Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits

Autor(es):Mostrar menos -

Peripolli, Elisa ^[1] ; Metzger, Julia ^[2] ; Antunes de Lemos, Marcos Vinicius ^[1] ; Stafuzza, Nedenia Bonvino ^[3] ; Kluska, Sabrina ^[1] ; Olivieri, Bianca Ferreira ^[1] ; Braga Feitosa, Fabieli Louise ^[1] ; Berton, Mariana Piatto ^[1] ; Lopes, Fernando Brito ^[1] ; Munari, Danisio Prado ^[3] ; Lobo, Raysildo Barbosa ^[4] ; Magnabosco, Claudio de Ulhoa ^[5] ; Di Croce, Fernando ^[6] ; Osterstock, Jason ^[6] ; Denise, Sue ^[6] ; Cravo Pereira, Angelica Simone ^[7] ; Baldi, Fernando ^[1]

Afiliação do(s) autor(es)

^[1] UNESP Univ Estadual Paulista Julio de Mesquita Fi, Fac Ciencias Agr & Vet, Dept Zootecnia, BR-14884900 Jaboticabal - Brazil

^[2] Univ Vet Med Hannover, Inst Anim Breeding & Genet, D-30559 Hannover - Germany

^[3] UNESP Univ Estadual Paulista Julio de Mesquita Fi, Dept Ciencias Exatas, Fac Ciencias Agr & Vet, BR-14884900 Jaboticabal - Brazil

^[4] ANCP, BR-14020230 Ribeirao Preto - Brazil

^[5] Embrapa Cerrados, BR-73310970 Planaltina - Brazil

^[6] Zoetis, Kalamazoo, MI 49007 - USA

^[7] Univ Sao Paulo, Dept Nutr & Prod Anim, BR-13635900 Pirassununga - Brazil

• Tipo de documento: Artigo Científico
• Fonte: BMC Genomics; v. 19, SEP 17 2018.
• Citações Web of Science: 2

Resumo

Background: The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (F-ROH), genomic relationship matrix (F-GRM), and pedigree-based coefficient (F-PED). Results: The average number of ROH per animal was 55.15 +/- 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of F(PED )and F-ROH, and their correlations (- 0.05 to 0.26) were low. Estimates of correlation between F-GRM-F-PED was zero, while the correlation (- 0.01 to - 0.07) between F-GRM- F-ROH decreased as a function of ROH length, except for F-ROH > (8Mb) (- 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions: Low F-PED-F-ROH correlation estimates indicate that F-PED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and F-ROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle. (AU)

• Processo FAPESP: 11/21241-0 - Estudo da variabilidade genética do perfil de ácidos graxos da carne de bovinos da raça Nelore terminados em confinamento
• Beneficiário: Fernando Sebastián Baldi Rey
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores