Please wait a minute...
Journal of Integrative Agriculture  2016, Vol. 15 Issue (8): 1693-1702    DOI: 10.1016/S2095-3119(15)61259-X
Crop Genetics · Breeding · Germplasm Resources Advanced Online Publication | Current Issue | Archive | Adv Search |
QTL mapping of grain appearance quality traits and grain weight using a recombinant inbred population in rice (Oryza sativa L.)
GAO Fang-yuan1*, ZENG Li-hua2*, QIU Ling1, 2, LU Xian-jun1, REN Juan-sheng1, WU Xian-ting1, SU Xiang-wen1, GAO Yong-ming3, REN Guang-jun1
1 Crop Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, P.R.China
2 Sichuan Normal University, Chengdu 610110, P.R.China
3 Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, P.R.China
Download:  PDF in ScienceDirect  
Export:  BibTeX | EndNote (RIS)      
Abstract     Grain appearance quality traits, measured as grain length (GL), grain width (GW), length to width ratio (LWR), grain thickness (GT) and the percentage of grain with chalkiness (PGWC), as well as 1 000-grain weight (TGW), are very important factors that contribute to rice grain quality and yield. To detect quantitative trait loci (QTLs) affecting these traits, we developed a set of recombinant inbred lines (RILs) derived from Gang46B (G46B) and K1075, a G46B introgression line with lower PGWC. Based on a linkage map containing 33 simple sequence repeat (SSR) markers, a total of 15 additive QTLs governing six measured traits were identified on 4 chromosomes across two environments. Of these, the five major QTLs which controlled GW, LWR, GT, PGWC, and TGW, each explaining up to 44.30, 55.29, 62.30, 30.94, and 28.78% of the variation, respectively, were found in the same interval of RM18004–RM18068 on chromosome 5. The G46B alleles contributed to the increase in GW, GT and PGWC at all loci, as well as the increase in TGW at its major QTL locus. Significant interactions between additive QTL and the environment were found at most loci, in which the largest, accounting for 15.06% of variation, was observed between qPGWC-5 and the environment. A total of 15 epistasis QTLs were detected for all the traits, and GL, GW and PGWC had significant epistasis QTLs based on environment interactions with minor effects. These results are valuable for future map-based cloning of the QTLs and the collaborative improvement of G46B in grain appearance quality and yield.
Keywords:  QTL        appearance quality        1 000-grain weight        recombination inbred lines (RIL)        rice  
Received: 29 July 2015   Accepted:

This work was supported by a grant from the National High-Tech R&D Program of China (2014AA10A603, 2014AA10A604), a grant from the Youth Foundation in Sichuan, China (2011JTD0022), the special fund for China Agricultural Research System (CARS-01-08) and the Provincial Specialized Funds for Innovation Ability Promotion in Sichuan, China (2013GXJS005).

Corresponding Authors:  REN Guang-jun, Tel: +86-28-84504006, Fax: +86-28-84790147, E-mail:   
About author:  GAO Fang-yuan, Mobile: +86-13618022481, Tel: +86-28-84504558, E-mail:; ZENG Li-hua, Tel: +86-28-84788266, E-mail:;

Cite this article: 

GAO Fang-yuan, ZENG Li-hua, QIU Ling, LU Xian-jun, REN Juan-sheng, WU Xian-ting, SU Xiangwen, GAO Yong-ming, REN Guang-jun. 2016. QTL mapping of grain appearance quality traits and grain weight using a recombinant inbred population in rice (Oryza sativa L.). Journal of Integrative Agriculture, 15(8): 1693-1702.

Bai X F, Luo L J, Yan W H, Kovi M R, Zhan W, Xing Y Z. 2010. Genetic dissection of rice grain shape using a recombinant inbred line population derived from two contrasting parents and fine mapping a pleiotropic quantitative trait locus qGL7. BMC Genetics, 11, 16.

