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ARS Home » Northeast Area » Geneva, New York » Grape Genetics Research Unit (GGRU) » Research » Research Project #434724

Research Project: Grapevine Genetics, Genomics and Molecular Breeding for Disease Resistance, Abiotic Stress Tolerance, and Improved Fruit Quality

Location: Grape Genetics Research Unit (GGRU)

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

First Report of Colletotrichum acutatum Causing Grapevine Anthracnose in New York - (Peer Reviewed Journal)

Berry anthocyanin, acid, and volatile trait analyses in a grapevine interspecific F2 population using an integrated GBS and rhAmpSeq genetic map Reprint Icon - (Peer Reviewed Journal)
Alahakoon, D., Fennell, A., Helget, Z., Bate, T., Karn, A., Manns, D., Mansfield, A., Reisch, B., Sacks, G., Sun, Q., Zou, C., Cadle Davidson, L.E., Londo, J.P. 2022. Berry anthocyanin, acid, and volatile trait analyses in a grapevine interspecific F2 population using an integrated GBS and rhAmpSeq genetic map. Plants. https://doi.org/10.3390/plants11050696.

Candidate resistance genes to foliar phylloxera identified at Rdv3 of hybrid grape Reprint Icon - (Peer Reviewed Journal)
Yin, L., Karn, A., Cadle Davidson, L.E., Zou, C., Londo, J.P., Sun, Q., Clark, M. 2022. Candidate resistance genes to foliar phylloxera identified at Rdv3 of hybrid grape. Horticulture Research. https://doi.org/10.1093/hr/uhac027.

The genetic basis of anthocyanin acylation in North American grapes (Vitis spp.) Reprint Icon - (Peer Reviewed Journal)
Karn, A., Diaz-Garcia, L., Reshef, N., Yang, S., Zou, C., Manns, D., Sun, Q., Cadle Davidson, L.E., Mansfield, A.K., Reisch, B.I., Sacks, G. 2021. The genetic basis of anthocyanin acylation in North American grapes (Vitis spp.). Genes. https://doi.org/10.3390/genes12121962.

QScout: A QGIS Plugin Tool Suite for Georeferencing and Analysis of Field Scouted and Remote Sensing Data Reprint Icon - (Peer Reviewed Journal)
Evans, J.R., Romero Galvan, F.E., Cadle Davidson, L.E., Gold, K.M. 2022. QScout: A QGIS Plugin Tool Suite for Georeferencing and Analysis of Field Scouted and Remote Sensing Data. The Plant Phenome Journal. https://doi.org/10.1002/ppj2.20031.

Stable QTL for malate levels in ripe fruit and their transferability across Vitis species Reprint Icon - (Peer Reviewed Journal)
Reshef, N., Karn, A., Manns, D., Mansfield, A., Cadle Davidson, L.E., Reisch, B., Sacks, G. 2022. Stable QTL for malate levels in ripe fruit and their transferability across Vitis species. Journal of Theoretical and Applied Genetics. https://doi.org/10.1093/hr/uhac009.

Chromosome-level genome sequence assembly and genome-wide association study of Vitis rotundifolia reveal the genetics for 12 berry-related traits Reprint Icon - (Peer Reviewed Journal)
Park, M., Vera, D., Kambrianda, D., Gajjar, P., Cadle Davidson, L.E., Tsolova, V., El-Sharkawy, I. 2022. Chromosome-level genome sequence assembly and genome-wide association study of Vitis rotundifolia reveal the genetics for 12 berry-related traits. Horticulture Research. https://doi.org/10.1093/hr/uhab011.

Discovery of the REN11 locus from Vitis aestivalis for stable resistance to grapevine powdery mildew in a family segregating for several unstable and tissue-specific quantitative resistance loci Reprint Icon - (Peer Reviewed Journal)
Karn, A., Zou, C., Brooks, S., Fresnedo-Ramirez, J., Gabler, F., Sun, Q., Ramming, D.W., Naegele, R.P., Ledbetter, C.A., Cadle Davidson, L.E. 2021. Discovery of the REN11 locus from Vitis aestivalis for stable resistance to grapevine powdery mildew in a family segregating for several unstable and tissue-specific quantitative resistance loci. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2021.733899.

