Crops ›› 2019, Vol. 35 ›› Issue (5): 15-21.doi: 10.16035/j.issn.1001-7283.2019.05.003

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Genetic Diversity Analysis of Rice Varieties in Tengchong, Yunnan Based on SSR Markers

Li Song1,Zhang Shicheng1,Dong Yunwu2,Shi Delin2,Shi Yundong1   

  1. 1 School of Chemical Biology and Environment, Yuxi Normal University, Yuxi 653100, Yunnan, China
    2 Yuxi Seed Management Station, Yuxi 653100, Yunnan, China
  • Received:2019-05-06 Revised:2019-08-15 Online:2019-10-15 Published:2019-11-07
  • Contact: Yundong Shi

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Abstract:

The genetic diversity analysis among several of indigenous waxy rice and it’s popularization grown in Tengchong were carried out based on SSR primers recommended by Chinese Agricultural Industry Standard (NY/T 1433-2014). The results showed that 18 pairs of SSR primers presented polymorphic among 20 varieties, and 82 polymorphic fragments were detected. The number of polymorphic fragments detected by each pair of primers was 2 to 8, with an average of 4.6. The Nei′s diversity index was 0.155 to 0.384, with an average of 0.284. The Shannon′s information index was 0.280 to 0.567, with an average of 0.398. The SSR polymorphism information content (PIC) distribution range from 0.26 to 0.84, with an average of 0.63. The genetic similarity coefficient range from 0.410 to 0.976, with an average of 0.710. The cluster analysis showed that when the genetic similarity coefficient was 0.70, 20 varieties were divided into 4 groups, of which groupsⅠand groupsⅡincluded 4 and 5 varieties, respectively, of which groupsⅢonly included indigenous waxy valley while the groupⅣincluded 10 varieties. The results showed that Tengchong waxy rice and extended varieties had rich genetic diversity and good polymorphism, which provided a reference for rice germplasm improvement and new variety breeding in Tengchong.

Key words: Rice, SSR markers, Germplasm resources, Genetic diversity

Table 1

The tested rice materials"

序号No. 品种Variety 来源地Source 类型Type 选育单位Breeding unit
1 内优5022 云南腾冲 籼型杂交水稻 云南绿晶种业有限公司
2 花优926 云南腾冲 籼型杂交水稻 四川省农业科学院水稻高粱研究所
3 两优2161 云南腾冲 籼型杂交水稻 福建省农业科学院水稻研究所,云南农业科学院粮食作物研究所
4 宜香优2115 云南腾冲 籼型杂交水稻 四川农业大学农学院,宜宾市农业科学院,四川省绿丹种业有限责任公司
5 腾冲糯谷 云南腾冲 粳型常规稻 腾冲本地水稻
6 协优46 云南腾冲 籼型杂交水稻 中国水稻研究所
7 明两优527 云南腾冲 籼型杂交水稻 福建省三明市农业科学研究所
8 软88 云南德宏 籼型杂交水稻 德宏本地水稻
9 内香8518 云南腾冲 籼型杂交水稻 内江杂交水稻科技开发中心
10 楚粳27号 云南腾冲 粳型常规稻 云南省楚雄州农业科学研究推广所
11 南粳9108 江苏扬州 粳型常规稻 江苏省农业科学院粮食作物研究所
12 连稻99 江苏徐州 粳型常规稻 江苏东海县守俊水稻研究所,江苏年年丰农业科技有限公司
13 连粳4号 江苏徐州 粳型常规稻 连云港市农业科学研究院
14 丹旱稻53 江苏连云港 粳型常规稻 丹东农业科学院
15 武运粳21号 江苏连云港 粳型常规稻 常州市武进区农业科学研究所
16 连糯1号 江苏宿迁 粳型常规稻 江苏胜田农业科技发展有限公司
17 临旱1号 安徽淮南 粳型常规稻 山东省临沂市水稻研究所
18 皖垦糯1号 安徽淮南 粳型常规稻 安徽皖垦种业有限公司
19 郑旱2号 安徽阜阳 粳型常规旱稻 河南省农业科学院
20 郑旱10号 安徽阜阳 粳型常规旱稻 河南省农业科学院

Fig.1

PCR products using primer RM19"

