Advertisement

3 Biotech

, 9:400 | Cite as

Genetic architecture related to contour feathers density in an F2 resource population via a genome-wide association study

  • Hongyan Sun
  • Yuping Hu
  • Taocun Dou
  • Liang Qu
  • Meng Ma
  • Jian Lu
  • Xingguo Wang
  • Manman Shen
  • Kehua WangEmail author
Original Article
  • 37 Downloads

Abstract

The density of contour feathers is an important trait as it is closely related to heat dissipation in birds. Thus, identification of the major genes that control this trait will be useful to improve heat tolerance in chicken. So far, no GWAS study for the density of contour feathers in birds has been previously published; therefore, this study was aimed to identify genomic regions controlling the density of contour feathers. A total of 1252 hens were genotyped, using the 600 K Affymetrix Axiom Chicken Genotyping Array. The association analyses were performed using the GenABEL package in the R program. In brief, 146 significant SNP markers were mainly located on chromosome 1 and were identified to associate with the density of contour feathers in the current GWAS analysis. Moreover, we identified several within/nearby candidate genes (SUCLA2, DNAJC15, DHRS12, MLNR, and RB1) that are either directly or indirectly involved in the genetic control of the density of contour feathers in chicken. This study laid the foundation for studying the mechanism that underlies the density of chicken feathers. Furthermore, it is feasible to shear the back feathers of live chickens and measure the density of the feathers to improve heat tolerance in breeding practice.

Keywords

Density of contour feather GWAS White leghorn Dongxiang blue-shelled chicken 

Notes

Funding

This work was supported by the China Agriculture Research Systems no. CARS-40-K01, Jiangsu Agriculture Research Systems no. JATS[2018]247, the Jiangsu Province Natural Science Foundation for Youths no. 205080274, the Yangzhou Municipal Natural Science Foundation for Youths no. 203310181.

Compliance with ethical standards

Conflict of interest

On behalf of all authors, the corresponding author states that there is no conflict of interest.

Human animal rights statement

All animal care and experimental procedures were approved by the Institutional Animal Care and Use of the Committee of the Jiangsu Institute of Poultry Science (permit number: SYXK 2007–0023).

Supplementary material

13205_2019_1918_MOESM1_ESM.xlsx (28 kb)
Supplementary material 1 (XLSX 27 kb)
13205_2019_1918_MOESM2_ESM.xlsx (18 kb)
Supplementary material 2 (XLSX 17 kb)
13205_2019_1918_MOESM3_ESM.docx (15 kb)
Supplementary material 3 (DOCX 37 kb)

