Current understanding of an Emerging Coronavirus using in silico approach: Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2)

Abstract Novel coronavirus (nCoV) namely SARS-CoV-2 is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the SARS-CoV-2 although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among SARS-CoV-2 and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that SARS-CoV-2 has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.

Resumo O novo coronavírus (nCoV), nomeadamente SARS-CoV-2, foi considerado responsável pela pandemia atual iniciada em Wuhan (China) desde dezembro de 2019 e foi descrito com ligação epidemiológica à China em cerca de 221 países e territórios até agora. Neste estudo, caracterizamos a linhagem genética do SARS-CoV-2 e relatamos a recombinação dentro do gênero e subgênero dos coronavírus. A relação filogenética de 39 coronavírus pertencentes a seus quatro gêneros e cinco subgêneros foi analisada usando o método de Neighbour-joining usando MEGA 6.0. Árvores filogenéticas do genoma de comprimento total, várias proteínas (espícula, envelope, membrana e nucleocapsídeo), sequências de nucleotídeos foram construídas separadamente. A recombinação putativa foi testada via RDP4. Nossa análise descreve que o SARS-CoV-2, embora mostre grande semelhança com as sequências de Bat-SARS-CoVs em todo o genoma (dando semelhança de sequência de 89%), exibe agrupamento conflitante com as sequências de coronavírus do tipo Bat-SARS (MG772933 e MG772934) Além disso, sete eventos de recombinação foram observados em SARS-CoV-2 (NC045512) por RDP4. Mas nem um único evento de recombinação preenche o alto nível de certeza. A recombinação está alojada mais em genes de proteína de pico, principalmente, do que no resto do genoma, indicando que o cluster de ponto de interrupção surge além dos intervalos de densidade de ponto de interrupção de 95% e 99%. Os níveis de similaridade genética observados entre SARS-CoV-2 e Bat-SARS-CoVs defendem que o último não exibe a variante específica que causa surto em humanos, sugerindo que SARS-CoV-2 tenha se originado possivelmente de morcegos. Essas características genômicas e sua provável associação com as características do vírus, juntamente com a virulência em humanos, requerem uma consideração mais aprofundada.

Current understanding of an Emerging Coronavirus usingin silico approach: Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) / Compreensão atual de um coronavírus emergente usando abordagem in silico: síndrome respiratória aguda grave - coronavírus-2 (SARS-CoV-2)

Novel coronavirus (nCoV) namely "SARS-CoV-2" is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the "SARS-CoV-2" although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among "SARS-CoV-2" and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that "SARS-CoV-2" has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.

O novo coronavírus (nCoV), nomeadamente "SARS-CoV-2", foi considerado responsável pela pandemia atual iniciada em Wuhan (China) desde dezembro de 2019 e foi descrito com ligação epidemiológica à China em cerca de 221 países e territórios até agora. Neste estudo, caracterizamos a linhagem genética do SARS-CoV-2 e relatamos a recombinação dentro do gênero e subgênero dos coronavírus. A relação filogenética de 39 coronavírus pertencentes a seus quatro gêneros e cinco subgêneros foi analisada usando o método de Neighbour-joining usando MEGA 6.0. Árvores filogenéticas do genoma de comprimento total, várias proteínas (espícula, envelope, membrana e nucleocapsídeo), sequências de nucleotídeos foram construídas separadamente. A recombinação putativa foi testada via RDP4. Nossa análise descreve que o "SARS-CoV-2", embora mostre grande semelhança com as sequências de Bat-SARS-CoVs em todo o genoma (dando semelhança de sequência de 89%), exibe agrupamento conflitante com as sequências de coronavírus do tipo Bat-SARS (MG772933 e MG772934) Além disso, sete eventos de recombinação foram observados em SARS-CoV-2 (NC045512) por RDP4. Mas nem um único evento de recombinação preenche o alto nível de certeza. A recombinação está alojada mais em genes de proteína de pico, principalmente, do que no resto do genoma, indicando que o cluster de ponto de interrupção surge além dos intervalos de densidade de ponto de interrupção de 95% e 99%. Os níveis de similaridade genética observados entre "SARS-CoV-2" e Bat-SARS-CoVs defendem que o último não exibe a variante específica que causa surto em humanos, sugerindo que "SARS-CoV-2" tenha se originado possivelmente de morcegos. Essas características genômicas e sua provável associação com as características do vírus, juntamente com a virulência em humanos, requerem uma consideração mais aprofundada.

