Tomato Fruits Show Wide Phenomic Diversity but Fruit Developmental Genes Show Low Genomic Diversity

<div><p>Domestication of tomato has resulted in large diversity in fruit phenotypes. An intensive phenotyping of 127 tomato accessions from 20 countries revealed extensive morphological diversity in fruit traits. The diversity in fruit traits clustered the accessions into nine classes and identified certain promising lines having desirable traits pertaining to total soluble salts (TSS), carotenoids, ripening index, weight and shape. Factor analysis of the morphometric data from Tomato Analyzer showed that the fruit shape is a complex trait shared by several factors. The 100% variance between round and flat fruit shapes was explained by one discriminant function having a canonical correlation of 0.874 by stepwise discriminant analysis. A set of 10 genes (<i>ACS2</i>, <i>COP1</i>, <i>CYC-B</i>, <i>RIN</i>, <i>MSH2</i>, <i>NAC-NOR</i>, <i>PHOT1</i>, <i>PHYA</i>, <i>PHYB</i> and <i>PSY1</i>) involved in various plant developmental processes were screened for SNP polymorphism by EcoTILLING. The genetic diversity in these genes revealed a total of 36 non-synonymous and 18 synonymous changes leading to the identification of 28 haplotypes. The average frequency of polymorphism across the genes was 0.038/Kb. Significant negative Tajima’D statistic in two of the genes, <i>ACS2</i> and <i>PHOT1</i> indicated the presence of rare alleles in low frequency. Our study indicates that while there is low polymorphic diversity in the genes regulating plant development, the population shows wider phenotype diversity. Nonetheless, morphological and genetic diversity of the present collection can be further exploited as potential resources in future.</p></div

Fruit traits associated with the factors extracted from factor analysis.

<p>Fruit traits associated with the factors extracted from factor analysis.</p

Clustering of accessions based on SNP polymorphism.

<p>The tree was made using the Neighbor-Joining method in MEGA4 taking together the sequences of all the genes. Substitutions are represented by branch lengths and the bootstrap value is indicated as numbers above the branches (10000 replicates).</p

Nucleotide polymorphism.

<p>Nucleotide polymorphism.</p

Clustering of the tomato accessions on the basis of 55 fruit attributes.

<p>Agglomerative hierarchical clustering by unweighted pair-group average method was used for clustering. The accessions were grouped into 9 classes (C1-C9). Each class is represented by a different color in the dendrogram. The dotted line on dendrogram represents the position of truncation for defining the 9 classes. The heat map on left side of dendrogram shows the relative values of five selected fruit attributes.</p