Genome scan for homozygosity islands and inbreeding effect on reproductive traits in nelore beef cattle
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Data
2018-07-30
Autores
Herrera Rios, Ana Cristina
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Universidade Estadual Paulista (Unesp)
Resumo
O uso intensivo de biotecnologias reprodutivas tem feito com que se eleve a taxa de nascimento de progênies com maior grau de parentesco (maior taxa de nascimento de meio-irmãos e irmãos completos). Assim, o conhecimento sobre o coeficiente da endogamia média do rebanho torna-se relevante para a eficiência do sistema de produção. Com o advento da genômica, o coeficiente de endogamia (F) pode ser estimado com base na informação de milhares de marcadores do tipo polimorfismos de base única (SNPs), espalhados por todo o genoma. No presente estudo, informações de 3.785 animais da raça Nelore (1,760 machos e 2,025 fêmeas) genotipados para 777.962 SNPs do BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) foram utilizadas com o objetivo de avaliar a taxa de endogamia em rebanhos comerciais da raça Nelore, bem como investigar o seu efeito (depressão endogâmica) sobre a expressão fenotípica de características reprodutivas (idade ao primeiro parto (IPP), ocorrência de prenhez precoce (OPP) e reconcepcão de novilhas (REC)). A estimativa do valor de F, bem como da depressão endogâmica, foi feita utilizando diferentes metodologias: (i) matriz de parentesco genômica com frequências alélicas obtidas da população base (FG); (ii) matriz de parentesco genômica com frequências alélicas fixadas em 0,5 (FGRM); (iii) com base no excesso de SNPs em homozigose (FSNP); e (iv) corrida de homosigose (FROH). Os resultados da corrida de homosigose também foram utilizados para identificar os padrões (tamanho e distribuição) dos segmentos ROH na raça Nelore bem como para identificar ilhas de homosigose (segmentos ROH compartilhados por mais de 50% da população). Foram identificados 210.636 segmentos ROH distribuídos nos 29 autossomos e cinco ilhas de homozigose localizadas nos cromossomos 5, 7, 12, 21 e 26, nas quais 43 genes foram identificados. Alguns destes genes (INHBE, INHBC, STAT6, FGF8 e DPCD) foram previamente associados com caracteristicas reproductivas, de crescimento, resposta inmume e adaptabilidade em bovinos. As médias para o coeficiente de endogamia calculado com base nas diferentes abordagens foram: -0,0006 (FG), 0,4376 (FGRM), 0,5500 (FSNP) e 0,0590 (FROH). As correlações foram ente baixas FG-FSNP (-0,28), FG-FGRM (-0,20), FG-FROH (0,21), a moderadas FROH-FSNP (0,68), FROH-FGRM (0,72) e fortemente alta para FSNP-FGRM (0,99). O valor médio de F variou de acordo com a metodologia utilizada. O valor extremamente alto do FSNP denota que este método tende a superestimar as taxas de endogamia. Independentemente do método utilizado para obter os valores de F, foi verificado que o aumento de 1% no coeficiente de endogamia médio do rebanho influenciou desfavoravelmente a média das características reprodutivas avaliadas.
