OpenLB
Open Library of Bioscience
Advanced Search
BMC genomics
May 27, 2024;25 (1): 522.

Whole-genome selection signature differences between Chaohu and Ji'an red ducks.

Ruiyi Lin, Huihuang Li, Weilong Lin, Fan Yang, Xinguo Bao, Chengfu Pan, Lianjie Lai, Weimin Lin
Author Information
  1. Ruiyi Lin: College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
  2. Huihuang Li: College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
  3. Weilong Lin: College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
  4. Fan Yang: College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
  5. Xinguo Bao: College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
  6. Chengfu Pan: College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
  7. Lianjie Lai: College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
  8. Weimin Lin: College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China. weiminlin@fafu.edu.cn.
PMID: 38802792 DOI: 10.1186/s12864-024-10339-6

Abstract

Assessing the genetic structure of local varieties and understanding their genetic data are crucial for effective management and preservation. However, the genetic differences among local breeds require further explanation. To enhance our understanding of their population structure and genetic diversity, we conducted a genome-wide comparative study of Chaohu and Ji'an Red ducks using genome sequence and restriction site-associated DNA sequencing technology. Our analysis revealed a distinct genetic distinction between the two breeds, leading to divided groups. The phylogenetic tree for Chaohu duck displayed two branches, potentially indicating minimal impact from artificial selection. Additionally, our ROH (runs of homozygosity) analysis revealed that Chaohu ducks had a lower average inbreeding coefficient than Ji'an Red ducks. We identified several genomic regions with high genetic similarity in these indigenous duck breeds. By conducting a selective sweep analysis, we identified 574 candidate genes associated with muscle growth (BMP2, ITGA8, MYLK, and PTCH1), fat deposits (ELOVL1 and HACD2), and pigmentation (ASIP and LOC101797494). These results offer valuable insights for the further enhancement and conservation of Chinese indigenous duck breeds.

