Assessment of runs of homozygosity islands and estimates of genomic inbreeding in Gyr (Bos indicus) dairy cattle.

Autor: Peripolli E; Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil., Stafuzza NB; Faculdade de Ciências Agrárias e Veterinárias, Departamento de Ciências Exatas, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil., Munari DP; Faculdade de Ciências Agrárias e Veterinárias, Departamento de Ciências Exatas, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil., Lima ALF; Centro de Ciências Agrárias, Departamento de Zootecnia e Desenvolvimento Rural, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil., Irgang R; Centro de Ciências Agrárias, Departamento de Zootecnia e Desenvolvimento Rural, Universidade Federal de Santa Catarina, Florianópolis, 88034-000, Brazil., Machado MA; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil.; Embrapa Gado de Leite, Juiz de Fora, 36038-330, Brazil., Panetto JCDC; Embrapa Gado de Leite, Juiz de Fora, 36038-330, Brazil., Ventura RV; Faculdade de Zootecnia e Engenharia de Alimentos, Universidade de São Paulo, Pirassununga, 13635-900, Brazil.; Beef Improvement Opportunities, Elora, ON, N0B 1S0, Canada.; University of Guelph, Centre for Genetic Improvement of Livestock, ABScBG, Guelph, N1G 2W1, Canada., Baldi F; Faculdade de Ciências Agrárias e Veterinárias, Departamento de Zootecnia, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil., da Silva MVGB; Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPQ), Lago Sul, 71605-001, Brazil. marcos.vb.silva@embrapa.br.; Embrapa Gado de Leite, Juiz de Fora, 36038-330, Brazil. marcos.vb.silva@embrapa.br.
Jazyk: angličtina
Zdroj: BMC genomics [BMC Genomics] 2018 Jan 09; Vol. 19 (1), pp. 34. Date of Electronic Publication: 2018 Jan 09.
DOI: 10.1186/s12864-017-4365-3
Abstrakt: Background: Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species. The aim of the present study was (i) to investigate genome-wide autozygosity to identify and characterize ROH patterns in Gyr dairy cattle genome; (ii) identify ROH islands for gene content and enrichment in segments shared by more than 50% of the samples, and (iii) compare estimates of molecular inbreeding calculated from ROH (F ROH ), genomic relationship matrix approach (F GRM ) and based on the observed versus expected number of homozygous genotypes (F HOM ), and from pedigree-based coefficient (F PED ).
Results: ROH were identified in all animals, with an average number of 55.12 ± 10.37 segments and a mean length of 3.17 Mb. Short segments (ROH 1-2 Mb ) were abundant through the genomes, which accounted for 60% of all segments identified, even though the proportion of the genome covered by them was relatively small. The findings obtained in this study suggest that on average 7.01% (175.28 Mb) of the genome of this population is autozygous. Overlapping ROH were evident across the genomes and 14 regions were identified with ROH frequencies exceeding 50% of the whole population. Genes associated with lactation (TRAPPC9), milk yield and composition (IRS2 and ANG), and heat adaptation (HSF1, HSPB1, and HSPE1), were identified. Inbreeding coefficients were estimated through the application of F ROH , F GRM , F HOM , and F PED approaches. F PED estimates ranged from 0.00 to 0.327 and F ROH from 0.001 to 0.201. Low to moderate correlations were observed between F PED -F ROH and F GRM -F ROH , with values ranging from -0.11 to 0.51. Low to high correlations were observed between F ROH -F HOM and moderate between F PED -F HOM and F GRM -F HOM . Correlations between F ROH from different lengths and F PED gradually increased with ROH length.
Conclusions: Genes inside ROH islands suggest a strong selection for dairy traits and enrichment for Gyr cattle environmental adaptation. Furthermore, low F PED- F ROH correlations for small segments indicate that F PED estimates are not the most suitable method to capture ancient inbreeding. The existence of a moderate correlation between larger ROH indicates that F ROH can be used as an alternative to inbreeding estimates in the absence of pedigree records.
Databáze: MEDLINE
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