Genome-wide association study identifies SNP markers and putative candidate genes for terpene traits important for<i>Leptocybe invasa</i>resistance in<i>Eucalyptus grandis</i>

Mhoswa, Lorraine; Myburg, Alexander Andrew; Slippers, Bernard; Külheim, Carsten; Naidoo, Sanushka

doi:10.1093/g3journal/jkac004

Cited by 3 publications

(2 citation statements)

References 74 publications

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“…There have been some previous examples pointing to that GGPPS is involved in the genetic regulation of certain traits. One study shown that an SNP associated with p-cymene in Eucalyptus grandis mapped to the gene encoding GGPPS, explaining 3.66% of the phenotypic variation (Mhoswa et al, 2022). However, no further validation was performed in this study.…”

Section: Function Of Vvggpps In Regulating Norisoprenoids Productionmentioning

confidence: 79%

Identification of SNP loci and candidate genes genetically controlling norisoprenoids in grape berry based on genome-wide association study

Sun

He²,

Sun³

et al. 2023

Front. Plant Sci.

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Obtaining new grapevine varieties with unique aromas has been a long-standing goal of breeders. Norisoprenoids are of particular interest to wine producers and researchers, as these compounds are responsible for the important varietal aromas in wine, characterized by a complex floral and fruity smell, and are likely present in all grape varieties. However, the single-nucleotide polymorphism (SNP) loci and candidate genes genetically controlling the norisoprenoid content in grape berry remain unknown. To this end, in this study, we investigated 13 norisoprenoid traits across two years in an F1 population consisting of 149 individuals from a hybrid of Vitis vinifera L. cv. Muscat Alexandria and V. vinifera L. cv. Christmas Rose. Based on 568,953 SNP markers, genome-wide association analysis revealed that 27 candidate SNP loci belonging to 18 genes were significantly associated with the concentrations of norisoprenoid components in grape berry. Among them, 13 SNPs were confirmed in a grapevine germplasm population comprising 97 varieties, including two non-synonymous mutations SNPs within the VvDXS1 and VvGGPPS genes, respectively in the isoprenoid metabolic pathway. Genotype analysis showed that the grapevine individuals with the heterozygous genotype C/T at chr5:2987350 of VvGGPPS accumulated higher average levels of 6-methyl-5-hepten-2-one and β-cyclocitral than those with the homozygous genotype C/C. Furthermore, VvGGPPS was highly expressed in individuals with high norisoprenoids concentrations. Transient overexpression of VvGGPPS in the leaves of Vitis quinquangularis and tobacco resulted in an increase in norisoprenoid concentrations. These findings indicate the importance of VvGGPPS in the genetic control of norisoprenoids in grape berries, serving as a potential molecular breeding target for aroma.

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Section: Function Of Vvggpps In Regulating Norisoprenoids Productionmentioning

confidence: 79%

Identification of SNP loci and candidate genes genetically controlling norisoprenoids in grape berry based on genome-wide association study

Sun

He²,

Sun³

et al. 2023

Front. Plant Sci.

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“…The variation in terpene traits, such as 1,8-cineole, γ-terpinene, and p-cymene, appears to be in uenced by a combination of loci with both minor and major effects, suggesting an oligogenic or potentially polygenic nature of these traits (Mhoswa et al 2022). In addition, variations in terpene pro les have been observed between resistant and susceptible Eucalyptus genotypes in response to L. invasa oviposition (Oates et al 2015;Naidoo et al 2018).…”

Section: Resultsmentioning

confidence: 99%

Innovating Eucalyptus resistance: A meta-analysis of gene associations for combatting Leptocybe invasa

Calazans

Souza

Nunes

et al. 2023

Preprint

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Our study aimed to enhance the current understanding of Leptocybe invasa, a pest affecting Eucalyptus trees, by exploring the intricate molecular interactions between plants and insects. Specifically, we sought to identify key genes and metabolic pathways involved in these plant-insect interactions to develop innovative strategies for effective pest control. To accomplish this, we embarked on a comprehensive investigation utilizing an array of scientific resources, including scientific articles, gene and protein sequence databases, and patents. This comprehensive search enabled us to gather valuable information on gene homology and predicted proteins specific to Eucalyptus species. Furthermore, we conducted an in-depth literature review that focused on the latest advancements in gene expression research and the intricate world of secondary metabolites. Through this exploration, we gained critical insights into the underlying mechanisms of plant resistance and the potential application of specific genes in selecting resilient Eucalyptus genotypes capable of withstanding the challenges posed by L. invasa. Our search for patents was facilitated by the utilization of the cutting-edge Orbit Intelligence patent research software, which allowed us to identify novel approaches and innovations in the field of pest control. This study underscores the significance of performing a meta-analysis that incorporates advancements in gene expression research and the exploration of secondary metabolite data. Such an approach deepens our understanding of plant resistance mechanisms, paving the way for the identification and selection of L. invasa resistant genotypes. Ultimately, our findings hold promise for the development of effective strategies to mitigate the impact of this destructive pest on Eucalyptus trees.

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Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection

Younessi-Hamzekhanlu

Gailing²

2022

IJMS

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The ecological and economic importance of forest trees is evident and their survival is necessary to provide the raw materials needed for wood and paper industries, to preserve the diversity of associated animal and plant species, to protect water and soil, and to regulate climate. Forest trees are threatened by anthropogenic factors and biotic and abiotic stresses. Various diseases, including those caused by fungal pathogens, are one of the main threats to forest trees that lead to their dieback. Genomics and transcriptomics studies using next-generation sequencing (NGS) methods can help reveal the architecture of resistance to various diseases and exploit natural genetic diversity to select elite genotypes with high resistance to diseases. In the last two decades, QTL mapping studies led to the identification of QTLs related to disease resistance traits and gene families and transcription factors involved in them, including NB-LRR, WRKY, bZIP and MYB. On the other hand, due to the limitation of recombination events in traditional QTL mapping in families derived from bi-parental crosses, genome-wide association studies (GWAS) that are based on linkage disequilibrium (LD) in unstructured populations overcame these limitations and were able to narrow down QTLs to single genes through genotyping of many individuals using high-throughput markers. Association and QTL mapping studies, by identifying markers closely linked to the target trait, are the prerequisite for marker-assisted selection (MAS) and reduce the breeding period in perennial forest trees. The genomic selection (GS) method uses the information on all markers across the whole genome, regardless of their significance for development of a predictive model for the performance of individuals in relation to a specific trait. GS studies also increase gain per unit of time and dramatically increase the speed of breeding programs. This review article is focused on the progress achieved in the field of dissecting forest tree disease resistance architecture through GWAS and QTL mapping studies. Finally, the merit of methods such as GS in accelerating forest tree breeding programs is also discussed.

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Genome-wide association study identifies SNP markers and putative candidate genes for terpene traits important forLeptocybe invasaresistance inEucalyptus grandis

Cited by 3 publications

References 74 publications

Identification of SNP loci and candidate genes genetically controlling norisoprenoids in grape berry based on genome-wide association study

Identification of SNP loci and candidate genes genetically controlling norisoprenoids in grape berry based on genome-wide association study

Innovating Eucalyptus resistance: A meta-analysis of gene associations for combatting Leptocybe invasa

Genome-Wide SNP Markers Accelerate Perennial Forest Tree Breeding Rate for Disease Resistance through Marker-Assisted and Genome-Wide Selection

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