Resequencing-based QTL mapping of girth and rubber yield traits in a full-sib rubber tree population GT1 × CATAS8-79

Abstract

Rubber tree (Hevea brasiliensis) provides the sole commercial source of natural rubber, a crucial industrial raw material. Rubber yield and girth are widely considered as the most important agronomic traits of rubber tree. However, due to the delayed initiation of rubber tree research, the identification of quantitative trait loci (QTLs) and candidate genes for these traits remains limited. Here, QTL mapping analysis was conducted on the full-sibling progeny population derived from a cross between the clones of GT1 and CATAS8–79. Phenotypes of girth, dry rubber yield (DRY) and yield per centimeter girth (YCG) were measured annually for four consecutive years. Meanwhile, the resequencing of 238 offspring individuals identified 29,140,529 high-confidence SNPs, which resulted in the generation of 3147 non-redundant bin markers. Based on these bin markers, 18 high-density linkage groups were constructed, with an average genetic distance ranging from 1.49 to 4.96 cM. Subsequently, a total of 37 environmentally stable QTLs were identified comprising 8 for girth, 16 for DRY, and 13 for YCG. These QTLs explained phenotypic variances spanning from 0.32 % to 17.71 %. The two most reliable QTLs, namely QGirth-4 and QGirth-7.2, were further investigated and 21 candidate genes were identified. Based on transcriptome sequencing and homologous annotation, a gibberellin receptor gene (GIBBERELLIN-INSENSITIVE DWARF1, GID1) was determined as the promising candidate for QGirth-7.2. Overexpression of HbGID1 led to early flowering and increased rosette-leaf branches in Arabidopsis, implying its significant role in girth development. These findings provide valuable insights into QTLs and target genes for enhancing growth and rubber yield traits, thereby contributing to molecular breeding of elite latex-timber rubber tree clones.