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United States Department of Agriculture

Agricultural Research Service

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Research Project: Conservation, Genetic Analyses, and Utilization of Subtropical/tropical Fruit Crops, Sugarcane, and Miscanthus Genetic Resources

Location: Subtropical Horticulture Research

Project Number: 6631-21000-022-00
Project Type: Appropriated

Start Date: Mar 28, 2013
End Date: Mar 27, 2018

Objective:
1. Efficiently and effectively maintain, back-up, regenerate, characterize, and evaluate tropical/subtropical fruit, sugarcane, Miscanthus, and Tripsacum genetic resources, and distribute samples and associated information worldwide. 1A Maintain, back-up, and regenerate tropical/subtropical fruit, sugarcane, Miscanthus, and Tripsacum genetic resources. 1B Characterize and evaluate tropical/subtropical fruit, sugarcane, Miscanthus, and Tripsacum genetic resources, and distribute samples and associated information worldwide. Standardize the format for evaluation data and improve access to this data by regular updating of GRIN/GRIN Global. 2. Aided by genetic marker information, strategically fill gaps in the current coverage of tropical/subtropical fruit, sugarcane and Miscanthus germplasm collections through domestic and international exchanges. 3. Identify new sets of single nucleotide polymorphism (SNP) markers for increasing the efficiency and effectiveness of mango and lychee genetic resource management and genetic improvement. 3A Identify SNPs from mango transcriptomes through next generation sequencing and apply to genetic resource management and genetic improvement. 3B Identify SNPs from lychee transcriptomes through next generation sequencing and apply to genetic resource management and genetic improvement. 4. Develop new genetic linkage maps for mango and avocado based on thousands of new SNP markers, and apply the new maps, markers, and phenotypic evaluations to identifying and mapping quantitative trait loci (QTLs) for anthracnose resistance in mango, as well as host-plant resistance to laurel wilt and root rot and tolerance to abiotic stresses for avocado. 4A Develop a genetic linkage map for avocado based on SNPs and apply it to identify QTLs for resistance/tolerance to laurel wilt, Phytophthora root rot (PRR), to abiotic stresses and for other horticultural traits. Improve the assembly of the avocado genome by applying knowledge from the genetic map. 4B Develop a genetic linkage map for mango based on SNPs and use to identify QTLs for anthracnose resistance and other horticultural traits.

Approach:
The curator and/or lead scientist will create a schedule and priority list to maintain, back-up, and regenerate the germplasm collections. Of current highest priority is the backing up of the avocado germplasm collection due to the threat of loss to laurel wilt. Laurel wilt causes a rapid wilting of mature avocado trees, so the germplasm collection is much more at risk than our mapping populations. The curator and/or lead scientist will create a schedule and priority list to characterize and evaluate the genetic resources and distribute samples and associated information worldwide. Through discussion with collaborators, the curator and/or lead scientist will standardize the format for evaluation data to allow convenient updating of GRIN/GRIN Global and improve access to the data. We will fill gaps in our collections by germplasm exchange with our collaborators. Cooperators at UF and FTBG will collaborate on tropical fruit germplasm collection in Central and South America and the Caribbean; ARS SY, TARS Mayaguez-PR, will collaborate on tropical fruit collection in the Caribbean; Dept. of Agriculture, Fisheries and Forestry, Australia will collaborate on germplasm exchange with Australia; and ARS SY, Hilo-HI, will collaborate on tropical fruit collection in Asia. The Volcani Institute, Israel will collaborate on avocado germplasm exchange and WICSCBS, Barbados will collaborate on sugarcane germplasm exchange. Univ. of Illinois will collaborate on germplasm exchange for Miscanthus. Single Nucleotide Polymorphism (SNP) discovery has been successfully accomplished for both cacao and avocado at the SHRS. The same approach will be implemented for SNP discovery in mango and lychee. The SNP discovery strategy for both mango and lychee is based on the transcriptome, the sequences of transcribed genes, rather than on the total genome sequence. The transcriptome will be assembled from 454 sequencing of the RNA from leaves, flowers and the developing fruit. RNA of the most commonly grown cultivar will be used to create a reference for calling SNPs. Linkage maps will be created from SNP marker information using JoinMap4.1. Phenotypic data collected from mapping populations are then analyzed to locate Qquantitative trait loci (QTLs) for the phenotypic traits on the linkage map using MapQTL6.0.

Last Modified: 10/1/2014
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