Comparison of short-read sequence aligners indicates strengths and weaknesses for biologists to consider Reprint Icon - (Peer Reviewed Journal)
Musich, R., Cadle Davidson, L.E., Osier, M.V. 2021. Comparison of short-read sequence aligners indicates strengths and weaknesses for biologists to consider. Frontiers in Plant Science. 12:657240. https://doi.org/10.3389/fpls.2021.657240.

Multiple independent recombinations led to hermaphrodism in domesticated grapevine Reprint Icon - (Peer Reviewed Journal)
Zou, C., Massonnet, M., Minio, A., Patel, S., Llaca, V., Avi, K., Gouker, F.E., Cadle Davidson, L.E., Reisch, B., Fennell, A., Cantu, D., Sun, Q., Londo, J.P. 2021. Multiple independent recombinations led to hermaphrodism in domesticated grapevine. Nature Genetics. https://doi.org/10.1073/pnas.2023548118.

Genetic mapping and fine mapping of leaf trichome density in cold-hardy hybrid wine grape populations Reprint Icon - (Peer Reviewed Journal)
Yin, L., Karn, A., Zou, C., Cadle Davidson, L.E., Underhill, A.N., Atkins, P., Voytas, D., Treiber, E., Clark, M. 2021. Genetic mapping and fine mapping of leaf trichome density in cold-hardy hybrid wine grape populations. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2021.587640.

Population structure of Erysiphe necator on domesticated and wild vines in the Middle East sheds a new light on the origins of the grapevine powdery mildew pathogen Reprint Icon - (Peer Reviewed Journal)
Gur, L., Reuveni, M., Cohen, Y., Cadle Davidson, L.E., Kisselstein, B., Ovadia, S., Frenkel, O. 2021. Population structure of Erysiphe necator on domesticated and wild vines in the Middle East sheds a new light on the origins of the grapevine powdery mildew pathogen. Molecular Ecology. https://doi.org/10.1111/1462-2920.15401.

Vein-to-blade ratio is an allometric indicator of climate-induced changes in grapevine leaf size and shape Reprint Icon - (Peer Reviewed Journal)
Mullins, J., Migicovsky, Z., Frank, M., Vanburen, R., Londo, J.P., Chitwood, D.H. 2020. Vein-to-blade ratio is an allometric indicator of climate-induced changes in grapevine leaf size and shape. American Journal of Botany. 1. https://doi.org/10.1002/ajb2.1639.

Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves Reprint Icon - (Peer Reviewed Journal)
Bryson, A.E., Brown, M.W., Mullins, J., Dong, W., Bahmani, K., Bornowski, N., Chiu, C., Engelgau, P., Gettings, B., Gomezcano, F., Gregory, L.M., Haber, A.C., Hoh, D., Jennings, E.E., Ji, Z., Kaur, P., Rafu Kenchanmane, S.K., Long, Y., Lotreck, S.G., Mathieu, D.T., Ranaweera, T., Ritter, E.J., Sadohara, R., Shrote, R.Z., Smith, K.E., Teresi, S.J., Venegas, J., Wang, H., Wilson, M.L., Tarrant, A.R., Frank, M.H., Migicovsky, Z., Kumar, J., Vanburen, R., Londo, J.P., Chitwood, D.H. 2020. Composite modeling of leaf shape across shoots discriminates Vitis species better than individual leaves. Applications in Plant Sciences. 1.

The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine Reprint Icon - (Peer Reviewed Journal)
Wang, Y., Xin, H., Fan, P., Zhang, J., Liu, Y., Dong, Y., Wang, Z., Yang, Y., Zhang, Q., Ming, R., Zhong, G., Li, S., Liang, Z. 2020. The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine. Plant Journal. https://doi.org/10.1111/tpj.15127.

Genomic consequences of apple improvement Reprint Icon - (Peer Reviewed Journal)
Migicovsky, Z., Gardner, K., Richards, C.M., Chao, T., Schwaninger, H., Fazio, G., Zhong, G., Myles, S. 2021. Genomic consequences of apple improvement. Horticulture Research. https://doi.org/10.1038/s41438-020-00441-7.

