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Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

da Silva JM, Giachetto PF, da Silva LO, Cintra LC, Paiva SR, Caetano AR, Yamagishi ME - PLoS ONE (2015)

Bottom Line: High density genotyping panels have been used in a wide range of applications.From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data.Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

View Article: PubMed Central - PubMed

Affiliation: Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso (UNEMAT), Nova Xavantina, Mato Grosso, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular-Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil.

ABSTRACT
High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

No MeSH data available.


GO annotation of biological processes affected by genes that were identified by SFNBs from the Illumina Bovine HD panel.
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pone.0136035.g008: GO annotation of biological processes affected by genes that were identified by SFNBs from the Illumina Bovine HD panel.

Mentions: GO annotation of SFNB-containing genes revealed several categories, including biological regulation, response to stimuli, signaling, immune system processes, growth, and reproduction (Fig 8). Genes involved in these biological processes are responsible for phenotypic differences that have already been described between taurine and zebuine cattle and which are target traits in breeding programs, such as reproductive function (age of puberty, estrous cycle patterns and behavior, ovulatory capacity, reproductive hormone levels, mean number of preantral follicles) [21], resistance to endo- and ecto-parasites [22], response to heat-stress [23], susceptibility to bovine spongiform encephalopathy [24], and growth, carcass, and meat quality traits [25]. Among the SFNB-containing genes found (S2 Table), some noteworthy genes include PPARG (peroxisome proliferator-activated receptor gamma), which is the main regulator of adipogenesis and which is involved in intramuscular fat deposition (marbling) [26–30] and has been associated with age of puberty [31] in cattle. The genes found also included CAST genes (calpastatins) and calpain (CAPN) inhibitors, which are both accountable for post-mortem muscle fiber proteolysis and associated with shear force and tenderness in the skeletal muscles [32, 33].


Genomic Variants Revealed by Invariably Missing Genotypes in Nelore Cattle.

da Silva JM, Giachetto PF, da Silva LO, Cintra LC, Paiva SR, Caetano AR, Yamagishi ME - PLoS ONE (2015)

GO annotation of biological processes affected by genes that were identified by SFNBs from the Illumina Bovine HD panel.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4549312&req=5

pone.0136035.g008: GO annotation of biological processes affected by genes that were identified by SFNBs from the Illumina Bovine HD panel.
Mentions: GO annotation of SFNB-containing genes revealed several categories, including biological regulation, response to stimuli, signaling, immune system processes, growth, and reproduction (Fig 8). Genes involved in these biological processes are responsible for phenotypic differences that have already been described between taurine and zebuine cattle and which are target traits in breeding programs, such as reproductive function (age of puberty, estrous cycle patterns and behavior, ovulatory capacity, reproductive hormone levels, mean number of preantral follicles) [21], resistance to endo- and ecto-parasites [22], response to heat-stress [23], susceptibility to bovine spongiform encephalopathy [24], and growth, carcass, and meat quality traits [25]. Among the SFNB-containing genes found (S2 Table), some noteworthy genes include PPARG (peroxisome proliferator-activated receptor gamma), which is the main regulator of adipogenesis and which is involved in intramuscular fat deposition (marbling) [26–30] and has been associated with age of puberty [31] in cattle. The genes found also included CAST genes (calpastatins) and calpain (CAPN) inhibitors, which are both accountable for post-mortem muscle fiber proteolysis and associated with shear force and tenderness in the skeletal muscles [32, 33].

Bottom Line: High density genotyping panels have been used in a wide range of applications.From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data.Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

View Article: PubMed Central - PubMed

Affiliation: Faculdade de Ciências Agrárias, Biológicas e Sociais Aplicadas, Universidade do Estado de Mato Grosso (UNEMAT), Nova Xavantina, Mato Grosso, Brazil; Programa de Pós-Graduação em Genética e Biologia Molecular-Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, São Paulo, Brazil.

ABSTRACT
High density genotyping panels have been used in a wide range of applications. From population genetics to genome-wide association studies, this technology still offers the lowest cost and the most consistent solution for generating SNP data. However, in spite of the application, part of the generated data is always discarded from final datasets based on quality control criteria used to remove unreliable markers. Some discarded data consists of markers that failed to generate genotypes, labeled as missing genotypes. A subset of missing genotypes that occur in the whole population under study may be caused by technical issues but can also be explained by the presence of genomic variations that are in the vicinity of the assayed SNP and that prevent genotyping probes from annealing. The latter case may contain relevant information because these missing genotypes might be used to identify population-specific genomic variants. In order to assess which case is more prevalent, we used Illumina HD Bovine chip genotypes from 1,709 Nelore (Bos indicus) samples. We found 3,200 missing genotypes among the whole population. NGS re-sequencing data from 8 sires were used to verify the presence of genomic variations within their flanking regions in 81.56% of these missing genotypes. Furthermore, we discovered 3,300 novel SNPs/Indels, 31% of which are located in genes that may affect traits of importance for the genetic improvement of cattle production.

No MeSH data available.