我们的网站为什么显示成这样?

可能因为您的浏览器不支持样式,您可以更新您的浏览器到最新版本,以获取对此功能的支持,访问下面的网站,获取关于浏览器的信息:

|Table of Contents|

Suitability test of SSR primer of Sinocalycanthus chinensis and its application in genetic diversity(PDF)

Journal of Nanjing Forestry University(Natural Science Edition)[ISSN:1000-2006/CN:32-1161/S]

Issue:
2018 03
Page:
58-66
Column:
lw
publishdate:
2018-05-15

Article Info:/Info

Title:
Suitability test of SSR primer of Sinocalycanthus chinensis and its application in genetic diversity
Article ID:
1000-2006(2018)03-0058-09
Author(s):
WU JingHUANG YaohuiDONG BinZHANG ChaoFU JianxinZHOU LihuaZHAO Hongbo*
School of Landscape Architecture, Zhejiang A & F University, Lin'an 311300, China
Keywords:
Keywords:Sinocalycanthus chinensis SSR molecular marker primer screening applicability verification genetic diversity
Classification number :
Q311
DOI:
10.3969/j.issn.1000-2006.201812037
Document Code:
A
Abstract:
Abstract: 【Objective】Our objective was to screen out the primers to analysis the intra-population and inter-population genetic diversity of Sinocalycanthus chinensis and genetic diversity analysis.【Methods】From the 125 014 unigene sequences assembled from the S. chinensis transcriptome database, 344 pairs of SSR(simple sequence repeats)primers were randomly selected. Firstly, six different populations of DNA were used as templates for polyacrylamide gel electrophoresis. Primers were screened to screen for polymorphic SSR primers based on the richness of amplified product bands; SSR primers with an amplification band number of 4 or more were selected to further verify that these primers were suitable within populations and among populations of S. chinensis.The applicability of the use of the validated primers was used to analyze the genetic diversity and genetic structure of six populations of S. chinensis.【Results】Our results showed that 148(43.02%)SSR primer pairs could amplify clear bands, and among them, 29(19.60%)pairs had polymorphisms. There were 15 primer pairs that could amplify more than 4 bands, and these primers had a higher polymorphism. Further analysis of the 15 primer pairs revealed that these primers all could be used for genetic diversity analysis among populations based on the number of bands amplified and genetic parameters. Additionally, the 15 primer pairs could be further divided into three groups, and the degree of genetic diversity in turn decreased. In the intra-population genetic diversity analysis, the amplified bands of P004 and P061 in the first, second and third class were high and had a uniform distribution, with higher polymorphism in each population according to the number of bands, their distribution, and genetic parameters. However, the genetic diversity of P021, P075, P095, P98 and P018 was a bit lower than that of the others. The diversity of species level(Ht)was 0.625 0. The genetic diversity index of each population ranged from 0.251 8 to 0.400 2. The Shannon index(I)ranged from 0.419 7 to 0.668 1, and the average genetic diversity index(Hs)was 0.323 0. 【Conclusion】The results indicated that the species level had high genetic diversity, but the genetic diversity intra-population is low. Cluster analysis divided the six populations into three groups, and the genetic distance was far between the groups. The genetic differentiation coefficient(Gst)was 0.437, the inbred coefficient(Fis)within the population was 0.430, and the inter-population gene flow(Nm)was 0.309 4. Based on the AMOVA molecular variance analysis, 56% of the variation was inter-population and 44% of the variation was intra-population. The above shows that there was significant genetic differentiation among populations of S. chinensis, there was a significant inbreeding phenomenon within populations, and gene exchange between various populations was blocked. In this study, we first published the SSR primer information of S. chinensis and provided the support for research on the mating system of S. chinensis in the future.

