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Genome-wide association study of reproductive traits in Nellore heifers using Bayesian inference.

Costa RB, Camargo GM, Diaz ID, Irano N, Dias MM, Carvalheiro R, Boligon AA, Baldi F, Oliveira HN, Tonhati H, Albuquerque LG - Genet. Sel. Evol. (2015)

Bottom Line: All significant SNPs for age at first calving were significant for heifer rebreeding.The use of Bayes factor to determine the significance of SNPs allowed us to identify two sets of 42 and 19 significant SNPs for heifer rebreeding and age at first calving, respectively, which explain 11.35 % and 6.42 % of their phenotypic variance, respectively.These SNPs provide relevant information to help elucidate which genes affect these traits.

View Article: PubMed Central - PubMed

Affiliation: UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, São Paulo, Brazil. raphaelbcosta@gmail.com.

ABSTRACT

Background: An important goal of Zebu breeding programs is to improve reproductive performance. A major problem faced with the genetic improvement of reproductive traits is that recording the time for an animal to reach sexual maturity is costly. Another issue is that accurate estimates of breeding values are obtained only a long time after the young bulls have gone through selection. An alternative to overcome these problems is to use traits that are indicators of the reproductive efficiency of the herd and are easier to measure, such as age at first calving. Another problem is that heifers that have conceived once may fail to conceive in the next breeding season, which increases production costs. Thus, increasing heifer's rebreeding rates should improve the economic efficiency of the herd. Response to selection for these traits tends to be slow, since they have a low heritability and phenotypic information is provided only later in the life of the animal. Genome-wide association studies (GWAS) are useful to investigate the genetic mechanisms that underlie these traits by identifying the genes and metabolic pathways involved.

Results: Data from 1853 females belonging to the Agricultural Jacarezinho LTDA were used. Genotyping was performed using the BovineHD BeadChip (777 962 single nucleotide polymorphisms (SNPs)) according to the protocol of Illumina - Infinium Assay II ® Multi-Sample HiScan with the unit SQ ™ System. After quality control, 305 348 SNPs were used for GWAS. Forty-two and 19 SNPs had a Bayes factor greater than 150 for heifer rebreeding and age at first calving, respectively. All significant SNPs for age at first calving were significant for heifer rebreeding. These 42 SNPs were next or within 35 genes that were distributed over 18 chromosomes and comprised 27 protein-encoding genes, six pseudogenes and two miscellaneous noncoding RNAs.

Conclusions: The use of Bayes factor to determine the significance of SNPs allowed us to identify two sets of 42 and 19 significant SNPs for heifer rebreeding and age at first calving, respectively, which explain 11.35 % and 6.42 % of their phenotypic variance, respectively. These SNPs provide relevant information to help elucidate which genes affect these traits.

No MeSH data available.


Manhattan plot for age at first calving. The y- and x-axes indicate the logarithm (base 10) of Bayes factor and chromosome number, respectively
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Fig1: Manhattan plot for age at first calving. The y- and x-axes indicate the logarithm (base 10) of Bayes factor and chromosome number, respectively

Mentions: Forty-two and 19 SNPs with a Bayes factor greater than 150 were detected for HR and AFC, respectively (Figs. 1 and 2). As expected, all SNPs that were significant for AFC were also significant for HR (Table 1), since both traits are indicators of reproductive efficiency in beef cattle and should be, at least in part, under the control of the same groups of genes. Gene symbols and their respective names are in Table 2.Fig. 1


Genome-wide association study of reproductive traits in Nellore heifers using Bayesian inference.

Costa RB, Camargo GM, Diaz ID, Irano N, Dias MM, Carvalheiro R, Boligon AA, Baldi F, Oliveira HN, Tonhati H, Albuquerque LG - Genet. Sel. Evol. (2015)

Manhattan plot for age at first calving. The y- and x-axes indicate the logarithm (base 10) of Bayes factor and chromosome number, respectively
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4541729&req=5

Fig1: Manhattan plot for age at first calving. The y- and x-axes indicate the logarithm (base 10) of Bayes factor and chromosome number, respectively
Mentions: Forty-two and 19 SNPs with a Bayes factor greater than 150 were detected for HR and AFC, respectively (Figs. 1 and 2). As expected, all SNPs that were significant for AFC were also significant for HR (Table 1), since both traits are indicators of reproductive efficiency in beef cattle and should be, at least in part, under the control of the same groups of genes. Gene symbols and their respective names are in Table 2.Fig. 1

Bottom Line: All significant SNPs for age at first calving were significant for heifer rebreeding.The use of Bayes factor to determine the significance of SNPs allowed us to identify two sets of 42 and 19 significant SNPs for heifer rebreeding and age at first calving, respectively, which explain 11.35 % and 6.42 % of their phenotypic variance, respectively.These SNPs provide relevant information to help elucidate which genes affect these traits.

View Article: PubMed Central - PubMed

Affiliation: UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal, 14884-900, São Paulo, Brazil. raphaelbcosta@gmail.com.

ABSTRACT

Background: An important goal of Zebu breeding programs is to improve reproductive performance. A major problem faced with the genetic improvement of reproductive traits is that recording the time for an animal to reach sexual maturity is costly. Another issue is that accurate estimates of breeding values are obtained only a long time after the young bulls have gone through selection. An alternative to overcome these problems is to use traits that are indicators of the reproductive efficiency of the herd and are easier to measure, such as age at first calving. Another problem is that heifers that have conceived once may fail to conceive in the next breeding season, which increases production costs. Thus, increasing heifer's rebreeding rates should improve the economic efficiency of the herd. Response to selection for these traits tends to be slow, since they have a low heritability and phenotypic information is provided only later in the life of the animal. Genome-wide association studies (GWAS) are useful to investigate the genetic mechanisms that underlie these traits by identifying the genes and metabolic pathways involved.

Results: Data from 1853 females belonging to the Agricultural Jacarezinho LTDA were used. Genotyping was performed using the BovineHD BeadChip (777 962 single nucleotide polymorphisms (SNPs)) according to the protocol of Illumina - Infinium Assay II ® Multi-Sample HiScan with the unit SQ ™ System. After quality control, 305 348 SNPs were used for GWAS. Forty-two and 19 SNPs had a Bayes factor greater than 150 for heifer rebreeding and age at first calving, respectively. All significant SNPs for age at first calving were significant for heifer rebreeding. These 42 SNPs were next or within 35 genes that were distributed over 18 chromosomes and comprised 27 protein-encoding genes, six pseudogenes and two miscellaneous noncoding RNAs.

Conclusions: The use of Bayes factor to determine the significance of SNPs allowed us to identify two sets of 42 and 19 significant SNPs for heifer rebreeding and age at first calving, respectively, which explain 11.35 % and 6.42 % of their phenotypic variance, respectively. These SNPs provide relevant information to help elucidate which genes affect these traits.

No MeSH data available.