Collard B C Y, Mackill D J. 2008. Marker-assisted selection: An approach for precision plant breeding in the 21st century. Philosophical Transacations of the Royal Society Lond (B Biological Sciences), 363, 557–572.

Fan C C, Xing Y Z, Mao H L, Lu T T, Han B, Xu C G, Li X H, Zhang Q F. 2006. GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theoretical and Applied Genetics, 112, 1164–1171.

Fan C C, Yu X Q, Xing Y Z,  Xu C G,  Luo L J, Zhang Q. 2005. The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theoretical and Applied Genetics, 110, 1445–1452.

Gao F Y, Lu X J, Wang W M, Sun S S, Li Z H, Li H J, Ren G J. 2009. Trait-specific improvement of a cytoplasmic male sterile line using molecular marker-assisted selection in rice. Crop Science, 49, 99–106.

Gao F Y, Qiu L, Lu X J, Ren J S, Wu X T, Ren G J, Zeng L H. 2014. QTL analysis on grain shape and chalkiness of an elite maintainer line Gang46B in hybrid rice (Oryza sativa L.). Chinese Journal of Rice Science, 28, 235–242. (in Chinese)

Gao F Y, Ren G J, Lu X J, Sun S S, Li H J, Gao Y M, Luo H, Yan W G, Zhang Y Z. 2008. QTL analysis for the resistance to pre-harvest sprouting in rice (Oryza sativa L.). Plant Breeding, 127, 268–273.

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. Nature Genetics, 45, 707–711.

Kepiro J L, McClung A M, Chen M H, Yeater K M, Fjellstrom R G. 2008. Mapping QTLs for milling yield and grain characteristics in a tropical japonica long grain cross. Journal of Cereal Science, 48, 477–485.

Liang Y S, Zhan X D, Gao Z Q, Lin Z C, Yang Z L, Zhang Y X, Shen X H, Cao L Y, Cheng S H. 2012. Mapping of QTLs associated with important agronomic traits using three populations derived from a super hybrid rice Xieyou 9308. Euphytica, 184, 1–13.

Lin H X, Min S K, Xiong Z M, Qian H R, Zhuang J Y, Lu J, Huang N, Zheng K. 1995. RFLP mapping of QTLs for grain shape traits in indica rice (Oryza sativa L. subsp. Indica). Scientia Agricultura Sinica, 28, 1–7. (in Chinese)

Liu W Q, Fan Y Y, Chen J, Shi Y F, Wu J L. 2009. Avoidance of linkage drag between blast resistance gene and the QTL conditioning spike let fertility based on genotype selection against heading date in rice. Chinese Journal of Rice Science, 16, 21–26. (in Chinese)

Li Y B, Fan C C, Xing Y Z, Jiang Y H, Luo L J, Sun L, Shao D, Xu C J, Li X H, Xiao J H, He Y Q, Zhang Q F. 2011. Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nature Genetics, 43, 1266–1269.

Li Y B, Fan C C, Xing Y Z, Yun P, Luo L J, Yan B, Peng B, Xie W B, Wang G W, Li X H, Xiao J H, Xu C G, He Y Q. 2014. Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice. Nature Genetics, 46, 398–404.

Li Z F, Wan J M, Xia J F, Zhai H Q. 2003. Mapping quantitative trait loci underlying appearance quality of rice grains (Oryza sativa L.). Acta Genetica Sinica, 30, 251–259.

Lou J, Chen L, Yue G H, Lou Q J, Mei H W, Xiong L, Luo L J. 2009. QTL mapping of grain quality traits in rice. Journal of Cereal Science, 50, 145–151.

McCouch S R, Cho Y G, Yano M. 1997. Report on QTL nomenclature. Rice Genetic Newsletter, 14, 11–13.

Murray M G, Thompson W F. 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Research, 8, 4321–4326.

Neeraja C N, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard B C, Septiningsih E M, Vergara G, Sanchez D, Xu K, Ismail A M, Mackill D J. 2007. A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theoretical and Applied Genetics, 115, 767–776.

