Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of solanum pimpinellifolium using genotyping by sequencing

• Published in: BMC genomics Vol. 18; no. 1; p. 1
• Main Authors: Celik, Ibrahim, Gurbuz, Nergiz, Uncu, Ali Tevfik, Frary, Anne, Doganlar, Sami
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 03.01.2017; BioMed Central
• Subjects: Alleles; Analysis; Breeding; Chromosome Mapping; Crosses, Genetic; Cultivars; Cultivation; Data analysis; Deoxyribonucleic acid; DNA; Fertilizers; Food Quality; Fruit - genetics; Fruit cultivation; Fruits; Gene mapping; Gene polymorphism; Genes, Plant; Genetic aspects; Genetic polymorphisms; Genome-Wide Association Study; Genomes; Genomics; Genotype; Genotype & phenotype; Genotyping; Health aspects; High-Throughput Nucleotide Sequencing; Identification; Inbreeding; Interspecific; Introduced species; Irrigation; Lycopersicon esculentum - genetics; Mapping; Next-generation sequencing; Nucleotide sequence; Phenotype; Pipelines; Polymorphism; Polymorphism, Single Nucleotide; Population; Quantitative trait loci; Quantitative Trait, Heritable; Single nucleotide polymorphisms; Single-nucleotide polymorphism; Software; Solanum - genetics; Solanum pimpinellifolium; Tags; Tomato breeding; Tomatoes; pH; Soluble solids content; Fruit weight; Tomato genome
• ISSN: 1471-2164; 1471-2164
• DOI: 10.1186/s12864-016-3406-7

Solanum pimpinellifolium has high breeding potential for fruit quality traits and has been used as a donor in tomato breeding programs. Unlocking the genetic potential of S. pimpinellifolium requires high-throughput polymorphism identification protocols for QTL mapping and introgression of favourable alleles into cultivated tomato by both positive and background selection. In this study we identified SNP loci using a genotyping by sequencing (GBS) approach in an IBL mapping population derived from the cross between a high yielding fresh market tomato and S. pimpinellifolium (LA1589) as the recurrent and donor parents, respectively. A total of 120,983,088 reads were generated by the Illumina HiSeq next-generation sequencing platform. From these reads 448,539 sequence tags were generated. A majority of the sequence tags (84.4%) were uniquely aligned to the tomato genome. A total of 3.125 unique SNP loci were identified as a result of tag alignment to the genome assembly and were used in QTL analysis of 11 fruit quality traits. As a result, 37 QTLs were identified. S. pimpinellifolium contributed favourable alleles for 16 QTLs (43.2%), thus confirming the high breeding potential of this wild species. The present work introduced a set of SNPs at sufficiently high density for QTL mapping in populations derived from S. pimpinellifolium (LA1589). Moreover, this study demonstrated the high efficiency of the GBS approach for SNP identification, genotyping and QTL mapping in an interspecific tomato population.