Location: Subtropical Horticulture Research
2013 Annual Report
2. Identify genetic variations (single nucleotide polymorphisms, or SNPs) in expressed genes from genetically diverse cultivars of these tree species for the development of SNP markers.
3. Generate and host web-based visualization of data and FTP sites for data analysis and distribution to project participants and to the scientific public when analyses are complete and a manuscript describing the work has been accepted.
A full SNP report will be generated. This report will identify: • Reference: the reference sequence against which the variant was detected. • Variant: an internal unique identifier for the variant. • Class: S=snp, I=insertion, D=deletion (relative to the reference). • Position: the base pair at which the variant occurs. • RefAllele: the allele for the reference sequence. • VarAllele: the allele for the variant reported. • Context: sub-sequence of the reference around the variant position. • BothStrands: has the variant been reported in reads from both strands? • AvgQual: the average quality of the bases in which the variant was reported. • MaxQual: the maximum quality of all bases in which the variant was reported. • NumReadsWithAllele: how many reads total exhibited the variant allele. • UniqAlns: how many reads exhibiting the allele were from unique alignments. • FreqDiff: the absolute value of the difference in frequency between varieties.
Results from this analysis will be used to generate single nucleotide polymorphisms (SNP_ panels for use in USDA-ARS breeding programs for these tree species, generation of genetic maps when mapping populations are available and evaluation of genetic diversity of the germplasm collection of these tree species.
RNA was isolated from leaves, flowers and five stages of developing fruit for the mango cultivar 'Tommy Atkins'. RNA was sent to Indiana University for sequencing on the Illumina HiSeq platform. In addition, RNA was isolated from leaves and flowers and where available fruit from three other genetically diverse cultivars representing the major categories of mango available on the station and sent to Indiana University for sequencing. The sequencing of 'Tommy Atkins' will create a mango transcriptome to which the other RNA sequences can be mapped for SNP calling. Sequencing and bioinformatics is currently underway.