Cis‐regulatory sequence variation and association with Mycoplasma load in natural populations of the house finch (Carpodacus mexicanus). Issue 3 (7th February 2013)

• Record Type: Journal Article
• Authors: Backström, Niclas; Shipilina, Daria; Blom, Mozes P. K.; Edwards, Scott V.
• Is Part Of: Ecology and evolution. Volume 3:Issue 3(2013:Mar.)
• Page Start: 655
• Page End: 666
• Publication Date: 2013-02-07
• Subjects: Association mapping -- cis‐regulatory element -- expression -- house finch -- Mycoplasma gallisepticum; Ecology -- Periodicals; Evolution -- Periodicals; 577.05
• DOI: 10.1002/ece3.484
• Languages: English
• ISSNs: 2045-7758

Abstract

Abstract: Characterization of the genetic basis of fitness traits in natural populations is important for understanding how organisms adapt to the changing environment 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, HSP90α, and LCP1 ) in populations of the house finch ( Carpodacus mexicanus ) historically exposed (Alabama) and naïve (Arizona) to Mycoplasma gallisepticum . Our study, the first to quantify variation in regulatory regions in wild birds, reveals that the upstream regions of CD74 and HSP90α 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 HSP90α, 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 NFYα and the other in a dinucleotide microsatellite ((GC)6 ). The genotype associated with pathogen load in the putative NFYα 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. Abstract : By taking a candidate gene approach, we investigate patterns of genetic variation in cis‐regulatory sequences of three genes previously shown to be differentially expressed between populations of house finches naive and historically exposed to the disease Mycoplasma gallisepticum . We show that upstream regions have high GC content, varying genetic variability, and contain several transcription factor‐binding sites. We identify two SNPs significantly associated with disease response that are located in cis‐regulatory sequences of the gene HSP90a and discuss their potential role in the evolution of resistance in this system.