Peng B, Wang L Q, Fan C C, Jiang G H, Luo L J, Li Y B, He Y Q. 2014. Comparative mapping of chalkiness components in rice using five populations across two environments. BMC Genetics, 15, 49.

Qiu X J, Gong R, Tan Y B, Yu S B. 2012. Mapping and characterization of the major quantitative trait locus qSS7 associated with increased length and decreased width of rice seeds. Theoretical and Applied Genetics, 125, 1717–1726.

Shanmugavadivel P S, Amitha Mithra S V, Dokku P, Anand Raj K K, Rao G J N, Singh V P, Singh A K, Singh N K, Mohapatra T. 2013. Mapping quantitative trait loci (QTL) for grain size in rice using a RIL population from basmati 3 indica cross showing high segregation distortion. Euphytica, 194, 401–416.

Shao G N, Wei X J, Chen M L, Tang S Q, Luo J, Jiao G A, Xie L H, Hu P S. 2012. Allelic variation for a candidate gene for GS7, responsible for grain shape in rice. Theoretical and Applied Genetics, 125, 1303–1312.

Shomura A, Izawa T, Ebana K, Ebitani T, Kanegae H, Konishi S, Yano M. 2008 . Deletion in a gene associated with grain size increased yields during rice domestication. Nature Genetics, 40, 1023–1028.

Song X J, Huang W, Shi M, Zhu M Z, Lin H X. 2007. A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase. Nature Genetics, 39, 623–630.

Sun W Q, Zhou Q L, Yao Y, Qiu X J, Xie K, Yu S B. 2015. Identification of genomic regions and the isoamylase gene for reduced grain chalkiness in rice. PLOS ONE, 10, e0122013.

Tan Y F, Xing Y Z, Li J X, Yu S B, Xu C G, Zhang Q F. 2000. Genetic bases of appearance quality of rice grains in Shanyou 63, an elite rice hybrid. Theoretical and Applied Genetics, 101, 823–829.

Takano-Kai N, Doi K, Yoshimura A. 2011. GS3 participates in stigma exsertion as well as seed length in rice. Breeding Science, 61, 244–250.

Teng S, Qian Q, Zeng D L, Kunihiro Y, Huang D N, Zhu L H. 2002. QTLs analysis of rice peduncle vascular bundle and panicle traits. Acta Botanica Sinica, 44, 301–306. (in Chinese)

Wan X Y, Wan J M, Weng J F, Jiang L, Bi J C, Wang C M, Zhai H Q. 2005. Stability of QTLs for rice grain dimension and endosperm chalkiness characteristics across eight environments. Theoretical and Applied Genetics, 110, 1334–1346.

Wang D L, Zhu J, Li Z K, Paterson A H. 1999. Mapping QTLs with epistatic effects and QTL environment interactions by mixed linear model approaches. Theoretical and Applied Genetics, 99, 1255–1264.

Wang S K, Wu K, Yuan Q B, Liu X Y, Liu Z B, Lin X Y, Zeng R Z, Zhu H T, Dong G J, Qian Q, Zhang G Q, Fu X D. 2012. Control of grain size, shape and quality by OsSPL16 in rice. Nature Genetics, 44, 950–954.

Wang Z, Cheng J, Chen Z, Huang J, Bao Y, Wang J, Zhang H. 2012. Identification of QTLs with main, epistatic and QTL×environment interaction effects for salt tolerance in rice seedlings under different salinity conditions. Theoretical and Applied Genetics, 125, 807–815.

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 Research, 18, 1199–1209.

Xing Z, Tan F, Hua P, Sun L, Xu G, Zhang Q. 2002. Characterization of the main effects, epistatic effects and their environmental interactions of QTLs on the genetic basis of yield traits in rice. Theoretical and Applied Genetics, 105, 248–257.

