Abstract Detail

Population Genetics/Genomics

Gavin-Smyth, Nora [1], Fant, Jeremie B [2], Grinage, Ayress [3], Zhang, Johnathan [4].

Using target capture data for population genetics: assessing allelic diversity within populations of three rare species.

Target enrichment approaches such as Hyb-Seq capture mutationally neutral regions, such as introns, increasing the potential use of these data for some population genetic analysis. Intron regions are linked to expressed regions, so they can be influenced by selective sweeps, thus limiting assumptions of Hardy-Weinberg equilibrium. Nonetheless, they can be useful for estimates of population genetic metrics such as inbreeding and as a metric of total diversity. GATK Haplotype Caller facilitates the identification of SNPs and phasing of alleles but has been complicated by the chiasmic reconstruction of contigs preventing accurate reconstruction of parental alleles, especially if there are long runs of identical sequences separating the SNPs. This problem has been addressed by an extension to the HybPiper pipeline called HybPhaser. HybPhaser uses reference mapping and phases alleles prior to assembly to detect hybrids. We modify the HybPhaser approach to identify alleles within populations. We used intensive population-level sampling of three rare species: two Asterids, Impatiens (Balsaminaceae) and Brighamia (Campanulaceae) and one monocot, Attalea (Arecaceae), to assess how these pipelines can allow us to accurately assess allelic diversity with target capture data. We did target capture with population sampling (15-45 individuals) from a single population using both Angiosperms353 probes and custom baits to assess allelic diversity and inbreeding. We used HybPiper to assemble contigs, GATK and HybPhaser to identify regions of SNP diversity and assess Hardy-Weinberg equilibrium and linkage. We identified the number of alleles for each locus and species, and used this to determine allelic diversity and estimated inbreeding.

1 - Chicago Botanic Garden, Plant Science Center, 1000 Lake Cook Rd., Glencoe, IL, 60022, United States
2 - Chicago Botanic Gardens, Plant Biology And Conservation , 1000 Lake Cook Rd, Glencoe, IL, 60022, United States
3 - Cornell University, Integrative Plant Science Plant Biology Section, 261 Plant Sciences, Ithaca, NY, 14853, USA
4 - Northwestern University, Plant Biology & Conservation

population genetics
Target Enrichment
Allele phasing.

Presentation Type: Oral Paper
Number: PGG3007
Abstract ID:689
Candidate for Awards:None

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