Ultrahigh-density genetic map construction and identification of quantitative trait loci for growth in rubber tree (Hevea brasiliensis)

Abstract

Ultrahigh-density genetic mapping is used extensively for gene discovery, mapping quantitative trait loci (QTL), and assisting in crop breeding. However, genetic mapping of rubber trees (Hevea brasiliensis) has hitherto been limited in terms of both types and resolution. In this study, 214 F1 progenies derived from a cross of IAN 873 × REYAN 106 were genotyped via a whole-genome resequencing-based (WGRS) approach. From the 44,438,656 single nucleotide polymorphisms (SNPs) obtained from the genotyping, an ultrahigh-density genetic map was constructed using 203,124 SNPs, which included 2099.12 cM across eighteen linkage groups of the entire rubber tree genome. To the best of our knowledge, an ultrahigh-density genetic map of a rubber tree constructed via the WGRS approach has not yet been reported in literature. Two phenotypes associated with growth, namely, the girth at breast height (GBH) and tree height (TH), were investigated under a six-month interval. A total of six QTLs were found, in which qGBH11 and qGBH18 were detected repeatedly. Based on the physical positions of the bin markers that flank the QTLs, 47 genes identified within the qGBH11 locus, as well as the gene HB11G00752, were selected as the candidate genes that encodes ent-kaur-16-ene synthase (KS), regulating gibberellin biosynthesis. The search results for the KS gene family in the genome indicated that six out of ten KS family members were located in the qGBH11 allele. Expression analysis further shed light on the differential expressions of the KS family genes between F1 individuals having fast and slow growth. These results are expected to provide new insight into the genomic regions that control growth in rubber trees, and also facilitate the development of more effective approaches for breeding fast-growing timber latex clones.