David Lopez

Ganoderma boninense, a soil-borne pathogenic fungus causing basal stem rot (BSR) disease in oil palm, is the major threat to cultivation in Southeast Asia, with the potential to reduce oil production by up to 80% in severely affected plantations. With a view to marker-assisted selection (MAS) of resistant planting material, we combined genetics and transcriptomics approaches to investigate the defense mechanisms of oil palm against infection by G. boninense. We first performed quantitative trait locus (QTL) mapping of BSR resistance using a multi-locus Bayesian variable selection approach applied to more than 10 years of data collected during pre-nursery tests of Deli and La Mé breeding populations. We found 6 and 5 BSR resistance loci segregating in Deli and La Mé respectively, with no overlap between them. Then we performed an RNA-sequencing approach on libraries of roots and bole of oil palm seedlings inoculated or not with G. boninense, focusing on Deli × La Mé crosses with contrasted BSR resistance. A Bayesian variable selection on predictors obtained by tracing the resistance loci haplotypes in profiled individuals identified 195 differentially expressed genes (DEGs) for the G. boninense inoculation × QTL interaction, among the 551 DEGs found for inoculation effects. The DEGs were located both in cis and trans positions compared to the segregating QTL intervals, enabling the prioritization of candidate genes and resistance mechanisms associated. Focusing on a strong effect QTL region on chromosome 4 in the Deli genetic background, we identified three candidate genes in cis positions that exhibited differential expression both in response to G. boninense inoculation and between resistant and susceptible haplotypes. Our study is the first combining QTL and RNA-seq approaches in oil palm based on genetically connected experimental setup, providing valuable information on the underlying mechanisms and paving the way for MAS of BSR resistant planting material.

Background: Quality traits are essential determinants of consumer preferences. Dioscorea alata (Greater Yam), is a starchy tuber crop in tropical regions. However, a comprehensive understanding of the genetic basis underlying yam tuber quality remains elusive. To address this knowledge gap, we employed population genomics and candidate gene association approaches to unravel the genetic factors influencing the quality attributes of boiled yam. Methods and Results: Comparative genomics analysis of 45 plant species revealed numerous novel genes absent in the existing D. alata gene annotation. This approach, adding 48% more genes, significantly enhanced the functional annotation of three crucial metabolic pathways associated with boiled yam quality traits: pentose and glucuronate interconversions, starch and sucrose metabolism, and flavonoid biosynthesis. In addition, the whole-genome sequencing of 127 genotypes identified 27 genes under selection and 22 genes linked to texture, starch content, and color through a candidate gene association analysis. Notably, five genes involved in starch content and cell wall composition, including 1,3-beta Glucan synthase, β-amylase, and Pectin methyl esterase, were common to both approaches and their expression levels were assessed by transcriptomic data. Conclusions: The analysis of the whole-genome of 127 genotypes of D. alata and the study of three specific pathways allowed the identification of important genes for tuber quality. Our findings provide insights into the genetic basis of yam quality traits and will help the enhancement of yam tuber quality through breeding programs.