Genome-wide patterns of genetic variation in two domestic chickens

Genome Biology and Evolution

Volumn 5, Issue 7, 2013, Pages 1376-1392

  Fan, Wen Lang ^a,b   Ng, Chen Siang ^a   Chen, Chih Feng ^c   Lu, Mei Yeh Jade ^a   Chen, Yu Hsiang ^a   Liu, Chia Jung ^a   Wu, Siao Man ^a   Chen, Chih Kuan ^a,d   Chen, Jiun Jie ^a   Mao, Chi Tang ^a,c,e   Lai, Yu Ting ^a   Lo, Wen Sui ^a   Chang, Wei Hua ^c   Li, Wen Hsiung ^a,b,f  

^a BIODIVERSITY RESEARCH CENTER   (Taiwan)

^b GENOMICS RESEARCH CENTER   (Taiwan)

^c NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

^d NATIONAL TAIWAN UNIVERSITY   (Taiwan)

^e ACADEMIA SINICA   (Taiwan)

^f UNIVERSITY OF CHICAGO   (United States)

Author keywords

Chicken; CNVs; Genetic variation; Single nucleotide polymorphism; Whole genome resequencing

Indexed keywords

ANIMAL; BREEDING; CHICKEN; COPY NUMBER VARIATION; DNA SEQUENCE; GENETIC VARIABILITY; GENETICS; GENOME; INDEL MUTATION; PHENOTYPE; PHYSIOLOGY; QUANTITATIVE TRAIT LOCUS; SEQUENCE ALIGNMENT; SINGLE NUCLEOTIDE POLYMORPHISM; ARTICLE; CNVS; WHOLE GENOME RESEQUENCING;

ANIMALS; BREEDING; CHICKENS; DNA COPY NUMBER VARIATIONS; GENETIC VARIATION; GENOME; INDEL MUTATION; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

CHICKEN; CNVS; GENETIC VARIATION; SINGLE NUCLEOTIDE POLYMORPHISM; WHOLE GENOME RESEQUENCING;

EID: 84891710670     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evt097     Document Type: Article

References (104)

