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Abstract
The sequencing of radish genome aids in the better understanding and tailoring of traits associated with economic importance. In order to accelerate the genomics assisted breeding and genetic selection, transcriptomes of 33 radish inbred lines with diverse traits were sequenced for the development of single nucleotide polymorphic (SNP) markers. The sequence reads ranged from 2,560,543,741 bp to 20,039,688,139 bp with the GC (%) of 47.80–49.34 and phred quality score (Q30) of 96.47–97.54%. A total of 4951 polymorphic SNPs were identified among the accessions after stringent filtering and 298 SNPs with efficient marker assisted backcross breeding (MAB) markers were generated from the polymorphic SNPs. Further, functional annotations of SNPs revealed the effects and importance of the SNPs identified in the flowering process. The SNPs were predominantly associated with the four major flowering related transcription factors such as MYB, MADS box (AG), AP2/EREB, and bHLH. In addition, SNPs in the vital flowering integrator gene (FT) and floral repressors (EMBRYONIC FLOWER 1, 2, and FRIGIDA) were identified among the radish inbred lines. Further, 50 SNPs were randomly selected from 298 SNPs and validated using Kompetitive Allele Specific PCR genotyping system (KASP) in 102 radish inbred lines. The homozygosity of the inbred lines varied from 56 to 96% and the phylogenetic analysis resulted in the clustering of inbred lines into three subgroups. Taken together, the SNP markers identified in the present study can be utilized for the discrimination, seed purity test, and adjusting parental combinations for breeding in radish.
Highlights
Radish (Raphanus sativus L., 2n = 18) is an important root vegetable in the Brassicaceae family
The objective of the present study is to discover single nucleotide polymorphic (SNP) markers from 33 inbred lines of radish by utilizing the information obtained from the transcriptome sequencing, functional annotation of the SNPs, and investigation of SNPs associated with flowering
The identified crude SNPs were filtered based on the criteria such as homozygous and diallelic SNPs, SNPs with the ability to classify at least 15 accessions, segregation ratio, flanking SNPs, and SNPs suitable for marker assisted backcross breeding
Summary
The tap root of radish has been widely consumed dietary part worldwide. Radish leaves, seedlings, siliques, and sprout possess dietary and medicinal importance[1]. Due to the higher consumption rate, several breeding efforts were implemented as well as researched to introduce cultivars with diverse phenotypic and economic qualities. The qualities such as shape, size, color, flowering. NGS approaches like transcriptome sequencing resulted in the generation of comprehensive sequence data in several horticultural plants such as pepper, cucumber, and eggplant,[7,8,9].
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