De novo sequencing of seed transcriptome and development of genic-SSR markers in common buckwheat (Fagopyrum esculentum)

Large-scale identification of simple sequence repeat (SSR) markers has not been reported in the genus Fagopyrum due to a lack of genomic resources. High-throughput transcriptomic sequencing can provide a rich resource for development of genic-SSR markers. In our study, the immature seeds transcripto...

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Bibliographic Details
Published in:Molecular breeding 2017-12, Vol.37 (12), p.1-15, Article 147
Main Authors: Shi, Taoxiong, Li, Ruiyuan, Chen, Qijiao, Li, Yue, Pan, Fan, Chen, Qingfu
Format: Article
Language:English
Subjects:
Biodiversity
Biomedical and Life Sciences
Biotechnology
Buckwheat
Encyclopedias
Fagopyrum
Fagopyrum esculentum
Filtration
Gene expression
Gene mapping
Genetic diversity
Genomes
Genotype & phenotype
Life Sciences
Low level
Marker-assisted selection
Markers
Molecular biology
Nucleotides
Pathogens
Plant biology
Plant Genetics and Genomics
Plant Pathology
Plant Physiology
Plant Sciences
Polymorphism
Proteins
Seeds
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Summary:Large-scale identification of simple sequence repeat (SSR) markers has not been reported in the genus Fagopyrum due to a lack of genomic resources. High-throughput transcriptomic sequencing can provide a rich resource for development of genic-SSR markers. In our study, the immature seeds transcriptome of common buckwheat ( Fagopyrum esculentum ) was sequenced using the Illumina HiSeq™ 2000 platform. We obtained a total of 21 million paired-end reads after filtering. The reads were assembled into 54,947 transcripts with an average length of 1235 bp. In total, 46,126 (83.95%) transcripts showed significant hits to known proteins or domains. Among these, 43,647 (79.43%) transcripts was assigned at least one gene ontology (GO) term. A total of 12,677 (23.07%) transcripts were mapped to the 141 Kyoto Encyclopedia of Genes and Genome (KEGG) pathways. Overall, 2326 transcripts contained at least one SSR with a frequency of one SSR per 1.17 kb. Mono-nucleotide repeats were the most abundant type (45.48%) followed by tri-nucleotide repeats (35.17%). Of the 150 SSRs chosen randomly, 36 markers showed polymorphism among 24 common buckwheat accessions, and 141 genic-SSRs (94.0%) were transferable to tartary buckwheat. A low level of genetic diversity was found among 35 registered tartary buckwheat varieties in China assessed using 31 polymorphic SSR markers. Genic-SSR markers developed herein will be valuable for construction of linkage maps, genetic diversity studies, and marker-assisted selection in Fagopyrum species.
ISSN:1380-3743
1572-9788
DOI:10.1007/s11032-017-0743-4