Table 2

18 SSR core primers of rice"

编号Code 引物Primer 染色体Chromosome 引物序列Primer sequence 扩增条带长度Length of amplify band (bp)
A02 RM71 2 F：CTAGAGGCGAAAACGAGATG 122~148
R：GGGTGGGCGAGGTAATAATG
A03 RM85 3 F：CCAAAGATGAAACCTGGATG 80~104
R：GCACAAGGTGAGCAGTCC
A05 RM274 5 F：CCTCGCTTATGGAGAGCTCG 149~162
R：CTTCTCCATCACTCCCATGG
A07 RM336 7 F：CTTACAGAGAAACGGCATCG 151~193
R：GCTGGTTTGTTTCAGGTTCG
A09 RM219 9 F：CGTCGGATGATGTAAAGCCT 194~222
R：CATATCGGCATTCGCCTG
A11 RM209 11 F：ATATGAGTTGCTGTCGTGCG 125~160
R：CAACTTGCATCCTCCCCTCC
A12 RM19 12 F：CAAAAACAGAGCAGATGAC 216~253
R：CTCAAGATGGACGCCAAGA
B01 RM1195 1 F：ATGGACCACAAACGACCTTC 142~152
R：CGACTCCCTTGTTCTTCTGG
B02 RM208 2 F：TCTGCAAGCCTTGTCTGATG 167~182
R：TAAGTCGATCATTGTGTGGACC
B03 RM232 3 F：CCGGTATCCTTCGATATTGC 141~161
R：CCGACTTTTCCTCCTGACG
B06 RM253 6 F：TCCTTCAAGAGTGCAAAACC 133~142
R：GCATTGTCATGTCGAAGCC
B09 RM278 9 F：GTAGTGAGCCTAACAATAATC 128~142
R：TCAACTCAGCATCTCTGTCC
B10 RM258 10 F：TGCTGTATGTAGCTCGCACC 128~146
R：TGGCCTTTAAAGCTGTCGC
B11 RM224 11 F：ATCGATCGATCTTCACGAGG 120~157
R：TGCTATAAAAGGCATTCGGG
B12 RM17 12 F：TGCCCTGTTATTTTCTTCTCTC 159~185
R：GGTGATCCTTTCCCATTTCA
- RM18 7 F：TTCCTCTCATGAGCTCCAT 142~183
R：GAGTGCCTGGCGCTGTAC
- RM273 4 F：GAAGCCGTCGTGAAGTTACC 152~172
R：GTTCCTACCTGATCGCGAC
- RM297 1 F：TCTTTGGAGGCGAGCTGAG 162~189
R：CGAAGGGTACATCTGCTTAG

Fig.2

Bands amplified by SSR primer RM219 for 20 rice materials"

Fig.3

Bands amplified by SSR primer RM19 for 20 rice materials"

Table 3

Polymorphism evaluation of 18 SSR core primers"

序号
No.		 引物
Primer		 染色体
Chromosome		 多态性片段
Polymorphic fragments		 Nei′s多样性指数
Nei′s diversity index		 Shannon′s信息指数
Shannon′s information index		 PIC值
PIC value
1 RM297 1 6 0.285 0.451 0.27
2 RM1195 1 3 0.301 0.461 0.41
3 RM71 2 2 0.309 0.471 0.26
4 RM208 2 4 0.311 0.481 0.71
5 RM232 3 5 0.295 0.451 0.73
6 RM85 3 4 0.240 0.386 0.64
7 RM273 4 2 0.384 0.567 0.42
8 RM274 5 5 0.328 0.493 0.76
9 RM253 6 3 0.335 0.517 0.66
10 RM336 7 8 0.195 0.339 0.84
11 RM18 7 5 0.195 0.326 0.63
12 RM219 9 6 0.222 0.360 0.72
13 RM278 9 6 0.155 0.280 0.76
14 RM258 10 6 0.198 0.337 0.78
15 RM224 11 6 0.174 0.302 0.75
16 RM209 11 4 0.280 0.450 0.68
17 RM17 12 4 0.201 0.334 0.62
18 RM19 12 4 0.322 0.482 0.68

Table 4

The genetic similarity coefficient of 20 rice materials"

