Welcome to Acta Agronomica Sinica,

Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (9): 1319-1326.doi: 10.3724/SP.J.1006.2019.82062

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genetic dissection of combining ability and heterosis of rice agronomic traits based on pathway analysis

XIANG Li-Yuan1,XU Kai1,SU Jing1,WU Chao1,YUAN Xiong1,ZHENG Xing-Fei2,DIAO Ying2,HU Zhong-Li2,LI Lan-Zhi1,*()   

  1. 1 Hunan Engineering & Technology Research Center for Agricultural Big Data Analysis & Decision-making/Hunan Agricultural University, Changsha 410128, Hunan, China;
    2 State Key Laboratory of Hybrid Rice/Wuhan University, Wuhan 430072, Hubei, China
  • Received:2018-12-13 Accepted:2019-05-12 Online:2019-09-12 Published:2019-05-31
  • Contact: Lan-Zhi LI E-mail:lancy0829@163.com
  • Supported by:
    The study was supported by the National Key Research and Development Program(2016YFD0100101);the Natural Science Foundation of Hunan Province(2016JJ3070);the State Key Laboratory of Crop Germplasm Innovation and Resource Utilization Breeding Base(16KFXM03)

Abstract:

In order to provide theoretical foundation of cultivating and improving rice, under North Carolina design II, we constructed test cross population and conducted pathway analysis of phenotype performance, combining ability and heterosis of agronomic trait in present study. The experiments’ results reveal that the filled grains per panicle, 1000-grain weight, main panicle length, primary/secondary branch of main panicle, plant height, spikelet per panicle, tillers per plant, and yield per plant were separately related to pathway of biological regulation, cysteine and methionine metabolism, snare interactions in vesicular transport, DNA-dependent transcription, macromolecular metabolism, recognition of pollen, hydrolase activity, purine nucleoside binding and so on. Therefore, in order to obtain elite hybrids with high combining ability and heterosis, it is feasible to start from studying related pathways of a certain trait and related genes regulating the pathway.

Key words: hybrid rice, GWAS, pathway analysis, combining ability, heterosis

Fig. 1

Pathways in the four datasets V: original phenotype in paternal population; GCA: general combining ability in paternal population; TC: original phenotype in test cross population; BP: heterosis over better of parents in test cross population."

Table 1

Common pathways in four datasets"

通路Pathway 类别Category 描述Description
CATALYTIC_ACTIVITY GO:0003824 催化活性Catalytic activity
CATION_BINDING GO:0043169 阳离子结合Cation binding
ION_BINDING GO:0043167 离子结合Ion binding
METABOLIC_PROCESS GO:0008152 代谢过程Metabolic process
PRIMARY_METABOLIC_PROCESS GO:0044238 初级代谢过程Primary metabolic process

Fig. 2

Pathways of nine traits in the four datasets FGPP: filled grains per panicle; KGW: 1000-grain weight; MPL: main panicle length; PBP: primary branch of main panicle; PH: plant height; SBP: secondary branch of main panicle; SPP: spikelet per panicle; TP: effective tillers per plant; YD: yield per plant."

Table 2

Number of paths contained in four datasets with different traits"

