国内外香稻资源遗传多样性研究

doi:10.7677/ynzwyj201515048

摘要/Abstract

摘要：

收集来源于16个国家和地区的345份香稻和89份非香材料开展了遗传多样性研究。利用分布于12条染色体上77对SSR标记，共检测出573个等位基因位点，多态信息含量（PIC）变幅为0090~0845，平均为0516；基因多样性（GD）变幅为0091~0859，平均为0573；主效等位基因频率（MAF）平均为0540，变幅从0251~0953。聚类分析和群体结构分析将434份材料分成3个亚群，亚群与亚群间FST平均为-0116，变幅从-0623~0494；据Nei’s方法计算的亚群间遗传距离从0207~0355；各亚群内的主效等位基因频率为0408~0746，基因多样性变幅为0354~0699，多态信息含量则从0320~0658。通过对18个水稻品种中的6个线粒体基因测序结果发现5个基因内不存在核苷酸的差异，仅Mit4中包含了3个SNP的两种基因型，可以作为反应籼粳分化与香味基因进化的重要功能标记。本研究较为系统地反映了不同香稻材料间以及与非香稻资源间的亲缘关系，为进一步了解国内外香稻种质资源和优质香稻育种提供了重要的参考依据。

关键词: 香稻, SSR标记, 遗传多样性, 聚类分析

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

中图分类号:

Q 16

余亚莹1, 邵高能1, 圣忠华1, 蒋汉伟2, 贺记外1, 孙园园2, 蔡怡聪1, 胡培松1**, 唐绍清1. 国内外香稻资源遗传多样性研究[J]. Plant Diversity, 2015, 37(06): 871-880.

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.

参考文献

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

[1]	孙旭东1、2. 拟南芥Rboh基因家族成员的分子和功能学比较[J]. Plant Diversity, 2015, 37(4): 463-471.
[2]	呼慧丽, 李波, 胡菀, 孙志霞, 张志勇, 范邓妹. 南天竹微卫星标记开发及特性分析[J]. Plant Diversity, 2015, 37(2): 141-144.
[3]	朱弘1, 库伟鹏1, 戎建涛2, 项佳娥3. 浙江南麂岛陆生维管束植物多样性及区系特征[J]. Plant Diversity, 2015, 37(06): 713-720.
[4]	姚雪芹, 张钦弟, 毕润成. 山西太岳山辽东栎群落林下草本植物功能群分类[J]. Plant Diversity, 2015, 37(06): 849-855.
[5]	徐玉仙, 张微微, 莫海波, 李春, 曹建国, 田代科. 基于ESTSSR标记的莲属种质资源遗传多样性分析[J]. Plant Diversity, 2015, 37(05): 595-604.
[6]	李苗苗, MEEGAHAKUMBURA M. Kasun, 严丽君, 刘杰, 高连明. 核基因组微卫星标记揭示大理茶参与了普洱茶的驯化过程[J]. Plant Diversity, 2015, 37(01): 29-37.
[7]	陈韵竹, 蒋丽娟, 陈景震, 刘强, 张路红, 刘健, 赵志伟. 光皮树不同无性系主要农艺性状多样性分析[J]. Plant Diversity, 2014, 36(06): 755-762.
[8]	叶林江, 王静, 孙鹏, 董书鹏, 张志勇. 四种栲属植物微卫星标记在钩栲中的通用性检测[J]. Plant Diversity, 2014, 36(04): 443-448.
[9]	黄菊, 许言福, 谢米雪, 李建粤. 分子标记分析二十三种香型水稻十个食味品质相关基因的基因型[J]. Plant Diversity, 2014, 36(03): 381-387.
[10]	黄家林, 李树云, 胡虹. 珍稀濒危植物硬叶兜兰的遗传多样性及遗传结构研究[J]. Plant Diversity, 2014, 36(02): 209-218.
[11]	官萌萌1、2, 马瑞1, 龚洵1. 金沙江河谷特有植物罂粟莲花的保护遗传学[J]. Plant Diversity, 2013, 35(5): 555-562.
[12]	赵凯1、2, 王德元2, 张文娟2, 邵剑文2 . 都支杜鹃遗传多样性的ISSR分析[J]. Plant Diversity, 2013, 35(5): 578-584.
[13]	何庆元1、2, 李正鹏1, 吴萍1, 杨红燕2, 王松华1. 起始密码子区域相关序列多态性的开发及在苜蓿遗传多样性上的应用[J]. Plant Diversity, 2013, 35(1): 48-54.
[14]	郑彦超, 沐先运, 李研南, 涂蔷, 张志翔. 卫矛属刺果卫矛组的数量分类学分析[J]. Plant Diversity, 2012, 34(3): 271-286.
[15]	董莉娜1, 李德铢1、2, 王红1. 中国西南特有翅茎草属的种间界定——基于形态学和分子系统学分析[J]. Plant Diversity, 2011, 33(6): 581-594.