Construction of a High-density Genetic Linkage Map and QTL Analysis of Resistance to Cucumber Mosaic Virus in Luffa cylindrica (L.) Roem. Based on Specific Length Amplified Fragment Sequencing

Abstract

Background: Luffa cylindrica L. is an economically important vegetable crop that is consumed globally. Cucumber mosaic virus (CMV) is an important virus affecting Luffa spp. No specific high-density maps have been constructed owing to a lack of efficient markers. Furthermore, no genes or quantitative trait loci (QTLs) are reportedly responsible for CMV resistance in Luffa spp. The development of next-generation sequencing has enabled discovery of single nucleotide polymorphisms and high-throughput genotyping of large populations. Results: A total of 271.01 Mb pair-end reads were generated. The average sequencing depth was 86.19× in both maternal and parental lines, and 14.57× in each F 2 individual. When filtering low-depth specific locus amplified fragment (SLAF) tags, 100,077 high-quality SLAFs were detected, and 7,405 of them were polymorphic. Finally, 3,701 of the polymorphic markers were selected for genetic map construction, and 13 linkage groups were generated. The map spanned 1,518.56 cM with an average distance of 0.41 cM between adjacent markers. Our results also revealed that CMV resistance was regulated by QTLs. Based on the newly constructed high-density map, two loci located on chromosome 1 (100.072 ~ 100.457 cM) and 4 (42.475 ~ 44.398 cM) were identified to regulate CMV resistance in L. cylindrica . A gag-polypeptide of LTR copia-type retrotransposon was predicted as the candidate gene responsible for CMV resistance in L. cylindrica . Conclusions: A high-density linkage map of L. cylindrica was constructed using SLAF. QTL mapping based on CMV disease phenotypes of F 2 led to the identification of two QTL on chromosome 1 and 4, respectively. Kompetitive allele-specific PCR analysis of 60 F 2 individuals, which gave rise to F 2:3 individuals, was carried out. We found that the QTL on chromosome 1 was associated with CMV resistance. Mapping of CMV QTL combined with the transcriptomic sequence alignment identified a gag-polypeptide of LTR copia-type retrotransposon as the most likely causal gene.