1. Andersson L. 2001. Genetic dissection of phenotypic diversity in farm animals. Nat Rev Genet. 2:130-138.
2. Andersson L, Georges M. 2004. Domestic-animal genomics: deciphering the genetics of complex traits. Nat Rev Genet. 5:202-212.
3. Anitha A, et al. 2008. Genetic analyses of roundabout (ROBO) axon guidance receptors in autism. Am J Med Genet B Neuropsychiatr Genet. 147B:1019-1027.
4. Bai Y, et al. 2012. Polymorphisms of the pro-opiomelanocortin and agoutirelated protein genes and their association with chicken production traits. Mol Biol Rep. 39:7533-7539.
5. Bamshad MJ, et al. 2011. Exome sequencing as a tool for Mendelian disease gene discovery. Nat Rev Genet. 12:745-755.
6. Biscarini F, et al. 2010. Across-line SNP association study for direct and associative effects on feather damage in laying hens. Behav Genet. 40: 715-727.
7. Burt D, Pourquie O. 2003. Genetics. Chicken genome - science nuggets to come soon. Science 300:1669.
8. Carroll SB. 2005. Evolution at two levels: on genes and form. PLoS Biol. 3: e245.
9. Chao CH, Lee YP. 2001. Relationship between reproductive performance and immunity in Taiwan country chickens. Poult Sci. 80:535-540.
10. Chen F, et al. 2011. NELL-1, an osteoinductive factor, is a direct transcriptional target of Osterix. PLoS One 6:e24638.
11. Clop A, Vidal O, Amills M. 2012. Copy number variation in the genomes of domestic animals. Anim Genet. 43:503-517.
12. Cowan CM, et al. 2012. NELL-1 increases pre-osteoblast mineralization using both phosphate transporter Pit1 and Pit2. Biochem Biophys Res Commun. 422:351-357.
13. Crawford RD. 1990. Poutry genetic resources: evolution, diversity, and conservation. In: Crawford RD, editor. Poutry breeding and genetics. New York (NY): Elsevier. p. 43-60.
14. Darwin C. 1859. On the origin of species by means of natural selection, or the preservation of favoured races in the struggle for life. London, UK: John Murray.
15. Darwin C. 1868. The variation of plants and animals under domestication. London, UK: John Murray.
16. Dean M, Annilo T. 2005. Evolution of the ATP-binding cassette (ABC) transporter super family in vertebrates. Annu Rev Genomics Hum Genet. 6:123-142.
17. Dittmar KA, et al. 2012. Genome-wide determination of a broad ESRP-regulated posttranscriptional network by high-throughput sequencing. Mol Cell Biol. 32:1468-1482.
18. Dohner JV. 2001. The encyclopedia of endangered livestock and poultry breeds. New Haven (CT): Yale University Press.
19. Dorshorst B, Okimoto R, Ashwell C. 2010. Genomic regions associated with dermal hyper pigmentation, polydactyly and other morphological traits in the Silkie chicken. J Hered. 101:339-350.
20. Dorshorst B, et al. 2011. A complex genomic rearrangement involving the endothelin 3 locus causes dermal hyperpigmentation in the chicken. PLoS Genet. 7:e1002412.
21. Elferink MG, Vallee AA, Jungerius AP, Crooijmans RP, Groenen MA. 2008. Partial duplication of the PRLR and SPEF2 genes at the late feathering locus in chicken. BMC Genomics 9:391.
22. Elferink MG, et al. 2012. Signatures of selection in the genomes of commercial and non-commercial chicken breeds. PLoS One 7:e32720.
23. Eriksson J, et al. 2008. Identification of the yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genet. 4:e1000010.
24. Ewald SJ, et al. 2011. Association of Mx1 Asn631 variant alleles with reductions in morbidity, early mortality, viral shedding, and cytokine responses in chickens infected with a highly pathogenic avian influenza virus. Immunogenetics 63:363-375.
25. Georges M. 2007. Mapping, fine mapping, and molecular dissection of quantitative trait Loci in domestic animals. Annu Rev Genomics Hum Genet. 8:131-162.
26. Georges M, Andersson L. 2003. Positional identification of structural and regulatory quantitative trait nucleotides in domestic animal species. Cold Spring Harb Symp Quant Biol. 68:179-187.
