A Genome-Wide Association Study for Resistance to the Insect Pest Leptocybe invasa in Eucalyptus grandis Reveals Genomic Regions and Positional Candidate Defense Genes

Abstract

The galling insect, Leptocybe invasa, causes significant losses in plantations of various Eucalyptus species and hybrids, threatening its economic viability. We applied a Genome-Wide Association Study (GWAS) to identify single nucleotide polymorphism (SNP) markers associated with resistance to L. invasa. A total of 563 insect-challenged Eucalyptus grandis trees, from 61 half-sib families, were genotyped using the EUChip60K SNP chip and we identified 15,445 informative SNP markers in the test population. Multi-Locus Mixed Model (MLMM) analysis identified 35 SNP markers putatively associated with resistance to L. invasa based on four discreet classes of insect damage scores: (0)- not infested, (1)- infested showing evidence of oviposition but no gall development, (2)- infested with galls on leaves, mid-ribs or petioles and (3)- stunting and lethal gall formation. MLMM analysis identified three associated genomic regions on chromosomes 3, 7 and 8 jointly explaining 17.6% of the total phenotypic variation. SNP analysis of a validation population of 494 E. grandis trees confirmed seven SNP markers that were also detected in the initial association analysis. Based on transcriptome profiles of resistant and susceptible genotypes from an independent experiment we identified several putative candidate genes in associated genomic loci including NB-ARC and TIR-NBS-LRR genes. Our results suggest that Leptocybe resistance in E. grandis may be influenced by a few large-effect loci in combination with minor effect loci segregating in our test and validation populations.

Genomic Breeding for Diameter Growth and Tolerance to Leptocybe Gall Wasp and Botryosphaeria/Teratosphaeria Fungal Disease Complex in Eucalyptus grandis

“…A recent genome-wide association study in an E. grandis breeding population identified candidate genomic regions on chromosomes 3, 7, and 8 that contained putative candidate genes for tolerance. These candidate genomic regions explained ∼17.6% of the total phenotypic variation of L. invasa tolerance (Mhoswa et al, 2020).…”

Differential development times of galls induced by Leptocybe invasa (Hymenoptera: Eulophidae) reveal differences in susceptibility between two Eucalyptus clones

“…To date, however, most studies have been limited to investigating the susceptibility of a particular genotype by counting the number of galls grown on plants in both nurseries and fields. It has recently been suggested that metabolites 21,23–27 and genes 28,29 may participate in this interaction, but such studies could not clarify whether the plant genotype affected the development time of the different gall stages. Based on the results of these studies, it remains not possible to determine the stages of gall development or the biological cycle of the insect when the defense mechanisms of each plant genotype are the most active.…”

Fungal Communities of Eucalyptus grandis Leaves Are Influenced by the Insect Pest Leptocybe invasa

“…The foliar fungal communities of 179 individual trees (0, n = 49; 1, n = 50; 2, n = 56; 3, n = 24) were analysed. The Eucalyptus population was analysed and genotyped in previous studies ( Naidoo et al, 2018 ; Mhoswa et al, 2020 ) and DNA extracts from those studies were used. Importantly, DNA was extracted from non-surface sterilised leaf punches of non-symptomatic leaf tissues and care was taken to avoid the galled areas of the leaves; thus, non-symptomatic tissue was used for all DNA samples.…”

“…Eucalyptus plantations are of high economic value globally ( Wingfield et al, 2015 ). In recent years, their yield has been jeopardised by the gall-forming wasp Leptocybe invasa Fisher and LaSalle (Hymenoptera: Eulophidae), which deposits eggs into new growth of Eucalyptus trees ( Naidoo et al, 2011 ; Dittrich-Schröder et al, 2018 ; Mhoswa et al, 2020 ). A high density of L .…”