Transcriptome Assisted Analysis of the Genome Sequence of Chromosome 7A

A high density molecular genetic map (over 4, 000 markers) has been combined with data from a BAC-based physical map, Illumina sequencing of BAC pools, mate pair libraries (0.5 to 20 kb), and optical maps (BioNano), using GYDLE software to generate a reference-quality genome assembly for chromosome 7A.

A large RNASeq data set generated from a controlled glasshouse experiment was used to assign functional attributes to regions of the genome assembly associated with agronomic traits.

The data showed that genes with variety specific and environment specific transcription patterns were located in the centromere region (unambiguously identified) as well as more generally in the genome space.  The transcriptome data analysis enhanced the analysis of QTL regions of agronomic significance.  In particular, the analysis helped to define suites of genes suitable for haplotype characterisation of genome segments and hence molecular markers for use in tracking key genome regions in breeding programs.