27. Gilissen C, Hoischen A, Brunner HG, Veltman JA. 2011. Unlocking Mendelian disease using exome sequencing. Genome Biol. 12:228.
28. Gilissen C, Hoischen A, Brunner HG, Veltman JA. 2012. Disease gene identification strategies for exome sequencing. Eur J Hum Genet. 20:490-497.
29. Gonzaga-Jauregui C, Lupski JR, Gibbs RA. 2012. Human genome sequencing in health and disease. Annu Rev Med. 63:35-61.
30. Gorbach DM. 2011. The prediction of single nucleotide polymorphisms and their utilization in mapping traits and determining population structure in production animals [PhD. Dissertation in Animal Science]. Paper 10336. [Ames (IA)]: Iowa State University.
31. Groenen MA, et al. 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature 491:393-398.
32. Habig C, Geffers R, Distl O. 2012. Differential gene expression from genome-wide microarray analyses distinguishes lohmann selected leghorn and lohmann brown layers. PLoS One 7:e46787.
33. Han R, et al. 2012. Novel SNPs in the PRDM16 gene and their associations with performance traits in chickens. Mol Biol Rep. 39: 3153-3160.
34. Hanon EA, et al. 2008. Ancestral TSH mechanism signals summer in a photoperiodic mammal. Curr Biol. 18:1147-1152.
35. Hashemi SM, Hund TJ, Mohler PJ. 2009. Cardiac ankyrins in health and disease. J Mol Cell Cardiol. 47:203-209.
36. Huang DW, Sherman BT, Lempicki RA. 2009. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37:1-13.
37. Huang DW, et al. 2007. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 8:R183.
38. Imsland F, et al. 2012. The Rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb morphology and defective sperm motility. PLoS Genet. 8:e1002775.
39. Jia X, et al. 2013. Copy number variations identified in the chicken using a 60K SNP BeadChip. Anim Genet. 44:276-284.
40. Johnsson M, et al. 2012. A sexual ornament in chickens is affected by pleiotropic alleles at HAO1 and BMP2, selected during domestication. PLoS Genet. 8:e1002914.
41. Kerstens HH, et al. 2011. Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries. BMC Genomics 12:94.
42. Klambauer G, et al. 2012. cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing datawith a low false discovery rate. Nucleic Acids Res. 40:e69.
43. Ku CS, Naidoo N, Pawitan Y. 2011. Revisiting Mendelian disorders through exome sequencing. Hum Genet. 129:351-370.
44. Kumar P, Henikoff S, Ng PC. 2009. Predicting the effects of coding nonsynonymous variants on protein function using the SIFT algorithm. Nat Protoc. 4:1073-1081.
45. Li H, Durbin R. 2010. Fast and accurate long-read alignment with Burrows- Wheeler transform. Bioinformatics 26:589-595.
46. Li H, et al. 2009. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25:2078-2079.
47. Li Q, et al. 2012. Gastrocnemius transcriptome analysis reveals domestication induced gene expression changes between wild and domestic chickens. Genomics 100:314-319.
48. Lipkin E, Fulton J, Cheng H, Yonash N, Soller M. 2002. Quantitative trait locus mapping in chickens by selective DNA pooling with dinucleotide micro satellite markers by using purified DNA and fresh or frozen red blood cells as applied to marker-assisted selection. Poult Sci. 81: 283-292.
49. Liu R, Wang YC, Sun DX, Yu Y, Zhang Y. 2006. Association between polymorphisms of lipoprotein lipase gene and chicken fat deposition. Asian-Austral J Anim Sci. 19:1409-1414.
50. Livak KJ, Schmittgen TD. 2001. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. Methods 25:402-408.
51. Livant EJ, et al. 2007. MX1 exon 13 polymorphisms in broiler breeder chickens and associations with commercial traits. Anim Genet. 38: 177-179.
52. Majewski J, Schwartzentruber J, Lalonde E, Montpetit A, Jabado N. 2011. What can exome sequencing do for you? J Med Genet. 48: 580-589.
53. Mamanova L, et al. 2010. Target-enrichment strategies for next-generation sequencing. Nat Methods. 7:111-118.
54. Mertes F, et al. 2011. Targeted enrichment of genomic DNA regions for next-generation sequencing. Brief Funct Genomics. 10:374-386.
