2024

  • Neale, D. B., Zimin, A. V., Meltzer, A., Bhattarai, A., Amee, M., Figueroa Corona, L., Allen, B. J., Puiu, D., Wright, J., De La Torre, A. R., McGuire, P. E., Timp, W., Salzberg, S. L., & Wegrzyn, J. L. (2024). A genome sequence for the threatened whitebark pine. G3: Genes, Genomes, Genetics, 14(5), jkae061. Full Text.

2023

  • Eckert, A. J., & Neale, D. B. (2022). Probing the dark matter of environmental associations yields novel insights into the architecture of adaptation. New Phytologist. 237 (5), 1479-1482. Full Text.
  • Neale, D. B. (2023) A short essay on genomic technologies toward understanding
    how forest trees are adapted to their environments. Forest Genetics and Tree Breeding 12: 48–51. Full Text.
  • Sepúlveda, S.L., Neale, D.B., Holliday, J., Famula, R., Fiehn, O., Stanton, B.J., & Guerra, F.P. (2023) GWAS on the attack of aspen borer Saperda calcarata to black cottonwood trees reveals a response mechanism involving secondary metabolism and independence of tree architecture. Forests. (Accepted).
  • Kaya, Z., Taşkıran, B., Uluğ, A., Güvendiren, A.D., Wegrzyn, J., Neale, D.B. (2023) Association genetics of wood traits in European black poplar (Populus nigra L.). Tree Genetics & Genomes. 19 (38). Full Text.

2022

  • Arab, M.M., Brown, P.J., Abdollahi-Arpanahi, R., Sohrabi, S.S., Askari, H., Aliniaeifard, S., Mokhtassi-Bidgoli, A., Mesgaran, M.B., Leslie, C.A., Marrano, A., Neale, D.B., Vahdati, K. (2022). Genome-wide association analysis and pathway enrichment provide insights into the genetic basis of photosynthetic responses to drought stress in Persian walnut. Horticulture Research, 9. Full Text.

2021

  • Castellana, S., Martin, M.A., Solla. A., Alcaide, F., Villani, F., Cherubini, M., Neale, D.B. (2021). Signatures of local adaptation to climate in natural populations of sweet chestnut (Castanea sativa Mill.) from southern Europe. Annals of Forest Science, 78(2), 1-21. Full Text.
  • David-Schwartz, R., Rosen, N., Riov, J., Osem, Y., Neale, D.B. (2021) Transcriptome-based single-nucleotide polymorphism markers between Pinus brutia and Pinus halepensis and the analysis of their hybrids. Tree Genetics & Genomes, 17(2), 1-11. Full Text.
  • De La Torre, A. R., Sekhwal, M. K., & Neale, D. B. (2021). Selective sweeps and polygenic adaptation drive local adaptation along moisture and temperature gradients in natural populations of coast redwood and giant sequoia. Genes, 12(11), 1826. Full Text.
  • De La Torre, A. R., Sekhwal, M. K., Puiu, D., Salzberg, S. L., Scott, A. D., Allen, B., Neale, D. B., Chin, A. R. O., & Buckley, T. N. (2021). Genome‐wide association identifies candidate genes for drought tolerance in coast redwood and giant sequoia. The Plant Journal, 109(1), 7-22. Full Text.
  • De La Torre, A., Wilhite, B., Puiu, D., St.Clair, J.B., Crepeau, M.W., Salzberg, S.L., Langley, C.H., Allen, B., & Neale, D.B. (2021). Dissecting the polygenic basis of cold adaptation using genome-wide association of traits and environmental data in Douglas-fir. Genes. 12(1):110. Full Text.
  • Neale, D. B., Zimin, A. V., Zaman, S., Scott, A. D., Shrestha, B., Workman, R. E., Puiu, D., Allen, B. J., Moore, Z. J., Sekhwal, M. K., De La Torre, A. R., McGuire, P. E., Burns, E., Timp, W., Wegrzyn, J. L., & Salzberg, S. L. (2021). Assembled and annotated 26.5 Gbp coast redwood genome: a resource for estimating evolutionary adaptive potential and investigating hexaploid origin. G3 Genes| Genomes| Genetics. 12(1). Full Text.

