Abstract
Key message
Large-scale faba bean transcriptome data are available, and the first genotyping platform based on liquid-phase probe targeted capture technology was developed for genetic and molecular breeding studies.
Abstract
Faba bean (Vicia faba L., 2n = 12) is an important food legume crop that is widely grown for multiple uses worldwide. However, no reference genome is currently available due to its very large genome size (approximately 13 Gb) and limited single nucleotide polymorphism (SNP) markers as well as highly efficient genotyping tools have been reported for faba bean. In this study, 16.7 billion clean reads were obtained from transcriptome libraries of flowers and leaves of 102 global faba bean accessions. A total of 243,120 unigenes were de novo assembled and functionally annotated. Moreover, a total of 1,579,411 SNPs were identified and further filtered according to a selection pipeline to develop a high-throughput, flexible, low-cost Faba_bean_130K targeted next-generation sequencing (TNGS) genotyping platform. A set of 69 Chinese faba bean accessions were genotyped with the TNGS genotyping platform, and the average mapping rate of captured reads to reference transcripts was 93.14%, of which 53.23% were located in the targeted regions. The TNGS genotyping results were validated by Sanger sequencing and the average consistency rate reached 93.6%. Comprehensive population genetic analysis was performed on the 69 Chinese faba bean accessions and identified four genetic subgroups correlated with the geographic distribution. This study provides valuable genomic resources and a reliable genotyping tool that could be implemented in genetic and molecular breeding studies to accelerate new cultivar development and improvement in faba bean.
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Data availability
The raw RNA sequencing data were deposited in the SRA under Bioproject No. PRJNA679419.
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Acknowledgements
We thank the Novogene Bioinformatics Institute (Beijing, China) for providing technical support in RNA sequencing and we also thank China Golden Marker (Beijing) Biotech Co., Ltd for providing technical support in the development, detection and data analysis of the panel. This study was supported by the Construction of Molecular Database of Faba Bean and Pea and Identification of Maize Germplasm Project (No.19200030), China Agriculture Research System of MOF and MARA-Food Legumes (CARS-08), the Crop Germplasm Resources Protection (2130135), the National Key R&D Program of China (2019YFD1001300), the Agricultural Science and Technology Independent Innovation Fund of Jiangsu Province (CX(18)2019) and also supported by Agricultural Science and Technology Innovation Program (ASTIP) in CAAS.
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X.Z. and T.Y. designed the study. Y.L., W.H., X.W., Y.M. and Y.H. conducted sample collections. C.W., R.L., Y.M., G.L., D.W., Y.J., H.Z., M.L. and X.Y. performed the experiment. C.W., R.L., and T.Y. finished data analyses. C.W., R.L., and T.Y. wrote the draft manuscript. X.Z. and Y.M. revised the manuscript.
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Figure S1
Classification of unigenes in GO (a), KEGG (b), and KOG (c). (PDF 370 kb)
Figure S2
Statistics of SNP numbers on target from genotyping results of 69 faba bean accessions under different filtrations. (a) No filtration on the SNP number within one read; (b) Reads with SNP number less than six were retained; (c) Reads with SNP number less than four were retained; (d) Reads with SNP number less than two were retained. (PDF 469 kb)
Table S1
Transcriptome data output and quality from the flowers and leaves of 102 global faba bean accessions. (PDF 150 kb)
Table S2
BUSCO analysis result of faba bean transcriptome. (PDF 5 kb)
Table S3
Similarity distribution of related species of V. faba assembled unigenes. (PDF 7 kb)
Table S4
Mapped rate of captured reads to the reference transcripts for 69 accessions. (PDF 60 kb)
Table S5
Specific primer pairs designed from flanking sequence of SNPs for PCR amplification. (PDF 162 kb)
Table S6
Verification of the sequencing results of Faba_bean_130K TNGS genotyping platform with Sanger sequencing. (PDF 63 kb)
File S1
The sequences of Faba_bean_130K TNGS liquid phase probes. (XLSX 8973 kb)
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Wang, C., Liu, R., Liu, Y. et al. Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing. Theor Appl Genet 134, 3195–3207 (2021). https://doi.org/10.1007/s00122-021-03885-0
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DOI: https://doi.org/10.1007/s00122-021-03885-0