivar Habataki were substituted into a japonica cultivar with a Sasanishiki background. We found the following two QTLs for increasing grain quality in the Habataki allele on chromosome 3: (1) qTW3-2, located near the marker RM14702, decreased the percentage of total white immature (TWI) grains, and (2) qRG3-2, located near RM3766, increased the percentage of regular grains. The effects of these two QTLs were more obvious under high-temperature ripening conditions; hence, these loci are considered QTLs not only for reducing TWI grains but also for increasing high-temperature tolerance. Additionally, we found two QTLs, i.e., qTW3-1 and qRG3-1, responsible for reduced grain quality near RM14314 on chromosome 3. Although the QTL for narrow grains in the Habataki allele qNG3 was genetically linked to qTW3-2, the effect was only slightly significant, and the length/width ratio of qNG3-carrying grains was within the range observed in widely grown japonica cultivars. Incorporating the Habataki region, including qRG3-2 and qTW3-2 but not qTW3-1 and qRG3-1, in addition to previously reported grain quality QTLs in breeding japonica cultivars will improve high-temperature tolerance and grain quality.
KeywordsHigh-temperature tolerance QTL Grain quality Rice (Oryza sativa L.)
We are grateful to Mr. Tokuya Genba, Mr. Hiroyuki Nakagawa, Mr. Tuyoshi Kotake, Mr. Masanori Ichihashi, Mr. Shinobu Yuminamochi, Mr. Koushi Yazaki, Mr. Susumu Saitou, Mr. Ken-ichi Koide, Ms. Keiko Nozaki, Ms. Setsuko Hayashi, and Ms. Kiiko Takatsuto for their excellent technical assistance.
This study was supported by Japan Society for the Promotion of Science KAKENHI grants 24580030 and 15K0280.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflicts of interest.
- Ando T, Yamamoto T, Shimizu T, Ma XF, Shomura A, Takeuchi Y, Lin SY, Yano M (2008) Genetic dissection and pyramiding of quantitative traits for panicle architecture by using chromosomal segment substitution lines in rice. Theor Appl Genet 116:881–890. https://doi.org/10.1007/s00122-008-0722-6 CrossRefPubMedGoogle Scholar
- Broman KW, Sen S (2009) A guide to QTL mapping with R/qtl. Springer, New York, pp 75–133Google Scholar
- Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, Onodera H, Kashiwagi T, Ujiie K, Shimizu B, Onishi 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. https://doi.org/10.1038/ng.2612 CrossRefPubMedGoogle Scholar
- Kobayashi A, Sonoda J, Sugimoto K, Kondo M, Iwasawa N, Hayashi T, Tomita K, Yano M, Shimizu T (2013) Detection and verification of QTLs associated with heat-induced quality decline of rice (Oryza sativa L.) using recombinant inbred lines and near-isogenic lines. Breed Sci 63:339–346. https://doi.org/10.1270/jsbbs.63.339 CrossRefPubMedPubMedCentralGoogle Scholar
- Kondo M, Iwasawa N, Yoshida H, Hakagawa H, Ohno H, Nakazono K, Usui Y, Tokida T, Hasegawa T, Kuwagata T, Morita S, Nagata K (2012) Factors influencing the appearance quality in rice under high temperature in 2010. Jpn J Crop Sci 81 (Extra issue 1):120–121. https://www.jstage.jst.go.jp/article/jcsproc/233/0/233_0_120/_pdf. Accessed 16 Oct 2017
- Li J, Xiao J, Grandillo S, Jiang L, Wan Y, Deng Q, Yuan L, McCouch SR (2004) QTL detection for rice grain quality traits using an interspecific backcross population derived from cultivated Asian (O. sativa L.) and African (O. Glaberrima S.) rice. Genome 47:697–704. https://doi.org/10.1139/g04-029 CrossRefPubMedGoogle Scholar
- Liu X, Wan X, Ma X, Wan J (2011) Dissecting the genetic basis for the effect of rice chalkiness, amylose content, protein content, and rapid viscosity analyzer profile characteristics on the eating quality of cooked rice using the chromosome segment substitution line population across eight environments. Genome 54:64–80. https://doi.org/10.1139/G10-070 CrossRefPubMedGoogle Scholar
- Murata K, Iyama Y, Yamaguchi T, Ozaki H, Kidani Y, Ebitani T (2014) Identification of a novel gene (Apq1) from the indica rice cultivar ‘Habataki’ that improves the quality of grains produced under high temperature stress. Breed Sci 64:273–281. https://doi.org/10.1270/jsbbs.64.273 CrossRefPubMedPubMedCentralGoogle 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 of 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. https://doi.org/10.1007/s00122-017-2862-z CrossRefPubMedPubMedCentralGoogle Scholar
- Shirasawa K, Sekii T, Ogihara Y, Yamada T, Shirasawa S, Kishitani S, Sasaki K, Nishimura M, Nagano K, Nishio T (2013) Identification of the chromosomal region responsible for high-temperature stress tolerance during the grain-filling period in rice. Mol Breed 32:223–232. https://doi.org/10.1007/s11032-013-9864-6 CrossRefGoogle Scholar
- Terao T, Nagata K, Morino K, Hirose T (2010b) A gene controlling the number of primary rachis branches also controls the vascular bundle formation and hence is responsible to increase the harvest index and grain yield in rice. Theor Appl Genet 120:875–893. https://doi.org/10.1007/s00122-009-1218-8 CrossRefPubMedGoogle Scholar
- Wang S, Basten CJ, Zeng Z-B (2012a) Windows QTL Cartographer 2.5. Department of Statistics. North Carolina State University, Raleigh, NC. http://statgen.ncsu.edu/qtlcart/WQTLCart.htm. Accessed 7 Aug 2017
- 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. https://doi.org/10.1038/cr.2008.307 CrossRefPubMedGoogle Scholar
- Yun YT, Chung CT, Lee YJ, Na HJ, Lee JC, Lee SG, Lee KW, Yoon YH, Kang JW, Lee HS, Lee JY, Ahn SN (2016) QTL mapping of grain quality traits using introgression lines carrying Oryza rufipogon chromosome segments in Japonica rice. Rice 9:62. https://doi.org/10.1186/s12284-016-0135-0 CrossRefPubMedPubMedCentralGoogle Scholar
- Zhu L, Shah F, Nie L, Cui K, Shah T, Wu W, Chen Y, Chen C, Wang K, Wang Q, Lian Y, Huang J (2013) Efficacy of sowing date adjustment as a management strategy to cope with rice (Oryza sativa L.) seed quality deterioration due to elevated temperature. Aust J Crop Sci 7:543–549Google Scholar