2020

  • Arab, M. M., Marrano, A., Abdollahi-Arpanahi, R., Leslie, C. A., Cheng, H., Neale, D. B., & Vahdati, K. (2020). Combining phenotype, genotype and environment to uncover genetic components underlying water use efficiency in Persian walnut. Journal of experimental botany. 71(3), 1107-1127. Full Text.
  • Bernard, A., Marrano, A., Donkpegan, A., Brown, P. J., Leslie, C. A., Neale, D. B., Lheureux, F., & Dirlewanger, E. (2020). Association and linkage mapping to unravel genetic architecture of phenological traits and lateral bearing in Persian walnut (Juglans regia L.). BMC Genomics, 21(1), 1-25. Full Text.
  • Marrano, A., Britton, M., Zaini, P. A., Zimin, A., Workman, R., Puiu, D., Bianco, L., Di Pierro, E. A., Allen, B. J., Chakraborty, S., Troggio, M., Leslie, C. A., Timp, W., Dandekar, A., Salzberg, S. L., Neale, D. B. (2020). High-quality chromosome-scale assembly of the walnut (Juglans regia L) reference genome. GigaScience, 9(5), giaa050. Full Text.
  • Montanari, S., Postman, J., Bassil, N. V., Neale, D. B. (2020) Reconstruction of the largest pedigree network for pear cultivars and evaluation of the genetic diversity of the USDA-ARS National Pyrus collection. G3: Genes|Genomes|Genetics. 10, 3285 – 3297. Full Text.
  • Scott, A.D., Zimin, A.V., Puiu, D., Workman, R., Britton, M., Zaman, S., Caballero, M., Read, A.C., Bogdanove, A.J., Burns, E., Wegrzyn, J., Timp, T., Salzberg, S.L., Neale, D.B. (2020) A Reference Genome Sequence for Giant Sequoia. G3: Genes, Genomes, Genetics, 10(11), 3907-3919. Full Text.
  • Sideli, G. M., McAtee, P., Marrano, A., Allen, B. J., Brown, P. J., Butterfield, T., Dandekar, A., Leslie, C. A., Neale, D. B. (2020) Genetic analysis of walnut (Juglans regia L.) pellicle pigment variation through a novel, high-throughput phenotyping platform. G3: Genes, Genomes, Genetics, 10(12), 4411-4424. Full Text.
  • Sideli, G. M., Marrano, A., Montanari, S., Leslie, C. A., Allen, B. J., Cheng, H., Brown, P. J., Neale, D. B. (2020) Quantitative phenotyping of shell suture strength in walnut (Juglans regia L.) enhances precision for detection of QTL and genome-wide association mapping. PloS one, 15(4), e0231144. Full Text.
  • Weiss, M., Sniezko, R., Puiu, D., Crepeau, M., Stevens, K., Salzberg, S., Langley, C., Neale, D.B., De la Torre, A. (2020) Genomic basis of white pine blister rust quantitative disease resistance and its relationship with qualitative resistance. The Plant Journal, 104(2), 365-376. Full Text.
  • Zurn, JD, Nyberg, A, Montanari, S, Postman, J, Neale, DB, Bassil, N. (2020) A new SSR fingerprinting set and its comparison to existing SSR- and SNP-based genotyping platforms to manage Pyrus germplasm resources. Tree Genetics & Genomes. 16(72). Full Text.