55. Miao YW, et al. 2013. Chicken domestication: an updated perspective based on mitochondrial genomes. Heredity (Edinb). 110:277-282.
56. Mohler PJ. 2006. Ankyrins and human disease: what the electrophysiologist should know. J Cardiovasc Electrophysiol. 17:1153-1159.
57. Mou C, et al. 2011. Cryptic patterning of avian skin confers a developmental facility for loss of neck feathering. PLoS Biol. 9:e1001028.
58. Nakao N, et al. 2008. Thyrotrophin in the pars tuberalis triggers photoperiodic response. Nature 452:317-322.
59. Ng CS, et al. 2012. The chicken frizzle feather is due to an alpha-keratin (KRT75) mutation that causes a defective rachis. PLoS Genet. 8: e1002748.
60. Ng PC, Henikoff S. 2003. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 31:3812-3814.
61. NishiboriM, Shimogiri T, Hayashi T, Yasue H. 2005. Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius. Anim Genet. 36:367-375.
62. OlsonMV. 1999. When less is more: gene loss as an engine of evolutionary change. Am J Hum Genet. 64:18-23.
63. Price EO. 2002. Animal domestication and behavior. Wallingford, UK: CABI Publ.
64. Quevillon E, et al. 2005. InterProScan: protein domains identifier. Nucleic Acids Res. 33:W116-W120.
65. Rabbani B, Mahdieh N, Hosomichi K, Nakaoka H, Inoue I. 2012. Next generation sequencing: impact of exome sequencing in characterizing Mendelian disorders. J Hum Genet. 57:621-632.
66. Ray SA, Drummond PB, Shi L, McDaniel GR, Smith EJ. 2006. Mutation analysis of the aggrecan gene in chickens with tibial dyschondroplasia. Poult Sci. 85:1169-1172.
67. Rozen S, Skaletsky SJ. 2000. Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S, editors. Bioinformatics methods and protocols: methods in molecular biology. Totowa (NJ): Humana Press. p. 365-386.
68. Rubin CJ, et al. 2010. Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464:587-591.
69. Sawai H, et al. 2010. The origin and genetic variation of domestic chickens with special reference to jungle fowls Gallus g. gallus and G. varius. PLoS One 5:e10639.
70. Schou TW, Permin A, Christensen JP, Cu HP, Juul-Madsen HR. 2010. Mannan-binding lectin (MBL) in two chicken breeds and the correlation with experimental Pasteurella multocida infection. Comp Immunol Microbiol Infect Dis. 33:183-195.
71. Sharma P, Bottje W, Okimoto R. 2008. Polymorphisms in uncoupling protein, melanocortin 3 receptor, melanocortin 4 receptor, and pro-opiomelanocortin genes and association with production traits in a commercial broiler line. Poult Sci. 87: 2073-2086.
72. Shinomiya A, et al. 2012. Gene duplication of endothelin 3 is closely correlated with the hyperpigmentation of the internal organs (Fibromelanosis) in silky chickens. Genetics 190:627-638.
73. Siegel PB, Dodgson JB, Andersson L. 2006. Progress from chicken genetics to the chicken genome. Poult Sci. 85:2050-2060.
74. Singh D, Singh PK, Chaudhary S, Mehla K, Kumar S. 2012. Exome sequencing and advances in crop improvement. Adv Genet. 79:87-121.
75. Siu RK, et al. 2012. NELL-1 promotes cartilage regeneration in an in vivo rabbit model. Tissue Eng Part A. 18:252-261.
76. Somes RG Jr. 1988. International Registry of Poultry Genetic Stocks. In. Storrs Agr. Exp. Sta Bull. 476. Storrs (CT): The University of Connecticut.
77. Song C, et al. 2011. Evaluation of SNPs in the chicken HMGA2 gene as markers for body weight gain. Anim Genet. 42:333-336.
78. Takahashi H, Sasaki O, Nirasawa K, Furukawa T. 2010. Association between ovocalyxin-32 gene haplotypes and eggshell quality traits in an F2 intercross between two chicken lines divergently selected for eggshell strength. Anim Genet. 41:541-544.
79. Tang S, et al. 2010. Evaluation of the IGFs (IGF1 and IGF2) genes as candidates for growth, body measurement, carcass, and reproduction traits in Beijing You and Silkie chickens. Anim Biotechnol. 21:104-113.
