Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus)

Citation:

Backstroem N, Shipilina D, Blom MPK, Edwards SV. Cis-regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus). Ecology and Evolution [Internet]. 2013;3 (3) :655-666.
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Abstract:

Characterization of the genetic basis of fitness traits in natural populations is
important for understanding how organisms adapt to the changing environ-
ment and to novel events, such as epizootics. However, candidate fitness-
influencing loci, such as regulatory regions, are usually unavailable in nonmodel
species. Here, we analyze sequence data from targeted resequencing of the cis-
regulatory regions of three candidate genes for disease resistance (CD74,
HSP90a, and LCP1) in populations of the house finch (Carpodacus mexicanus)
historically exposed (Alabama) and na
ıve (Arizona) to Mycoplasma gallisepti-
cum. Our study, the first to quantify variation in regulatory regions in wild
birds, reveals that the upstream regions of CD74 and HSP90a are GC-rich, with
the former exhibiting unusually low sequence variation for this species. We
identified two SNPs, located in a GC-rich region immediately upstream of an
inferred promoter site in the gene HSP90a, that were significantly associated
with Mycoplasma pathogen load in the two populations. The SNPs are closely
linked and situated in potential regulatory sequences: one in a binding site for
the transcription factor nuclear NFYa and the other in a dinucleotide microsat-
ellite ((GC)
6
). The genotype associated with pathogen load in the putative
NFYa binding site was significantly overrepresented in the Alabama birds.
However, we did not see strong effects of selection at this SNP, perhaps because
selection has acted on standing genetic variation over an extremely short time
in a highly recombining region. Our study is a useful starting point to explore
functional relationships between sequence polymorphisms, gene expression, and
phenotypic traits, such as pathogen resistance that affect fitness in the wild.

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