SSR based association mapping analysis for fatty acid content in coconut flesh and exploration of the elite alleles in Cocos nucifera L

Exploring the elite alleles based on the association mapping related to fatty acid content in coconut flesh will expedite the breeding of coconut varieties for human welfare. In the present study, a total of eighty representative Cocos nucifera accessions belonging to 6 populations (Red dwarf, Yellow dwarf, Hainan red, Hainan tall, MAWA and Aromatica green dwarf) were selected from China as an association mapping population. The fatty acid content in mature flesh of the selected coconut accessions was measured by gas chromatography-mass spectrometry (GCMS). Ninety one SSR (simple sequence repeat) markers distributed across the 16 chromosomes of coconut were adopted for association mapping analysis with the aim to explore the elite alleles for the fatty acid content related traits. The results clearly showed the significant variation in fatty acid content among the analyzed coconut accessions. Based on the population structure analysis, we categorized eighty accessions in to two subgroups, the higher-fatty acid containing germplasm subgroup (HFA) and the lower-fatty acid containing germplasm subgroup (LFA). An admixed population structure was also observed through the PCoA (two groups), and UPGMA (two clusters). A Total of 10 SSR loci associated with fatty acid content of coconut flesh, were identified by the general linear model (GLM) and mixed linear model (MLM), with the maximum number of association loci across the chromosome 14. SSR loci with high explanation of phenotypic variation and stable expression were selected from the comparative analysis, with the phenotypic effect of their elite alleles ranging from -1.02～3.12. Among the identified elite alleles, CnFatB3-359 demonstrated the strongest positive effect with (mean of 2.35) the typical carrier material of Aromatica green dwarf, while CnFatB2-830 had the strongest negative effect (mean of -0.65) with the carrier material of MAWA. The present research detected favorable quantitative trait loci’s alleles and typical accessions for fatty acid content associated traits for breeding nutritional rich coconut varieties