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Journal of Integrative Agriculture  2014, Vol. 13 Issue (1): 18-30    DOI: 10.1016/S2095-3119(13)60353-6
Crop Genetics · Breeding · Germplasm Resources Advanced Online Publication | Current Issue | Archive | Adv Search |
Effect of Environment and Genetic Recombination on Subspecies and Economic Trait Differentiation in the F2 and F3 Generations from indicajaponica Hybridization
 WANG He-tong, JIN Feng, JIANG Yi-jun, LIN Qing-shan, XU Hai, CHENG Ling, XIA Ying-jun, LIU Chun-xiang, CHEN Wen-fu , XU Zheng-jin
1.Rice Research Institute, Shenyang Agricultural University, Shenyang 110010, P.R.China
2.Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510000, P.R.China
3.Agricultural Technology Extension Station, Department of Agriculture of Guangdong Province, Guangzhou 510000, P.R.China
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摘要  indica and japonica are the two most important subspecies of Asian cultivated rice. Identifying mechanisms responsible for population differentiation in these subspecies is important for indica-japonica hybridization breeding. In this study, subspecies and economic trait differentiation patterns were analyzed using morphological and molecular (InDel and Intron Length Polymorphism) data in F2 and F3 populations derived from indica-japonica hybridization. Populations were grown in Liaoning and Guangdong provinces, China, with F3 populations generated from F2 populations using bulk harvesting (BM) and single-seed descent methods (SSD). Segregation distortion was detected in F3-BM populations, but not in F3- SSD or in F2 populations. Superior performance was observed with respect to economic traits in Liaoning compared with that in Guangdong and 1 000-grain weight (KW), seed setting rate (SSR) and grain yield per plant (GYP) were significantly correlated with indica and japonica subspecies types. Analysis of molecular and morphological data demonstrated that the environment is the main factor giving rise to population differentiation in indica-japonica hybridization. In addition, we also found that KW, SSR and GYP are related to subspecies characteristics and kinship, which is possibly a significant factor resulting in economic trait differentiation and determining environmental adaptability. Our study has provided new insights into the process of population differentiation in these subspecies to inform indica-japonica hybridization breeding.

Abstract  indica and japonica are the two most important subspecies of Asian cultivated rice. Identifying mechanisms responsible for population differentiation in these subspecies is important for indica-japonica hybridization breeding. In this study, subspecies and economic trait differentiation patterns were analyzed using morphological and molecular (InDel and Intron Length Polymorphism) data in F2 and F3 populations derived from indica-japonica hybridization. Populations were grown in Liaoning and Guangdong provinces, China, with F3 populations generated from F2 populations using bulk harvesting (BM) and single-seed descent methods (SSD). Segregation distortion was detected in F3-BM populations, but not in F3- SSD or in F2 populations. Superior performance was observed with respect to economic traits in Liaoning compared with that in Guangdong and 1 000-grain weight (KW), seed setting rate (SSR) and grain yield per plant (GYP) were significantly correlated with indica and japonica subspecies types. Analysis of molecular and morphological data demonstrated that the environment is the main factor giving rise to population differentiation in indica-japonica hybridization. In addition, we also found that KW, SSR and GYP are related to subspecies characteristics and kinship, which is possibly a significant factor resulting in economic trait differentiation and determining environmental adaptability. Our study has provided new insights into the process of population differentiation in these subspecies to inform indica-japonica hybridization breeding.
Keywords:  indica-japonica hybridization       subspecies differentiation       environment       economic traits       recombinant inbred line       rice  
Received: 19 November 2012   Accepted:
Fund: 

This study was supported by the National Natural Science Foundation of China (30971845).

Corresponding Authors:  XU Zheng-jin, Tel: +86-24-88487183, E-mail: xuzhengjin@126.com     E-mail:  xuzhengjin@126.com
About author:  WANG He-tong, E-mail: tony.w.china@gmail.com

Cite this article: 

WANG He-tong, JIN Feng, JIANG Yi-jun, LIN Qing-shan, XU Hai, CHENG Ling, XIA Ying-jun, LIU Chun-xiang, CHEN Wen-fu , XU Zheng-jin. 2014. Effect of Environment and Genetic Recombination on Subspecies and Economic Trait Differentiation in the F2 and F3 Generations from indicajaponica Hybridization. Journal of Integrative Agriculture, 13(1): 18-30.