品种
Variety		 内优5022
Neiyou
5022		 花优926
Huayou
926		 两优2161
Liangyou
2161		 宜香优2115
Yixiangyou
2115		 腾冲糯谷
Tengchong
waxy rice		 协优46
Xieyou
46		 明两优527
Mingliangyou
527		 软88
Ruan
88		 内香8518
Neixiang 8518		 楚粳
27号
Chujing 27		 南粳9108
Nanjing 9108		 连稻99
Liandao 99		 连粳4号
Lianjing 4		 丹旱稻53
Danhandao
53		 皖垦糯1号
Wankennuo 1		 连糯1号
Liannuo 1		 临旱1号
Linhan 1		 武运粳21号
Wuyunjing 21		 郑旱2号
Zhenghan 2		 郑旱10号
Zhenghan
10
内优5022
Neiyou 5022		 1.000
花优926
Huayou 926		 0.759 1.000
两优2161
Liangyou 2161		 0.651 0.723 1.000
宜香优2115
Yixiangyou 2115		 0.675 0.747 0.711 1.000
腾冲糯谷
Tengchong waxy rice		 0.602 0.578 0.528 0.590 1.000
协优46
Xieyou 46		 0.651 0.699 0.783 0.663 0.542 1.000
明两优527
Mingliangyou 527		 0.614 0.711 0.699 0.651 0.530 0.843 1.000
软88
Ruan 88		 0.663 0.759 0.578 0.747 0.530 0.627 0.687 1.000
内香8518
Neixiang 8518		 0.590 0.663 0.795 0.651 0.506 0.867 0.855 0.639 1.000
楚粳27号
Chujing 27		 0.663 0.687 0.867 0.675 0.554 0.843 0.783 0.663 0.855 1.000
南粳9108
Nanjing 9108		 0.578 0.506 0.494 0.590 0.687 0.566 0.530 0.627 0.530 0.602 1.000
连稻99
Liandao 99		 0.590 0.542 0.482 0.554 0.747 0.554 0.470 0.542 0.494 0.518 0.723 1.000
连粳4号
Lianjing 4		 0.554 0.482 0.470 0.470 0.663 0.518 0.434 0.554 0.482 0.530 0.759 0.795 1.000
丹旱稻53
Danhandao 53		 0.554 0.506 0.494 0.542 0.687 0.518 0.482 0.627 0.506 0.530 0.783 0.771 0.880 1.000
皖垦糯1号
Wankennuo 1		 0.578 0.506 0.494 0.542 0.687 0.518 0.434 0.602 0.482 0.506 0.783 0.795 0.880 0.928 1.000
连糯1号
Liannuo 1		 0.554 0.482 0.494 0.566 0.663 0.518 0.434 0.578 0.482 0.506 0.783 0.771 0.855 0.904 0.976 1.000
临旱1号
Linhan 1		 0.554 0.482 0.446 0.518 0.687 0.494 0.434 0.627 0.482 0.506 0.759 0.795 0.904 0.904 0.928 0.904 1.000
武运粳21号
Wuyunjing 21		 0.530 0.458 0.422 0.518 0.663 0.470 0.410 0.602 0.458 0.482 0.783 0.771 0.880 0.880 0.904 0.904 0.976 1.000
郑旱2号
Zhenghan 2		 0.590 0.518 0.482 0.506 0.723 0.530 0.446 0.542 0.494 0.518 0.771 0.855 0.892 0.843 0.867 0.843 0.867 0.843 1.000
郑旱10号
Zhenghan 10		 0.590 0.494 0.434 0.530 0.699 0.506 0.422 0.614 0.446 0.518 0.771 0.783 0.819 0.819 0.867 0.843 0.916 0.892 0.855 1.000

Fig.4

The clustering analysis of 20 rice varieties"

