Delineating Population Structure and Genetic Erosion in Tropical Tomato Germplasm for Lowland Breeding Initiatives (Early view)

Abstract

Understanding population structure and mitigating genetic erosion are critical for developing climate-resilient crop varieties tailored to tropical climates. Due to an intensive domestication history, cultivated tomato (Solanum lycopersicum) germplasm suffers from a narrowed genetic base that severely limits potential advancements in lowland breeding initiatives. This study delineates the population structure and assesses genetic erosion within a diverse collection of cultivated tomato accessions maintained by the Malaysian Agricultural Research and Development Institute (MARDI). The germplasm panel comprises breeding lines from MARDI and the World Vegetable Centre (WorldVeg), commercial varieties from local seed companies (Green World Genetics and Chia Hup Agriculture), regional accessions from Thailand, and landraces from Sabah and Sarawak. Genotypic profiling using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers revealed moderate genetic variation coupled with high inbreeding coefficients (f). These metrics signify severe genetic erosion and restricted gene flow, likely driven by historical bottlenecks and population stratification. Both SSR- and SNP-based cluster analyses resolved the germplasm into two primary clusters, clearly demarcating standard-type from cherry-type tomato accessions. Population structure analysis identified an optimal sub-population structure of K = 6, capturing the distinct genetic groups within the repository. Notably, WorldVeg-derived accessions (CLN3125A, CLN3125Q, CLN3125L, CLN2026D, and CLN5915-206D4) exhibited a highly distinct genetic background. Given their established heat and disease tolerance, these lines serve as vital parental candidates to counter genetic erosion and widen the genetic base in future tropical lowland tomato breeding programmes.