title: Detection and characterization of small insertion and deletion genetic variants in modern layer chicken genomes.
abstract: BACKGROUND
  Small insertions and deletions (InDels) constitute the second most abundant class of genetic variants and have been found to be associated with many traits and diseases. The present study reports on the detection and characterisation of about 883 K high quality InDels from the whole-genome analysis of several modern layer chicken lines from diverse breeds.
  
  
  RESULTS
  To reduce the error rates seen in InDel detection, this study used the consensus set from two InDel-calling packages: SAMtools and Dindel, as well as stringent post-filtering criteria. By analysing sequence data from 163 chickens from 11 commercial and 5 experimental layer lines, this study detected about 883 K high quality consensus InDels with 93% validation rate and an average density of 0.78 InDels/kb over the genome. Certain chromosomes, viz, GGAZ, 16, 22 and 25 showed very low densities of InDels whereas the highest rate was observed on GGA6. In spite of the higher recombination rates on microchromosomes, the InDel density on these chromosomes was generally lower relative to macrochromosomes possibly due to their higher gene density. About 43-87% of the InDels were found to be fixed within each line. The majority of detected InDels (86%) were 1-5 bases and about 63% were non-repetitive in nature while the rest were tandem repeats of various motif types. Functional annotation identified 613 frameshift, 465 non-frameshift and 10 stop-gain/loss InDels. Apart from the frameshift and stopgain/loss InDels that are expected to affect the translation of protein sequences and their biological activity, 33% of the non-frameshift were predicted as evolutionary intolerant with potential impact on protein functions. Moreover, about 2.5% of the InDels coincided with the most-conserved elements previously mapped on the chicken genome and are likely to define functional elements. InDels potentially affecting protein function were found to be enriched for certain gene-classes e.g. those associated with cell proliferation, chromosome and Golgi organization, spermatogenesis, and muscle contraction.
  
  
  CONCLUSIONS
  The large catalogue of InDels presented in this study along with their associated information such as functional annotation, estimated allele frequency, etc. are expected to serve as a rich resource for application in future research and breeding in the chicken.
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK. clarissaboschi@yahoo.com.|Current Address: Departamento de Zootecnia, University of Sao Paulo/ESALQ, Piracicaba, SP, 13418-900, Brazil. clarissaboschi@yahoo.com.
authors.forename: Clarissa
authors.initials: C
authors.lastname: Boschiero
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK. almas.gheyas@roslin.ed.ac.uk.
authors.forename: Almas A
authors.initials: AA
authors.lastname: Gheyas
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK. hannahralph@aol.com.
authors.forename: Hannah K
authors.initials: HK
authors.lastname: Ralph
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK. lel.eory@roslin.ed.ac.uk.
authors.forename: Lel
authors.initials: L
authors.lastname: Eory
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK. bob.paton@roslin.ed.ac.uk.
authors.forename: Bob
authors.initials: B
authors.lastname: Paton
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK. richard.kuo@roslin.ed.ac.uk.
authors.forename: Richard
authors.initials: R
authors.lastname: Kuo
authors.affiliation: Hy-Line International, Dallas Center, IA, USA. jfulton@hyline.com.
authors.forename: Janet
authors.initials: J
authors.lastname: Fulton
authors.affiliation: Lohmann Tierzucht GmbH, Cuxhaven, Germany. preisinger@ltz.de.
authors.forename: Rudolf
authors.initials: R
authors.lastname: Preisinger
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK. pete.kaiser@roslin.ed.ac.uk.
authors.forename: Pete
authors.initials: P
authors.lastname: Kaiser
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK. dave.burt@roslin.ed.ac.uk.
authors.forename: David W
authors.initials: DW
authors.lastname: Burt
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D002645:Chickens / Q000235:genetics*; D016678:Genome; D054643:INDEL Mutation / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017384:Sequence Deletion / Q000235:genetics*