|
|
|
|
|
| Development of a core set of SNP markers for the identification of upland cotton cultivars in China |
| KUANG Meng1, 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 |
|
|
|
|
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.
|
|
Received: 13 July 2015
Accepted:
|
| Fund: 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). |
|
Corresponding Authors:
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 |
Cite this article:
KUANG Meng, WEI Shou-jun, WANG Yan-qin, ZHOU Da-yun, MA Lei, FANG Dan, YANG Wei-hua.
2016.
Development of a core set of SNP markers for the identification of upland cotton cultivars in China. Journal of Integrative Agriculture, 15(05): 954-962.
|
| Anderson J A, Churchill G A, Autrique J E, Tanksley S D, Sorrells M E. 1993. Optimizing parental selection for genetic linkage maps. Genome, 36, 181–186.Ashok B D, Mamta P R, Manoj R B, Kshanada J M. 2011. Identification and genetic purity testing of cotton F1 hybrid using molecular markers. Indian Journal of Biotechnology, 10, 301–306.Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape J M, Yu J Z, Jesudurai C, Jung S, Muthukumar S, Yellambalase P, Ficklin S, Staton M, Eshelma R, Ulloa M, Saha S, Burr B, Liu S, Zhang T, Fang D, Pepper A, et al. 2006. CMD: A cotton microsatellite database resource for Gossypium genomics. BMC Genomics, 7, 132.Borys J, Kowalczyk B, Waszak J. 2000. Distinctness, uniformity and stability testing of tomato varieties in Poland. Acta Physiologiae Plantarum, 22, 225–229.Buanec B L. 2006. Protection of plant-related innovations: evolution and current discussion. World Patent Information, 28, 50–62.Byers R L, Harker D B, Yourstone S M, Maughan P J, Udall J A. 2012. Development and mapping of SNP assays in allotetraploid cotton. Theoretical and Applied Genetics, 124, 1201–1214.Van Deynze A, Stoffel K, Lee M, Wilkins T A, Kozik A, Cantrell R G, Yu J Z, Kohel R J, Stelly D M. 2009. Sampling nucleotide diversity in cotton. BMC Plant Biology, 9, 125.Eillis J R, Burke J M. 2007. EST-SSRs as a resource for population genetic analyses. Heredity, 99, 125–132.Frelichowski J E, Palmer M B, Main D, Tomkins J P, Cantrell R G, Stelly D M, Yu J, Kohel R J, Ulloa M. 2006. Cotton genome mapping with new microsatellites from Acala ‘Maxxa’ BAC-ends. Molecular Genetics and Genomics, 275, 479–491.Guo W Z, Cai C P, Wang C B, Han Z G, Song X L, Wang K, Niu X W, Wang C, Lu K Y, Shi B, Zhang T Z. 2007. A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics, 176, 527–541.Higgins J, Evans J L. 1984. Standards employed in distinctness, uniformity and stability tests of faba bean cultivars. Advances in Agricultural Biotechnology, 11, 118–125.Jones E S, Sullivan H, Bhattramakki D, Smith J S C. 2007. A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.). Theoretical and Applied Genetics, 115, 361–371.Kuang M, Wang Y Q, Zhou D Y, Fang D, Ma L, Yang W H. 2015. Construction of SSR fingerprinting database of standard varieties on cotton in DUS testing. Cotton Science, 27, 46–52. (in Chinese)Kuang M, Yang W H, Wang F, Xu H X, Wang Y Q, Zhou D Y, Fang D, Ma L, Feng X A. 2014. Screening of highly informative and representative microsatellite markers for genotyping of major cultivated cotton variety. Genetics and Molecular Research, 13, 9777–9786.Kuang M, Yang W H, Xu H X, Wang Y Q, Zhou D Y, Feng X A. 2010. A rapid method of DNA extraction from single cotton seed. Molecular Plant Breeding, 8, 827–831. (in Chinese)Kuang M, Yang W H, Xu HX, Wang Y Q, Zhou D Y, Feng X A. 2011. Construction of DNA fingerprinting and analysis of genetic diversity with SSR markers for cotton major cultivars in China. Scientia Agricultura Sinica, 44, 20–27. (in Chinese)Lacape J M, Claverie M, Vidal R O, Carazzolle M F, Guimaraes Pereira G A, Ruiz M, Pré M, Llewellyn D, Al-Ghazi Y, Jacobs J, Dereeper A, Huguet S, Giband M, Lanaud C. 2012. Deep sequencing reveals differences in the transcriptional landscapes of fibers from two cultivated species of cotton. PLoS ONE, 7, e48855.Lacape