数据集
Dataset
性状个数
Number of traits
通路个数
Number of pathways
V 1 86
2 13
3 1
GCA 1 52
2 11
3 11
4 25
5 7
6 1
TC 1 51
2 20
3 32
4 4
5 7
7 1
8 3
BP 1 33
[1] Beló A, Zheng P Z, Luck S, Shen B, Meyer DJ, Li B, Tingey S, Rafalski A . Whole genome scan detects an allelic variant of fad2 associated with increased oleic acid levels in maize. Mol Genet Genomics, 2008,279:1-10.
[2] Yonemaru J, Mizobuchi R, Kato H, Yamamoto T, Yamamoto E, Matasubara K, Hirabayashi H, Takeuchi Y, Tsunematsu H, Ishii T . Genomic regions involved in yield potential detected by genome-wide association analysis in Japanese high-yielding rice cultivars. BMC Genomics, 2014,15:346.
[3] 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, Huang T, Zhou T Y, Jing Y F, Li W, Lin Z, Buckler E S, Qian Q, Zhang Q F, Li J Y, Han B . Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet, 2010,42:961-967.
[4] 王彩红 . 水稻苗期稻瘟病抗性的全基因组关联分析. 中国农业科学院博士论文, 北京, 2014.
Wang C H . Genome-wide Association Study of Rice Seedling Resistance to Blast. PhD Dissertation of Chinese Academy of Agricultural Sciences, Beijing, China, 2014 (in Chinese with English abstract).
[5] Wang K, Li M, Bucan M . Pathway-based approaches for analysis of genome-wide association studies. Am J Hum Genet, 2007,81:1278-1283.
[6] Wang S B, Feng J Y, Ren W L, Huang B, Zhou L, Wen Y J, Zhang J, Jim M D, Xu S Z, Zhang Y M . Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology. Sci Rep, 2016,6:19444.
[7] Hirschhorn J N . Genomewide association studies-illuminating biologic pathways. N Engl J Med, 2009,360:1699-1701.
[8] 王钰嫣, 王子兴, 胡耀达, 王蕾, 李宁, 张彪, 韩伟, 姜晶梅 . 全基因组关联研究通路分析方法现状. 遗传, 2017,39:707-716.
Wang Y Y, Wang Z X, Hu Y D, Wang L, Li N, Zhang B, Han W, Jiang J M . Current status of pathway analysis in genome-wide association study. Hereditas (Beijing), 2017,39:707-716 (in Chinese with English abstract).
[9] 张远森 . 基于通路分析法诠释水稻农艺性状全基因组关联研究. 昆明理工大学硕士学位论文, 云南昆明, 2015.
Zhang Y S . Explanation the Genome-wide Association Study of Agronomic Traits in Rice by Pathway. MS Thesis of Kunming University of Science and Technology, Kunming, Yunnan, China, 2015 (in Chinese with English abstract).
[10] 张征, 张雪丽, 莫博程, 代志军, 胡中立, 李兰芝, 郑兴飞 . 籼型杂交水稻农艺性状的配合力研究. 作物学报, 2017,43:1448-1457.
Zhang Z, Zhang X L, Mo B C, Dai Z J, Hu Z L, Li L Z, Zheng X F . Combining ability analysis of agronomic trait in indica × indica hybrid rice. Acta Agron Sin, 2017,43:1448-1457 (in Chinese with English abstract).
[11] Liu C, Song G Y, Zhou Y H, Qu X F, Guo Z B, Liu Z W, Jiang D M, Yang D C . OsPRR37 and Ghd7 are the major genes for general combining ability of DTH, PH and SPP in rice. Sci Rep, 2015,5:12803.
[12] 付新民, 王岩, 高冠军, 何予卿 . 利用水稻重组自交系进行配合力遗传分析. 华中农业大学学报, 2010,29:397-402.
Fu X M, Wang Y, Gao G J, He Y Q . Combining ability analysis in rice using recombinant inbred lines. J Huazhong Agric Univ, 2010,29:397-402 (in Chinese).
[13] 梁康迳 . 基因型×环境互作效应对水稻穗部性状杂种优势的影响. 应用生态学报, 1999,10:683-688.
Liang K J . Interactive effect of genotype and environment on heterosis of panicle traits of rice (Oryza sative L.). Chin J Appl Ecol, 1999,10:683-688 (in Chinese with English abstract).
[14] Tang Y, Liu X L, Wang J B, Li M, Wang Q S, Tian F, Su Z B, Pan Y C, Liu D, Su Z B, Pan Y C, Lipka A E, Buckler E S, Zhang Z W . GAPIT version 2: an enhanced integrated tool for genomic association and prediction. Plant Genome-US, 2016,9:1-9.
[15] 王杰, 刘璐, 刘杰, 赵桂苹, 刘冉冉, 郑麦青, 文杰 . 基于通路分析方法诠释肉鸡体重性状全基因组关联研究. 畜牧兽医学报, 2017,48:810-817.
Wang J, Liu L, Liu J, Zhou G P, Liu R R, Zheng M Q, Wen J . Genome-wide association study on body weight traits of broilers based on pathway. Acta Veter Zootech Sin, 2017,48:810-817 (in Chinese with English abstract).