The intensive use of reproductive biotechnologies has increased the birth rate of progenies with high degree of relationships (higher birth rate of half- and full-sibs). Thus, the control of herd inbreeding becomes relevant for the efficiency of the production system. With genomics, the inbreeding coefficient can be estimated using thousands of single nucleotide polymorphisms (SNPs), spread throughout the genome. In the present study, information of 3,785 Nelore animals (1,760 males and 2,025 females) genotyped with 777,962 SNP markers of BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) was used with the objective of evaluating the inbreeding rates of Nelore commercial herds, as well as to investigate the effects of inbreeding (inbreeding depression) on the phenotypic expression of reproductive traits (age at first calving (AFC), heifer early pregnancy (EP), and heifer rebreeding (HR)). The inbreeding coefficient (F) and inbreeding depression were estimated based on (i) genomic relationship matrix considering allele frequencies estimated from the base population (FG); (ii) genomic relationship matrix considering allele frequencies fixed at 0.5 (FGRM); (iii) excess of homozygous SNPs (FSNP); and (iv) runs of homozygosity (FROH). The runs of homozygosity results were also used to identify the pattern (size and distribution) of ROH segments as well as to identify ROH islands (ROH segments shared by more than 50% of the population). In total, there were identified 210,636 ROH segments and five ROH Islands located on the chromosomes 5, 7, 12, 21 and 26, in which 43 annotated genes were identified. Some of these genes (INHBE, INHBC, STAT6, FGF8 and DPCD) were previously associated with reproduction and growth traits, inmume response and adaptability in cattle. The average inbreeding calculated based on different approaches were -0.0006 (FG), 0.4376 (FGRM), 0.5500 (FSNP) e 0.0590 (FROH). These correlations ranged from low FG-FSNP (-0.28), FG-FGRM (-0.20), FG-FROH (0.21), to moderated FROH-FSNP (0.68), FROH-FGRM (0.72) and extremely high FSNP-FGRM (0.99). The average population inbreeding coefficient ranged according to the method used. The extremely high value of FSNP indicates that this approach tend to overestimate the inbreeding rates. Independently of the method used to obtain the F values, it was verified that the increase of 1% in the average herd inbreeding unfavorably influenced the mean value of the evaluated reproductive traits.
The intensive use of reproductive biotechnologies has increased the birth rate of progenies with high degree of relationships (higher birth rate of half- and full-sibs). Thus, the control of herd inbreeding becomes relevant for the efficiency of the production system. With genomics, the inbreeding coefficient can be estimated using thousands of single nucleotide polymorphisms (SNPs), spread throughout the genome. In the present study, information of 3,785 Nelore animals (1,760 males and 2,025 females) genotyped with 777,962 SNP markers of BovineHD BeadChip (Illumina Inc., San Diego, CA, USA) was used with the objective of evaluating the inbreeding rates of Nelore commercial herds, as well as to investigate the effects of inbreeding (inbreeding depression) on the phenotypic expression of reproductive traits (age at first calving (AFC), heifer early pregnancy (EP), and heifer rebreeding (HR)). The inbreeding coefficient (F) and inbreeding depression were estimated based on (i) genomic relationship matrix considering allele frequencies estimated from the base population (FG); (ii) genomic relationship matrix considering allele frequencies fixed at 0.5 (FGRM); (iii) excess of homozygous SNPs (FSNP); and (iv) runs of homozygosity (FROH). The runs of homozygosity results were also used to identify the pattern (size and distribution) of ROH segments as well as to identify ROH islands (ROH segments shared by more than 50% of the population). In total, there were identified 210,636 ROH segments and five ROH Islands located on the chromosomes 5, 7, 12, 21 and 26, in which 43 annotated genes were identified. Some of these genes (INHBE, INHBC, STAT6, FGF8 and DPCD) were previously associated with reproduction and growth traits, inmume response and adaptability in cattle. The average inbreeding calculated based on different approaches were -0.0006 (FG), 0.4376 (FGRM), 0.5500 (FSNP) e 0.0590 (FROH). These correlations ranged from low FG-FSNP (-0.28), FG-FGRM (-0.20), FG-FROH (0.21), to moderated FROH-FSNP (0.68), FROH-FGRM (0.72) and extremely high FSNP-FGRM (0.99). The average population inbreeding coefficient ranged according to the method used. The extremely high value of FSNP indicates that this approach tend to overestimate the inbreeding rates. Independently of the method used to obtain the F values, it was verified that the increase of 1% in the average herd inbreeding unfavorably influenced the mean value of the evaluated reproductive traits.
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Palavras-chave
Autozygosity, Beef cattle, Inbreeding depression, Runs of homozygosity