TITLE:
Genetic Diversity and Population Structure of Tomato (Solanum lycopersicum) Germplasm Developed by Texas A&M Breeding Programs
AUTHORS:
Devi R. Kandel, Renesh H. Bedre, Kranthi K. Mandadi, Kevin Crosby, Carlos A. Avila
KEYWORDS:
Genetic Diversity, Single-Nucleotide Polymorphism (SNP), Solanum lycopersicum, Tomato, Genotyping by Sequencing (GBS)
JOURNAL NAME:
American Journal of Plant Sciences,
Vol.10 No.7,
July
25,
2019
ABSTRACT: Genetic variation developed in plant breeding
programs is fundamental to creating new combinations that result in cultivars
with enhanced characteristics. Over the years, tomato (Solanum lycopersicum) breeding programs associated with the Texas A&M
University system have developed morphologically diverse lines of tomatoes
selected for heat tolerance, fruit quality, and disease resistance to adapt
them to Texas growing conditions. Here we explored the intraspecific genetic
variations of 322 cultivated tomato genotypes, including 300 breeding lines
developed by three Texas A&M breeding programs, as an initial step toward
implementing molecular breeding approaches. Genotyping by sequencing using low
coverage whole-genome sequencing (SkimGBS) identified 10,236 high-quality
single-nucleotide polymorphisms (SNPs) that were used to assess genetic
diversity, population structure, and phylogenetic relationship between
genotypes and breeding programs. Model-based population structure analysis,
phylogenetic tree construction, and principal component analysis indicated that
the genotypes were grouped into two main clusters. Genetic distance analysis
revealed greater genetic diversity among
the products of the three breeding programs. The germplasm developed at Texas A&M
programs at Weslaco, College Station, and by Dr. Paul Leeper exhibited genetic
diversity ranges of 0.175 - 0.434, 0.099 - 0.392, and 0.183 - 0.347, respectively,
suggesting that there is enough variation within and between the lines from the
three programs to perform selection for cultivar development. The SNPs
identified here could be used to develop molecular tools for selecting various
traits of interest and to select parents for future tomato breeding.