Genetic Diversity of Global Aromatic Rice Varieties

doi:10.7677/ynzwyj201515048

Abstract

Abstract:

Genetic diversity of 434 rice accessions collected from 16 countries, including 345 fragrance rice varieties and 89 nonfragrance rice varieties, have been analyzed. A total of 573 alleles were detected by using 77 simple sequence repeats (SSR) primer pairs covering all rice 12 chromosomes. The value of allelic polymorphism information content (PIC) ranged from 0090 to 0845, with an average of 0516 per locus; Gene diversity (GD) varied from 0091 to 0859, with an average of 0573; The mean value of major allele frequencies (MAF) was 0540, covering from 0251 to 0953. In addition, 434 rice accessions are divided into three subpopulations by cluster and population structure analysis, and FST between subpopulations showed a mean of -0116, ranging from -0623 to 0494; The score of genetic distance calculated by Nei′s method appeared from 0207 to 0355. Major allele frequencies within each subpopulation distributed from 0408 to 0746, and gene diversity level from 0354 to 0699, while PIC from 0320 to 0658. Sequencing 6 mitochondrion genes in 18 rice varieties exhibited no different in 5 genes, whereas Mit4 contains a 3 SNPs in the gene body, which acts as an important marker to understanding the relationship between Indica/Japonica differentiation and the evolution of fragrant gene. Finally, genetic diversity and mitochondrion gene sequencing would help to know about the origin of fragrant resource and benefit rice breeding.

Key words: Aromatic rice, SSR markers, Genetic diversity, Cluster analysis

CLC Number:

Q 16

YU Ya-Ying-, SHAO Gao-Neng-, SHENG Zhong-Hua-, JIANG Han-Wei-, HE Ji-Wai-, SUN Yuan-Yuan-, CA Yi-Cong-, HU Pei-Song-**, TANG Shao-Qing. Genetic Diversity of Global Aromatic Rice Varieties[J]. Plant Diversity, 2015, 37(06): 871-880.