J M, Jacobs J, Arioli T, Derijcker R, Forestier-Chiron N, Llewellyn D, Jean J, Thomas E, Viot C. 2009. A new interspecific, Gossypium hirsutum×G. barbadense, RIL population: Towards a unified consensus linkage map of tetraploid cotton. Theoretical and Applied Genetics, 119, 281–292.Li F, Fan G, Lu C, Xiao G, Zou C, Kohel R J, Ma Z, Shang H, Ma X, Wu J, Liang X, Huang G, Percy RG, Liu K, Yang W, Chen W, Du X, Shi C, Yuan Y, Ye W, et al. 2015. Genome sequence of cultivated upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nature Biotechnology, 33, 524–530.Li F, Fan G, Wang K, Sun F, Yuan Y, Song G, Li Q, Ma Z, Lu C, Zou C, Chen W, Liang X, Shang H, Liu W, Shi C, Xiao G, Gou C, Ye W, Xu X, Zhang X, et al. 2014. Genome sequence of the cultivated cotton Gossypium arboreum. Nature Genetics, 46, 567–572.Li X M, Gao W H, Guo H L, Zhang X L, Fang D D, Lin Z X. 2014. Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping. BMC Genomics, doi: 10.1186/1471-2164-15-1046Liu Y F, Zhang J H, LÜ B, Yang X H, Li Y G, Wang Y, Wang J M, Zhang H, Guan J J. 2013. Statistic analysis on quantitative characteristics for developing the DUS test guideline of Ranunculus asiaticus L. Journal of Integrative Agriculture, 12, 971–978.Lu C R, Zou C S, Zhang Y P, Yu D Q, Cheng H L, Jiang P F, Yang W C, Wang Q L, Feng X X, Prosper M A, Guo X P, Song G L. 2015. Development of chromosome-specific markers with high polymorphism for allotetraploid cotton based on genome-wide characterization of simple sequence repeats in diploid cottons (Gossypium arboreum L. and Gossypium raimondii Ulbrich). BMC Genomics, doi: 10.1186/s12864-015-1265-2Matsuoka Y, Mitchell S E, Kresovich S, Goodman M, Doebley J. 2002. Microsatellites in Zea-variability, patterns of mutations, and use for evolutionary studies. Theoretical and Applied Genetics, 104, 436–450.Paterson A H, Wendel J F, Gundlach H, Guo H, Jenkins J, Jin D, Llewellyn D, Showmaker K C S, Shu S, Udall J, Yoo M, Byers R, Chen W, Doron-Faigenboim A, Duke M V, Gong L, Grimwood J, Grover C, Grupp K, Hu G, et al. 2012. Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature, 492, 423–427.Rafalski A. 2002. Applications of single nucleotide polymorphisms in crop genetics. Current Opinion in Plant Biology, 5, 94–100.Tripp R, Louwaars N, Eaton D. 2007. Plant variety protection in developing countries. A report from the field. Food Policy, 32, 354–371.UPOV (Union for the Protection of New Varieties of Plants). 2007. Guidelines for DNA-Profiling: Molecular Marker Selection and Database Construction//BMT Guidelines (proj.9). UPOV, Geneva. pp. 3–4.Varshney R K, Thiel T, Sretenovic-Rajicic T, Baum M, Valkoun J, Guo P, Grando S, Ceccarelli S, Graner A. 2008. Identification and validation of a core set of informative genic SSR and SNP markers for assaying functional diversity in barley. Molecular Breeding, 22, 1–13.Wang K, Wang Z, Li F, Ye W, Wang J, Song G, You Z, Cong L, Shang H, Zhu S, Zou C, Li Q, Yuan Y, Lu C, Wei H, Gou C, Zheng Z, Yin Y, Zhang X, Liu K, et al. 2012. The draft genome of a diploid cotton Gossypium raimondii. Nature Genetics, 44, 1098–1103.Yu J Z, Fang D D, Kohel R J, Ulloa M, Hinze L L, Percy R G, Zhang J, Chee P, Scheffler B E, Jones D C. 2012. Development of a core set of SSR markers for the characterization of Gossypium germplasm. Euphytica, 187, 203–213.Zhang H B, Li Y, Wang B, Chee P W. 2008. Recent advances in cotton genomics. International Journal of Plant Genomics, doi: 10.1155/2008/742304Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski C A, Scheffler B E, Stelly D M, Hulse-Kemp A M, Wan Q, Liu B, Liu C, Wang S, Pan M, Wang Y, Wang D, Ye W, Chang L, et al. 2015. Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nature Biotechnology, 33, 531–537.Zhang Y C, Kuang M, Yang W H, Xu H X, Zhou D Y, Wang Y Q, Feng X A, Su C, Wang F. 2013. Construction of a primary DNA fingerprint database for cotton cultivars. Genetics and Molecular Research, 12, 1897–1906. |
| No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