Keywords

genetic diversity indigenous duck population structure selection signatures

References

  1. BMC Ecol Evol. 2021 Sep 6;21(1):165 [PMID: 34488647]
  2. Anim Biotechnol. 2022 Apr;33(2):242-249 [PMID: 32634039]
  3. Animal. 2018 Jun;12(6):1126-1134 [PMID: 29065939]
  4. BMC Genomics. 2017 Nov 21;18(1):892 [PMID: 29162033]
  5. Genet Sel Evol. 2019 Apr 15;51(1):12 [PMID: 30987584]
  6. J Exp Biol. 2021 Jun 15;224(12): [PMID: 34142139]
  7. Biochim Biophys Acta Mol Cell Biol Lipids. 2021 Jan;1866(1):158842 [PMID: 33069870]
  8. Acta Med Litu. 2019;26(4):211-216 [PMID: 32355459]
  9. PLoS One. 2018 Mar 9;13(3):e0191598 [PMID: 29522515]
  10. IEEE Trans Med Imaging. 2023 Feb;42(2):493-506 [PMID: 36318557]
  11. BMC Genomics. 2023 Jul 1;24(1):367 [PMID: 37391702]
  12. Curr Biol. 2016 Jun 6;26(11):1435-40 [PMID: 27212402]
  13. Bioinformatics. 2009 Jul 15;25(14):1754-60 [PMID: 19451168]
  14. Nat Struct Mol Biol. 2004 May;11(5):481-8 [PMID: 15064755]
  15. J Poult Sci. 2019 Apr 25;56(2):84-90 [PMID: 32055201]
  16. BMC Genomics. 2022 Oct 17;23(1):705 [PMID: 36253734]
  17. PLoS One. 2018 May 29;13(5):e0197937 [PMID: 29813125]
  18. Mol Cell Biol. 1995 Jul;15(7):3479-86 [PMID: 7791754]
  19. Nucleic Acids Res. 2022 Jul 5;50(W1):W216-W221 [PMID: 35325185]
  20. PLoS One. 2019 Aug 8;14(8):e0220904 [PMID: 31393948]
  21. Diabetologia. 2016 May;59(5):1049-58 [PMID: 26852333]
  22. Genet Sel Evol. 2021 Dec 20;53(1):98 [PMID: 34930109]
  23. Curr Protoc Bioinformatics. 2016 Jun 20;54:1.30.1-1.30.33 [PMID: 27322403]
  24. Br Poult Sci. 2022 Aug;63(4):466-474 [PMID: 35094630]
  25. Nat Commun. 2018 Jul 17;9(1):2648 [PMID: 30018292]
  26. Nucleic Acids Res. 2019 Jul 2;47(W1):W199-W205 [PMID: 31114916]
  27. Development. 2000 Nov;127(22):4905-13 [PMID: 11044404]
  28. Heredity (Edinb). 2018 Dec;121(6):564-578 [PMID: 29588508]
  29. J Bone Miner Res. 2008 Mar;23(3):314-25 [PMID: 17967138]
  30. BMC Genomics. 2021 May 31;22(1):401 [PMID: 34058976]
  31. Int J Obes (Lond). 2020 Feb;44(2):377-387 [PMID: 31164724]
  32. Annu Rev Anim Biosci. 2015;3:169-95 [PMID: 25387232]
  33. Anim Genet. 2020 Dec;51(6):890-898 [PMID: 33058234]
  34. Evolution. 2020 Oct;74(10):2348-2364 [PMID: 32749066]
  35. Bioinformatics. 2018 Sep 1;34(17):i884-i890 [PMID: 30423086]
  36. Asian-Australas J Anim Sci. 2018 Aug;31(8):1110-1118 [PMID: 29268585]
  37. Front Genet. 2021 Oct 05;12:719215 [PMID: 34675962]
  38. Curr Protoc Bioinformatics. 2020 Mar;69(1):e96 [PMID: 32162851]
  39. Gigascience. 2021 Feb 16;10(2): [PMID: 33590861]
  40. Nucleic Acids Res. 2015 Jan;43(Database issue):D1049-56 [PMID: 25428369]
  41. Genomics. 2022 Jul;114(4):110406 [PMID: 35709924]
  42. Poult Sci. 2008 Sep;87(9):1823-33 [PMID: 18753451]
  43. Ecol Evol. 2016 Jan 22;6(4):1104-27 [PMID: 26811749]
  44. Animals (Basel). 2022 May 31;12(11): [PMID: 35681891]
  45. BMC Genet. 2016 Aug 26;17(1):122 [PMID: 27565946]
  46. Asian-Australas J Anim Sci. 2020 Dec;33(12):1957-1964 [PMID: 32054153]
  47. Genome Res. 2010 Mar;20(3):393-402 [PMID: 20086244]
  48. Genes (Basel). 2022 Jul 14;13(7): [PMID: 35886032]
  49. Diabetes. 2022 Jun 1;71(6):1218-1232 [PMID: 35287172]
  50. Genome Biol Evol. 2016 Apr 13;8(4):1115-31 [PMID: 26979796]
  51. Int J Mol Sci. 2023 Jan 26;24(3): [PMID: 36768740]
  52. Animals (Basel). 2022 May 26;12(11): [PMID: 35681821]
  53. Br Poult Sci. 2020 Dec;61(6):609-614 [PMID: 33012177]
  54. Animals (Basel). 2023 Mar 24;13(7): [PMID: 37048411]
  55. Evolution. 2017 Mar;71(3):797-799 [PMID: 28071784]
  56. Mol Biol Evol. 2021 Jun 25;38(7):3022-3027 [PMID: 33892491]
  57. Am J Hum Genet. 2007 Sep;81(3):559-75 [PMID: 17701901]
  58. Curr Protoc Bioinformatics. 2013;43:11.10.1-11.10.33 [PMID: 25431634]
  59. PLoS Genet. 2012;8(8):e1002914 [PMID: 22956912]
  60. Genome Res. 2009 Sep;19(9):1655-64 [PMID: 19648217]
  61. J Exp Zool B Mol Dev Evol. 2003 Aug 15;298(1):1-11 [PMID: 12949766]
  62. Genomics Proteomics Bioinformatics. 2021 Aug;19(4):619-628 [PMID: 33662620]
  63. Nucleic Acids Res. 2000 Jan 1;28(1):27-30 [PMID: 10592173]
  64. Poult Sci. 2023 Sep;102(9):102857 [PMID: 37390555]
  65. Genet Sel Evol. 2021 Jan 4;53(1):2 [PMID: 33397285]
  66. BMC Syst Biol. 2017 Feb 24;11(1):29 [PMID: 28235404]
  67. Mol Biol Evol. 2014 Jul;31(7):1929-36 [PMID: 24739305]
  68. Front Genet. 2020 Dec 21;11:582355 [PMID: 33424922]
  69. Br Poult Sci. 2016 Jun;57(3):288-94 [PMID: 26750999]

MeSH Term

Animals
Ducks
Selection, Genetic
Genome
Phylogeny
Genomics
Genetic Variation
Polymorphism, Single Nucleotide
Breeding
Journal Article

Word Cloud

Created with Highcharts 10.0.0geneticbreedsChaohuducksduckstructureJi'ananalysisselectionindigenouslocalunderstandingdifferencespopulationdiversityRedrevealedtwoidentifiedAssessingvarietiesdatacrucialeffectivemanagementpreservationHoweveramongrequireexplanationenhanceconductedgenome-widecomparativestudyusinggenomesequencerestrictionsite-associatedDNAsequencingtechnologydistinctdistinctionleadingdividedgroupsphylogenetictreedisplayedbranchespotentiallyindicatingminimalimpactartificialAdditionallyROHrunshomozygosityloweraverageinbreedingcoefficientseveralgenomicregionshighsimilarityconductingselectivesweep574candidategenesassociatedmusclegrowthBMP2ITGA8MYLKPTCH1fatdepositsELOVL1HACD2pigmentationASIPLOC101797494resultsoffervaluableinsightsenhancementconservationChineseWhole-genomesignatureredsignatures

Similar Articles

Cited By