[16] She K C, Kusano H, Koizumi K, Yamakawa H, Hakata M, Imamura T, Fukuda M, Naito N, Tsurumaki Y, Yaeshima M, Tsuge T, Matsumoto K, Kudoh M, Itoh E, Kikuchi S, Kishimoto N, Yazaki J, Ando T, Yano M, Aoyama T, Sasaki T, Satoh H, Shimada H . A novel factor FLOURY ENDOSPERM2 is involved in regulation of rice grain size and starch quality. Plant Cell, 2010,22:3280-3294.
[17] Mao H, Sun S, Yao J L, Wang C G, Yu S B, Xu C G, Li X H, Zhang Q F . Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA, 2010,107:19579-19584.
[18] Long Y M, Zhao L F, Niu B X, Su J, Wu H, Chen Y L, Zhang Q Y, Guo J X, Zhuang C X, Mei M T, Xia J X, Wang L, Wu H B, Liu Y G . Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc Natl Acad Sci USA, 2008,105:18871-18876.
[19] 鲍永美 . 水稻SNARE蛋白基因的克隆与功能分析. 南京农业大学硕士学位论文, 江苏南京, 2007.
Bao Y M . Cloning and Functional Analysis of SNARE Protein Genes from Rice (Oryza sativa L.). MS Thesis of Nanjing Agricultural University, Nanjing, Jiangsu, China, 2007 (in Chinese with English abstract).
[20] Yaish M W, El-Kereamy A, Zhu T, Beatty P H, Good A G, Bi Y M, Rothstein S J . The APETALA-2-like transcription factor OsAP2-39 controls key interactions between abscisic acid and gibberellin in rice. PLoS Genet, 2010,6:e1001098.
[21] Li M, Xiong G Y, Li R, Cui J J, Tang D, Zhang B C, Pauly M, Cheng Z K, Zhou Y H . Rice cellulose synthase-like D4 is essential for normal cell-wall biosynthesis and plant growth. Plant J, 2009,60:1055-1069.
[22] 石晗 . 不同类型水稻种质资源农艺性状鉴定与抗逆性筛选. 华中农业大学硕士学位论文, 湖北武汉, 2017.
Shi H . Evaluation of Agronomic Traits and Screening of Stress Resistance in Different Types of Rice Germplasm. MS Thesis of Huazhong Agricultural University, Wuhan, Hubei, China, 2017 (in Chinese with English abstract).
[23] 黄利兴, 游年顺, 雷捷成, 郑向华 . 杂交水稻配合力分析及高产地优组合选配的探讨. 福建稻麦科技, 1994, (12):11-17.
Huang L X, You N S, Lei J C, Zheng X H . Analysis of combining ability of hybrid rice and selection of high-yield combinations. Fujian Sci & Technol Rice & Wheat, 1994, (12):11-17 (in Chinese with English abstract).
[24] 廖伏明, 周坤炉, 盛孝邦, 阳和华, 徐秋生 . 籼型三系杂交水稻主要农艺性状配合力研究. 作物学报, 1999,25:622-631.
Liao F M, Zhou K L, Sheng X B, Yang H H, Xu Q S . Studies on combining ability of major agronomic characters in three-line indica hybrid rice. Acta Agron Sin, 1999,25:622-631 (in Chinese with English abstract).
[25] 王玉 . 利用复合性状开展QTL作图的有效性研究. 沈阳农业大学硕士学位论文, 辽宁沈阳, 2010.
Wang Y . On the Use of Mathematically-derived Composite Traits and Their Efficiency in Quantitative Trait Locus Mapping. MS Thesis of Shenyang Agricultural University, Shenyang, Liaoning, China, 2010 (in Chinese with English abstract).
[26] Li J M, Xiao J H, Grandillo S, Jiang L Y, Wan Y Z, Deng Q Y, Yuan L P, McCouch S R . 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, 2004,47:697-704.
[27] Rabiei B, Valizadeh M, Ghareyazie B, Moghaddam M, Ali A J . Identification of QTLs for rice grain size and shape of Iranian cultivars using SSR markers. Euphytica, 2004,137:325-332.
[1] CHEN Ling-Ling, LI Zhan, LIU Ting-Xuan, GU Yong-Zhe, SONG Jian, WANG Jun, QIU Li-Juan. Genome wide association analysis of petiole angle based on 783 soybean resources (Glycine max L.) [J]. Acta Agronomica Sinica, 2022, 48(6): 1333-1345.
[2] DENG Zhao, JIANG Nan, FU Chen-Jian, YAN Tian-Zhe, FU Xing-Xue, HU Xiao-Chun, QIN Peng, LIU Shan-Shan, WANG Kai, YANG Yuan-Zhu. Analysis of blast resistance genes in Longliangyou and Jingliangyou hybrid rice varieties [J]. Acta Agronomica Sinica, 2022, 48(5): 1071-1080.