Bai X F, Luo L J, Yan W H, Mallikarjuna R K, Zhan W,Xing Y Z. 2010. Genetic dissection of rice grain shapeusing a recombinant inbred line population derived fromtwo contrasting parents and fine mapping a pleiotropic quantitative trait locus qGL7. BMC Genomics, 11, 16.

Cai X X, Liu J, Qiu Y Q, Zhao W, Song Z P, Lu B R. 2007.Differentiation of indica-japonica rice revealed byinsertion/deletion (InDel) fragments obtained from the comparative genomic study of DNA sequences between93-11 (indica) and Nipponbare (japonica) Frontiers ofBiology in China, 2, 291-296.

Chang T T, Oka H I. 1976. Genetic variousness in the climatic adaption of rice cultivars. In: Proceedings of the Symposium on Climate and Rice. International RiceResearch Institute, Los Banǒs, Philippines. pp. 87-111

Chen W F, Xu Z J, Zhang L B. 1995a. Comparative study ofstomata density and gas diffusion resistance in leaves ofvarious types of rice. Korean Journal of Crop Science,40, 125-132

Chen W F, Xu Z J, Zhang L B. 1995b. Physiological Basisof Rice Breeding for Super High Yield. Liaoning Scienceand Technology Press, Shenyang. (in Chinese)

Cheng K S, Zhou J W, Lu Y X, Luo J, Huang N W, LiuG R, Wang X K. 1984. Studies on the indigenous inYunnan and their utilization II-A revised classificationof Asian culture rice. Acta Agronomica Sinica, 4, 271. (inChinese)

Ding Y. 1983. Classification of Chinese culture rice. In: Anthology of Ding Ying’s Paper in Rice. Agricultural Publishing Company, Beijing. pp. 74-93 (in Chinese)

Fan Y Y, Zhuang J Y, Wu J L, Sun B L, Zheng K L. 2000.SSLP based identification of subspecies in rice (Oryzasativa L.). Hereditas (Beijing), 6, 392-394. (in Chinese)

Gu M H. 2010. Discussion on the aspects of high-yieldingbreeding in rice. Acta Agronomica Sinica, 36, 1431-1439.

He G H, Zhen J K, Li Y, Yang Z L. 1993. A comparativestudy on yield components of various type of rice.Journal of Southwest Agricultural University, 15, 438-440. (in Chinese)

Jiang S K, Zhong M, Xu Z J, Zhang L, Ma H, Liu S X. 2006.Classification of rice cultivars with RAPD molecular markers. Journal of Shenyang Agricultural University,37, 639-641. (in Chinese)

Kanbar A, Shahriari H E. 2011. Participatory selectionassisted by DNA markers for enhanced drought resistance and productivity in rice (Oryza sativa L.).Euphytica, 178, 137-150

Kato S, Kosaka H, Hara S. 1928. On the affinity of rice varieties as shown by fertility of hybrid plants. Bulletinof Scienses of Faculty of Agriculture Kyushu University.3, 132-147

Li S G, Li H Y, Zhou K D, Ma Y Q. 1995. Genetic analysison exterior quality traits in hybrid rice. Journal of Southwest Agricultural University, 17, 197-201 (inChinese)

Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C,Li X, Xiao J, et al. 2011. Natural variation in GS5 playsan important role in regulating grain size and yield inrice. Nature Genetics, 43, 1266-1269

Li Y H, Xu C G, Sun C Q, Li Z C, Wang X K. 1999.Genotypic divergence and classification of Asiancultivated rice (Oryza sativa L.). Acta AgronomicaSinica, 25, 518-526 (in Chinese)

Lin H X, Qian H R, Zhuang J Y, Lu J, Min S K, Xiong ZM, Huang N, Zheng K L. 1996. RFLP mapping of QTLsfor yield and related characters in rice. Theoretical andApplied Genetics, 92, 920-927

