The value of avian genomics to the conservation of wildlife

Michael N Romanov,Jarret Glasscock,Vincent Magrini,Yang Da,Tanya Renner,Sugandha Dandekar,Sean Mcgrath,Emily M Stremel Mork ,Keithly G Jones ,Elaine R Mardis ,Leona G Chemnick ,Christie A Otten ,Marisa L Korody ,Matthew T Hickenbotham ,Elaina M Tuttle ,Marlys L Houck ,William S Modi ,Eric D Green ,Jeanette C Papp ,Oliver A Ryder

doi:10.1186/1471-2164-10-s2-s10

Abstract

BackgroundGenomic studies in non-domestic avian models, such as the California condor and white-throated sparrow, can lead to more comprehensive conservation plans and provide clues for understanding mechanisms affecting genetic variation, adaptation and evolution.Developing genomic tools and resources including genomic libraries and a genetic map of the California condor is a prerequisite for identification of candidate loci for a heritable embryonic lethal condition. The white-throated sparrow exhibits a stable genetic polymorphism (i.e. chromosomal rearrangements) associated with variation in morphology, physiology, and behavior (e.g., aggression, social behavior, sexual behavior, parental care).In this paper we outline the utility of these species as well as report on recent advances in the study of their genomes.ResultsGenotyping of the condor resource population at 17 microsatellite loci provided a better assessment of the current population's genetic variation. Specific New World vulture repeats were found in the condor genome. Using condor BAC library and clones, chicken-condor comparative maps were generated. A condor fibroblast cell line transcriptome was characterized using the 454 sequencing technology.Our karyotypic analyses of the sparrow in combination with other studies indicate that the rearrangements in both chromosomes 2m and 3a are complex and likely involve multiple inversions, interchromosomal linkage, and pleiotropy. At least a portion of the rearrangement in chromosome 2m existed in the common ancestor of the four North American species of Zonotrichia, but not in the one South American species, and that the 2m form, originally thought to be the derived condition, might actually be the ancestral one.ConclusionMining and characterization of candidate loci in the California condor using molecular genetic and genomic techniques as well as linkage and comparative genomic mapping will eventually enable the identification of carriers of the chondrodystrophy allele, resulting in improved genetic management of this disease.In the white-throated sparrow, genomic studies, combined with ecological data, will help elucidate the basis of genic selection in a natural population. Morphs of the sparrow provide us with a unique opportunity to study intraspecific genomic differences, which have resulted from two separate yet linked evolutionary trajectories. Such results can transform our understanding of evolutionary and conservation biology.

Highlights

Genomic studies in non-domestic avian models, such as the California condor and white-throated sparrow, can lead to more comprehensive conservation plans and provide clues for understanding mechanisms affecting genetic variation, adaptation and evolution.Developing genomic tools and resources including genomic libraries and a genetic map of the California condor is a prerequisite for identification of candidate loci for a heritable embryonic lethal condition
Mining and characterization of candidate loci in the California condor using molecular genetic and genomic techniques as well as linkage and comparative genomic mapping will eventually enable the identification of carriers of the chondrodystrophy allele, resulting in improved genetic management of this disease
California condor studies Genetic diversity and linkage analysis For genetic diversity assessment, linkage analysis and construction of the condor genetic map, we chose 121 related individuals that formed a condor resource population. Their genotyping at 17 microsatellite loci resulted in the estimates of within-population genetic variation shown in the Table 2

Summary

Introduction

Genomic studies in non-domestic avian models, such as the California condor and white-throated sparrow, can lead to more comprehensive conservation plans and provide clues for understanding mechanisms affecting genetic variation, adaptation and evolution.Developing genomic tools and resources including genomic libraries and a genetic map of the California condor is a prerequisite for identification of candidate loci for a heritable embryonic lethal condition. Genomic studies in non-domestic avian models, such as the California condor and white-throated sparrow, can lead to more comprehensive conservation plans and provide clues for understanding mechanisms affecting genetic variation, adaptation and evolution. Introduction Genomic studies in a variety of mammalian taxa have contributed to the development of more comprehensive plans for their conservation, as well as to our understanding of the generation and maintenance of genetic diversity in general (e.g., [1,2,3]). Non-domesticated species of birds are emerging as new animal models with great potential to advance comparative avian genomics and contribute to conservation efforts for threatened species. With the completion of the chicken genome, as well as significant advances in turkey and zebra finch genomic resources, it is possible to examine the genetic bases of complex traits using "tools" borrowed from these species. Because many avian species are relatively easy to observe in the wild, they have been intensely studied for decades

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