References

[1] 徐耀良, 张若蕙, 周骋. 夏蜡梅的群落学研究[J]. 浙江林学院学报,1997,14(4): 43-50. XU Y L, ZHANG R H, ZHOU P. Study on communities of Sinocalycanthus chinensis[J]. Journal of Zhejiang Forestry College,1997,14(4): 43-50.
[2] 刘华红, 周莉花, 黄耀辉, 等. 群落演替对夏蜡梅种群分布和数量的影响[J]. 生态学报, 2016,36(3): 620-628.DOI: 10.5846/stxb201405221054. LIU H H, ZHOU L H, HUANG Y H,et al. Effects of community succession on population distribution and size of Sinocalycanthus chinensis(Cheng et S. Y. Chang)Cheng et S. Y. Chang [J]. Acta Ecologica Sinica, 2016, 36(3): 620-628.
[3] 赵宏波, 周莉花, 郝日明, 等. 中国特有濒危植物夏蜡梅的交配系统[J]. 生态学报, 2011, 31(3): 602-610. ZHAO H B, ZHOU L H, HAO R M,et al. Mating system of Sinocalycanthus chinensis(Cheng et S. Y. Chang)Cheng et S. Y. Chang,an endangered,indigenous species in China[J]. Acta Ecologica Sinica, 2011, 31(3): 602-610.
[4] AGARWAL M, SHRIVASTAVA N, PADH H. Advances in molecular marker techniques and their applications in plant sciences[J]. Plant Cell Reports, 2008, 27(4): 617-631.DOI:10.1007/s00299-008-0507-z.
[5] 李小湘, 刘勇, 段永红, 等. 利用SSR分析普通野生稻自然居群交配系统[J]. 中国水稻科学,2010, 24(6): 601-607.DOI: 10.3969/j.issn.1001-7216.2010.06.007. LI X X, LIU Y, DUAN Y H, et al. Estimation of mating system in natural Oryza rufipogon populations by SSR markers[J]. Chin J Rice Sci, 2010, 24(6): 601-607.
[6] KALIA R K, RAI M K, KALIA S, et al. Microsatellite markers: an overview of the recent progress in plants[J]. Euphytica, 2011, 177(3): 309-334.DOI: 10.1007/s10681-010-0286-9.
[7] LI F, GAN S. An optimised protocol for fluorescent-dUTP based SSR genotyping and its application to genetic mapping in Eucalyptus[J]. Silvae Genetica, 2011, 60(1): 18-25.DOI:10.1515/sg-2011-0003.
[8] 程小毛, 黄晓霞. SSR标记开发及其在植物中的应用[J]. 中国农学通报, 2011, 27(5): 304-307. CHENG X M, HUANG X X. Development and application of SSR markers in plants[J]. Chinese Agricultural Science Bulletin, 2011, 27(5): 304-307.
[9] 黄耀辉, 张超, 周莉花, 等. 基于转录组序列的夏蜡梅SSR位点特征与引物开发[J]. 浙江农林大学学报, 2017, 34(4): 589-596.DOI:10.11833/j.issn.2095-0756.2017.04.004. HUANG Y H, ZHAO C, ZHOU L H, et al. Development and primer screening of SSR markers based on transcriptome sequences in Sinocalycanthus chinensis[J]. Journal of Zhejiang A & F University,2017, 34(4): 589-596.
[10] WU J, CAI C, CHENG F, et al. Characterisation and development of EST-SSR markers in tree peony using transcriptome sequences[J]. Molecular Breeding, 2014, 34(4): 1853-1866.DOI: 10.1007/s11032-014-0144-x.
[11] 万宣伍, 刘映红,张彬, 等. 基于微卫星分子标记的重庆地区桔小实蝇遗传分化研究[J]. 中国农业科学, 2010, 43(13): 2688-2696.DOI: 10.3864/j.issn.0578-1752.2010.13.008. WANG X W, LIU Y H, ZHANG B,et al. Genetic differentiation among poupulations of the oriental fruit fly Bactrocera dorsalis(Hendel)in Chongqing based on microsatellite markers[J]. Scientia Agricultura Sinica, 2010, 43(13): 2688-2696.
[12] SAAD Y M. Analysis of genetic variations in two savothrodon galilaeus sexes using popgene[J]. Global Veterinaria, 2009, 3(1): 22-25.
[13] GUO J J, SHANG S B, WANG C S, et al. Twenty microsatellite markers for the endangered Vatica mangachapoi (Dipterocarpaceae)[J]. Applications in Plant Sciences, 2017, 5(2): 1600134.DOI: 10.3732/apps.1600134.
