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Title: Appliation of rad-sequencing to linkage mapping in citrus

Author
item ROOSE, MIKEAL - University Of California
item GNUTTER, FRED - University Of Florida
item Stover, Eddie
item FEDERICI, CLAIRE - University Of California

Submitted to: International Horticultural Congress
Publication Type: Abstract Only
Publication Acceptance Date: 11/7/2013
Publication Date: 11/17/2013
Citation: Roose, M., Gnutter, F., Stover, E.W., Federici, C. 2013. Application f rad-sequencing to linkage mapping in citrus [abstract]. International Horticultural Congress.

Interpretive Summary:

Technical Abstract: High density linkage maps can be developed for modest cost using high-throughput DNA sequencing to genotype a defined fraction (representation) of the genome. We developed linkage maps in two citrus populations using the RAD (Restriction site Associated DNA) genotyping method which involves restriction digestion, ligation of barcoded adaptors and size selection to generate sequencing libraries that represent a small fraction of the genome. This method was applied to a population of 169 hybrids between sweet orange (Citrus sinensis) and trifoliate orange (Poncirus trifoliata), and other Poncirus hybrids, to map disease resistance genes from Poncirus. The average number of reads per sample was about 4.5 million and the average read depth was about 21. Approximately 6000 and 1900 heterozygous single nucleotide polymorphism (SNPs) were found in sweet orange and trifoliate orange respectively. SNPs were well distributed over the reference genome sequence although some regions with lower marker density were found. Three duplicated samples differed for only 0.4 to 1.2% of the loci analysed. In the initial analysis 33% of individuals had more than 10% of markers with missing data and were considered unsuitable for mapping. Apparently the problem with these samples was that the DNA did not digest well with PstI so new DNA preparations were sequenced. The second population analysed was 98 progeny, parents and grandparents from a cross of two mandarin hybrids, Fortune x Fairchild, which is used primarily for mapping fruit quality traits. Details of maps generated from these populations will be described.