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Journal of Integrative Agriculture  2021, Vol. 20 Issue (1): 35-45    DOI: 10.1016/S2095-3119(20)63256-7
Special Issue: 水稻遗传育种合辑Rice Genetics · Breeding · Germplasm Resources
Crop Science Advanced Online Publication | Current Issue | Archive | Adv Search |
Genome-wide pedigree analysis of elite rice Shuhui 527 reveals key regions for breeding
REN Yun1, 2, CHEN Dan1, LI Wen-jie1, TAO Luo1, YUAN Guo-qiang1, CAO Ye1, LI Xue-mei1, DENG Qi-ming1, WANG Shi-quan1, ZHENG Ai-ping1, ZHU Jun1, LIU Huai-nian1, WANG Ling-xia1, LI Ping1, LI Shuang-cheng1 
1 State Key Laboratory of Hybrid Rice/Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, P.R.China
2 College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, P.R.China
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杂交水稻为世界粮食的供应做出了重大贡献,而骨干亲本在杂交水稻品种选育中发挥着重要作用。为明确水稻骨干亲本蜀恢527(SH527,Oryza sativa)在育种过程中所利用的关键基因组区域,本研究对其进行了基于系谱的全基因组分析。利用高密度单核苷酸多态性(SNP)阵列对包括SH527、6个亲本品种及17个衍生恢复系在内的24个品种进行了扫描,分析了上游亲本对SH527基因组的独特贡献,确定了SH527及其衍生品种中保守的关键基因组区域。同时,利用多年的产量性状数据和SNP 芯片结果进行全基因组关联分析,发现了一些可能的已知或新的产量性状的关联位点。这项研究初步揭示了SH527育种的关键区域,将为后续育种提供参考。杂交水稻为世界粮食的供应做出了重大贡献,而骨干亲本在杂交水稻品种选育中发挥着重要作用。为明确水稻骨干亲本蜀恢527(SH527,Oryza sativa)在育种过程中所利用的关键基因组区域,本研究对其进行了基于系谱的全基因组分析。利用高密度单核苷酸多态性(SNP)阵列对包括SH527、6个亲本品种及17个衍生恢复系在内的24个品种进行了扫描,分析了上游亲本对SH527基因组的独特贡献,确定了SH527及其衍生品种中保守的关键基因组区域。同时,利用多年的产量性状数据和SNP 芯片结果进行全基因组关联分析,发现了一些可能的已知或新的产量性状的关联位点。这项研究初步揭示了SH527育种的关键区域,将为后续育种提供参考。

Hybrid rice significantly contributes to the food supply worldwide.  Backbone parents play important roles in elite hybrid rice breeding systems.  In this study, we performed pedigree-based analysis of the elite backbone parent rice variety, namely, Shuhui 527 (SH527, Oryza sativa), to exploit key genome regions during breeding.  Twenty-four cultivars (including SH527, its six progenitors and 17 derived cultivars) were collected and analyzed with high-density single nucleotide polymorphism (SNP) array.  Scanning all these cultivars with genome-wide SNP data indicated the unique contributions of progenitors to the SH527 genome and identified the key genomic regions of SH527 conserved within all its derivatives.  These findings were further supported by known rice yield-related genes or unknown QTLs identified by genome-wide association study.  This study reveals several key regions for SH527 and provides insights into hybrid rice breeding.
Keywords:  backbone parent        Shuhui 527        SNPs        genome-wide association study  
Received: 09 October 2019   Accepted:
Fund: This study was supported by the Sichuan Science and Technology Support Project, China (2016NZ0103), the National Natural Science Foundation of China (91435102 and 31570004), the Sichuan Provincial Founding for Distinguished Young Scholars, China (2015JQ0048), and the Open Research Fund of State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, China (2016KF10).
Corresponding Authors:  Correspondence LI Shuang-cheng, Tel: +86-28-86290898, E-mail:    
About author:  REN Yun, Tel: +86-23-49685266, E-mail:;

Cite this article: 

REN Yun, CHEN Dan, LI Wen-jie, TAO Luo, YUAN Guo-qiang, CAO Ye, LI Xue-mei, DENG Qi-ming, WANG Shi-quan, ZHENG Ai-ping, ZHU Jun, LIU Huai-nian, WANG Ling-xia, LI Ping, LI Shuang-cheng . 2021. Genome-wide pedigree analysis of elite rice Shuhui 527 reveals key regions for breeding. Journal of Integrative Agriculture, 20(1): 35-45.