[14] 陈娇, 王小蓉, 汤浩茹, 等. 基于SSR标记的四川野生中国樱桃遗传多样性和居群遗传结构分析[J]. 园艺学报, 2013, 40(2): 333-340.DOI: 10.16420/j.issn.0513-353x.2010.02.028. CHEN J, WANG X Y, TANG H R, et al. Assessment of genetic diversity and populations genetic structure in wild Chinese cherry from sichuan province using SSR markers[J]. Acta Horticulturae Sinica, 2013, 40(2): 333-340.
[15] 李海渤, 杨军, 吕泽文, 等. 甘蓝型油菜SSR核心引物研究[J]. 中国油料作物学报, 2010, 32(3): 329-336. LI H B, YANG J, LV Z W,et al. Screening of Brassica napus core SSR priners[J]. Chinese Joumal of Oil Crop Sciences, 2010, 32(3): 329-336.
[16] 唐荣华, 张君诚, 吴为人. SSR分子标记的开发技术研究进展[J]. 西南农业学报, 2002,15(4): 106-109. TANG R H, ZHANG J C, WU W R. Progress in the way to develop SSR molecular marker[J]. Southwest China Journal of Agricultural Sciences, 2002,15(4):106-109.
[17] 李炎林, 杨星星, 张家银, 等. 南方红豆杉转录组SSR挖掘及分子标记的研究[J]. 园艺学报, 2014, 41(4):735-745. LI Y L, YANG X X, ZHANG J Y,et al. Studies on SSR molecular markers based on transcriptome of Taxus chinensis var. mairei[J]. Acta Horticulturae Sinica, 2014, 41(4): 735-745.
[18] 李响, 杨楠, 赵凯歌, 等. 蜡梅转录组EST-SSR标记开发与引物筛选[J]. 北京林业大学学报, 2013, 35(S1): 25-32.DOI:10.13332/j.1000-1522.2013.s1.010. LI X, YANG N, ZHAO K G, et al. Development and primer selection of EST-SSR molecular markers based on transcriptome sequencing of Chimonanthus praecox[J]. Journal of Beijing Forestry University, 2013, 35(S1): 25-32.
[19] 赵明晓, 范国强. 蜡梅SSR反应体系建立及引物筛选[J]. 河南农业大学学报, 2011, 45(1): 46-50. ZHAO M X, FAN G Q. Establishment of Chimonanthus SSR reaction system and its primer selection[J]. Journal of Henan Agricultural University, 2011, 45(1): 46-50.
[20] 廖娇, 黄春辉, 辜青青, 等. 猕猴桃EST-SSR引物筛选及通用性分析[J]. 果树学报, 2011, 28(6): 1111-1116. LIAO J, HUANG C H, GU Q Q,et al. Mining and transferability analysis of EST-SSR primers in Kiwifruit(Actinidia spp.)[J]. Journal of Fruit Science, 2011, 28(6):1111-1116.
[21] 姜德波, 栾林, 吕锐, 等. HAP 鲍曼不动杆菌耐药谱型与 IRS-PCR 基因型关联性研究[J]. 交通医学, 2009, 23(4): 340-343. JIANG D B,LUAN L,LV R,et al.Investigation the correlation between resistance phenotype and IRS-PCR genotype of Acinetobacter baumannii in HAP[J]. Med. J. of Communications, 2009,23(4): 340-343.
[22] BOTSTEIN D, WHITE R L, SKOLNICK M, et al. Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J]. American Journal of Human Genetics, 1980, 32(3): 314.
[23] 周世良, 叶文国. 夏腊梅的遗传多样性及其保护[J]. 生物多样性, 2002, 10(1): 1-6. ZHOU S L, YE W G. The genetic diversity and conservation of Sinocalycanthus chinensis [J]. Biodiversity Science, 2002, 10(1): 1-6.
[24] 汪琼, 姚青菊, 徐增莱, 等. 基于ISSR和RAPD 标记的四个夏蜡梅种群的遗传多样性研究[J]. 广西植物, 2013, 33(1): 30-34.DOI: 10.3969/j.issn.1000-3142.2013.01.004. WANG Q, YAO Q J, XU Z L,et al. Genetic diversity of four populations of Calycanthus chinensis based on ISSR and RAPD markers[J]. Guihaia, 2013,33(1): 30-34.
[25] 张文标, 金则新, 李钧敏. 不同生境夏蜡梅群体遗传多样性的 RAPD 分析[J]. 植物研究, 2007, 27(3): 313-318. ZHANG W B, JIN Z X, LI J M. Genetic diversity of Sinocalycanthus chinensis in four different habitats revealed by RAPD[J]. Bulletin of Botanical Research, 2007, 27(3): 313-318.
[26] 金则新, 李钧敏. 珍稀濒危植物夏蜡梅遗传多样性的 ISSR分析[J]. 应用生态学报, 2007, 18(2): 247-253. JIN Z X, LI J M. ISSR analysis on genetic diversity of endangered relic shrub Sinocalycanthus chinensis[J]. Chinese Journal of Applied Ecology, 2007, 18(2): 247-253.

Last Update: 2018-06-06