Yamamoto T, Lin H, Sasaki T, Yano M. 2000. Identification of heading date quantitative trait locus Hd6 and characterization of its epistatic interactions with Hd2 in rice using advanced backcross progeny. Genetics, 154, 885–891.

Yu S B, Li J X, Xu C G, Tan Y F, Gao Y J, Li X H, Zhang Q, Saghai Maroof M A. 1997. Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proceedings of the National Academy of Sciences of the United States of America, 94, 9226–9231.

Zhang Y D, Zhang Y H, Dong S L, Chen T, Zhao Q Y, Zhu Z, Zhou L H, Yao S, Zhao L, Yu X, Wang C L. 2013. Identification of QTL for rice grain traits based on an extra-large grain material. Chinese Journal of Rice Science, 27, 122–128. (in Chinese)

Zhou L, Chen L, Jiang L, Zhang W, Liu L, Liu X, Zhao Z, Liu S, Zhang L, Wang J, Wan J. 2009 Fine mapping of the grain chalkiness QTL qPGWC-7 in rice (Oryza sativa L.). Theoretical and Applied Genetics, 118, 581–590.

Zhuang J Y, Fan Y Y, Rao Z M, Wu J L, Xia Y W, Zheng K L. 2002. Analysis on additive effects and additive-by-additive epistatic effects of QTLs for yield traits in a recombinant inbred line population of rice. Theoretical and Applied Genetics, 105, 1137–1145.
[1] LIU Dan, ZHAO De-hui, ZENG Jian-qi, Rabiu Sani SHAWAI, TONG Jing-yang, LI Ming, LI Fa-ji, ZHOU Shuo, HU Wen-li, XIA Xian-chun, TIAN Yu-bing, ZHU Qian, WANG Chun-ping, WANG De-sen, HE Zhong-hu, LIU Jin-dong, ZHANG Yong. Identification of genetic loci for grain yield‑related traits in the wheat population Zhongmai 578/Jimai 22[J]. >Journal of Integrative Agriculture, 2023, 22(7): 1985-1999.
[2] GAO Peng, ZHANG Tuo, LEI Xing-yu, CUI Xin-wei, LU Yao-xiong, FAN Peng-fei, LONG Shi-ping, HUANG Jing, GAO Ju-sheng, ZHANG Zhen-hua, ZHANG Hui-min. Improvement of soil fertility and rice yield after long-term application of cow manure combined with inorganic fertilizers[J]. >Journal of Integrative Agriculture, 2023, 22(7): 2221-2232.
[3] GAO Ri-xin, HU Ming-jian, ZHAO Hai-ming, LAI Jin-sheng, SONG Wei-bin.

Genetic dissection of ear-related traits using immortalized F2 population in maize [J]. >Journal of Integrative Agriculture, 2022, 21(9): 2492-2507.

