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

Abstract

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.

Pipeline to Design Inbred Lines and F1 Hybrids of Leaf Chicory (Radicchio) Using Male Sterility and Genotyping-by-Sequencing

“…It is noteworthy that, in the current scientific literature, the only case study in which RADseq technology is used for genotyping Cichorium species is the work of Patella et al, in which endive accessions were analysed using RADseq to identify the genes responsible for leaf shape in this crop [ 45 ]. Moreover, germplasm characterisation and population genetics studies based on RADseq genotyping have been performed, which showed the potential of this tool in other crop plants, such as peanut [ 46 ] and faba bean [ 47 ], as well as in other non-plant organisms. An example of this is represented in Sunde et al, where a comparison between codominant PCR-based microsatellite and RADseq is also provided [ 48 ], highlighting the higher informativeness of the GBS approach compared to conventional PCR.…”