An ultra-high density map allowed for mapping QTL and candidate genes controlling dry latex yield in rubber tree

Rubber tree (Hevea brasiliensis) is the most important commercial producer of high-quality natural rubber in the world. Here, we identified 571,267 SNPs and 134,184 indels, and constructed the first ultra-high density genetic linkage map in rubber tree population. This map consisted of 6940 markers, with average marker density and recombination rate 0.30 cM and 0.97 cM/Mb, respectively. Then the whole genome QTL scanning for dry latex yield (DLY) trait were performed and seventeen repQTLs were obtained, among which qDFY-10 and qDFY-18-4 could explain up to 38.3% and 33.3% phenotypic variability, respectively. Numerous highly-promising QTL candidate genes were identified and then verified significant associated with DLY trait, including some first found in rubber tree, such as thioredoxin h, plastin-like protein, calmodulin binding protein, cytochrome-c oxidase and methylglutaconyl-CoA hydratase. This ultra-high density linkage map supplies a base for important traits QTL mapping and will be useful in the improvement of the assembly of genome sequences in rubber tree. The verification of candidate QTL genes showed great importance for understanding the possible function of mapped QTLs and the comprehensive relations between phenotypes and genotypes. Accurate QTL mapping will be enhance genetic studies that can be applied in rubber tree breeding programs.