Development of a core set of SNP markers for the identification of upland cotton cultivars in China

doi:10.1016/S2095-3119(15)61226-6

Journal of Integrative Agriculture ›› 2016, Vol. 15 ›› Issue (05): 954-962.DOI: 10.1016/S2095-3119(15)61226-6

Development of a core set of SNP markers for the identification of upland cotton cultivars in China

KUANG Meng^{1, 2}, WEI Shou-jun², WANG Yan-qin², ZHOU Da-yun², MA Lei², FANG Dan², YANG Wei-hua², MA Zhi-ying¹

¹Hebei Research Base for State Key Laboratory of Cotton Biology/College of Agronomy, Hebei Agricultural University, Baoding 071001, P.R.China
² Institute of Cotton Research, Chinese Academy of Agriculture Sciences, Anyang 455000, P.R.China

收稿日期:2015-07-13 出版日期:2016-05-03 发布日期:2016-05-03
通讯作者: MA Zhi-ying, Tel/Fax: +86-312-7528401, E-mail: mzhy@hebau.edu.cn; YANG Wei-hua, Tel/Fax: +86-372-2525389, E-mail: cottontest@126.com
作者简介:KUANG Meng, Mobile: +86-15836313471, E-mail: kuangmeng 007@163.com
基金资助:
This work was supported by the the Basic R&D Operation Special Fund for the Central Level, Non-Profit, Scientific Research Institutes, Ministry of Agriculture, China (1610162015A08) and the National Key Technologies R&D Program of China during the 12th Five-Year Plan period (2011BAD35B09).

Development of a core set of SNP markers for the identification of upland cotton cultivars in China

KUANG Meng^{1, 2}, WEI Shou-jun², WANG Yan-qin², ZHOU Da-yun², MA Lei², FANG Dan², YANG Wei-hua², MA Zhi-ying¹

¹ Hebei Research Base for State Key Laboratory of Cotton Biology/College of Agronomy, Hebei Agricultural University, Baoding 071001, P.R.China
² Institute of Cotton Research, Chinese Academy of Agriculture Sciences, Anyang 455000, P.R.China

Received:2015-07-13 Online:2016-05-03 Published:2016-05-03
Contact: MA Zhi-ying, Tel/Fax: +86-312-7528401, E-mail: mzhy@hebau.edu.cn; YANG Wei-hua, Tel/Fax: +86-372-2525389, E-mail: cottontest@126.com
About author:KUANG Meng, Mobile: +86-15836313471, E-mail: kuangmeng 007@163.com
Supported by:
This work was supported by the the Basic R&D Operation Special Fund for the Central Level, Non-Profit, Scientific Research Institutes, Ministry of Agriculture, China (1610162015A08) and the National Key Technologies R&D Program of China during the 12th Five-Year Plan period (2011BAD35B09).

摘要/Abstract

关键词: upland cotton , core SNP , DUS , genotyping

Abstract: Considering the advantages of single nucleotide polymorphisms (SNP) in genotyping and variety identification, the first set public SNP markers at Cotton Marker Database (http://www.cottonmarker.org/) were validated and screened across standard varieties of cotton distinctness, uniformity and stability (DUS) test, aiming to obtain an appropriate set of core SNP markers suitable for upland cotton cultivars in China. A total of 399 out of 1 005 SNPs from 270 loci including 170 insertions-deletions (InDels) were evaluated for their polymorphisms among 30 standard varieties using Sanger sequencing. As a result, 147 loci were sequenced successfully, 377 SNPs and 49 InDels markers were obtained. Among the 377 SNP markers, 333 markers (88.3%) were polymorphic between Gossypium hirsutum and G. barbadense, while 164 markers (43.5%) were polymorphic within upland cotton. As for InDel markers, the polymorphic rate is relatively lower than that of SNP both between species and within species. The homozygous DNA locus ratio of 121 SNPs was higher than 86.2% while that of other 43 SNPs was less than 70%. Only 64 SNPs displayed completely homozygous genotypes among all of the detected upland cotton varieties with 100% homozygous DNA locus ratio. At last, a set of 23 pairs of core SNPs were achieved in view of avoidance of linkage, with polymorphism information content (PIC) values varying from 0.21 to 0.38 with an average of 0.28. Genotype characteristics and genetic diversity were analyzed based on the set of core markers, while 40 pairs of core simple-sequence repeats (SSR) primers comprised of 10 sets of four multiplex PCR combinations were also used for analysis based on fluorescence detection system. Comparison results indicated that the genetic diversity level was almost equal, while various varieties were significantly different from each other. Genetic relationship revealed by SSR markers is related to geographic source to a certain extent. Meanwhile clustering results analyzed by SNP markers are more consistent with kinship, which demonstrated that the screen strategy for core SNP marker is effective.

Key words: upland cotton , core SNP , DUS , genotyping

KUANG Meng, WEI Shou-jun, WANG Yan-qin, ZHOU Da-yun, MA Lei, FANG Dan, YANG Wei-hua. Development of a core set of SNP markers for the identification of upland cotton cultivars in China[J]. Journal of Integrative Agriculture, 2016, 15(05): 954-962.

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Development of a core set of SNP markers for the identification of upland cotton cultivars in China

Development of a core set of SNP markers for the identification of upland cotton cultivars in China

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