Pyramiding superior haplotypes and epistatic alleles to accelerate wood quality and yield improvement in poplar breeding

Abstract

Abstract Genetic improvement of woody bioenergy crops is essential to maximize the genetic gain of industrially useful products. Conventional selective breeding to improve complex traits is laborious and time-consuming. A molecular marker-assisted selection approach based on multi-omics genetic dissection and pyramiding gene module utilization has not been developed for woody industrial crops. We initially identified 80 correlated genes enriched in co-expression modules that sustainably participate in lignocellulosic biosynthesis during various developmental periods in Populus. Using an adult germplasm population (15 years old, 435 accessions) of Populus tomentosa, we integrated association mapping, expression quantitative trait loci, and epistasis analyses to reveal the pleiotropy of causative genes within the core co-expression modules, such as ALG14, GSL8, SMT1, and IRX15-L.2, that drive natural variations in gene expression and harvested wood traits. We further pyramided two superior haplotypes and one desirable epistatic allele (Hap_01PtoSMT1+Hap_01PtoALG14+SNP2PtoIRX15-L.2) to alleviate linkage drag in multi-trait selection and improve industrial pulpwood products. Early-period selection study and genetic interpretation of the allelic differences of candidate elite trees in a juvenile germplasm population (5 years old, 435 accessions) demonstrated the accuracy and efficiency of our haplotype-based selection method relative to phenotype-based selection. This study provides novel insights into the improvement of industrial wood traits and also facilitates the rational breeding of perennial trees.