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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Publications at this Location » Publication #344941

Research Project: Genetic Improvement of Hard Winter Wheat to Biotic and Abiotic Stresses

Location: Hard Winter Wheat Genetics Research

Title: Development of EST-SSR markers in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) based on de novo transcriptomeic assemblies

Author
item Chen, Jingfang - Guangzhou University
item Li, Ronghua - Guangzhou University
item Xia, Yanshi - Guangzhou University
item Bai, Guihua
item Peiguo, Guo - Guangzhou University
item Zhiliang, Wang - Guangzhou University
item Hua, Zhang - Guangzhou University
item Siddique, Kadambot H.m. - University Of Western Australia

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/30/2017
Publication Date: 9/13/2017
Publication URL: http://handle.nal.usda.gov/10113/5863788
Citation: Chen, J., Li, R., Xia, Y., Bai, G., Peiguo, G., Zhiliang, W., Hua, Z., Siddique, K. 2017. Development of EST-SSR markers in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee) based on de novo transcriptomeic assemblies. PLoS One. 12(9):e0184736. https://doi.org/10.1371/journal.pone.0184736.
DOI: https://doi.org/10.1371/journal.pone.0184736

Interpretive Summary: Flowering Chinese cabbage is one of the most important vegetable crops in southern China. The limited number of molecular markers available for this crop hampered progress in genetic improvement of Chinese cabbage cultivars. We used transcriptome sequences of flowering Chinese cabbage generated by a method called RNA-seq and developed new molecular markers. We designed primers for 4,912 SSR markers. Of these, 170 were randomly selected for marker validation and 48 showed high reproducibility. Cluster analysis using the 48 SSRs classified 34 flowering Chinese cabbage cultivars into three groups. The large number of new SSR markers identified in this study will facilitate marker-assisted selection in the breeding programs for flowering Chinese cabbage.

Technical Abstract: Flowering Chinese cabbage is one of the most important vegetable crops in southern China. Genetic improvement of various agronomic traits in this crop is underway to meet high market demand in the region, but the progress is hampered by limited number of molecular markers available in this crop. This study aimed to develop EST-SSR markers from transcriptome sequences generated by next-generation sequencing. RNA-seq of eight cabbage samples identified 48,975 unigenes. Of these unigenes, 23,267 were annotated in 56 gene ontology (GO) categories, 6,033 were mapped to 131 KEGG pathways, and 7,825 were assigned to clusters of orthologous groups (COGs). From the unigenes, 8,165 EST-SSR loci were identified and 98.57% of them were 1–3 nucleotide repeats with 14.32%, 41.08% and 43.17% of mono-, di- and tri-nucleotide repeats, respectively. Fifty-eight types of motifs were identified with A/T, AG/CT, AT/AT, AC/GT, AAG/CTT and AGG/CCT the most abundant. The lengths of repeated nucleotide sequences in all SSR loci ranged from 12 to 60 bp, with most (88.51%) under 20 bp. Among 170 primer pairs that were randomly selected from a total of 4,912 SSR primers we designed, 48 yielded unambiguously polymorphic bands with high reproducibility. Cluster analysis using using 48 SSRs classified 34 flowering Chinese cabbage cultivars into three groups. A large number of EST-SSR markers identified in this study will facilitate marker-assisted selection in the breeding programs of flowering Chinese cabbage.