Assessing genomic diversity and signatures of selection in Jiaxian Red cattle using whole-genome sequencing data.
Bos indicus
Bos taurus
Chinese cattle
Genetic diversity
Genetic signatures
Population structure
Journal
BMC genomics
ISSN: 1471-2164
Titre abrégé: BMC Genomics
Pays: England
ID NLM: 100965258
Informations de publication
Date de publication:
09 Jan 2021
09 Jan 2021
Historique:
received:
01
07
2020
accepted:
22
12
2020
entrez:
10
1
2021
pubmed:
11
1
2021
medline:
15
5
2021
Statut:
epublish
Résumé
Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, F We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.
Sections du résumé
BACKGROUND
BACKGROUND
Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle.
RESULTS
RESULTS
The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, F
CONCLUSION
CONCLUSIONS
We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.
Identifiants
pubmed: 33421990
doi: 10.1186/s12864-020-07340-0
pii: 10.1186/s12864-020-07340-0
pmc: PMC7796570
doi:
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
43Subventions
Organisme : Program of National Beef Cattle and Yak Industrial Technology system
ID : CARS-37
Organisme : Henan Beef Cattle Industrial Technology System
ID : S2013-08
Organisme : Special Program for Self-Innovation of Henan Academy of Agricultural Sciences
ID : 2019ZC41
Organisme : National Natural Science Foundation of China
ID : 31872317
Organisme : Science-Technology Foundation for innovation and creativity of Henan Academy of Agricultural Sciences
ID : 2020CX09
Références
Science. 2009 Apr 24;324(5926):528-32
pubmed: 19390050
Genome Res. 2005 Nov;15(11):1566-75
pubmed: 16251466
Nucleic Acids Res. 2011 Jul;39(Web Server issue):W316-22
pubmed: 21715386
Genomics. 2020 Jan;112(1):831-836
pubmed: 31145994
BMC Dev Biol. 2008 Dec 22;8:118
pubmed: 19102749
J Proteomics. 2014 Sep 23;109:63-75
pubmed: 24972320
Genet Sel Evol. 2018 Aug 22;50(1):43
pubmed: 30134820
PLoS Genet. 2016 Oct 28;12(10):e1006367
pubmed: 27792790
Front Immunol. 2016 Jan 20;7:4
pubmed: 26834746
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Genomics. 2019 Dec;111(6):1736-1744
pubmed: 30529539
J Med Genet. 2013 Mar;50(3):194-7
pubmed: 23355746
Anim Biotechnol. 2019 Jan;30(1):30-35
pubmed: 29540101
Mol Biol Evol. 2018 Mar 1;35(3):688-699
pubmed: 29294071
J Biol Chem. 2010 Sep 24;285(39):30181-91
pubmed: 20630863
Poult Sci. 2012 Jun;91(6):1299-307
pubmed: 22582286
Anim Genet. 2012 Aug;43(4):367-74
pubmed: 22497295
BMC Genet. 2012 Aug 14;13:70
pubmed: 22888858
J Anim Sci. 2018 Mar 6;96(2):375-397
pubmed: 29390120
Anim Biotechnol. 2019 Jul;30(3):202-211
pubmed: 30595081
Mol Cells. 2015 May;38(5):466-73
pubmed: 26018558
PLoS Genet. 2014 Mar 27;10(3):e1004254
pubmed: 24675901
Mol Biol Evol. 2014 Oct;31(10):2824-7
pubmed: 25015648
BMC Bioinformatics. 2011 Jun 18;12:246
pubmed: 21682921
Front Genet. 2019 Jan 11;9:728
pubmed: 30687392
Nucleic Acids Res. 2010 Sep;38(16):e164
pubmed: 20601685
Bioinformatics. 2019 May 15;35(10):1786-1788
pubmed: 30321304
BMC Genomics. 2011 Feb 10;12:103
pubmed: 21310019
Dev Biol. 2006 Jun 1;294(1):220-31
pubmed: 16595131
Mol Biol Evol. 2011 Oct;28(10):2731-9
pubmed: 21546353
Nat Commun. 2018 Jun 14;9(1):2337
pubmed: 29904051
J Anim Sci. 2012 Sep;90(9):2894-906
pubmed: 22739780
Anim Reprod Sci. 2014 May;146(3-4):89-97
pubmed: 24612955
Bioinformatics. 2016 Jun 15;32(12):1895-7
pubmed: 27153702
J Biol Chem. 2002 Dec 20;277(51):49158-66
pubmed: 12364336
Nature. 2003 Nov 20;426(6964):247-54
pubmed: 14628042
Clin Immunol. 2019 Jul;204:57-63
pubmed: 30415085
J Proteomics. 2011 Dec 21;75(2):352-65
pubmed: 21855665
BMC Genet. 2017 Feb 9;18(1):11
pubmed: 28183280
PLoS One. 2012;7(3):e33763
pubmed: 22470472
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
BMC Genomics. 2010 Jun 11;11:372
pubmed: 20540717
J Biol Chem. 2008 Oct 24;283(43):29285-91
pubmed: 18682384
Anim Sci J. 2019 Apr;90(4):467-472
pubmed: 30780197
Genome Biol. 2017 Feb 20;18(1):34
pubmed: 28219390
Anim Genet. 2019 Feb;50(1):64-69
pubmed: 30421442
PLoS Genet. 2006 Dec;2(12):e190
pubmed: 17194218
BMC Genomics. 2011 Nov 15;12:559
pubmed: 22085807
Am J Hum Genet. 2007 Sep;81(3):559-75
pubmed: 17701901
Genet Mol Res. 2013 Oct 29;12(4):5085-101
pubmed: 24301769
J Anim Sci. 2010 Jan;88(1):16-22
pubmed: 19749024
Anim Genet. 2019 Feb;50(1):70-73
pubmed: 30421479