Genetic Diversity, Gene Discovery and Combining Ability for Yield and Fruit Quality Traits in Tomato (Solanum lycopersicum L.)

Abstract

Tomato is a major vegetable crop in Ethiopia, contributing to nutrition, household income, and serving as a raw material for agro-processing and export markets. However, national tomato productivity remains low due to the prevalence of diseases, insect pests, and weeds. The shortage of improved varieties with high yield, superior fruit quality, and resistance to both biotic and abiotic stresses further limits production. Developing high-yielding OPVs and hybrids with superior fruit quality and tolerance to biotic and abiotic stresses is essential to enhance tomato productivity and utilization in Ethiopia. Therefore, the study aimed to develop high-yielding and fruit-quality varieties with large fruit size, and extended shelf life to contribute to improvement in productivity and utilization. The specific objectives were to: (i) assess the phenotypic diversity among tomato germplasm; (ii) determine the interrelationships among yield, yield-related, and fruit quality; (iii) determine molecular genetic diversity and population structure using SNP markers; (iv) identify QTLs or genomic regions associated with yield, yield-related, and fruit quality; (v) estimate combining ability and heterosis and identify parental lines for the production of hybrids that combine high yield and fruit quality. One hundred and forty-three (143) tomato genotypes were characterized for 15 quantitative and 18 qualitative traits for two seasons in 2021 and 2022. Most traits showed a highly significant difference (p<0.01) among tomato germplasm. The genotype-by-season interaction was also highly significant (p<0.01) for some traits. High (79 92%; 24–84%) to medium (41-46%; 12–13%) broad sense heritability and genetic advance as a percent of the mean, respectively, were detected for most traits. Fruit size traits (fruit weight, fruit length, fruit width, fruit shape index, and pericarp thickness), along with days to 50% flowering, fruit number per plant, fruits per cluster, and total soluble solids, showed strong genetic correlations with marketable and total yield. These correlations ranged from –0.552 to +0.55 and were highly significant (p < 0.01). Principal component analysis showed that the first five components together accounted for 82.86% of the total variation. The first two components explained 51%, primarily contributed by fruits per plant, fruit weight, fruit width, fruit length, number of locules, and fruit skin thickness. Genetic diversity was also observed for 18 qualitative traits, including flower, growth pattern, and fruit traits. Genotypes were classified into three groups, with multiple correspondence analysis (MCA) biplots capturing 18.5% of the total variation. A molecular diversity analysis was conducted on 187 tomato germplasm, including 63 fresh-market, 112 processing, and 12 cherry types, using 4,729 high-quality SNP markers generated through DArTseq. The study revealed low to moderate gene diversity (0.04–0.50), polymorphic information content (0.04–0.37), and minor allele frequency (0.02–0.497). Two distinct population structures and admixtures comprising 6, 172, and 9 genotypes were detected. PCoA revealed two distinct genetic clusters and admixtures, with PCoA1 (29.02%) and PCoA2 (10.78%) accounting for 39.8% of the total molecular genetic diversity. Analysis of molecular variance further elucidated high or moderate and highly significant genetic differentiation among the structured (FST = 0.496, p≤ 0.001) and pre-defined (FST = 0.134, p≤ 0.001) populations. The variation within a cluster (50%) was comparable to the variation accounted for among the population (50%) for the structured population; variation within the predefined population (87%) was much higher than among populations (13%). A genome-wide association study using 2,709 informative SNP markers identified 121 marker-trait associations (−log10p ≥ 3.5; FDR ≤ 0.05) related to ten traits. These associations corresponded to 104 QTLs, which were clustered based on linkage disequilibrium decay (0.157–28.826 Mbp at r² = 0.2) for each chromosome. Some of the identified QTLs were located in the vicinity of previously identified marker-trait associations, while others were new. A combining ability study was conducted using five male and five female parental lines selected for phenotypic diversity in yield per plant, fruit size, fruit number per plant, fruit shape, and total soluble solids (TSS). The study revealed highly significant genetic variation (p < 0.01) among hybrids, parents, their specific combining ability (male × female), and interactions with the environment. The additive and dominance genetic variances were important, while the additive variance dominated for most traits. The highest positive midparent (81%) and better parent (75%) were recorded for fruit yield per plant for the hybrid G2xG7. Female parental line G2 was the best combiner for fruit yield and number per plant, and parental line G3 was the best for fruit number per plant. Male parental lines G7 and G10 were the best combiners for fruit weight, fruit wall thickness, and fruit width. Hybrids G2 x G7, G3 x G7, and G3 x G6 showed high positive specific combining ability effects, better performance per se, and heterosis over the mid and better parent for yield and related traits.