Haplotype mining panel for genetic dissection and breeding in Eucalyptus

Abstract

SUMMARY To improve our understanding of genetic mechanisms underlying complex traits in plants, a comprehensive analysis of gene variants is required. Eucalyptus is an important forest plantation genus that is highly outbred. Trait dissection and molecular breeding in eucalypts currently relies on biallelic single‐nucleotide polymorphism (SNP) markers. These markers fail to capture the large amount of haplotype diversity in these species, and thus multi‐allelic markers are required. We aimed to develop a gene‐based haplotype mining panel for Eucalyptus species. We generated 17 999 oligonucleotide probe sets for targeted sequencing of selected regions of 6293 genes implicated in growth and wood properties, pest and disease resistance, and abiotic stress responses. We identified and phased 195 834 SNPs using a read‐based phasing approach to reveal SNP‐based haplotypes. A total of 8915 target regions (at 4637 gene loci) passed tests for Mendelian inheritance. We evaluated the haplotype panel in four Eucalyptus species (E. grandis, E. urophylla, E. dunnii and E. nitens) to determine its ability to capture diversity across eucalypt species. This revealed an average of 3.13–4.52 haplotypes per target region in each species, and 33.36% of the identified haplotypes were shared by at least two species. This haplotype mining panel will enable the analysis of haplotype diversity within and between species, and provide multi‐allelic markers that can be used for genome‐wide association studies and gene‐based breeding approaches.

Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)

“…In the Eucalyptus genus, despite its high cost, WGS was applied in some cases ( Kainer et al, 2019 ; Yong et al, 2021 ). RRS has been applied for association studies by using target re-sequencing of specific genes ( Ghosh Dasgupta et al, 2021 ; Candotti et al, 2023 ). Besides, sequence capture, where E. grandis reference genome ( Bartholomé et al, 2014 ; Myburg et al, 2014 ) was used to design probes and capture genomic regions to be sequenced, was evaluated ( de Moraes et al, 2018 ).…”

Tendencias en investigación de marcadores moleculares en especies forestales, con énfasis en Eucalyptus: análisis bibliométrico

“…Resaltan los trabajos desarrollados por Candotti et al (2023) la translocación de metales en la planta. Estos hallazgos proporcionan una mejor comprensión de la función de los genes EgMTP en la tolerancia a los metales y su potencial aplicación en la selección asistida por marcadores en Eucalyptus grandis.…”