2019

  • Arab, M.M., Marrano, A., Abdollahi-Arpanahi, R., Leslie, C.A., Hossein, A., Neale, D.B., Vahdati, K. (2019). Genome-wide patterns of population structure and association mapping of nut-related traits in Persian walnut populations from Iran using the Axiom J. regia 700K SNP array. Scientific Reports, 9(1), 6376. Full Text.
  • De La Torre, A. R., Wilhite, B., & Neale, D. B. (2019). Environmental Genome-Wide Association Reveals Climate Adaptation Is Shaped by Subtle to Moderate Allele Frequency Shifts in Loblolly Pine. Genome biology and evolution, 11(10), 2976-2989. Full Text.
  • Durán, R., Rodriguez, V., Carrasco, A., Neale, D.B., Balocchi, C., Valenzuela, S.A. (2019) SNP discovery in radiata pine using a de novo transcriptome assembly. Trees, 33(5), 1505-1511. Full Text.
  • Guerra, F.P., Suren, H., Holliday, J., Richards, J.H., Fiehn, O., Famula, R., Stanton, B.J., Shuren, R., Sykes, R., Davis, M.F., Neale, D.B. (2019) Exome resequencing and GWAS for growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa. BMC genomics, 20(1), 1-14. Full Text.
  • Linsmith, G., Rombauts, S., Montanari, S., Deng, C.H., Celton, J.M., Guérif, P., Liu, C., Lohaus, R., Zurn, J.D., Cestaro, A., Bassil, N.V., Bakker, L.V., Schijlen, E., Gardiner, S.E., Lespinasse, Y. Durel, C.E., Velasco, R., Neale, D.B., Chagné, D., Van de Peer, Y., Troggio,, Bianco, L. (2019). Pseudo-chromosome length genome assembly of a double haploid ‘Bartlett’ pear (Pyrus communis L.). GigaScience, 8(12), giz138. Full Text.
  • Marrano, A., Martínez-García, P.J., Bianco, L., Sideli, G., Di Pierro, E., Leslie, C., Stevens, K., Crepeau, M., Troggio, M., Langley, C., Neale, D.B. (2019) A new genomic tool for walnut (Juglans regia L.): development and validation of the high-density AxiomTM J. regia 700K SNP genotyping array. Plant Biotechnology Journal, 17(6), 1027-1036. Full Text.
  • Marrano, A. and Neale, D.B. (2019). “Towards sustainable production of walnut (Juglans regia L.)” in Serdar, U., and Fulbright, D. (eds.) “Achieving sustainable cultivation of tree nuts.” Sawston, Cambridge: Burleigh Dodds Science Publishing Limited.
  • Marrano, A., Sideli, G. M., Leslie, C. A., Cheng, H., & Neale, D. B. (2019). Deciphering of the genetic control of phenology, yield and pellicle color in Persian walnut (Juglans regia L.). Frontiers in Plant Science, 10, 1140. Full Text.
  • Montanari, S., Bianco, L., Allen, B.J., Martínez-García, P.J., Bassil, N.V., Postman, J., Knäbel, M., Kitson, B., Deng, C.H., Chagné, D., Crepeau, M.W., Langley, C., Evans, K., Dhingra, A., Troggio, M., Neale, D.B. (2019) Development of a highly efficient Axiom™ 70K SNP Array for Pyrus and evaluation for high-density mapping and germplasm characterization. BCM Genomics, 20(1), 331. Full Text.
  • Mosca, E., Cruz, F., Gómez Garrido, J., Bianco, L., Rellstab, C., Brodbeck, S., Csilléry, K., Fady, B., Fladung, M., Fussi, B., Gömöry, D., González-Martínez, S.C., Grivet, D., Gut, M., Hansen, O.K., Heer, K., Kaya, Z., Krutovsky, K.V., Kersten, B., Liepelt, S., Opgenoorth, L., Sperisen, C., Ullrich, K.K., Vendramin, G.G., Westergren, M., Ziegenhagen, B., Alioto, T., Gugerli, F., Heinze, B., Höhn, M., Troggio, M., Neale, D.B. (2019). A reference genome sequence for the European silver fir (Abies alba Mill.): a community-generated genomic resource. G3: Genes, Genomes, Genetics, 9(7): 2039-2049. Full Text.
  • Neale, D. B., & Wheeler, N. C. (2019). The Conifers: Genomes, Variation and Evolution. Cham, Switzerland: Springer.
  • Trouern-Trend, A.J., Falk, T.A., Zaman, Caballero, M., Neale, D.B., Langley, C.H., Dandekar, A., Stevens, K., Wegrzyn, J. (2019). Comparative Genomics of Six Juglans Species Reveals Patterns of Disease-associated Gene Family Contractions. The Plant Journal, 102, 410–423 Full Text.