[1] 林春雨, 梁效宇, 马淑梅 , 等. 亚洲不同生态区水稻群体遗传多样性与特异性分析. 中国农学通报, 2018,34(14):1-5.
[2] 明跃成 . 腾冲市水稻种植主要病虫害类型及防治技术探讨. 南方农业, 2018,12(14):14-15.
[3] 穆家伟 . 腾冲县水稻产业发展现状存在问题与对策. 中国农业信息, 2012(22):49-52.
[4] Glaszmann J C . Isozymes and classification of Asian rice varieties. Theoretical and Applied Genetics, 1987,74(1):21-30.
[5] Li Z, Rutger J N . Geographic distribution and multilocus organization of isozyme variation of rice (Oryza sativa L. ). Theoretical and Applied Genetics, 2000,101(3):379-387.
[6] Singh A K, Singh P K, Arya M , et al. Molecular screening of blast resistance genes in rice using SSR markers. Plant Pathology Journal, 2015,31(1):12-24.
[7] 牛付安, 程灿, 周继华 , 等. 分子标记在杂交粳稻育种上的应用现状及展望. 中国稻米, 2015,21(1):18-23.
doi: 10.3969/j.issn.1006-8082.2015.01.004
[8] Chakravarthi B K, Naravaneni R . SSR maker based DNA fingerprinting and diversity study in rice. African Journal of Biotechnology, 2006,5(9):684-688.
[9] 肖小余, 王玉平, 张建勇 , 等. 四川省主要杂交稻亲本的SSR分析和指纹图谱的构建与应用. 中国水稻科学, 2006,20(1):1-7.
[10] 马孟莉, 郑云, 周晓梅 , 等. 云南哈尼梯田红米地方品种遗传多样性分析. 作物杂志, 2018(5):21-26.
[11] 马作斌, 王昌华, 王辉 , 等. 不同国家水稻品种的遗传多样性分析. 植物遗传资源学报, 2014,15(3):540-545.
[12] 张燕红, 王奉斌, 布哈丽且木·阿不力孜 , 等. 粳稻种质资源SSR指纹图谱构建及遗传多样性分析. 新疆农业科学, 2016,53(11):1961-1968.
[13] 徐艳, 徐继法, 陈磊 , 等. 小麦TILLING突变体检测基因组DNA提取方法的优化. 麦类作物学报, 2017,37(2):185-191.
[14] NY/T 1433-2014,水稻品种鉴定技术规程SSR标记法. 北京:中华人民共和国农业部, 2014.
[15] 邓姗, 褚云霞, 黄志城 , 等. 上海地区水稻已知品种SSR指纹图谱库构建. 中国农学通报, 2015,31(3):7-15.
[16] Smith J S C, Chin E C L, Shu H , et al. An evalution of the utilize of SSR loci as molecular in maize (Zea mays L.):comparisons with data from RFLPs and pedigree. Theoretical and Applied Genetics, 1997,95(1/2):163-173.
[17] Yeh F C, Yang R C, Boyle T , et al. Popgene Version 1.32 Microsoft Windows-based Freeware for Populations Genetic Analysis. University of Alberta,Centre for International Forestry Research, 1999.
[18] Rohlf F J . NTSYS-pc:Microcomputer programs for numerical taxonomy and multivariate analysis. American Statistician, 1987,41(4):330.
[19] 谷静丛, 王冲, 王国琴 , 等. 110份普通玉米自交系SSR聚类分析. 华北农学报, 2014,29(6):101-105.
doi: 10.7668/hbnxb.2014.06.018
[20] Botstein D, White R L, Skolnick M , et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 1980,32(3):314-331.
[21] 吕瑞玲, 吴小凤, 刘敏超 . 分子标记技术及在水稻遗传研究中的应用. 中国农学通报, 2009,25(4):65-73.
[22] 张晓丽, 吕荣华, 唐茂艳 , 等. 东南亚国家引进水稻种质的遗传多样性和遗传结构分析. 植物遗传资源学报, 2018,19(1):29-38.
[23] 华蕾, 袁筱萍, 余汉勇 , 等. 我国水稻主载品种SSR多样性的比较分析. 中国水稻科学, 2007,21(2):150-154.
[24] 张丽娜, 曹桂兰, 韩龙植 . 利用SSR标记揭示中国粳稻地方品种多样性. 中国农业科学, 2012,45(3):405-423.
doi: 10.3864/j.issn.0578-1752.2012.03.001
[25] 翟婉婉, 李雪萍, 徐返 , 等. 云南水稻地方品种月亮谷的群体多样性分析. 植物遗传资源学报, 2016,17(3):423-432.
[26] 赵庆勇, 张亚东, 朱镇 , 等. 30个粳稻品种SSR标记遗传多样性分析. 植物遗传资源学报, 2010,11(2):218-223.
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