Corymbia-Association-Colinearity

Title

Association mapping and Co-linearity of genome-wide high-throughput SNPs in Corymbia.

Abstract

Corymbia commonly referred as spotted gums or Cadaga, is popularly emerging as one of the most preferred commercial hardwood species throughout the world due to its superior growth, wood properties and adaptability to marginal-rainfall areas (Shepherd et al., 2007). Despite of its potential, the availability of genomic resources in Corymbia is inadequate and the whole genome sequence is yet to be available in the public databases. Diversity arrays coupled with NGS platform (DArTseq) provides a low-cost, high-throughput, robust markers with uniform genome-wide coverage, preferentially targeting gene-rich regions (Jaccoud et al. 2001 & Petroli et al., 2012). Furthermore, the delivery of large number of dominant and co-dominant markers with the same platform like DArTseq, increases the selection accuracy in predictive models (Sansaloni et al. 2011). We describe the development of genome-wide Silico DArTs and SNPs using DArT genotyping-by-sequencing platform in three major species of Corymbia viz., Corymbia citriodora subsp. variegata (CCV), Corymbia citriodora subsp. citriodora (CCC) and Corymbia torelliana (CT). Of the 96,751 DArTs, a total of 37047 SNPs were discovered in CCV with slightly lesser numbers in CCC and CT with high stringency in selection, at 99% call rate and reproducibility. Overall number of markers in all three species were reported 63718 DArTs and 17602 SNPs. The SNPs were used for studying population genetic structure, linkage disequilibrium and genome-wide association analysis using a natural germplasm of CCV. Co-linearity of the 37047 DArT sequences were assessed with whole genome sequence of E. grandis (Phytosome V10) and E. camaldulensis (unpublished) with minimum of 90 % similarity and e-value of 10-5. About 20,464 SNPs were mapped on 11 chromosomes and 1559 SNPs on other scaffolds, however the remaining 15024 unassigned SNPs could be attributed to Corymbia genome. Similarly with E. camaldulensis genome, only 9676 hits were mapped, which could be due to incomplete coverage of E. camaldulensis genome. Further, the SNPs discovered in CCV population were annotated with the E. grandis database for functional validation of SNPs. Diversity and population structure analyses using 2500 functionally annotated polymorphic SNPs, association analysis for growth parameters were carried out using a natural population of 168 individuals from CCV. The detailed results will be discussed in this presentation.

References

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