80. Teer JK, Mullikin JC. 2010. Exome sequencing: the sweet spot before whole genomes. Hum Mol Genet. 19:R145-R151.
81. Vallejo RL, et al. 1998. Genetic mapping of quantitative trait loci affecting susceptibility to Marek's disease virus induced tumors in F2 intercross chickens. Genetics 148:349-360.
82. Wang J, et al. 2005. ChickVD: a sequence variation database for the chicken genome. Nucleic Acids Res. 33:D438-D441.
83. Wang K, Li M, Hakonarson H. 2010a. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38:e164.
84. Wang X, Nahashon S, Feaster TK, Bohannon-Stewart A, Adefope N. 2010b. An initial map of chromosomal segmental copy number variations in the chicken. BMC Genomics 11:351.
85. Wang Y, et al. 2012a. The crest phenotype in chicken is associated with ectopic expression of HOXC8 in cranial skin. PLoS One 7:e34012.
86. Wang Y, et al. 2012b. A genome-wide survey of copy number variation regions in various chicken breeds by array comparative genomic hybridization method. Anim Genet. 43:282-289.
87. Warzecha CC, Sato TK, Nabet B, Hogenesch JB, Carstens RP. 2009a. ESRP1 and ESRP2 are epithelial cell-type-specific regulators of FGFR2 splicing. Mol Cell. 33:591-601.
88. Warzecha CC, Shen S, Xing Y, Carstens RP. 2009b. The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events. RNA Biol. 6:546-562.
89. Warzecha CC, et al. 2010. An ESRP-regulated splicing programme is abrogated during the epithelial-mesenchymal transition. EMBO J. 29: 3286-3300.
90. Winter SF, Lukes L, Walker RC, Welch DR, Hunter KW. 2012. Allelic variation and differential expression of the mSIN3A histone deacetylase complex gene Arid4b promote mammary tumor growth and metastasis. PLoS Genet. 8:e1002735.
91. Wong GK, et al. 2004. A genetic variation map for chicken with 2.8million single-nucleotide polymorphisms. Nature 432:717-722.
92. Wright D, et al. 2009. Copy number variation in intron 1 of SOX5 causes the Pea-comb phenotype in chickens. PLoS Genet. 5:e1000512.
93. Wu MY, Tsai TF, Beaudet AL. 2006. Deficiency of Rbbp1/Arid4a and Rbbp1l1/Arid4b alters epigenetic modifications and suppresses an imprinting defect in the PWS/AS domain. Genes Dev. 20: 2859-2870.
94. Wu X, et al. 2007. Associations of Gonadotropin-Releasing Hormone Receptor (GnRHR) and Neuropeptide Y (NPY) Genes' Polymorphisms with Egg-Laying Traits in Wenchang Chicken. Agr Sci China. 6: 499-504.
95. Xie C, Tammi MT. 2009. CNV-seq, a new method to detect copy number variation using high-throughput sequencing. BMC Bioinformatics 10:80.
96. Xie X, et al. 2012. Genome-wide analysis of the ATP-binding cassette (ABC) transporter gene family in the silkworm, Bombyx mori. Mol Biol Rep. 39:7281-7291.
97. Ye K, Schulz MH, Long Q, Apweiler R, Ning Z. 2009. Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25:2865-2871.
98. Ye X, Avendano S, Dekkers JC, Lamont SJ. 2006. Association of twelve immune-related genes with performance of three broiler lines in two different hygiene environments. Poult Sci. 85: 1555-1569.
99. Yoshimura T, et al. 2003. Light-induced hormone conversion of T4 to T3 regulates photoperiodic response of gonads in birds. Nature 426: 178-181.
100. Zhang H, et al. 2012. Selection signature analysis implicates the PC1/PCSK1 region for chicken abdominal fat content. PLoS One 7: e40736.
101. Zhang X, Zara J, Siu RK, Ting K, Soo C. 2010. The role of NELL-1, a growth factor associated with craniosynostosis, in promoting bone regeneration. J Dent Res. 89:865-878.
102. Zhang X, et al. 2011. The Nell-1 growth factor stimulates bone formation by purified human perivascular cells. Tissue Eng Part A. 17:2497-2509.
103. Zhu JJ, et al. 2001. Screening for highly heterozygous chickens in out bred commercial broiler lines to increase detection power for mapping quantitative trait loci. Poult Sci. 80:6-12.
104. Zou X, et al. 2011. NELL-1 binds to APR3 affecting human osteoblast proliferation and differentiation. FEBS Lett. 585:2410-2418.