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United States Department of Agriculture

Agricultural Research Service


Location: Subtropical Horticulture Research

2012 Annual Report

1a. Objectives (from AD-416):
The primary goals for this project are to conserve, collect, evaluate, and distribute germplasm and associated information for subtropical/tropical fruit, sugarcane, and Tripsacum. A secondary goal is to investigate the genetic basis of important horticultural traits such as disease resistance and to select improved germplasm. Molecular markers have been developed for genetic diversity analysis and for the production of molecular genetic linkage maps. Families of avocado, mango, and jackfruit have been produced that should allow the mapping of Quantitative Trait Loci (QTL) involved with disease resistance, fruit quality, and yield. A candidate gene approach (CGA) is also being used to find genes involved with disease resistance and for control of flowering. Establish at other National Plant Germplasm System sites duplicate, back-up field plantings of Subtropical Horticulture Research Station priority germplasm; rejuvenate current Subtropical Horticulture Research Station field collections in Miami; and, as determined by annual demand, expand the curatorial capacity for distributing germplasm of sugarcane and tropical/subtropical tree crops.

1b. Approach (from AD-416):
Maintain healthy field collections of current accessions of tropical/subtropical fruit trees and grasses. We recognize that the genetic diversity available in tropical fruit species is not fully represented in the current collections. Significant loss of biodiversity and increasing difficulty in collecting germplasm in tropical countries makes it imperative that new accessions be collected as quickly as possible. Implement improved horticultural practices to ensure the longevity of current collections by re-propagating old clones on new rootstocks in new fields. Add new accessions as they become available from foreign collaborators and breeding programs. Because most of the species and location priorities for collection have been established, it is essential that we support international collecting expeditions with appropriate benefit sharing. After quarantine requirements have been satisfied, the new accessions will be maintained in field plantings. Backup core collections have been established in Mayaguez, Puerto Rico or Hilo, Hawaii. Adequate daily maintenance and periodic replanting of the sugarcane and Tripsacum collection is required to maintain these genetic resources, some 1,800 accessions, as healthy clones.

3. Progress Report:
The redbay ambrosia beetle, Xyloborus glabratus Eichhoff was introduced into the U.S. near Savannah, GA in 2002. The symbiotic fungus (Raffaelea lauricola T. C. Harr., Fraedrich & Aghayeva,) carried by the beetle infects and kills members of Lauraceae including avocado, Persea americana Mill., and has recently been found in avocado groves in Miami-Dade County, Florida. The USDA ARS NPGS collection of avocado is conserved at the National Germplasm Repository (NGR) in Miami-Dade County, Florida. Although the avocado collection is currently free from the ambrosia beetle and the laurel wilt disease, it is believed to be only a matter of time before this insect/disease complex reaches the collection. We have developed a protocol to secure the USDA ARS, NPGS avocado collection at Miami and to establish a backup collection at the ARS germplasm repository in Hilo, HI. Single nucleotide polymorphism (SNP) markers were identified for avocado, used to design an Illumina Infinium SNP chip and the mapping populations and germplasm collections were genotyped. On May 31 - June 1, SHRS hosted a meeting for the California Avocado Commission and the Florida Avocado Association to present recent research results on avocado breeding in Florida and research on red bay ambrosia beetle and laurel wilt. Three members of the California Avocado Commission attended. The head of the Florida Avocado Association and seven other avocado growers represented Florida. Eight Ivorian scientists and technicians were trained in the use of a SNP assay based on endpoint fluorescence and a real time polymerase chain reaction (PCR) SNP assay from July 14 - 24, 2012 at CNRA, Abidjan, Côte d'Ivoire. A presentation was given at the Plant and Animal Genome meetings in San Diego, CA January 15-18, 2012 on the assay (Maul et al. 2012).

4. Accomplishments
1. New tools for avocado genomics. In 2011, a single nucleotide polymorphism (SNP) discovery project was supported by funding from NPS to identify SNPs in the parents of the two avocado mapping populations (Simmonds x Tonnage and reciprocal) and (Bacon x Hass and reciprocal). The project discovered ~600,000 SNPs and, in 2012, 6000 were used in the design of an Illumina Infinium SNP chip also funded by NPS. ARS researchers at the Miami SHRS genotyped 2021 individual trees, including the mapping populations at SHRS, the mapping population at the South Coast Field Station, UC Riverside, CA and germplasm collections at SHRS, Fairchild Tropical Garden and UC Riverside. The genetic map for avocado created from this genotype data will identify genes that are involved in cold tolerance, salinity tolerance, disease resistance and other favorable traits to enhance avocado breeding.

2. Protecting avocado genetic diversity. A protocol with three stages was developed to secure the SHRS avocado collection from the threat of laurel wilt. First, using the ARS Foreign Disease/Weed Science lab in Fort Detrick, MD as an intermediate quarantine, rootstocks were grown from seed sent from Miami. Staff from the National Germplasm Repository (NGR) in Miami hand-carried scions to Ft. Detrick and grafted them onto the rootstocks until at least one representative of each of the clones at SHRS has been grafted at Fort Detrick. The grafted scions remain in the greenhouse for at least one year or longer as necessary to ensure successful establishment in Hawaii. Second, budwood is sent from Fort Detrick to Hilo and grafted on avocado rootstock. Third, research is ongoing at the National Center for Genetic Resource Preservation (NCGRP) to maintain avocado buds and meristems under cryogenic storage, however, initial experiments with 30 pieces of two cultivars were not successful. Preservation of the SHRS germplasm collection provides needed genetic diversity for avocado breeding programs seeking to identify cold tolerant, salinity tolerant and disease resistant cultivars.

3. Sugarcane and energycane evaluation. Enhancement of the sugarcane collection was accomplished by the addition of 121 clones of Saccharum hybrid, S. officinarum, S. barberi, S. sinensis, S. robustum and S. spontaneum. In collaboration with ARS scientists at Canal Point and researchers at the University of Florida, these seedlings and others in the germplasm collection are under evaluation for vigor and enhanced biomass production. Evaluation of genetically diverse sugarcane aids in identifying clones with the greatest biofuel potential.

Review Publications
Reed, S.T., Ayala Silva, T., Brown, J., Glaz, B.S., Comstock, J.C. 2012. Screening Saccharum barberi and sinense accessions for flood tolerance and biomass production. Journal of Agronomy and Crop Science. 198(3):236-244.

Zhang, J., Nagai, C., Yu, Q., Pan, Y., Ayala Silva, T., Schnell Ii, R.J., Comstock, J.C., Arumuganathan, A.K., Ming, R. 2012. Genome size variation in three Saccharum species. Euphytica. 185:511-519. DOI: 10.1007/S10681-012-0664-6.

Arias De Ares, R.S., Borrone, J.W., Tondo, C.L., Kuhn, D.N., Schnell Ii, R.J. 2012. Genomics of Tropical Fruit Tree Crops. Book Chapter. In: Schnell, R.J., Priyadarshan, P.M., editors. Genomics of Tree Crops. Heidelberg, Germany: Springer. p. 209-239.

Gubbuk, H., Gunes, E., Ayala Silva, T., Ercisli, S. 2011. Rapid vegetative propagation method for carob. University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca. 39(1):251-254.

Ayala Silva, T., Schnell Ii, R.J., Gordon, G.G., Winterstein, M.C. 2012. APPLICATION OF PROPICONAZOLE IN MANAGEMENT OF LAUREL WILT DISEASE IN AVOCADO (Persea americana Mill.) TREES. Acta Horticulturae. 948:71-78.

Last Modified: 05/29/2017
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