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Accueil du site → Master → Etats Unis → 2021 → The Application of Angiosperms-353 Target Enrichment Data for the Assessment of Genetic Variation among Populations of Cheatgrass in Northern New Mexico (Bromus tectorum)

New Mexico State University (2021)

The Application of Angiosperms-353 Target Enrichment Data for the Assessment of Genetic Variation among Populations of Cheatgrass in Northern New Mexico (Bromus tectorum)

Tamrakar, Rubin M

Titre : The Application of Angiosperms-353 Target Enrichment Data for the Assessment of Genetic Variation among Populations of Cheatgrass in Northern New Mexico (Bromus tectorum)

Auteur : Tamrakar, Rubin M

Université de soutenance : New Mexico State University

Grade : Master of Science (MS) in Biology 2021

Résumé partiel
Bromus tectorum (cheatgrass) is an invasive grass from North Africa and Eurasia whose introduction and expansion in the US has particularly impacted rangeland systems across the Western USA. Previous studies found lower inter- but higher intra-population genetic variation in US populations than in native Old-World populations. This finding is consistent with the presence of genetic variation in US populations being derived from multiple founder events that may be contributing to invasive genotypes. In northern New Mexico, Bureau of Land Management land managers have observed populations of cheatgrass that differ in recovery after fire. Some populations demonstrate post-fire vigorous regrowth and even expansion while others do not. These observations suggest that NM population may contain genetic variation relevant to land management decisions. We have conducted a population genomic study using Angiosperms-353 genomic targets on 25 individuals for each of six populations from northern NM and 19 individuals from Red Bluff, Montana to test if target enrichment can be useful for studying within species population genomic variation in NM populations that might inform management practices. Sequencing results obtained from enriched genomic libraries were used for locus reconstruction using HybPiper with an average of 31.3% reads on target. Two methods, 1) SNPs as haplotypes, and 2) Sequences as consensus “haplotypes”, were followed for comparing population assignments. SNP variant calling was performed to generate a SNP map using VCFtools, which was filtered through PLINK v1.9 for generating population assignment plot through ADMIXTURE software. Reconstructed loci using HybPiper were called and aligned for selecting regions without missing data for consensus haplotype construction.

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Page publiée le 3 décembre 2021