Localization of genomic region associated with the leaf resistance to grapevine phylloxera (Daktulosphaira vitifoliae)

Abstract

The present study aimed to identify genomic regions associated with leaf resistance to grapevine phylloxera (Daktulosphairavitifoliae). Amapping population (MP), derived from a cross between ‘Moscato Giallo’ (Vitis vinifera) and the rootstock ‘IAC766’{‘106 8 Mgt’ [V. riparia × (V. rupestris × V. cordifolia)] × V. caribaea}, was used for this study. The MP and parental genotypes were grown under greenhouse conditions, and phylloxera infestation occurred naturally. The MP population was evaluated for phylloxera incidence, number of leaf galls, and damage severity on the fourth and fifth leaves from the shoot apex toward the base. The MP wasgenotyped using 2,000 rhAmpSeq DNAmolecular markers in collaboration with Dr. Lance Caddle Davidson. PCR amplicons were purified, quantified, and sequenced using an Illumina platform (Illumina, San Diego, CA, USA). Genotypic data were initially converted into a VCF file and imported into TASSEL 5 software for genotype and marker filtering. Markers were further filtered using Lep MAP3 v.0.2, assigned to 19 linkage groups, and ordered. These linkage groups were used to construct genetic maps with MapChart software. For the identification of genomic regions associated with resistance, genetic map data were combined with phylloxera phenotypic data. QTL mapping was performed in R using the R/qtl package. Interval mapping was conducted using the scanone function, based on abinary model (incidence data) and Haley–Knott regression. The significance threshold for the logarithm of the odds (LOD) score wasdetermined by 1,000 permutation tests at α = 0.05. Approximately two-thirds of the population exhibited complete resistance tophylloxera, frequently characterized by the presence of necrotic spots on leaves. Among progenies showing infestation, quantitative variation was observed for gall number and damage severity.

These results indicate the presence of a major resistance gene associated with additional genes of minor effect. QTL analysis identifieda genomic region located on chromosome 18 significantly associated with leaf resistance to phylloxera. The QTL was detected in the same genomic region for all three evaluated traits (α = 0.05), with LOD values up to 15.9. This study identified a novel source of leaf resistance to grapevine phylloxera and paves the way for the gene(s) underlying the resistance and the development of molecularmarkers for marker-assisted selection.

Acknowledgements

We are grateful to the Coordination for the Improvement of Higher Education Personnel (CAPES) and CNPq for scholarships. Thisresearch was financially supported by the National Council for Scientific and Technological Development (CNPq), Brazil (Grant: CNPq/409471/2021-6).

References

BRADBURY, P. J. et al. TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics, v. 23, n. 19, p. 2633-2635, 2007.

BROMAN, K. W. et al. R/qtl: QTL mapping in experimental crosses. Bioinformatics, v. 19, n. 7, p. 889-890, 2003.

CLARK, M. D. et al. Quantitative trait loci identified for foliar phylloxera resistance in a hybrid grape population. Australian journal of grape and wine research, v. 24, n. 3, p. 292-300, 2018.

EDWARDS, J. et al. Relationships between grape phylloxera abundance, fungal interactions and grapevine decline. Acta Horticulturae, v. 733, p. 151-157, 2007.

GRANETT, J. et al. Biology and management of grape phylloxera. Annual review of entomology, v. 46, n. 1, p. 387-412, 2001.

GRANETT, J.; TIMPER, P.; LIDER, L. A. Grape phylloxera (Daktulosphaira vitifoliae) (Homoptera: Phylloxeridae) biotypes in California. Journal of Economic Entomology, v. 78, n. 6, p. 1463-1467, 1985.

JI, W.; GAO, G.; WEI, J. Potential global distribution of Daktulosphaira vitifoliae under climate change based on MaxEnt. Insects, v. 12, n. 4, p. 347, 2021.

NABITY, P. D. et al. Leaf-galling phylloxera on grapes reprograms host metabolism and morphology. Proceedings of the National Academy of Sciences, v. 110, n. 41, p. 16663-16668, 2013.

RASTAS, P. Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data. Bioinformatics, v. 33, n. 23, p. 3726-3732, 2017.

VOORRIPS, R. E. MapChart: software for the graphical presentation of linkage maps and QTLs. Journal of heredity, v. 93, n. 1, p. 77-78, 2002.

YIN, L. et al. Effects of foliar phylloxera (Hemiptera: Phylloxeridae) infestations on wine grape photosynthesis, yield, and fruit quality. Journal of Entomological Science, v. 56, n. 4, p. 504-518, 2021.

ZOU, C. et al. Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nature communications, v. 11, n. 1, p. 413, 2020.