Genome-wide Identification of SSR and SNP Markers from the Non-heading Chinese Cabbage for Comparative Genomic Analyses

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2015 Apr 25

PMID 25908429

Citations 26

Authors

Xiaoming Song

Tingting Ge

Ying Li

Xilin Hou

Affiliations

Soon will be listed here.

Abstract

Background: Non-heading Chinese cabbage (NHCC), belonging to Brassica, is an important leaf vegetable in Asia. Although genetic analyses have been performed through conventional selection and breeding efforts, the domestication history of NHCC and the genetics underlying its morphological diversity remain unclear. Thus, the reliable molecular markers representative of the whole genome are required for molecular-assisted selection in NHCC.

Results: A total of 20,836 simple sequence repeats (SSRs) were detected in NHCC, containing repeat types from mononucleotide to nonanucleotide. The average density was 62.93 SSRs/Mb. In gene regions, 5,435 SSRs were identified in 4,569 genes. A total of 5,008 primer pairs were designed, and 74 were randomly selected for validation. Among these, 60 (81.08%) were polymorphic in 18 Cruciferae. The number of polymorphic bands ranged from two to five, with an average of 2.70 for each primer. The average values of the polymorphism information content, observed heterozygosity, Hardy-Weinberg equilibrium, and Shannon's information index were 0.2970, 0.4136, 0.5706, and 0.5885, respectively. Four clusters were classified according to the unweighted pair-group method with arithmetic average cluster analysis of 18 genotypes. In addition, a total of 1,228,979 single nucleotide polymorphisms (SNPs) were identified in the NHCC through a comparison with the genome of Chinese cabbage, and the average SNP density in the whole genome was 4.33/Kb. The number of SNPs ranged from 341,939 to 591,586 in the 10 accessions, and the average heterozygous SNPs ratio was ~42.53%. All analyses showed these markers were high quality and reliable. Therefore, they could be used in the construction of a linkage map and for genetic diversity studies for NHCC in future.

Conclusions: This is the first systematic and comprehensive analysis and identification of SSRs in NHCC and 17 species. The development of a large number of SNP and SSR markers was successfully achieved for NHCC. These novel markers are valuable for constructing genetic linkage maps, comparative genome analysis, quantitative trait locus (QTL) mapping, genome-wide association studies, and marker-assisted selection in NHCC breeding system research.

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References

Cline M, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C . Integration of biological networks and gene expression data using Cytoscape. Nat Protoc. 2007; 2(10):2366-82. PMC: 3685583. DOI: 10.1038/nprot.2007.324. View

Bus A, Hecht J, Huettel B, Reinhardt R, Stich B . High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing. BMC Genomics. 2012; 13:281. PMC: 3442993. DOI: 10.1186/1471-2164-13-281. View

Barchi L, Lanteri S, Portis E, Acquadro A, Vale G, Toppino L . Identification of SNP and SSR markers in eggplant using RAD tag sequencing. BMC Genomics. 2011; 12:304. PMC: 3128069. DOI: 10.1186/1471-2164-12-304. View

Wang X, Wang H, Sun R, Wu J, Liu S, Bai Y . The genome of the mesopolyploid crop species Brassica rapa. Nat Genet. 2011; 43(10):1035-9. DOI: 10.1038/ng.919. View

Simko I, Haynes K, Jones R . Assessment of linkage disequilibrium in potato genome with single nucleotide polymorphism markers. Genetics. 2006; 173(4):2237-45. PMC: 1569688. DOI: 10.1534/genetics.106.060905. View

Raman H, Raman R, Nelson M, Aslam M, Rajasekaran R, Wratten N . Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.). DNA Res. 2011; 19(1):51-65. PMC: 3276259. DOI: 10.1093/dnares/dsr041. View

Kim J, Chung T, King G, Jin M, Yang T, Jin Y . A sequence-tagged linkage map of Brassica rapa. Genetics. 2006; 174(1):29-39. PMC: 1569789. DOI: 10.1534/genetics.106.060152. View

Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y . Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010; 42(11):961-7. DOI: 10.1038/ng.695. View

Wang H, Wu J, Sun S, Liu B, Cheng F, Sun R . Glucosinolate biosynthetic genes in Brassica rapa. Gene. 2011; 487(2):135-42. DOI: 10.1016/j.gene.2011.07.021. View

10.

Terol J, Naranjo M, Ollitrault P, Talon M . Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences. BMC Genomics. 2008; 9:423. PMC: 2561056. DOI: 10.1186/1471-2164-9-423. View

11.

Sarwat M, Nabi G, Das S, Srivastava P . Molecular markers in medicinal plant biotechnology: past and present. Crit Rev Biotechnol. 2011; 32(1):74-92. DOI: 10.3109/07388551.2011.551872. View

12.

Srikanth A, Schmid M . Regulation of flowering time: all roads lead to Rome. Cell Mol Life Sci. 2011; 68(12):2013-37. PMC: 11115107. DOI: 10.1007/s00018-011-0673-y. View

13.

Agarwal M, Shrivastava N, Padh H . Advances in molecular marker techniques and their applications in plant sciences. Plant Cell Rep. 2008; 27(4):617-31. DOI: 10.1007/s00299-008-0507-z. View

14.

Soengas P, Hand P, Vicente J, Pole J, Pink D . Identification of quantitative trait loci for resistance to Xanthomonas campestris pv. campestris in Brassica rapa. Theor Appl Genet. 2006; 114(4):637-45. DOI: 10.1007/s00122-006-0464-2. View

15.

Blanca J, Esteras C, Ziarsolo P, Perez D, Ferna Ndez-Pedrosa V, Collado C . Transcriptome sequencing for SNP discovery across Cucumis melo. BMC Genomics. 2012; 13:280. PMC: 3473316. DOI: 10.1186/1471-2164-13-280. View

16.

Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S . MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011; 28(10):2731-9. PMC: 3203626. DOI: 10.1093/molbev/msr121. View

17.

Saldanha A . Java Treeview--extensible visualization of microarray data. Bioinformatics. 2004; 20(17):3246-8. DOI: 10.1093/bioinformatics/bth349. View

18.

Hampl V, Pavlicek A, Flegr J . Construction and bootstrap analysis of DNA fingerprinting-based phylogenetic trees with the freeware program FreeTree: application to trichomonad parasites. Int J Syst Evol Microbiol. 2001; 51(Pt 3):731-5. DOI: 10.1099/00207713-51-3-731. View

19.

Hubisz M, Falush D, Stephens M, Pritchard J . Inferring weak population structure with the assistance of sample group information. Mol Ecol Resour. 2011; 9(5):1322-32. PMC: 3518025. DOI: 10.1111/j.1755-0998.2009.02591.x. View

20.

Gao Z, Luo W, Liu H, Zeng C, Liu X, Yi S . Transcriptome analysis and SSR/SNP markers information of the blunt snout bream (Megalobrama amblycephala). PLoS One. 2012; 7(8):e42637. PMC: 3412804. DOI: 10.1371/journal.pone.0042637. View