Genome-wide association study identifies candidate genes responsible for inorganic phosphorus and sucrose content in rubber tree latex

Abstract

Rubber tree (Hevea brasiliensis) provides the sole commercial source of natural rubber in the world. Over the past three decades, a number of latex physiological parameters has been applied to construct tapping systems, enhance natural rubber production, monitor tapping panel dryness, and evaluate rubber clone performance. Inorganic phosphorus and sucrose content (Pi and Suc) are two well-interpreted parameters to describe the latex metabolic status of rubber trees, whereas the candidate genes responsible for regulating Pi and Suc have never been reported. Here, a natural population consisting of 218 rubber tree individuals was exploited to identify candidate genes associated with Pi and Suc. The phenotype of this population was measured over a period of two years. Genome-wide association study (GWAS) was conducted using mixed linear models and 7,835,736 single-nucleotide polymorphisms (SNP). A total of 26 and 11 SNPs were significantly associated with Pi and Suc, respectively. By combining the GWAS results with genomic annotation data, 57 and 29 candidate genes within 50 kb of the significant SNPs were identified for Pi and Suc, respectively. The expression patterns of these candidates were further investigated, and five for Pi and three for Suc were identified to be specifically expressed in the latex. A DOF transcription factor and a histone H2A gene have been interpreted, while the annotations for the other candidate genes remain limited. These findings contribute to understanding the genetic foundation of Pi and Suc in the latex as well as the breeding of high-yielding rubber clones by employing latex physiological parameters.