Transcriptome Sequencing of Two Parental Lines of Cabbage (Brassica Oleracea L. Var. Capitata L.) and Construction of an EST-based Genetic Map

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2014 Feb 25

PMID 24559437

Citations 18

Authors

Nur Kholilatul Izzah

Jonghoon Lee

Murukarthick Jayakodi

Sampath Perumal

Mina Jin

Beom-Seok Park

Kyounggu Ahn

Tae-Jin Yang

Affiliations

Soon will be listed here.

Abstract

Background: Expressed sequence tag (EST)-based markers are preferred because they reflect transcribed portions of the genome. We report the development of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers derived from transcriptome sequences in cabbage, and their utility for map construction.

Results: Transcriptome sequences were obtained from two cabbage parental lines, C1184 and C1234, which are susceptible and resistant to black rot disease, respectively, using the 454 platform. A total of 92,255 and 127,522 reads were generated and clustered into 34,688 and 40,947 unigenes, respectively. We identified 2,405 SSR motifs from the unigenes of the black rot-resistant parent C1234. Trinucleotide motifs were the most abundant (66.15%) among the repeat motifs. In addition, 1,167 SNPs were detected between the two parental lines. A total of 937 EST-based SSR and 97 SNP-based dCAPS markers were designed and used for detection of polymorphism between parents. Using an F2 population, we built a genetic map comprising 265 loci, and consisting of 98 EST-based SSRs, 21 SNP-based dCAPS, 55 IBP markers derived from B. rapa genome sequence and 91 public SSRs, distributed on nine linkage groups spanning a total of 1,331.88 cM with an average distance of 5.03 cM between adjacent loci. The parental lines used in this study are elite breeding lines with little genetic diversity; therefore, the markers that mapped in our genetic map will have broad spectrum utility.

Conclusions: This genetic map provides additional genetic information to the existing B. oleracea map. Moreover, the new set of EST-based SSR and dCAPS markers developed herein is a valuable resource for genetic studies and will facilitate cabbage breeding. Additionally, this study demonstrates the usefulness of NGS transcriptomes for the development of genetic maps even with little genetic diversity in the mapping population.

Citing Articles

Genetic dissection of morphological variation between cauliflower and a rapid cycling Brassica oleracea line.

Shuang L, Cuevas H, Lemke C, Kim C, Shehzad T, Paterson A G3 (Bethesda). 2023; 13(11).

PMID: 37506262 PMC: 10627287. DOI: 10.1093/g3journal/jkad163.

Genome-wide analysis-based single nucleotide polymorphism marker sets to identify diverse genotypes in cabbage cultivars (Brassica oleracea var. capitata).

Jo J, Kang M, Kim K, Youk H, Shim E, Kim H Sci Rep. 2022; 12(1):20030.

PMID: 36414667 PMC: 9681867. DOI: 10.1038/s41598-022-24477-y.

Advances in Multi-Omics Approaches for Molecular Breeding of Black Rot Resistance in L.

Shaw R, Shen Y, Wang J, Sheng X, Zhao Z, Yu H Front Plant Sci. 2021; 12:742553.

PMID: 34938304 PMC: 8687090. DOI: 10.3389/fpls.2021.742553.

Development of a new set of genic SSR markers in the genus : in silico mining, characterization and validation.

Malhotra E, Jain R, Bansal S, Mali S, Sharma N, Agrawal A 3 Biotech. 2021; 11(10):430.

PMID: 34527507 PMC: 8433281. DOI: 10.1007/s13205-021-02969-4.

Transcriptomic analysis of resistant and susceptible cabbage lines reveals differential expressions and candidate genes involved in cabbage early responses to black rot.

Song L, Tang J, Yan J, Zeng A, Lv S, Gao B 3 Biotech. 2020; 10(7):308.

PMID: 32582505 PMC: 7297882. DOI: 10.1007/s13205-020-02256-8.

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