Developing a core collection of litchi (Litchi chinensis Sonn.) based on EST-SSR genotype data and agronomic traits

► We analyzed genetic diversity of a litchi germplasm of 96 accessions. ► Two core collections of litchi using the PowerCore program were constructed. ► Core set is better with genotypic and phenotypic dataset than only genotypic data. ► Core set should be on molecular and phenotypic data when markers had a low coverage.