Single nucleotide polymorphism discovery through Illumina-based transcriptome sequencing and mapping in lentil

Lentil, which belongs to the family Leguminosae (Fabaceae), is a diploid (2n = 2x = 14 chromosomes) self-pollinating crop with a genome size of 4063 Mbp. Because of its nutritional importance and role in the fixation of nitrogen from the atmosphere, lentil is a widely used crop species in molecular genetic studies. By using DNA markers, to date, a limited number of polymorphic bands have been generated. Therefore, it is necessary to develop additional markers to saturate the genome at high density. Single nucleotide polymorphism (SNP) markers are promising for this purpose because of their abundance, stability, and heredity; they can be used to generate a large number of markers over a short distance that are distributed in both intragenic and intergenic regions. Transcriptome sequencing technology was applied to 2 lentil genotypes, and cDNAs were sequenced using the Illumina platform. A total of 111,105,153 sequence reads were generated after trimming. The high-quality reads were assembled, producing 97,528 contigs with an N50 of 1996 bp. The Genome Analysis Tool Kit Unified Genotyper algorithm detected 50,960 putative SNP primers. A genetic linkage map was constructed by using JoinMap4.0 and the map consists of 7 major linkage groups that could be represented as 7 chromosomes of lentil. The extensive sequence information and large number of SNPs obtained in this study could potentially be used for future high-density linkage map construction and association mapping. The large number of contigs obtained in this study could be used for the identification of orthologous transcripts from cDNA data on other organisms.Lentil, which belongs to the family Leguminosae (Fabaceae), is a diploid (2n = 2x = 14 chromosomes) self-pollinating crop with a genome size of 4063 Mbp. Because of its nutritional importance and role in the fixation of nitrogen from the atmosphere, lentil is a widely used crop species in molecular genetic studies. By using DNA markers, to date, a limited number of polymorphic bands have been generated. Therefore, it is necessary to develop additional markers to saturate the genome at high density. Single nucleotide polymorphism (SNP) markers are promising for this purpose because of their abundance, stability, and heredity; they can be used to generate a large number of markers over a short distance that are distributed in both intragenic and intergenic regions. Transcriptome sequencing technology was applied to 2 lentil genotypes, and cDNAs were sequenced using the Illumina platform. A total of 111,105,153 sequence reads were generated after trimming. The high-quality reads were assembled, producing 97,528 contigs with an N50 of 1996 bp. The Genome Analysis Tool Kit Unified Genotyper algorithm detected 50,960 putative SNP primers. A genetic linkage map was constructed by using JoinMap4.0 and the map consists of 7 major linkage groups that could be represented as 7 chromosomes of lentil. The extensive sequence information and large number of SNPs obtained in this study could potentially be used for future high-density linkage map construction and association mapping. The large number of contigs obtained in this study could be used for the identification of orthologous transcripts from cDNA data on other organisms