Lu B R, Cai X X, Jin X. 2009. Efficient indica and japonicarice identification based on the InDel molecular method:its implication in rice breeding and evolutionaryresearch. Progress in Natural Science, 19, 1241-1252

Mao T, Xu H, Guo YH, Zhu C J, Chen K, Wang J Y, XuZ J. 2009. Establishment of subspecies classificationof indica and japonica system by SSR markers. ActaAgriculturae Boreall-Sinca, 24, 119-124

Motoyuki A, Hitoshi S, Lin S Y, Toshio Y, Tomonori T,Asuka N, Enrique R A, Qian Q, Hidemi K, Maoto M.2005. Cytokinin oxidase regulates rice grain productio.Science, 309, 741-745

Murray M G, Thompson W F. 1980. Rapid isolation of highmolecular weight plant DNA. Nucleic Acids Research, 8,4321-4325

Ni J J, Colowit P M, Mackill D J. 2002. Evaluation of genetic diversity in rice subspecies using microsatellite markers. Crop Science, 42, 601-607

Oka H I. 1958. Variation and classification of cultivatedrice. Indian Journal of Genetics and Plant Breeding, 18,79.

Peng J H. 1991. An analysis of genotype × environmentinteraction on grain yield and the differentiationof ecologic type region in rice. Journal of Sichuan Agricultural University, 9, 327-333 (in Chinese)

Peng J H, Li Y C. 1990. The dissection and comparison ofyield formation for indica and japonica subspecies inrice. Journal of Sichuan Agricultural University, 8, 162-168. (in Chinese)

Qian Q, He P, Zheng X W, Chen Y, Zhu L H. 2000.Genetic analysis of morphological index and its relatedtaxonomic traits for classification of indica/japonicarice. Science in China (Series C, Life Sciences), 43, 113-119

Shao G, Tang S, Luo J, Jiao G, Wei X, Tang A, Wu J,Zhuang J, Hu P. 2010. Mapping of qGL7-2, a grainlength QTL on chromosome 7 of rice Journal of Genetics and Genomics, 37, 523-531

Shen Y J, Jiang H, Jin J P, Zhang Z B, Xi B, He Y Y, WangG, Wang C, Qian L, Li X, et al. 2004. Development ofgenome-wide DNA polymorphism database for map-based cloning of rice genes. Plant Physiology, 135,1198-1205

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

Sun C Q, Jiang T B, Cheng L, Wu C M, Li Z C, Wang X K.2000. Studies on the relationship between heterosis andgenetic differentiation in hybrid rice (Oryza sativa L.).Acta Agronomica Sinica, 26, 641-649

Sun C Q, Yuan P Y, Yoshimura A. 1998. Comparative studyon the indica-japonica differentiation of nuclear DNA, mitochondrial DNA and chloroplast DNA in cultivated rice (Oryza sativa L.). Acta Agronomica Sinica, 98, 677-686 (in Chinese)

Sun J, Liu D, Wang J Y, Ma D R, Tang L, Gao H, Xu Z J,Chen W F. 2012. The contribution of intersubspecific hybridization to the breeding of super-high-yieldingjaponica rice in northeast China. Theoretical andApplied Genetics, 125, 1149-1157

Wang X K, Cheng K S, Hang N W, Luo J, Lu Y X, Liu G R.1987. Studies on two important rice types concerning the origin and differentiation of Asian cultivated rice. ActaGenetica Sinica, 14, 262-270

Wang X K, Li R H, Sun C Q. 1997. Identification andtaxonomy of subspecies of Asia cultivated rice and thehybrids between subspecies. Chinese Science Bulletin,42, 2596-2603. (in Chinese)

Wang X S, Zhao X Q, Zhu J, Wu W R. 2005. Genome-wideinvestigation of intron length polymorphisms and their potential as molecular markers in rice. DNA Research,12, 417-427

Wang Z, Yu C, Liu X, Liu S, Yin C, Liu L, Lei J, Jiang L,Yang C, Chen L, et al. 2012. Identification of indica ricechromosome segments for the improvement of japonicainbreds and hybrids. Theoretical and Applied Genetics,124, 1351-1364