Phased diploid and pan-genomes of cultivated and wild apples unravel genetic basis of apple domestication Reprint Icon - (Peer Reviewed Journal)
Sun, X., Jiao, C., Schwaninger, H., Chao, T., Ma, Y., Duan, N., Khan, A., Xu, K., Cheng, L., Zhong, G., Fei, Z. 2020. Phased diploid and pan-genomes of cultivated and wild apples unravel genetic basis of apple domestication. Nature Genetics. https://doi.org/10.1038/s41588-020-00723-9.

Transfer of endogenous small RNAs between branches of scions and rootstocks in grafted sweet cherry trees Reprint Icon - (Peer Reviewed Journal)
Zhao, D., Zhong, G., Song, G. 2020. Transfer of endogenous small RNAs between branches of scions and rootstocks in grafted sweet cherry trees. PLoS ONE. https://doi.org/10.1371/journal.pone.0236376.

Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. 'Manitoba 37' Reprint Icon - (Peer Reviewed Journal)
Patel, S., Robben, M., Fennell, A., Londo, J.P., Alahakoon, D., Villegas-Diaz, R., Swaminathan, P. 2020. Draft genome of the Native American cold hardy grapevine Vitis riparia Michx. 'Manitoba 37'. Horticulture Research. doi.org/10.1038/s41438-020-0316-2.

A key ‘foxy’ aroma gene is regulated by homology-induced promoter indels in the iconic juice grape ‘Concord’ Reprint Icon - (Peer Reviewed Journal)
Yang, Y., Cuenca, J., Wang, N., Liang, Z., Sun, H., Gutierrez, B.L., Xi, X., Arro, J., Wang, Y., Fan, P., Londo, J.P., Cousins, P., Li, S., Fei, Z., Zhong, G. 2020. A key ‘foxy’ aroma gene is regulated by homology-induced promoter indels in the iconic juice grape ‘Concord’. Horticulture Research. 7(67). https://doi.org/10.1038/s41438-020-0304-6.

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus - (Peer Reviewed Journal)
Zou, C., Karn, A., Reisch, B., Nguyen, A., Sun, Y., Bao, Y., Campbell, M.S., Church, D., Williams, S., Xu, X., Ledbetter, C.A., Patel, S., Fennell, A., Glaubitz, J., Clark, M., Ware, D., Londo, J.P., Sun, Q., Cadle Davidson, L.E. 2020. Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus. Nature Communications. https://doi.org/10.1038/s41467-019-14280-1.

Grape breeders search for reliable DNA markers: Why the Pinot Noir PN40024 reference genome is not enough - (Trade Journal)
Martinson, T., Sun, Q., Zou, C., Cadle Davidson, L.E. 2019. Grape breeders search for reliable DNA markers: Why the Pinot Noir PN40024 reference genome is not enough. Wine Business Monthly. 1.

X-ray phase contrast imaging of Vitis spp. buds reveals freezing pattern and correlation between volume and cold hardiness Reprint Icon - (Peer Reviewed Journal)
Kovaleski, A.P., Londo, J.P., Finkelstein, K. 2019. X-ray phase contrast imaging of Vitis spp. buds reveals freezing pattern and correlation between volume and cold hardiness. Scientific Reports. 9:14949. https://doi.org/10.1038/s41598-019-51415-2.

RNA-Seq reveals new DELLA targets and regulation in transgenic GA-insensitive grapevines Reprint Icon - (Peer Reviewed Journal)
Arro, J., Yang, Y., Song, G., Zhong, G. 2019. RNA-Seq reveals new DELLA targets and regulation in transgenic GA-insensitive grapevines. Biomed Central (BMC) Plant Biology. 9(1):80. https://doi.org/10.1186/s12870-019-1675-4.

Extracing DNA from the grape berry surface, beginning in the vineyard - (Trade Journal)
Hall, M., Cadle Davidson, L.E., Fang, Z., Wilcox, W. 2019. Extracing DNA from the grape berry surface, beginning in the vineyard. Heliyon. 5 (10).

