Hybridity testing of tomato F1 progenies derived from parents with varying fruit quality and shelf life using single nucleotide polymorphism (SNPs)

Abstract

The demand for tomato is increasing day by day mostly because of the increased per capita fresh fruit consumption. Nonetheless as a perishable fruit crop, it has relatively short life after ripening thus experiences remarkable post-harvest losses. The study was to select true F1 hybrids using SNPs for the development of inbred lines with long shelf life character through marker assisted backcrossing. Nine out of the one hundred and forty SNP markers failed, 93 were uninformative and 38 were polymorphic and spread across the 12 chromosomes. The major allele frequency, gene diversity, heterozygosity and Polymorphic Information Content (PIC) for each locus were calculated for SNP markers using Power Marker 3.5. The mean value of the major allele frequency was 0.673, ranging between 0.529 and 0.794. The average gene diversity and Heterozygosity values were 0.419 and 0.125 respectively. The PIC ranged from 0.273 (Sly11-Rx4) to 0.375 (Sly04-9) with a mean of 0.329. Of the 31 polymorphic SNPs, two SNPs (Sly04-9 and Sly07-2) exhibited the maximum PIC and a gene diversity value of 0.50. The markers Sly11-13 and Sly11-Rx4 were found to be the least informative with PIC and gene diversity values equaling 0.327 and major allele frequency of 0.794. The maximum heterozygosity was observed with SNP markers Sly03-8, Sly06-7, Sly08-1, Sly08-8, while the minimum heterozygosity was observed with SNPs marker Sly02-9, Sly06-1, Sly10-4, Sly10-5, Sly11-13, Sly11-Rx4, and Sly12-9.The SNPs tested for shelf life genes rin (Sly05-rin1 and Sly05-rin2) and nor (Sly10-nor) were monomorphic within the seven different plants (parentals). The SNP (Sly10-alc) tested for the alc gene was however, polymorphic within the seven lines. The result indicates that only one SNP (Sly10-alc) is a functional SNP to detect a long shelf life gene. Tomato genotypes CSIR/CRI-P002 and CSIR/CRI-ATS064 were however, polymorphic for alc. The other SNPs for rin and nor were not useful and new SNPs are needed to be redesigned. The molecular test revealed two superior F1 hybrids which were selected for evaluation as lines for improvement. The advantage is the reduction in cost, time, labor and field space requirement.