Weng J, Gu S, Wan X, Gao H, Guo T, Su N, Lei C, ZhangX, Cheng Z, Guo X, et al. 2008. Isolation and initial characterization of GW5, a major QTL associated withrice grain width and weight. Cell Research, 18, 1199-1209

Xiong Z Y, Zhang S J, Wang Y Y, Ford-Lioyd B V, TuM, Jin X, Wu Y, Yan H X, Yang X, Liu P, et al. 2010.Differentiation and distribution of indica and japonica rice varieties along the altitude gradients in Yunnan Province of China as revealed by InDel molecular markers. Genetic Resources and Crop Evolution, 57,891-902

Xu H, Liu H G, Yang L, Zhu C J, Wang J Y, Yang Q H, XuZ J, Zheng J K. 2007. Subspeices characteristics in filialgeneration of cross between indica and japonica riceunder different environments. Frontiers of Agriculture inChina 1, 281-288

Xu H, Liu H G, Zhu C J, Yang L, Guo Y H, Wang J Y,Yang Q H, Xu Z J, Zheng J K, Chen W F. 2008. Effectof ecological environments on subspecies characteristicsand economic traits in filial generations of cross betweenindica and japonica rice. Frontiers of Agriculture inChina, 2, 23-29

Xu Z J, Chen W F, Cao H Y, Zhang L B, Yang S R.1998. Relationships between the characters of panicle and vascular bundles in neck-panicle of rice. Acta Agronomica Sinica, 24, 47-54 (in Chinese)

Xu Z J, Chen W F, Ma D R, Wu X D, Zheng X Y, Wang JY. 2005. Relationship between eating quality and otherquality characters of rice in Liaoning. Acta AgronomicaSinica, 31, 1092-1094

Xu Z J, Li J Q, Huang R D, Jiang J, Chen W F, Zhang LB. 2003a. Subspecies characteristics and classificationof rice varieties developed through indica and japonicacrossing. Scientia Agricultural Sinica, 36, 1571-1675 (inChinese)

Xu Z J, Li J Q, Jiang J, Jing Y H, Zhang W Z, Chen W F, Zhang L B. 2003b. Subspecies characteristics andtheir relationships with economic characters. ActaAgronomica Sinica, 29, 735-739

Xu Z J, Quan T Y, Ma Y M, Wang J D. 1997. Relationshipsbetween the number of the vascular bundle of neck-panicle and the characters of panicle in the filial generation from indica and japonica rice. Journal of Shenyang Agricultural University, 28, 1-6 (in Chinese)

Yang S R, Shen X Y, Gu W L, Cao D J. 1962. Studies onrice cross-breeding between indica and japonica (II).Acta Agronomica Sinica, 1, 97-102. (in Chinese)

Yang S R, Zhao J S. 1959. Studies on indica and japonicarice breeding. Acta Agronomica Sinica, 10, 256-268. (inChinese)

Yuan L P. 1997. Hybrid rice breeding for super high yield.Hybrid Rice, 12, 1-3

Zeder M A, Emshwiller E, Smith B D, Bradley D G. 2006.Documenting domestication: the intersection of geneticsand archaeology. Trends in Genetics, 22, 139-155

Zhang P, Li J Q, Li X L, Liu X D, Zhao X J, Lu Y G. 2011.Population structure and genetic diversity in a rice corecollection (Oryza sativa L.) investigated with SSR markers. PloS One, 6, e27565.

Zhang Q E, Saghai-Maroof M A, Lu T Y, Shen B Z. 1992.Genetic diversity and differentiation of indica andjaponica rice detected by RFLP an alysis. Theoretical and Applied Genetics, 83, 495-499

Zhao A C, Rui C Q. 1982. Analysis of combining abilityon main quantitative characters in hsien rice. ActaAgronomica Sinica, 8, 113-117 (in Chinese)

Zhou J S, Lu C G. 2005. Practice and thinking on rice breeding for high yield. Acta Agronomica Sinica, 31,254-258 (in Chinese)

Zhu L H, Zhou Y Z, Tao S C. 1964. Breeding studies onhybridization between O. sativa L. subsp. hsien andO. sativa L. subsp. keng in the cultivated rice. ActaAgronomica Sinica, 3, 69-84. (in Chinese)
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