Location: Nat'l Clonal Germplasm Rep - Tree Fruit & Nut Crops & Grapes
2019 Annual Report
Accomplishments
1. New technology changes the conservation status of northern California black walnut. A study was done by ARS researchers in Davis, California, using microsatellite markers to determine the genetic purity status of the northern California black walnut (Juglans hindsii). DNA was extracted from 158 mostly wild J. hindsii trees from 10 counties in northern and southern California and one county in southern Oregon. The study found that at least 71.5% of the wild J. hindsii trees represent pure members of that species. As a result, the California Native Plant Society has reclassified the species so that it is no longer given conservation status. The species is robust.
2. Sequencing and complete assembly of heterozygous genomes of J. regia and J.microcarpa. Members of the genus Juglans are monoecious wind-pollinated trees in the family Juglandaceae with highly heterozygous genomes, which greatly complicates genome sequence assembly. However, ARS researchers in Davis, California, in collaboration with University of California, Davis, Plant Sciences Department, sequenced an interspecific hybrid Juglans microcarpa x J. regia using a novel combination of single-molecule sequencing and optical genome mapping technologies. The resulting assemblies were remarkably complete including chromosome termini and centromere regions. Given the importance of J. microcarpa x J. regia hybrids as potential walnut rootstocks, the researchers catalogued disease resistance genes in the parental genomes and studied their chromosomal distribution. They also estimated the molecular clock rates for woody perennials and deployed them in estimating divergence times of Juglans genomes and those of other woody perennials.
3. Walnut genetic linkage map and QTL analysis of economic traits. A genetic linkage map of walnut containing 2220 single nucleotide polymorphisms (SNPs) in 16 linkage groups (LGs) was constructed by ARS researchers in Davis, California, in collaboration with University of California, Davis, Plant Sciences Department, using an F1 mapping population from a cross between ‘Chandler’ and ‘Idaho’, two contrasting heterozygous parents. Five quantitative yield traits; lateral fruitfulness, harvest date and three nut traits (shell thickness, nut weight, and kernel fill) were then mapped on to the linkage groups. A significant quantitative trait locus (QTL) in LG 11 with negative additive effects suggested heterozygote superiority in the expression of lateral bearing. A set of three QTLs explaining ~10% of the variation in harvest date was located in LG 1. Shell thickness, nut weight, and kernel fill were under the control of two to three linked pleiotropic QTLs in LG 1 segregating from ‘Idaho’. The marginal positive additive effects of QTLs for harvest date, shell thickness, and nut weight and small negative additive effects for kernel fill suggested the QTLs had marginal effect on the expression of these traits.
4. Pistachio genome sequencing and phenotyping. ARS researchers in Davis, California, are collaborating with the University of California, Davis, Genome Center and the Foundation Plant Service on phenotyping and genotyping about 1,000 trees each of grafted and nongrafted hybrid pistachio rootstock seedlings. This is an interspecific hybrid between Pistacia atlantica and P. integerrima that is known as UCB-1. During the previous year, the genomes were sequenced. Recently, the focus was on the phenotypic data and the researchers discovered that early growth is a poor predictor of ultimate growth and vigor of the rootstock. Detailed analysis of the first five years of growth of the UCB-1 seedlings was accomplished.
5. Germplasm backup. The collections at the National Clonal Germplasm Repository (NCGR) in Davis, California, are generally not backed up at another location and represent a vulnerability and an important objective for the NCGR. Therefore, the NCGR has been working with the NLGRP in Fort Collins, Colorado, for cryopreservation studies focused on the Prunus and grapes. Success has been achieved with cryopreservation of pollen of peach and other members of the Prunus genus and with vegetative shoot tips of grape. Pollen was collected from 10 Prunus accessions and shipped to Fort Collins for cryopreservation.
Review Publications
Gradziel, T., Lampinen, B., Preece, J.E. 2019. Propagation from basal epicormic meristems remediates an agring-related disorder in almond clones. Horticulturae. 5(28):1-9. https://doi.org/10.3390/horticulturae5020028.
Diaz-Lara, A., Klaassen, V., Stevens, K., Sudarshana, M.R., Rowhani, A., Maree, H.J., Chooi, K.M., Blouin, A.G., Habili, N., Song, Y., Aram, K., Arnold, K., Cooper, M.L., Wunderlich, L., Battany, M.C., Bettiga, L.J., Smith, R.J., Bester, R., Xiao, H., Meng, B., Preece, J.E., Golino, D., Alrwahnih, M. 2018. Characterization of grapevine leafroll-associated virus 3 genetic variants and application towards RT-qPCR assay design. PLoS One. 13(12):e0208862. https://doi.org/10.1371/journal.pone.0208862.
Preece, J.E., Aradhya, M.K. 2019. Temperate nut crops: chestnut, hazelnut, pecan, pistachio, and walnut. In: Greene S., Williams K., Khoury C., Kantar M., Marek L., editors. North American Crop Wild Relatives, Volume 2. Cham, Switzerland: Springer. p. 417-449.
Chater, J.M., Mathon, C., Larive, C.K., Merhaut, D.J., Tinoco, L.W., Mauk, P.A., Preece, J.E. 2019. Juice quality traits, potassium content, and 1H NMR derived metabolites of 14 pomegranate cultivars. Journal of Berry Research. 9(2):209-225.
Aradhya, M.K., Ibrahimov, Z., Toktoraliev, B., Maghradze, D., Musayev, M., Bobokashvili, Z., Velasco, D., Preece, J.E. 2017. Genetic and ecological insights into glacial refugia of walnut (Juglans regia L.). PLoS One. 12(10):e0185974. https://doi.org/10.1371/journal.pone.0185974.
Riaz, S., De Lorenzis, G., Velasco, D., Koehmstedt, A., Maghradze, D., Bobokashvili, Z., Musayev, M., Zdunic, G., Laucou, V., Walker, A.M., Failla, O., Preece, J.E., Aradhya, M.K., Arroyo-Garcia, R. 2018. Genetic diversity analysis of cultivated and wild grapevine (Vitis vinifera L.) accessions around the Mediterranean basin and Central Asia. Biomed Central (BMC) Plant Biology. 18:137. https://doi.org/10.1186/s12870-018-1351-0.
Guzman, F., Segura, S., Aradhya, M.K., Potter, D. 2018. Evaluation of the genetic structure present in natural populations of four subspecies of black cherry (Prunus serotina Ehrh.) from North America using SSR markers. Scientia Horticulturae. 232:206-215. https://doi.org/10.1016/j.scienta.2018.01.013.
Milczarek, R.R., Liang, P., Wong, T., Augustine, M.P., Smith, J.L., Woods, R., Sedej, I., Olsen, C.W., Vilches, A.M., Haff, R.P., Preece, J.E., Breksa, A.P. 2019. Nondestructive determination of the astringency of pollination-variant persimmons (Diospyros kaki) using near-infrared (NIR) spectroscopy and nuclear magnetic resonance (NMR) relaxometry. Postharvest Biology and Technology. 149:50-57. https://doi.org/10.1016/j.postharvbio.2018.11.006.
