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ARS Home » Midwest Area » Madison, Wisconsin » U.S. Dairy Forage Research Center » Cell Wall Biology and Utilization Research » Research » Publications at this Location » Publication #348465

Research Project: Investigating Microbial, Digestive, and Animal Factors to Increase Dairy Cow Performance and Nutrient Use Efficiency

Location: Cell Wall Biology and Utilization Research

Title: New-world quail population genomics reveal structure, divergence, and evidence for selection

item WILSON, MIRANDA - Texas A&M University
item OLDESCHULTE, DAVID - Texas A&M University
item HALLEY, YVETTE - West Virginia University
item BHATTARAI, E - Texas A&M University
item HILL, JOSH - Texas A&M University
item METZ, RICHARD - Texas A&M Agrilife
item JOHNSON, CHARLES - Texas A&M University
item ROLLINS, DALE - Texas A&M University
item PETERSON, MARKUS - University Of Texas - El Paso
item Bickhart, Derek
item DECKER, JARED - University Of Missouri
item SEWELL, JOHN - Texas A&M University
item SEABURY, CHRISTOPHER - Texas A&M University

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 1/16/2018
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: North American quail species have been a focus of wildlife researchers for decades, primarily due to more recent broad-scale population declines. The scaled quail (Callipepla squamata) is a desert niche species whose range extends across the southwestern United States and into Mexico, and also overlaps in Texas with the range of the more widely distributed and phenotypically diverse northern bobwhite (Colinus virginianus). A first-generation draft genome assembly for the scaled quail, and a second-generation draft genome assembly for the northern bobwhite, have recently been published. We annotated these genomes using a combination of cDNA and protein evidence from the northern bobwhite (Colinus virginianus), chicken (Gallus gallus), zebra finch (Taeniopygia guttata), and turkey (Meleagris gallopavo). These assemblies are currently being used for northern bobwhite and scaled quail population genomics, with a primary focus on population structure, divergence, and the detection of genomic regions that may be subject to intense selective pressures. To date, we have identified and are examining thousands of genomic regions that do not follow a neutral model, based on the frequency distribution(s) of predicted polymorphisms for 57 scaled quail and 126 northern bobwhites that were sampled from diverse ecoregions across the southern United States of America. We hypothesize that the underlying biological function(s) of genes and/or regulatory features present among loci putatively subject to intense selective pressures may potentially reveal new insights regarding some factors contributing to modern quail declines.