Transcriptomatic profiling of acute cold stress-induced disease resistance (SIDR) genes and pathways in the grapevine powdery mildew pathosystem - (Peer Reviewed Journal)
Weldon, W., Palumbo, C.D., Kovaleski, A.P., Tancos, K., Gadoury, D.M., Osier, M.V., Cadle Davidson, L.E. 2020. Transcriptomatic profiling of acute cold stress-induced disease resistance (SIDR) genes and pathways in the grapevine powdery mildew pathosystem. Molecular Plant-Microbe Interactions. 33(2):284-295. https://doi.org/10.1094/MPMI-07-19-0183-R.

Characterizing grapevine (Vitis spp.) inflorescence architecture using X-ray imaging: implications for understanding cluster density Reprint Icon - (Peer Reviewed Journal)
Li, M., Klein, L.L., Duncan, K., Jiang, N., Londo, J.P., Miller, A.J., Topp, C.N. 2019. Characterizing grapevine (Vitis spp.) inflorescence architecture using X-ray imaging: implications for understanding cluster density. Journal of Experimental Botany. https://doi.org/10.1093/jxb/erz394.

QTL analysis of leaf morphology indicates conserved shape loci in grapevine Reprint Icon - (Peer Reviewed Journal)
Demmings, E.M., Williams, B., Lee, C., Barba, P., Yang, S., Hwang, C., Reisch, B.I., Chitwood, D.H., Londo, J.P. 2019. QTL analysis of leaf morphology indicates conserved shape loci in grapevine. Frontiers in Plant Science. 10:1373. doi: 10.3389/fpls.2019.01373.

VcFT-induced mobile florigenic signals in transgenic and transgrafted blueberries Reprint Icon - (Peer Reviewed Journal)
Song, G., Walworth, A., Lin, T., Chen, Q., Han, X., Zaharia, L., Zhong, G. 2019. VcFT-induced mobile florigenic signals in transgenic and transgrafted blueberries. Horticulture Research. 6(105). https://doi.org/10.1038/s41438-019-0188-5.

VcRR2 regulates chilling-mediated flowering through expression of hormone genes in a trangenic blue berry mutant Reprint Icon - (Peer Reviewed Journal)
Lin, T., Walworth, A., Zong, X., Danial, G., Tomaszewski, E., Callow, P., Han, X., Zaharia, L., Edger, P., Zhong, G., Song, G. 2019. VcRR2 regulates chilling-mediated flowering through expression of hormone genes in a trangenic blue berry mutant. Horticulture Research. (2019) 6:96. https://doi.org/10.1038/s41438-019-0180-0.

A high-throughput phenotyping system using machine vision to quantify severity of grapevine powdery mildew - (Peer Reviewed Journal)
Bierman, A., Laplumm, T., Cadle Davidson, L.E., Gadoury, D., Martinez, D., Sapkota, S., Rea, M. 2019. A high-throughput phenotyping system using machine vision to quantify severity of grapevine powdery mildew. Plant Phenomics. 1..

Effects of sunlight on anthocyanin accumulation and associated co-expression gene networks in developing grape berries Reprint Icon - (Peer Reviewed Journal)
Zou, L., Zhong, G., Wu, B., Yang, Y., Li, S., Liang, Z. 2019. Effects of sunlight on anthocyanin accumulation and associated co-expression gene networks in developing grape berries. Environmental and Experimental Botany. 166. https://doi.org/10.1016/j.envexpbot.2019.103811.

Tempo of gene regulation in wild and cultivated Vitis species shows coordination between cold deacclimation and budbreak Reprint Icon - (Peer Reviewed Journal)
Kovaleski, A.P., Londo, J.P. 2019. Tempo of gene regulation in wild and cultivated Vitis species shows coordination between cold deacclimation and budbreak. Plant Science. 287:110178. https://doi.org/10.1016/j.plantsci.2019.110178.