Arite T, Umehara M, Ishikawa S, Hanada A, Maekawa M, Yamaguchi S, Kyozuka J. 2009. D14, a strigolactone-insensitive mutant of rice, shows an accelerated outgrowth of tillers. Plant and Cell Physiology, 50, 1416–1424.
Ashikari M, Sakakibara H, Lin S, Yamamoto T, Takashi T, Nishimura A, Angeles E R, Qian Q, Kitano H, Matsuoka M. 2005. Cytokinin oxidase regulates rice grain production. Science, 309, 741–745.
Chen B X, Li Z K, Liu H Y, Shi Y Y, Cui J T, Qian Y L, Zhang L K, Wang H, Gao Y M, Zhu L H. 2008. QTL detection of grain size and shape with BC2F2 advanced backcross population of rice. Acta Agronomica Sinica, 34, 1299–1307. (in Chinese)
Chen H D, Xie W B, He H, Yu H H, Chen W, Li J, Yu R B, Yao Y, Zhang W H, He Y Q, Tang X Y, Zhou F S, Deng X W, Zhang Q F. 2014. A high-density SNP genotyping array for rice biology and molecular breeding. Molecular Plant, 7, 541–553.
Chen J M, Su J, Liu H Q, Luo J M, Wu M J, Wang F. 2013. Breeding and utilization of super hybrid rice “Tianyou 3301”. Fujian Journal of Agricultural Sciences, 28, 1218–1223. (in Chinese)
Chen J P, Guo W, Liu X Y, Jiang M B, Xu H, Cheng Z M, Zhang S, Li Q G, Zhang B, Gao C. 2005. Breeding of a new rice variety B You 827 with high yeld, good quality and wide variety. Journal of Henan Agricultural Sciences, 34, 41–42. (in Chinese)
Chen Y, Fan X, Song W, Zhang Y, Xu G. 2011. Over-expression of OsPIN2 leads to increased tiller numbers, angle and shorter plant height through suppression of OsLAZY1. Plant Biotechnology Journal, 10, 139–149.
Cui J T, Chen B R, Shi Y Y, Zhang R, Wang H, Qian Y L, Liu H Y, Zhu L H, Li Z K, Gao Y M. 2008. Genetic diversity of involved varieties and improvement of elite restorer of indica rice using backcross introgression. Molecular Plant Breeding, 6, 25–31.
Guo L, Gao Z, Qian Q. 2014. Application of resequencing to rice genomics, functional genomics and evolutionary analysis. Rice, 7, 1–10.
Huang X, Lu T, Han B. 2013. Resequencing rice genomes: An emerging new era of rice genomics. Trends in Genetics, 29, 225–232.
Huang X H, Feng Q, Qian Q, Zhao Q, Wang L, Wang A, Guan J, Fan D, Weng Q, Huang T, Dong G, Sang T, Han B. 2009. High-throughput genotyping by whole genome resequencing. Genome Research, 19, 1068–1076.
Huang X H, Wei X H, Sang T, Zhao Q, Feng Q, Zhao Y, Li C Y, Zhu C R, Lu T T, Zhang Z W, Li M, Fan D L, Guo Y L, Wang A H, Wang L, Deng L W, Li W J, Lu Y Q, Weng Q J, Liu K Y, et al. 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nature Genetics, 42, 961–967.
IRGSP (International Rice Genome Sequencing Project). 2005. The map-based sequence of the rice genome. Nature, 436, 793–800.
Ishimaru K, Hirotsu N, Madoka Y, Murakami N, Hara N, Onodera H, Kashiwaqi 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.
Izawa T, Shimamoto K. 1996. Becoming a model plant: The importance of rice to plant science. Trends in Plant Science, 1, 95–99.
Jie R S, Liu F P, Yang C H, Ping H E, Mao J X. 2005. Breeding of new rice restorer line Nanhui 511 with high combining ability. Hybrid Rice, 20, 15–16. (in Chinese)
Jin S J, Kim J K. 2010. Root-specific expression of OsNAC10 improves drought tolerance and grain yield in rice under field drought conditions. Plant Physiology, 153, 185–197.
