Working group session:
Structural Genomics
Presentation type:
poster
Authors:
Buyyarapu, Ramesh; Rider, Kelly; McEwan, Robert; Premchand, Gandra; Marri, Pradeep; Evans, Clive; Kumpatla, Siva ; Meyer, David; Channabasavaradhya, Chandra
Presenter:
Buyyarapu, Ramesh
Correspondent:
Buyyarapu, Ramesh
Abstract:
Cotton is one of the most cultivated natural fiber crops in the world. Molecular markers help genome characterization, tagging of key traits and also facilitate marker assisted selection to improve crop productivity. Development of Single Nucleotide Polymorphic (SNP) markers directly from gene sequences are more informative than those from intergenic regions. However, SNP marker development in tetraploid cotton species is highly challenging due to genome complexity and polyploidy nature. Use of available Expressed Sequence Tag (EST) information directly for SNP detection may not provide enough information about the homolog, paralog and homoelog gene copies from both sub-genomes and that would directly impact the rate of false positive SNPs. To overcome this problem, we used Fluidigm Access Array instrument in combination with NGS technologies to generate the gene sequences from diverse germplasm. Fluidigm Access Array technology allows generating the sequencing ready libraries in a multiplexed manner (48x48) to reduce the sequencing cost further by pooling the amplicon libraries. Gene sequences derived from NGS platforms were deconvoluted to each genotype using barcode sequence information from the raw reads. Mapping of the sequences against the target amplicon provide the paralogs and homoeologs in each genotype, and comparison of sequences from multiple genotypes help to identify candidate SNPs from homologous sequences by allele frequency and haplotype clustering. The targeted re-sequencing using NGS instruments provide high sequence depth and thus improve the efficiency of SNP detection process and also assist in distinguishing homologs and paralogs in complex polyploid genomes.