2018

  • Baker, E.A.G., Wegrzyn, J.L., Sezen, U.U., Falk, T., Maloney, P.E., Vogler, D.R., Delfino-Mix, A., Jensen, C., Mitton, J., Wright, J., Knaus, B., Rai, H., Cronn, R., Gonzalez-Ibeas, D., Vasquez-Gross, H.A., Famula, R.A., Liu, J., Kueppers, L.M., Neale, D.B. (2018). Comparative Transcriptomics Among Four White Pine Species. G3: Genes|Genomes|Genetics 8(5): 1461 – 1474. Full Text.
  • De La Torre, A. R., Puiu, D., Crepeau, M. W., Stevens, K., Salzberg, S. L., Langley, C. H., & Neale, D. B. (2018). Genomic architecture of complex traits in loblolly pine. New Phytologist, 221: 1789 – 1801. Full Text.
  • Famula, R.A., Richards, J.A., Famula, T.R., & Neale, D.B. (2018). Association genetics of carbon isotope discrimination and leaf morphology in a breeding population of Juglans regia L. Tree Genetics & Genomes, 15(1), 6. Full Text.
  • Marrano, A., Micheletti, D., Lorenzi, S., Neale, D., & Grando, M. S. (2018). Genomic signatures of different adaptations to environmental stimuli between wild and cultivated Vitis vinifera L. Horticulture research, 5(1), 34. Full Text.
  • Mosca, E., Di Pierro, E. A., Budde, K. B., Neale, D. B., & González‐Martínez, S. C. (2018). Environmental effects on fine‐scale spatial genetic structure in four Alpine keystone forest tree species. Molecular Ecology, 27(3):647-658. Full Text.
  • Stevens, K. A., Woeste, K., Chakraborty, S., Crepeau, M. W., Leslie, C. A., Martínez-García, P. J., Puiu, D., Romero-Severson, J., Coggeshall, M., Dandekar, A.M., Kluepfel, D., Neale, D.B., Salzberg, S.L., & Langley, C.H. (2018). Genomic Variation Among and Within Six Juglans Species. G3: Genes, Genomes, Genetics 8(7): 2153 – 2165. Full Text.
  • Vangestel, C., Eckert, A.J., Wegrzyn, J.L., St. Clair, J.B., & Neale, D.B. (2018). Linking phenotype, genotype and environment to unravel genetic components underlying cold hardiness in coastal Douglas-fir (Pseudotsuga menziesii var. menziesii). Tree Genetics & Genomes, 14(1), 10. Full Text.

