Genomic diversity and population structure of understudied cattle populations of Sri Lanka in relation to established indigenous breeds.

Indigenous local cattle constitute one of the major components and primary contributors to the livestock sector in Sri Lanka. Understanding the genetic makeup of local cattle is essential for their effective utilization in national breed improvement programs aimed at enhancing productivity, as well as elucidating their historical development and ancestry. Accordingly, this study was conducted to assess the genomic diversity and population structure of two understudied local cattle populations of Sri Lanka, Northern Local and Kinniya cattle in addition to three well established indigenous breeds, Batu, Thawalam and White cattle. Estimates of genomic diversity indices revealed moderately high observed heterozygosity across all populations. FROH estimates indicated moderate levels of inbreeding in Thawalam and Kinniya cattle. The linkage disequilibrium persisted over short genomic regions and estimates of effective population size revealed sharp decline over recent generations in all populations. Pairwise FST values indicated low genetic differentiation among Sri Lankan local cattle with values varying between 0.01 and 0.03. Principal components analysis indicated relative genetic distinctness of Kinniya cattle. ADMITURE analysis revealed both Indus valley and South Indian cattle ancestries in Sri Lankan cattle, indicating an admixed genomic background shaped by historical and recent introgression events. White and Kinniya cattle exhibited the lowest level of exotic introgression (< 2%) while Batu, Thawalam and Northern Local cattle exhibited notable taurine admixture of 14%, 8% and 9% respectively. The results provided critical insights for guiding future breeding programs and developing effective conservation strategies to preserve the genetic diversity and ecological adaptability of Sri Lankan cattle.