References

  1. Aulchenko YS, Ripke S, Isaacs A, Van Duijn CM (2007) GenABEL: an R library for genome-wide association analysis. Bioinformatics 23(10):1294–1296CrossRefGoogle Scholar
  2. Barrett JC, Fry B, Maller J, Daly MJ (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21(2):263–265CrossRefGoogle Scholar
  3. Browning BL, Browning SR (2009) A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 84(2):210–223CrossRefGoogle Scholar
  4. Bukau B, Horwich AL (1998) The Hsp70 and Hsp60 chaperone machines. Cell 92:351–366CrossRefGoogle Scholar
  5. Cahaner A, Ajuh JA, Siegmund-Schultze M, Azoulay Y, Druyan S, Valle Zarate A (2008) Effects of the genetically reduced feather coverage in naked neck and featherless broilers on their performance under hot conditions. Poult Sci 87:2517–2527CrossRefGoogle Scholar
  6. Craig E, Weissman JS, Horwich AL (1994) Heat shock proteins and molecular chaperones: mediators of protein conformation and turnover in the cell. Cell 78:365–372CrossRefGoogle Scholar
  7. Deeb N, Cahaner A (1999) The effect of naked-neck genotypes, ambient temperature, feeding status and their interactions on body temperature and performance of broilers. Poult Sci 78:1341–1346CrossRefGoogle Scholar
  8. Elpeleg O, Miller C, Hershkovitz E et al (2005) Deficiency of the ADP-forming succinyl-CoA synthase activity is associated with encephalomyopathy and mitochondrial DNA depletion. Am J Hum Genet 76(6):1081–1086CrossRefGoogle Scholar
  9. Fotsa JC, Merat P, Bordas A (2001) Effect of the slow (K) or rapid (k +) feathering gene on body and feather growth and fatness according to ambient temperature in a Leghorn × brown egg type cross. Genet Sel Evol 33:659–670CrossRefGoogle Scholar
  10. Gething MJ, Sambrook J (1992) Protein folding in the cell. Nature 355:33–45CrossRefGoogle Scholar
  11. Gilmour AR, Gogel B, Cullis B, Thompson R (2009) ASReml user guide release 3.0. VSN International Ltd, Hemel HempsteadGoogle Scholar
  12. Hartl FU (1996) Molecular chaperones in cellular protein folding. Nature 381:571–580CrossRefGoogle Scholar
  13. Hohfeld J, Minami Y, Hartl FU (1995) Hip, a novel cochaperone involved in the eukaryotic hsc70/hsp40 reaction cycle. Cell 83:589–598CrossRefGoogle Scholar
  14. Jiang RS, Xia WT, Chen XY, Geng ZY, Hu ZY (2010) Density of contour feathers and heat tolerance in chickens. J Appl Anim Res 38:253–255CrossRefGoogle Scholar
  15. Johnson JD, Mehus JG, Tews K, Milavetz BI, Lambeth DO (1998) Genetic evidence for the expression of ATP- and GTP-specific succinyl-CoA synthetases in multicellular eucaryotes. J Biol Chem 273(42):27580–27586CrossRefGoogle Scholar
  16. Kiat Y, Vortman Y, Sapir N (2019) Feather moult and bird appearance are correlated with global warming over the last 200 years. Nat Commun 10:2540CrossRefGoogle Scholar
  17. Kinsella RJ, Kähäri A, Haider S et al (2011) Ensembl BioMarts: a hub for data retrieval across taxonomic space. Database 23:bar030Google Scholar
  18. McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP effect predictor. Bioinformatics 26(16):2069–2070CrossRefGoogle Scholar
  19. N’dri AL, Mignon-Grasteau S, Sellier N, Beaumont C, Tixier-Boichard M (2007) Interactions between naked neck gene, sex, and fluctuating ambient temperature on heat tolerance, growth, body composition, meat quality, and sensory analysis of slow growing meat-type broilers. Livest Sci 110:33–45CrossRefGoogle Scholar
  20. Ng CS, Wu P, Foley J et al (2012) The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachils. PLoS Genet 8(7):e1002748CrossRefGoogle Scholar
  21. Ng CS, Chen CK, Fan WL et al (2015) Transcriptomic analyses of regenerating adult feathers in chicken. BMC Genom 16:756CrossRefGoogle Scholar
  22. Pap P, Vincze O, Wekerle B, Daubner T, Vagasi C, Nudds R et al (2017) A phylogenetic comparative analysis reveals correlations between body feather structure and habitat. Funct Ecol 31:1241–1251CrossRefGoogle Scholar
  23. Purcell S, Neale B, Todd-Brown K et al (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559–575CrossRefGoogle Scholar
  24. Renaudeau D, Collin A, Yahav S, de Basilio V, Gourdine JL, Collier RJ (2012) Adaptation to hot climate and strategies to alleviate heat stress in livestock production. Animal 6(5):707–728CrossRefGoogle Scholar
  25. Rothman JE (1989) Polypeptide chain binding proteins: catalysts of protein folding and related processes in cells. Cell 59:591–601CrossRefGoogle Scholar
  26. Saarela S, Klapper B, Heldmaier G (1995) Daily rhythm of oxygen consumption and thermoregulatory responses in some European winter- or summer-acclimatized finches at different ambient temperatures. J Comp Physiol B 165:366–376CrossRefGoogle Scholar
  27. Shen M, Qu L, Ma M et al (2016) Genome-wide association studies for comb traits in chickens. PLoS One 11(7):e0159081CrossRefGoogle Scholar
  28. Song Z, Liu L, Sheikhahmadi A, Jiao H, Lin H (2012) Effect of heat exposure on gene expression of feed intake regulatory peptides in laying hens. J Biomed Biotechnol 2012:484869PubMedPubMedCentralGoogle Scholar
  29. Stettenheim PR (2000) The integumentary morphology of modern birds. Integr Comp Biol 40:461–477Google Scholar
  30. Stuart-Fox D, Newton E, Mulder RA, D’Alba L, Shawkey MD, Igic B (2018) The microstructure of white feathers predicts their visible and near-infrared reflectance properties. PLoS One 13:e0199129CrossRefGoogle Scholar
  31. Swanson DL (1991) Seasonal adjustments in metabolism and insulation in the dark-eyed junco. Condor 93:538–545CrossRefGoogle Scholar
  32. Ungermann C, Neupert W, Cyr DM (1994) The role of Hsp70 in conferring unidirectionality on protein translocation into mitochondria. Science 266:1250–1253CrossRefGoogle Scholar
  33. Wolf BO, Walsberg GE (2000) The role of the plumage in heat transfer processes of birds. Am Zool 40:575–584Google Scholar
  34. Yahav S, Luger D, Cahaner A, Dotan M, Rusal M, Hurwitz S (1998) Thermoregulation in naked-neck chickens subjected to different ambient temperatures. Br Poult Sci 39:133–138CrossRefGoogle Scholar
  35. Yahav S, Shinder D, Tanny J et al (2005) Sensible heat loss: the broiler’s paradox. World’s Poultry Sci J 61:419–434CrossRefGoogle Scholar
  36. Yamamoto I, Kaiya H, Tsutsui C et al (2008) Primary structure, tissue distribution, and biological activity of chicken motilin receptor. Gen Comp Endocrinol 156:509–514CrossRefGoogle Scholar
  37. Yi G, Shen M, Yuan J et al (2015) Genome-wide association study dissects genetic architecture underlying longitudinal egg weights in chickens. BMC Genom 16:746CrossRefGoogle Scholar
  38. Yu JM, Pressoir G, Briggs WH et al (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38(2):203–208CrossRefGoogle Scholar
  39. Zhang H, Liu SH, Zhang Q et al (2011) Fine-mapping of quantitative trait loci for body weight and bone traits and positional cloning of the RB1 gene in chicken. J Anim Breed Genet 128:366–375CrossRefGoogle Scholar
  40. Zhang J, Li C, Tang X, Lu Q, Sa R, Zhang H (2015) High concentrations of atmospheric ammonia induce alterations in the hepatic proteome of broilers (Gallus gallus): an iTRAQ-based quantitative proteomic analysis. PLoS One 10(4):e0123596CrossRefGoogle Scholar

Copyright information

© King Abdulaziz City for Science and Technology 2019

Authors and Affiliations

  1. 1.College of Animal Science and TechnologyYangzhou UniversityYangzhouChina
  2. 2.Jiangsu Institute of Poultry ScienceChinese Academy of Agricultural ScienceYangzhouChina
  3. 3.College of BiotechnologyJiangsu University of Science and TechnologyZhenjiangChina

Personalised recommendations