Keyan Z, Mark W, Jennifer K, Eizenga G, McCkung A, Kovach M, Tyaqi W, Ali M L, Tung C W, Reynolds A, Bustamante C D, McCouch S R. 2010. Genomic diversity and introgression in O. sativa reveal the impact of domestication and breeding on the rice genome. PLoS ONE, 5, e10780-e10780.
Kim E H, Kim Y S, Park S H, Koo Y J, Choi Y D, Chung Y Y, Lee I J, Kim J K. 2009. Methyl jasmonate reduces grain yield by mediating stress signals to alter spikelet development in rice. Plant Physiology, 149, 1751–1760.
Kitagawa K, Kurinami S, Oki K, Abe Y, Ando T, Kono I, Yano M, Kitano H, Iwasaki Y. 2010. A novel kinesin 13 protein regulating rice seed length. Plant and Cell Physiology, 51, 1315–1329.
Li S B, Qian Q, Fu Z M, Zeng D, Meng X B, Kyozuka J, Maekawa M, Zhu X, Zhang J, Li J, Wang Y. 2009. Short panicle1 encodes a putative PTR family transporter and determines rice panicle size. The Plant Journal, 58, 592–605.
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. Nature Genetics, 43, 1266–1269.
Lin H, Wang R, Qian Q, Yan M, Meng X, Fu Z, Yan C, Jiang B, Su Z, Li J, Wang Y. 2009. Dwarf27, an iron-containing protein required for the biosynthesis of strigolactones, regulates rice tiller bud out growth. The Plant Cell, 21, 1512–1525.
Lin Q B, Wang D, Dong H, Gu S H, Cheng Z J, Gong J, Qin R Z, Jiang L, Li G, Wang J L, Wu F Q, Guo X P, Zhang X, Lei C L, Wang H Y, Wan J M. 2012. Rice APC/CTE controls tillering by mediating the degradation of MONOCULM 1. Nature Communications, 3, 132–136.
Lin S C, Min S K. 1991. Rice Varieties and Their Pdigree in China. Shanghai Scientific and Technical Publishers, China. p. 414. (in Chinese)
Liu H L, Zhi J Y, Li X, Yi N X, Le Q Q. 2012. Identification and evaluation of ω-3 fatty acid desaturase genes for hyperfortifying α-linolenic acid in transgenic rice seed. Journal of Experimental Botany, 63, 3279–3287.
Liu H N. 2011. Genomic scanning of rice (Oryza sativa L.) backbone parent Shuhui 527 and QTLs analysis of yield related characters. Ph D thesis, Sichuan Agricultural University, China. (in Chinese)
Luan W J, Liu Y Q, Zhang F X, Song Y L, Wang Z Y, Peng Y K, Sun Z X. 2011. OsCD1 encodes a putative member of the cellulose synthase-liked D sub-family and is essential for rice plant architecture and growth. Plant Biotechnology Journal, 9, 513–524.
Manavalan L P, Chen X, Joseph C, John S, Nguyen H T. 2012. RNAi-mediated disruption of squalene synthase improves drought tolerance and yield in rice. Journal of Experimental Botany, 63, 163–175.
Mosa K A, Kumar K, Chhikara S, Mcdermott J, Liu Z, Musante C, White J C, Dhankher O P. 2012. Members of rice plasma membrane intrinsic proteins subfamily are involved in arsenite permeability and tolerance in plants. Transgenic Research, 21, 1265–1277.
Nakagawa H, Tanaka A, Tanabata T, Ohtake M, Fujioka S, Nakamura H, Ichikawa H, Mori M. 2012. SHORT GRAIN1 decreases organ elongation and brassinosteroid response in rice. Plant Physiology, 158, 1208–1219.
Piao R, Jiang W, Ham T H, Choi M S, Qiao Y, Chu S H, Park J H, Woo M O, Jin Z, An G, Lee J, Koh H J. 2009. Map-based cloning of the ERECT PANICLE 3 gene in rice. Theoretical and Applied Genetics, 119, 1497–1506.
Qi P, Lin Y S, Song X J, Shen J B, Huang W, Shan J X, Zhu M Z, Jiang L, Gao J P, Lin H X. 2012. The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3. Cell Research, 22, 1666–1680.
Qian Y L, Wang H, Chen M Y. 2009. Detection of salt-tolerant QTL using BC2F3 yield selected introgression lines of rice. Molecular Plant Breeding, 7, 224–232.
