Research Article

SNP Identification from RAD-Seq Data in Faba Bean (Vicia faba L.)  

Yujie Zhu1 , Tingfu Liu2 , Hanmei Li3 , Baogen Wang4 , Suqi Wu4 , Sujuan Li5 , Linlin Wang2 , Guojing Li4 , Xinyi Wu4
1 School of Agriculture and Food Science, Zhejiang A&F university, Hangzhou, 311300, China
2 Lishui Academy of Agricultural and Forestry Sciences, Lishui 323000, China
3 Lishui Vocational and Technical College, Lishui, 323000, China
4 Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
5 Central Laboratory of Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
Author    Correspondence author
Plant Gene and Trait, 2021, Vol. 12, No. 2   doi: 10.5376/pgt.2021.12.0002
Received: 04 Aug., 2021    Accepted: 12 Aug., 2021    Published: 20 Aug., 2021
© 2021 BioPublisher Publishing Platform
This article was first published in Molecular Plant Breeding in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Preferred citation for this article:

Zhu Y.J., Liu T.F., Li H.M., Wang B.G., Wu S.Q., Li S.J., Wang L.L., Li G.J., and Wu X.Y., SNP identification from RAD-Seq data in faba bean (Vicia faba L.), Plant Gene and Trait, 12(2): 1-8(doi: 10.5376/pgt.2021.12.0002)


Faba bean is an important edible legume crop in China. Due to its huge genome size and no available reference genome, SNP marker is very limited in faba bean. To identify genome-wide SNP markers, we obtained 35.47 Gb data from eight landraces by RAD-sequencing, with an average of 4.77 Gb data for each accession. A total of 245443516 reads were generated, the single accession has an average of 30680439.5 reads, and the average length of the reads reaches to 144 bp. The Q20 and Q30 values were over 97.89% and 93.83%, respectively. The GC content between the reads varied from 38.05% to 40.09%. Using a special Bayesian method under the situation of no reference genome, we identified 3722 SNPs among the eight landraces. Regarding the single accession, the detected SNPs varied from 3278 to 3578, and the homozygous SNPs number was larger than that of heterozygous SNPs for most of accessions. For the SNP types, T:A->C:G type has the largest proportion (38.8%), followed by C:G->T:A (28.0%) and the smallest is T:A->A:T (7.5%). 31 SNPs were selected to convert into KASP markers, and they showed a success rate of 66.7% through amplifying on 46 accessions. The SNPs in this study provide a strong genetic tool for germplasm identification, gene mapping and molecular breeding in faba bean.

Faba bean; SNP; RAD-Sequencing; KASP
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