Sequencing-based High-density Genetic Map Construction And Mutation Mapping In Cucumber

Genetic linkage maps are important tools for molecular breeding, gene cloning, and study of meiotic recombination. In cucumber(Cucumis sativus L.), the marker density, resolution and genome coverage of previously developed genetic maps using PCR-based molecular markers are relatively low. In this study we generated an ultra-high density linkage map by conducting low-coverage sequencing of 147 recombinant inbred lines(RILs) derived from two cultivated cucumber inbred lines. This map spanned 1384.4 c M in length and consisted of 115,933 SNPs that were grouped into 759 bins. Comparison of the genetic map and the 9930 draft genome assembly revealed more than 98% genome coverage of this map, and a high degree of concordance between marker orders and their physical locations. Based on this, we corrected the inaccurate anchor of nine scaffolds on chromosome 5. Genomic regions with high recombination frequency and segregation distortion were also identified. The quality of the map was authenticated by resolving the bitterness gene Bi and a major QTL for fruit wart size fws5 into single bins harboring the cloned genes. Furthermore, we localized 28 QTLs for ten agronomical traits, and revealed a genomic region for multiple fruit epidermal features. This high-density genetic map should be a valuable tool for molecular breeding in cucumber and facilitate our understanding of cucumber biology.The peel color of fruit is an important commercial trait in cucumber. A mutant showing light green exocarp was discovered from ethylmethane sulfonate(EMS) mutagenized cucumber line 406 with dark green exocarp. Genetic analysis showed the mutant phenotype is conferred by a single recessive gene, which is designated as lgp(light green peel). By re-sequencing of bulked segregants, we identified the candidate gene Csa7G051430 encoding ACCUMULATION AND REPLICATION OF CHLOROPLASTS 5(ARC5) that plays a vital role in chloroplast division in Arabidopsis. A single nucleotide polymorphism(SNP) causing amino acid alteration in the conserved GTPase domain of Csa7G051430 showed co-segregation with the altered phenotype. Furthermore, a transient RNA interference of this gene resulted in reduced number and enlarged size of chloroplasts, which were also observed in the lgp mutant. These evidences support that the non-synonymous SNP in Csa7G051430 is the causative mutation for the light green peel. This study provides a new allele for cucumber breeding for light green fruits and additional resource for the study of chloroplast development.