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 Z X, E Z G, Wang L, Zhu D F, Zhang Y P, Hu G C, Liu W Z, Fu Y P. 2014. Exploring assessment method of chinese rice backbone parents. Acta Agronomica Sinica, 40, 973–983. (in Chinese)
Tang S X, Wang X D, Liu X. 2012. Study on turnover tendency and core backbone of conventional rice varieties in China. Scientia Agricultura Sinica, 45, 1455–1464. (in Chinese)
Takagi H, Abe A, Yoshida K, Kosuqi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S, Innan H, Cano LM, Kamoun S, Terauchi R. 2013. QTL-seq: Rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. The Plant Journal, 74, 174–183.
Takeda T, Suwa Y, Suzuki M, Kitano H, Ueguchi-Tanaka M, Ashikari M, Matsuoka M, Uequchi C. 2003. The ostb1 gene negatively regulates lateral branching in rice. The Plant Journal, 33, 513–520.
Terao T, Nagata K, Morino K, Hirose T. 2010. 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. Theoretical and Applied Genetics, 120, 875–933.
Wan J M. 2006. Crop molecular design breeding. Acta Agronomica Sinica, 32, 455–462. (in Chinese)
Wan J M. 2010. Rice Genetic Breeding and Pedigree in China. China Agriculture Press, China. p. 741. (in Chinese)
Wang S, Wu K, Yuan 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. Nature Genetics, 44, 950–954.
Wang Y P, Li S G, Li H Y, Gao K M. 2004. Breeding and utilization of restorer line Shuhui 527 with good grain quality and high combining ability in grain yield. Hybrid Rice, 19, 12–14. (in Chinese)
Wang Z, Liu D Y, Hu Y G, Song D M, Yan X D, Xiang Z F, Shi S P. 2004. Breeding and application of high quality and high yield hybrid rice Mian 5 You 527. Chinese Seed Industry, 11, 39–40. (in Chinese)
Weng X. 2008. Natural variation in ghd7 is an important regulator of heading date and yield potential in rice. Nature Genetics, 40, 761–767.
Xiao J P, Zhang J X. 2010. Jinyou 238, a new late-cropping hybrid rice combination with medium maturity. Hybrid Rice, 25, 98–99. (in Chinese)
Xu M, Zhu L, Shou H, Wu P. 2005. A PIN1 family gene, OsPIN1, involved in auxin-dependent adventitious root emergence and tillering in rice. Plant and Cell Physiology, 46, 1674–1681.
Yan D W, Zhou Y, Ye S H, Zeng L J, Zhang X M, He Z H. 2013. BEAK-SHAPED GRAIN 1/TRIANGULAR HULL 1, a DUF640 gene, is associated with grain shape, size and weight in rice. Science in China (Life Sciences), 56, 275–283.
Yu G P, Zhu H Y. 2009. Current situation and development countermeasures of rice production in China. Modern Agricultural Science and Technology, 6, 122–126. (in Chinese)
Yu J, Ni P, Wong G K. 2006. Comparing the whole-genome-shot gun and map-based sequences of the rice genome. Trends in Plant Science, 11, 387–391.
Zhang X, Wang J, Huang J, Lan H, Wang C, Yin C, Wu Y, Tang H, Qian Q, Li J, Zhang H. 2012. Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice. Proceedings of the National Academy of Sciences of the United States of America, 109, 21534–21539.
Zhang Y, Zhu Y, Yu P, Yan D, Li Q, Wang J, Wang L, He L. 2008. Gibberellin homeostasis and plant height control by eui and a role for gibberellin in root gravity responses in rice. Cell Research, 18, 412–421.
Zhao Z G , Zhu S S, Zhang Y H, Bian X F, Wang Y, Jiang L, Liu X, Chen L M, Liu S J, Zhang W W, Ikehashi H, Wan J M. 2011. Molecular analysis of an additional case of hybrid sterility in rice (Oryza sativa L.). Planta, 233, 485–494.
Zhu K, Tang D, Yan C, Chi Z, Yu H, Chen J M, Liang J S, Gu M H, Chen Z K. 2010. ERECT PANICLE 2 encodes a novel protein that regulates panicle erectness in indica rice. Genetics, 184, 343–350.
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