Progress 10/01/12 to 09/30/13
Outputs
Progress Report Objectives (from AD-416): To improve the existing sequencing and assembly of the Prunus domestica genome. Approach (from AD-416): DNA will be purified from Prunus domestica cultivars. Purified DNA will be outsourced to a sequencing service provider to obtain 3X genome coverage via long read sequencing (>500 base pair reads). This project was funded with the aim of sequencing and assembling the most important commercial plum variety named �Improved French�. This variety currently accounts for 99% of the prune acreage in the U.S. State-of-the-art technologies were used to sequence the �Improved French� genome. The data was used to study the familial relationships of worldwide prune germplasm which has been murky up until now. The results showed that so-called �French� types that are commonly used for dried fruit production have a distinct heritage from the majority of fresh fruit varieties. This information is critical to ongoing breeding efforts. The availability of the plum genome will also provide a valuable scientific resource to plant biologists and medical researchers seeking to identify compounds in prunes known to promote digestive, coronary, and bone health.
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Progress 10/01/11 to 09/30/12
Outputs
Progress Report Objectives (from AD-416): To improve the existing sequencing and assembly of the Prunus domestica genome. Approach (from AD-416): DNA will be purified from Prunus domestica cultivars. Purified DNA will be outsourced to a sequencing service provider to obtain 3X genome coverage via long read sequencing (>500 base pair reads). A more fully assembled genome will aid molecular marker development as well as genomic studies in this species. Prior to performing additional sequencing, computational analyses were performed using existing data. The results showed that the hexaploid nature of the genome was a limiting factor and that additional sequencing would not likely lead to significant improvements beyond the current plum-peach reference assembly. Thus, we moved to the next step of molecular marker development. A technician was hired to design a set of genome spanning molecular markers that should discriminate between the industry standard cultivar, Improved French, and an Eastern-type transgenic plum, HoneySweet. Markers were designed against a set of Deletion/Insertion Polymorphisms and tested on approximately 70 plum cultivars. Twenty-four markers could effectively discriminate Improved French from HoneySweet. The data also revealed that Improved French is distinctly different from the bulk of Prunus domestica germplasm. In addition, several DIP positions were found to have six distinct alleles representing each allele in the hexaploid genome. This is now being used to assess the precise genetic segregation pattern in Prunus domestica.
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