Constitutive expression of an apple gene promotes flowering in transgenic blueberry under nonchilling conditions Reprint Icon - (Peer Reviewed Journal)
Zong, X., Zhang, Y., Walworth, A., Tomaszewski, E.M., Callow, P., Zhong, G., Song, G. 2019. Constitutive expression of an apple FLC3-like gene promotes flowering in transgenic blueberry under nonchilling conditions. International Journal of Molecular Sciences. 20(11):2775. https://doi.org/10.3390/ijms20112775.

From phenotyping to phenomics: Present and future approaches in grape trait analysis to inform grape gene function - (Book / Chapter)

Computational analysis of AmpSeq data for targeted, high-throughput genotyping of amplicons Reprint Icon - (Peer Reviewed Journal)
Fresnedo-Ramirez, J., Yang, S., Sun, Q., Karn, A., Reisch, B., Cadle Davidson, L.E. 2019. Computational analysis of AmpSeq data for targeted, high-throughput genotyping of amplicons. Frontiers in Plant Science. 10:599. https://doi.org/10.3389/fpls.2019.00599.

Disease-resistant varieties are on the way: Can we ensure they last? - (Trade Journal)
Moyer, M., Martinson, T., Cadle Davidson, L.E. 2019. Disease-resistant varieties are on the way: Can we ensure they last?. Nature Biotechnology. 1.

Rootstock effects on scion phenotypes in a 'Chambourcin' experimental vineyard - (Peer Reviewed Journal)
Migicovsky, Z., Harris, Z.H., Klein, L.L., Li, M., Mcdermaid, A., Chitwood, D.H., Fennell, A., Kovacs, L.G., Kwasniewski, M., Londo, J.P., Ma, Q., Miller, A. 2019. Rootstock effects on scion phenotypes in a 'Chambourcin' experimental vineyard. Horticulture Research. 1.

The epiphytic microbiota of sour rot-affected grapes differs minimally from that of healthy grapes, indicating causal organisms are already present on healthy berries Reprint Icon - (Peer Reviewed Journal)
Hall, M.E., O'Bryon, I., Osier, M.V., Wilcox, W.F., Cadle Davidson, L.E. 2019. The epiphytic microbiota of sour rot-affected grapes differs minimally from that of healthy grapes, indicating causal organisms are already present on healthy berries. PLoS One. https://doi.org/10.1371/journal.pone.0211378.

Deconstructing cold hardiness: Supercooling ability and chilling requirements in the wild North American grapevine vitis riparia - (Peer Reviewed Journal)
Londo, J.P., Kovaleski, A.P. 2019. Deconstructing cold hardiness: Supercooling ability and chilling requirements in the wild North American grapevine vitis riparia. Australian Journal of Grape and Wine Research. 25:276-285.

A perspective on breeding and implementing durable powdery mildew resistance - (Peer Reviewed Journal)
Cadle-Davidson, L.E. 2019. A perspective on breeding and implementing durable powdery mildew resistance. Acta Hortic. 1248:541-548. https://doi.org/10.17660/ActaHortic.2019.1248.72.

QTL mapping of downy mildew and botrytis bunch rot resistance in a Vitis aestivalis-derived 'Norton'-based population - (Peer Reviewed Journal)
Sapkota, S.D., Chen, L.L., Yang, S., Hyma, K.E., Cadle-Davidson, L.E. and Hwang, C.F. 2019. Quantitative trait locus mapping of downy mildew and botrytis bunch rot resistance in a Vitis aestivalis-derived 'Norton'-based population. Acta Hortic. 1248:305-312. https://doi.org/10.17660/ActaHortic.2019.1248.44.

The phenotyping bottleneck: How grape breeders link desired traits to DNA markers - (Trade Journal)
Martinson, T., Cadle Davidson, L.E. 2019. The phenotyping bottleneck: How grape breeders link desired traits to DNA markers. Wine and Vines. 142-145.

Construction of a high-density linkage map and QTL detection of downy mildew resistance in Vitis aestivalis-derived ‘Norton’ - (Peer Reviewed Journal)
Saptoka, S., Chen, L., Yang, S., Hyma, K.E., Cadle Davidson, L.E., Hwang, C. 2018. Construction of a high-density linkage map and QTL detection of downy mildew resistance in Vitis aestivalis-derived ‘Norton’. Theoretical and Applied Genetics. 132:137-147.