Genetic characterization of coconut (Cocos nucifera L.) varieties conserved in Vietnam through SCoT marker-based polymorphisms

Coconut (Cocos nucifera L.) production sustains millions of smallholder farmers and their families around the globe, and also powers a thriving industry of climate-adaptive nutrition and biomaterials. Demand for high-quality planting materials has risen sharply in recent years, calling for greater understanding and potential utilization of the genetic diversity in coconut populations. Genetic diversity among several conserved coconut varieties in Vietnam was investigated to assess the suitability of 15 start codon targeted (SCoT) primers for future selective breeding programs. Amplification of 15 SCoT primers in 57 individuals from 19 coconut varieties revealed high intra-varietal diversity (Nei’s genetic diversity index = 0.237, Shannon’s Information index = 0.352), especially among the Vietnamese Dwarfs. Intriguingly, inter-varietal differentiation accounted for only 9.41% of total genetic variation. The designated SCoT primers were moderately informative. On average, each primer had 9.5 reproducible polymorphic bands per reaction. Polymorphism Information Content (PIC) per locus ranged between 0.217 and 0.390, with Resolving power (Rp) between 0.271 and 0.599. Principal Coordinate Analysis (PCoA) and Unweighted Pair Group Method with Arithmetic mean (UPGMA) analyses revealed distinct clusters for non-native Dwarf, native Dwarf, and Tall varieties. This paper represents the first-of-its-kind attempt to shed light on coconut genetic diversity in Vietnam using molecular markers.