[4] CHAO Kai-xiang, WU Cai-juan, LI Juan, WANG Wen-li, WANG Bao-tong, LI Qiang. Genetic analysis of adult plant, quantitative resistance to stripe rust in wheat landrace Wudubaijian in multi-environment trials[J]. >Journal of Integrative Agriculture, 2022, 21(8): 2305-2318.
[5] GAO Zhi-ping, XU Min-li, ZHANG Hai-zi, LÜ Chuan-gen, CHEN Guo-xiang. Photosynthetic properties of the mid-vein and leaf lamina of field-grown, high-yield hybrid rice during senescence[J]. >Journal of Integrative Agriculture, 2022, 21(7): 1913-1926.
[6] PAN Wen-jing, HAN Xue, HUANG Shi-yu, YU Jing-yao, ZHAO Ying, QU Ke-xin, ZHANG Ze-xin, YIN Zhen-gong, QI Hui-dong, YU Guo-long, ZHANG Yong, XIN Da-wei, ZHU Rong-sheng, LIU Chun-yan, WU Xiao-xia, JIANG Hong-wei, HU Zhen-bang, ZUO Yu-hu, CHEN Qing-shan, QI Zhao-ming. Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses[J]. >Journal of Integrative Agriculture, 2022, 21(7): 1886-1902.
[7] LIU Chen, TIAN Yu, LIU Zhang-xiong, GU Yong-zhe, ZHANG Bo, LI Ying-hui, NA Jie, QIU Li-juan. Identification and characterization of long-InDels through whole genome resequencing to facilitate fine-mapping of a QTL for plant height in soybean (Glycine max L. Merr.)[J]. >Journal of Integrative Agriculture, 2022, 21(7): 1903-1912.
[8] TIAN Chang, SUN Ming-xue, ZHOU Xuan, LI Juan, XIE Gui-xian, YANG Xiang-dong, PENG Jian-wei. Increase in yield and nitrogen use efficiency of double rice with long-term application of controlled-release urea[J]. >Journal of Integrative Agriculture, 2022, 21(7): 2106-2118.
[9] ZHOU Tian-yang, LI Zhi-kang, LI En-peng, WANG Wei-lu, YUAN Li-min, ZHANG Hao, LIU Li-jun, WANG Zhi-qin, GU Jun-fei, YANG Jian-chang. Optimization of nitrogen fertilization improves rice quality by affecting the structure and physicochemical properties of starch at high yield levels[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1576-1592.
[10] DING Pu-yang, MO Zi-qiang, TANG Hua-ping, MU Yang, DENG Mei, JIANG Qian-tao, LIU Ya-xi, CHEN Guang-deng, CHEN Guo-yue, WANG Ji-rui, LI Wei, QI Peng-fei, JIANG Yun-feng, KANG Hou-yang, YAN Gui-jun, Wei Yu-ming, ZHENG You-liang, LAN Xiu-jin, MA Jian. A major and stable QTL for wheat spikelet number per spike validated in different genetic backgrounds[J]. >Journal of Integrative Agriculture, 2022, 21(6): 1551-1562.
[11] TIAN Yu, YANG Lei, LU Hong-feng, ZHANG Bo, LI Yan-fei, LIU Chen, GE Tian-li, LIU Yu-lin, HAN Jia-nan, LI Ying-hui, QIU Li-juan. QTL analysis for plant height and fine mapping of two environmentally stable QTLs with major effects in soybean[J]. >Journal of Integrative Agriculture, 2022, 21(4): 933-946.
[12] JIANG Xue-qian, ZHANG Fan, WANG Zhen, LONG Rui-cai, LI Ming-na, HE Fei, YANG Xi-jiang, YANG Chang-fu, JIANG Xu, YANG Qing-chuan, WANG Quan-zhen, KANG Jun-mei. Detection of quantitative trait loci (QTL) associated with spring regrowth in alfalfa (Medicago sativa L.)[J]. >Journal of Integrative Agriculture, 2022, 21(3): 812-818.
[13] Christian Adler PHARES, Selorm AKABA. Co-application of compost or inorganic NPK fertilizer with biochar influenced soil quality, grain yield and net income of rice[J]. >Journal of Integrative Agriculture, 2022, 21(12): 3600-3610.
[14] Muhammad Amjad BASHIR, ZHAI Li-mei, WANG Hong-yuan, LIU Jian, Qurat-Ul-Ain RAZA, GENG Yu-cong, Abdur REHIM, LIU Hong-bin. Apparent variations in nitrogen runoff and its uptake in paddy rice under straw incorporation[J]. >Journal of Integrative Agriculture, 2022, 21(11): 3356-3367.
[15] HUANG Li-ying, Li Xiao-xiao, ZHANG Yun-bo, Shah FAHAD, WANG Fei. dep1 improves rice grain yield and nitrogen use efficiency simultaneously by enhancing nitrogen and dry matter translocation[J]. >Journal of Integrative Agriculture, 2022, 21(11): 3185-3198.
No Suggested Reading articles found!