[3] SUN Si-Min, HAN Bei, CHEN Lin, SUN Wei-Nan, ZHANG Xian-Long, YANG Xi-Yan. Root system architecture analysis and genome-wide association study of root system architecture related traits in cotton [J]. Acta Agronomica Sinica, 2022, 48(5): 1081-1090.
[4] QIN Qin, TAO You-Feng, HUANG Bang-Chao, LI Hui, GAO Yun-Tian, ZHONG Xiao-Yuan, ZHOU Zhong-Lin, ZHU Li, LEI Xiao-Long, FENG Sheng-Qiang, WANG Xu, REN Wan-Jun. Characteristics of panicle stem growth and flowering period of the parents of hybrid rice in machine-transplanted seed production [J]. Acta Agronomica Sinica, 2022, 48(4): 988-1004.
[5] ZHAO Hai-Han, LIAN Wang-Min, ZHAN Xiao-Deng, XU Hai-Ming, ZHANG Ying-Xin, CHENG Shi-Hua, LOU Xiang-Yang, CAO Li-Yong, HONG Yong-Bo. Genetic dissection of the bacterial blight disease resistance in super hybrid rice RILs using genome-wide association study [J]. Acta Agronomica Sinica, 2022, 48(1): 121-137.
[6] WANG Ya-Liang, ZHU De-Feng, ZHANG Yu-Ping, CHEN Ruo-Xia, XIANG Jing, CHEN Hui-Zhe, CHEN Jiang-Hua, WANG Feng. Analysis on the plant growth and yield formation of double cropping late season hybrid rice in machine transplanting with long seedling age by precision drill sowing [J]. Acta Agronomica Sinica, 2022, 48(1): 215-225.
[7] YANG Zhi-Yuan, SHU Chuan-Hai, ZHANG Rong-Ping, YANG Guo-Tao, WANG Ming-Tian, QIN Jian, SUN Yong-Jian, MA Jun, LI Na. Comparison of tolerances to nitrogen fertilizer between compact and loose hybrid indica rice varieties [J]. Acta Agronomica Sinica, 2021, 47(8): 1593-1602.
[8] WANG Yan-Hua, LIU Jing-Sen, LI Jia-Na. Integrating GWAS and WGCNA to screen and identify candidate genes for biological yield in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(8): 1491-1510.
[9] MA Juan, CAO Yan-Yong, LI Hui-Yong. Genome-wide association study of ear cob diameter in maize [J]. Acta Agronomica Sinica, 2021, 47(7): 1228-1238.
[10] KE Jian, CHEN Ting-Ting, XU Hao-Cong, ZHU Tie-Zhong, WU Han, HE Hai-Bing, YOU Cui-Cui, ZHU De-Quan, WU Li-Quan. Effects of different application methods of controlled-release nitrogen fertilizer on grain yield and nitrogen utilization of indica-japonica hybrid rice in pot-seedling mechanically transplanted [J]. Acta Agronomica Sinica, 2021, 47(7): 1372-1382.
[11] GENG La, HUANG Ye-Chang, LI Meng-Di, XIE Shang-Geng, YE Ling-Zhen, ZHANG Guo-Ping. Genome-wide association study of β-glucan content in barley grains [J]. Acta Agronomica Sinica, 2021, 47(7): 1205-1214.
[12] CHEN Can, NONG Bao-Xuan, XIA Xiu-Zhong, ZHANG Zong-Qiong, ZENG Yu, FENG Rui, GUO Hui, DENG Guo-Fu, LI Dan-Ting, YANG Xing-Hai. Genome-wide association study of blast resistance loci in the core germplasm of rice landraces from Guangxi [J]. Acta Agronomica Sinica, 2021, 47(6): 1114-1123.
[13] ZHANG Chun, ZHAO Xiao-Zhen, PANG Cheng-Ke, PENG Men-Lu, WANG Xiao-Dong, CHEN Feng, ZHANG Wei, CHEN Song, PENG Qi, YI Bin, SUN Cheng-Ming, ZHANG Jie-Fu, FU Ting-Dong. Genome-wide association study of 1000-seed weight in rapeseed (Brassica napus L.) [J]. Acta Agronomica Sinica, 2021, 47(4): 650-659.
[14] JIN Yi-Rong, LIU Jin-Dong, LIU Cai-Yun, JIA De-Xin, LIU Peng, WANG Ya-Mei. Genome-wide association study of nitrogen use efficiency related traits in common wheat (Triticum aestivum L.) [J]. Acta Agronomica Sinica, 2021, 47(3): 394-404.
[15] WEI Li-Juan, SHEN Shu-Lin, HUANG Xiao-Hu, MA Guo-Qiang, WANG Xi-Tong, YANG Yi-Ling, LI Huan-Dong, WANG Shu-Xian, ZHU Mei-Chen, TANG Zhang-Lin, LU Kun, LI Jia-Na, QU Cun-Min. Genome-wide association analysis reveals zinc-tolerant loci of rapeseed at germination stage [J]. Acta Agronomica Sinica, 2021, 47(2): 262-274.
Viewed
Full text


Abstract

Cited

  Shared   
  Discussed   
No Suggested Reading articles found!