2017

  • Ćalić, I., Koch, J., Carey, D., Addo-Quaye, C., Carlson, J.E., Neale, D.B. (2017). Genome-wide association study identifies a major gene for beech bark disease resistance in American beech (Fagus grandifolia Ehrh.). BMC Genomics, 18:547. Full Text.
  • Carrasco, A., Wegrzyn, J.L., Durán, R., Fernández, M., Donoso, A., Rodriguez, V., Neale, D.B., Valenzuela, S. (2017) Expression profiling in Pinus radiata infected with Fusarium circinatum. Tree Genetics and Genomes, 13(2):46-46. Full Text.
  • Cronn, R., Dolan, P.C., Jogdeo, S., Wegrzyn, J.L., Neale, D.B., St. Clair, J.B., Denver, D.R. (2017). Transcription through the eye of a needle: daily and annual cyclic gene expression variation in Douglas-fir needles. BMC Genomics, 18:558. Full Text.
  • Di Pierro, E.A., Mosca, E., González-Martínez, S.C., Binelli, G., Neale, D.B., La Porta, N. (2017). Adaptive variation in natural Alpine populations of Norway spruce (Picea abies [L.] Karst) at regional scale: Landscape features and altitudinal gradient effects. Forest Ecology and Management, 405:350-359. Full Text.
  • Grivet, D., Avia, K., Vaattovaara, A., Eckert, A. J., Neale, D. B., Savolainen, O., & González‐Martínez, S. C. (2017). High rate of adaptive evolution in two widespread European pines. Molecular Ecology, 26(24):6857-6870. Full Text.
  • Lind, B.M., Friedline, C.J., Wegrzyn, J.L., Maloney, P.E., Vogler, D.R., Neale, D.B., Eckert, A.J. (2017) Water availability drives signatures of local adaptation in whitebark pine (Pinus albicaulis Englm.) across fine spatial scales of the Lake Tahoe Basin, USA. Molecular Ecology, 26(12):3168–3185. Full Text.
  • Martínez-García, P.J., Famula, R.A., Leslie, C., McGranahan, G.H., Famula, T.R., Neale, D.B. (2017). Predicting breeding values and genetic components using generalized linear mixed models for categorical and continuous traits in walnut (Juglans regia). Tree Genetics and Genomes, 13:109. Full Text.
  • Neale, D.B., Martinez-Garcia, P.J., De La Torre, A.R., Montanari, S., Wei, X. (2017) Novel Insights into Tree Biology and Genome Evolution as Revealed Through Genomics. Annual Review of Plant Biology, 68(6):1-1. Full Text.
  • Neale, D.B., McGuire, P.E., Wheeler, N.C., Stevens, K.A., Crepeau, M.W., Cardeno, C., Zimin, A.V. Puiu, D., Pertea, G.M., Sezen, U. U., Casola, C., Koralewski, T.E., Paul, R., Gonzalez-Ibeas, D., Zaman, S., Cronn, R., Yandell, M., C. Holt, Langley, C.H., Yorke, J.A., Salzberg, S.L., Wegrzyn, J.L.(2017). The Douglas-Fir Genome Sequence Reveals Specialization of the Photosynthetic Apparatus in Pinaceae. G3: Genes|Genomes|Genetics, 7(9):3157-3167. Full Text.
  • Vázquez-Lobo, A., De La Torre, A. R., Martínez-García, P.J., Vangestel, C., Wegrzyn, J.L., Ćalić, I., Burton, D., Davis, D., Kinloch, B., Vogler, D., Neale, D.B. (2017) Finding loci associated to partial resistance to white pine blister rust in sugar pine (Pinus lambertiana Dougl.). Tree Genetics and Genomes, 13:108. Full Text.
  • Zimin, A.V., Stevens, K.A., Crepeau, M.W., Puiu, D., Wegrzyn, J.L., Yorke, J.A., Langley, C.H., Neale, D.B., Salzberg, S.L. (2017) An Improved Assembly of the Loblolly Pine Mega-Genome Using Long-Read Single-Molecule Sequencing. Giga Science, 6(1):1-4. Full Text.

