Journal Article

Chromosome‐level wild Hevea brasiliensis genome provides new tools for genomic‐assisted breeding and valuable loci to elevate rubber yield

Cheng, Han, Feng, Shuyan, Wu, Wenguan, Zeng, Xia, Yang, Qihang, Wang, Xiyin, Tu, Min, Song, Xiaoming, Huang, Huasun, Wu, Tingkai, Hu, Yanshi, An, Zewei, Deng, Zhi

2023

Overview

Summary The rubber tree (Hevea brasiliensis) is grown in tropical regions and is the major source of natural rubber. Using traditional breeding approaches, the latex yield has increased by sixfold in the last century. However, the underlying genetic basis of rubber yield improvement is largely unknown. Here, we present a high‐quality, chromosome‐level genome sequence of the wild rubber tree, the first report on selection signatures and a genome‐wide association study (GWAS) of its yield traits. Population genomic analysis revealed a moderate population divergence between the Wickham clones and wild accessions. Interestingly, it is suggestive that H. brasiliensis and six relatives of the Hevea genus might belong to the same species. The selective sweep analysis found 361 obvious signatures in the domesticated clones associated with 245 genes. In a 15‐year field trial, GWAS identified 155 marker–trait associations with latex yield, in which 326 candidate genes were found. Notably, six genes related to sugar transport and metabolism, and four genes related to ethylene biosynthesis and signalling are associated with latex yield. The homozygote frequencies of the causal nonsynonymous SNPs have been greatly increased under selection, which may have contributed to the fast latex yield improvement during the short domestication history. Our study provides insights into the genetic basis of the latex yield trait and has implications for genomic‐assisted breeding by offering valuable resources in this new domesticated crop.

• Publisher: John Wiley & Sons, Inc,John Wiley and Sons Inc
• Subject: Biosynthesis / biotechnology / Breeding / Chromosomes / Chromosomes - metabolism / Cloning / Divergence / Domestication / ethylene production / field experimentation / Gene expression / Gene Expression Regulation, Plant / Genes / Genetic diversity / genome / Genome-wide association studies / Genome-Wide Association Study / Genomes / Genomic analysis / Genomics / Germplasm / Hevea - genetics / Hevea - metabolism / Hevea brasiliensis / homozygosity / Latex / Latex - metabolism / metabolism / Natural rubber / nonsynonymous SNP / Nucleotide sequence / nucleotide sequences / Phylogenetics / Plant Breeding / Plant Proteins - genetics / Rubber / Rubber - metabolism / Rubber trees / selective sweep / Signatures / Single-nucleotide polymorphism / Trees / Tropical environment / Tropical environments