References

胡培松, 唐绍清, 顾海华等, 2006. 水稻香味的遗传研究与育种利用［J］. 中国稻米, 6: 5
黄发松, 胡培松, 唐绍清等, 1999. 食用优质稻米新品种的研究开发［J］. 中国稻米, 6: 24—26
栾霁, 2013. 水稻线粒体DNA遗传多态性及相关基因表达的研究［D］. 长沙: 湖南师范大学
谢黎虹, 段斌伍, 孙成效, 2003. 香稻的渊源, 香味及遗传［J］. 世界农业, 11
张天真, 2003. 作物育种学总论［M］. 北京: 中国农业出版社, 46
赵国超, 2010. 香稻分子育种及香味形成分子机理的初步研究［D］. 上海: 上海师范大学
Bai XG (白现广), Cheng ZQ (程在全), Lin ZL (蔺忠龙) et al., 2009. Comparison of genetic diversity between local cultivated aromatic and nonaromatic rice in Yunnan Province［J］. Journal of Anhui Agricultural Science (安徽农业科学), 10 (1): 56—59
Botstein D, White RL, Skolnick M et al., 1980. Construction of a genetic linkage map in man using restriction fragment length polymorphisms［J］. American Journal of Human Genetics, 32 (3): 314
Chen ML, Wei XJ, Shao GN et al., 2012. Fragrance of the rice grain achieved via artificial microRNAinduced downregulation of OsBADH2［J］. Plant Breeding, 131 (5): 584—590
Chen YM (陈远孟), Zhang XJ (张向军), Chen CH (陈传华), 2008a. Developm ent and current：research of aromatic rice［J］. Guangxi Agricultural Sciences (广西农业科学), 38: 597—600
Chen YM (陈远孟), Zhang XJ (张向军), Chen CH (陈传华) et al., 2008b. Assessment of genetic diversity of aromatic rice (Oryza sativa) from Guangxi and South Asia by using SSR markers［J］. Guihaia (广西植物), 28 (2): 154—159
Falush D, Stephens M, Pritchard JK, 2003. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies［J］. Genetics, 164 (4): 1567—1587
Fitzgerald MA, Mccouch SR, Hall RD, 2009. Not just a grain of rice: the quest for quality［J］. Trends in Plant Science, 14 (3): 133—139
Garris AJ, Tai TH, Coburn J et al., 2005. Genetic structure and diversity in Oryza sativa L.［J］. Genetics, 169 (3): 1631—1638
Hashemi FG, Rafii M, Ismail M et al., 2013. Biochemical, genetic and molecular advances of fragrance characteristics in rice［J］. Critical Reviews in Plant Sciences, 32 (6): 445—457
Huang J (黄菊), Xu YF (许言福), Xie MX (谢米雪) et al., 2014. Genotypes analyses of ten genes related to eating quality of twentythree fragrant rice cultivars by molecular marker［J］. Plant Diversity and Resources (植物分类与资源学报), 36 (3): 381—387
Huang TX (黄庭旭), Jiang WQ (江文清), You QR (游晴如) et al., 2006. Breeding and utilization of fragrant restoring line Dalixiang 15 of indica hybrid rice［J］. Fujian Journal of Agricultural Science (福建农业学报), 21 (2): 83—88
Jain S, Jain RK, Mccouch SR, 2004. Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescentlylabeled microsatellite markers［J］. Theoretical and Applied Genetics, 109 (5): 965—977
Jiao GA (焦桂爱), Hu PS (胡培松), Tang SQ (唐绍清) et al., 2010. Diversity analysis of RVA profiles of aromatic rice［J］. Journal of Nuclear Agricultural Science (核农学报), 24 (1): 78—82
Jin L, Lu Y, Xiao P et al., 2010. Genetic diversity and population structure of a diverse set of rice germplasm for association mapping［J］. Theoretical and Applied Genetics, 121 (3): 475—487
Kaur S, Panesar PS, Bera MB et al., 2015. Simple sequence repeat markers in genetic divergence and markerassisted selection of rice cultivars: a review［J］. Critical Reviews in Food Science and Nutrition, 55 (1): 41—49
Kovach MJ, Calingacion MN, Fitzgerald MA et al., 2009. The origin and evolution of fragrance in rice (Oryza sativa L.) ［J］. Proceedings of the National Academy of Sciences of the United States of America, 106 (34): 14444—14449
Liu K, Muse SV, 2005. PowerMarker: an integrated analysis environment for genetic marker analysis［J］. Bioinformatics, 21 (9): 2128—2129
Ma J (马静), Sun JC (孙建昌), An YP (安永平) et al., 2013. Analysis of genetic diversity with population of Japonica rice from Ningxia using microsatellite markers［J］. Journal of Plant Genetic Resources (植物遗传资源学报), 14 (5): 826—832
Nakazono M, Ishikawa M, Yoshida KT et al., 1996. Multiple initiation sites for transcription of a gene for subunit 1 of F1ATPase (atp1) in rice mitochondria［J］. Current Genetics, 29 (5): 417—422
Nei M, 1973. Analysis of gene diversity in subdivided populations［J］. Proceedings of the National Academy of Sciences of the United States of America, 70 (12): 3321—3323
Ni J, Colowit PM, Mackill DJ, 2002. Evaluation of genetic diversity in rice subspecies using microsatellite markers［J］. Crop Science, 42 (2): 601—607
Pachauri V, Singh MK, Singh AK et al., 2010. Origin and genetic diversity of aromatic rice varieties, molecular breeding and chemical and genetic basis of rice aroma［J］. Journal of Plant Biochemistry and Biotechnology, 19 (2): 127—143
Shao GN, Tang A, Tang SQ et al., 2011. A new deletion mutation of fragrant gene and the development of three molecular markers for fragrance in rice［J］. Plant Breeding, 130 (2): 172—176
Shao GN, Tang SQ, Chen ML et al., 2013. Haplotype variation at Badh2, the gene determining fragrance in rice［J］. Genomics, 101 (2): 157—162
Tang A (唐傲), Shao GN (邵高能), Jiao GA (焦桂爱) et al., 2009. Comparative assessment of SSR diversity in aromatic rice germplasm［J］. Hereditas (遗传), 31 (4): 412—419
Tautz D, 1989. Hypervariabflity of simple sequences as a general source for polymorphic DNA markers［J］. Nucleic Acids Research, 17 (16): 6463—6471
Wang J (王军), Zhong WG (仲维功), Chen ZD (陈志德) et al., 2008. Progress of studies on the fragrance of rice and its application［J］. Journal of Jinlin Institute of Technology (金陵科技学院学报), 24 (2): 53—57
Xie H, Wang J, Qian M et al., 2014. Mitotypespecific sequences related to cytoplasmic male sterility in Oryza species［J］. Molecular Breeding, 33 (4): 803—811
Yang WX (杨旺兴), Xu XM (许旭明), Qi JM (祁建民) et al., 2013. Genetic diversity of parents and derived lines based on phenotypic characters and SSR cluster analysis［J］. Fujian Journal of Agricultural Science (福建农业学报), 28 (3): 211—216
Zhang T, Hu S, Zhang G et al., 2012.The organelle genomes of hassawi rice (Oryza sativa L.) and its hybrid in saudi arabia: genome variation, rearrangement, and origins［J］. PLoS ONE, 7 (7): e42041
Zhu YL (朱勇良), Xie YL (谢裕林), Huang LZ (黄凌哲) et al., 2012. Establishment of SSR fingerprint M ap and preliminary analysis of genetic diversity among aromatic rice from Taihu and other Areasin China［J］. Journal of Plant Genetic Resources (植物遗传资源学报), 13 (4): 666—671

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