2016

  • Calic I., Bussotti F., Martinez-García P. J., Neale D. B., (2016) Recent landscape genomics studies in forest trees–what can we believe? Tree Genetics and Genomes. 12(3):1-7. Full Text. Supplemental.
  • DiPierro E.A., Mosca E., Rocchini D., Binelli G., Neale D.B., La Porta N. (2016) Climate-related adaptive genetic variation and population structure in natural stands of Norway spruce in the South-Eastern Alps. Tree Genetics and Genomes. 12(2):1-16. Full Text.
  • Gonzalez-Ibeas, D., Martinez-Garcia, P.J., Famula, R.A., Delfino-Mix, A., Stevens, K.A., Loopstra, C.A., Langley, C.H., Neale, D.B., Wegrzyn, J.L. (2016) Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana). G3: Genes|Genomes|Genetics. 1(1):3787-3802. Full Text.
  • Guerra F.P., Richards J.H., Fiehn O., Famula R., Stanton B.J., Shuren R., Sykes R., Davis M.F., Neale D.B. (2016) Analysis of the genetic variation in growth, ecophysiology, and chemical and metabolomic composition of wood of Populus trichocarpa provenances. Tree Genetics and Genomes. 12(6):1-16. Full Text.
  • Kujala, S.T., Knürr, T., Kärkkäinen, K., Neale, D.B., Sillanpää, M.J., Savolainen, O. (2016) Genetic Heterogeneity Underlying Variation in a Locally Adaptive Clinal Trait in Pinus sylvestris Revealed by a Bayesian Multipopulation Analysis. Heredity. 115(11):1-1. Full Text.
  • Maloney P.E., Eckert A.J., Vogler D.R., Jensen C.E., Delfino Mix A., Neale D.B. (2016) Landscape Biology of Western White Pine: Implications for Conservation of a Widely-Distributed Five-Needle Pine at Its Southern Range Limit. Forests. 7(5):93-102. Full Text.
  • Martínez-García, P. J., Crepeau, M. W., Puiu, D., Gonzalez-Ibeas, D., Whalen, J., Stevens, K. A., Paul, R., Butterfield, T. S., Britton, M. T., Reagan, R. L., Chakraborty, S., Walawage, S. L., Vasquez-Gross, H. A., Cardeno, C., Famula, R. A., Pratt, K., Kuruganti, S., Aradhya, M. K., Leslie, C. A., Dandekar, A. M., Salzberg, S. L., Wegrzyn, J. L., Langley, C. H., Neale, D. B. (2016) The walnut (Juglans regia) genome sequence reveals diversity in genes coding for the biosynthesis of nonstructural polyphenols. The Plant Journal, 87(5), 507-532. Full Text.
  • Mosca E., Gugerli F., Eckert A. J., Neale D. B. (2016) Signature of natural selection on Pinus cemba and P. mugo along elevational gradients in the Alps. Tree Genetics and Genomes. 12(3):1-1. Full Text. Supplemental.
  • Stevens, K.A., Wegrzyn, J., Zimin, A., Puiu, D., Crepeau, M., Cardeno, C., Paul, R., Gonzalez-Ibeaz, D., Koriabine, M., Holtz-Morris, A., Martinez-Garcia, P., Sezen, U., Marcais, G., Jermstad, K., McGuire, P., Loopstra, C.A., Davis, J.M., Eckert, A., deJong, P., Yorke, J.A., Salzberg, S.L., Neale, D.B., Langley, C.H. (2016) Sequence of the Sugar Pine Megagenome. Genetics. 204(3): 1613-1626. Full Text.
  • Vangestel, C., Vázquez-Lobo, A., Martínez-García, P.J., Calic, I., Wegrzyn, J.L., Neale,, D.B. (2016) Patterns of neutral and adaptive genetic diversity across the natural range of sugar pine (Pinus lambertiana Dougl.). Tree Genetics and Genomes. 12(3):51-51. Full Text.
  • Wegrzyn J. L., Whalen J., Kinlaw C. S., Harry D. E., Puryear J., Loopstra C. A., Gonzalez-Ibeas D., Vasquez-Gross H.A., Famula R. A., Neale D.B (2016) Transcriptomic profile of leaf tissue from the leguminous tree, Millettia pinnata. Tree Genetics and Genomes. 12(3):1-12. Full Text.
  • Xiong, J.S., McKeand, S.E., Isik, F., Wegrzyn, J., Neale, D.B., Zeng, Z., da Costa e Silva, L., Whetten, R.W. (2016) Quantitative Trait Loci Influencing Forking Defects in an Outbred Pedigree of Loblolly Pine. BCM Genetics. 17(1):138-138. Full Text.

Publications by Year

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