Current understanding of an Emerging Coronavirus usingin silico approach: Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) / Compreensão atual de um coronavírus emergente usando abordagem in silico: síndrome respiratória aguda grave - coronavírus-2 (SARS-CoV-2)

Novel coronavirus (nCoV) namely "SARS-CoV-2" is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the "SARS-CoV-2" although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among "SARS-CoV-2" and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that "SARS-CoV-2" has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.(AU)

O novo coronavírus (nCoV), nomeadamente "SARS-CoV-2", foi considerado responsável pela pandemia atual iniciada em Wuhan (China) desde dezembro de 2019 e foi descrito com ligação epidemiológica à China em cerca de 221 países e territórios até agora. Neste estudo, caracterizamos a linhagem genética do SARS-CoV-2 e relatamos a recombinação dentro do gênero e subgênero dos coronavírus. A relação filogenética de 39 coronavírus pertencentes a seus quatro gêneros e cinco subgêneros foi analisada usando o método de Neighbour-joining usando MEGA 6.0. Árvores filogenéticas do genoma de comprimento total, várias proteínas (espícula, envelope, membrana e nucleocapsídeo), sequências de nucleotídeos foram construídas separadamente. A recombinação putativa foi testada via RDP4. Nossa análise descreve que o "SARS-CoV-2", embora mostre grande semelhança com as sequências de Bat-SARS-CoVs em todo o genoma (dando semelhança de sequência de 89%), exibe agrupamento conflitante com as sequências de coronavírus do tipo Bat-SARS (MG772933 e MG772934) Além disso, sete eventos de recombinação foram observados em SARS-CoV-2 (NC045512) por RDP4. Mas nem um único evento de recombinação preenche o alto nível de certeza. A recombinação está alojada mais em genes de proteína de pico, principalmente, do que no resto do genoma, indicando que o cluster de ponto de interrupção surge além dos intervalos de densidade de ponto de interrupção de 95% e 99%. Os níveis de similaridade genética observados entre "SARS-CoV-2" e Bat-SARS-CoVs defendem que o último não exibe a variante específica que causa surto em humanos, sugerindo que "SARS-CoV-2" tenha se originado possivelmente de morcegos. Essas características genômicas e sua provável associação com as características do vírus, juntamente com a virulência em humanos, requerem uma consideração mais aprofundada.(AU)

Current understanding of an Emerging Coronavirus using in silico approach: Severe Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2) / Compreensão atual de um coronavírus emergente usando abordagem in silico: síndrome respiratória aguda grave - coronavírus-2 (SARS-CoV-2)

Abstract Novel coronavirus (nCoV) namely "SARS-CoV-2" is being found responsible for current PANDEMIC commenced from Wuhan (China) since December 2019 and has been described with epidemiological linkage to China in about 221 countries and territories until now. In this study we have characterized the genetic lineage of SARS-CoV-2 and report the recombination within the genus and subgenus of coronaviruses. Phylogenetic relationship of thirty nine coronaviruses belonging to its four genera and five subgenera was analyzed by using the Neighbor-joining method using MEGA 6.0. Phylogenetic trees of full length genome, various proteins (spike, envelope, membrane and nucleocapsid) nucleotide sequences were constructed separately. Putative recombination was probed via RDP4. Our analysis describes that the "SARS-CoV-2" although shows great similarity to Bat-SARS-CoVs sequences through whole genome (giving sequence similarity 89%), exhibits conflicting grouping with the Bat-SARS-like coronavirus sequences (MG772933 and MG772934). Furthermore, seven recombination events were observed in SARS-CoV-2 (NC_045512) by RDP4. But not a single recombination event fulfills the high level of certainty. Recombination mostly housed in spike protein genes than rest of the genome indicating breakpoint cluster arises beyond the 95% and 99% breakpoint density intervals. Genetic similarity levels observed among "SARS-CoV-2" and Bat-SARS-CoVs advocated that the latter did not exhibit the specific variant that cause outbreak in humans, proposing a suggestion that "SARS-CoV-2" has originated possibly from bats. These genomic features and their probable association with virus characteristics along with virulence in humans require further consideration.

Resumo O novo coronavírus (nCoV), nomeadamente "SARS-CoV-2", foi considerado responsável pela pandemia atual iniciada em Wuhan (China) desde dezembro de 2019 e foi descrito com ligação epidemiológica à China em cerca de 221 países e territórios até agora. Neste estudo, caracterizamos a linhagem genética do SARS-CoV-2 e relatamos a recombinação dentro do gênero e subgênero dos coronavírus. A relação filogenética de 39 coronavírus pertencentes a seus quatro gêneros e cinco subgêneros foi analisada usando o método de Neighbour-joining usando MEGA 6.0. Árvores filogenéticas do genoma de comprimento total, várias proteínas (espícula, envelope, membrana e nucleocapsídeo), sequências de nucleotídeos foram construídas separadamente. A recombinação putativa foi testada via RDP4. Nossa análise descreve que o "SARS-CoV-2", embora mostre grande semelhança com as sequências de Bat-SARS-CoVs em todo o genoma (dando semelhança de sequência de 89%), exibe agrupamento conflitante com as sequências de coronavírus do tipo Bat-SARS (MG772933 e MG772934) Além disso, sete eventos de recombinação foram observados em SARS-CoV-2 (NC045512) por RDP4. Mas nem um único evento de recombinação preenche o alto nível de certeza. A recombinação está alojada mais em genes de proteína de pico, principalmente, do que no resto do genoma, indicando que o cluster de ponto de interrupção surge além dos intervalos de densidade de ponto de interrupção de 95% e 99%. Os níveis de similaridade genética observados entre "SARS-CoV-2" e Bat-SARS-CoVs defendem que o último não exibe a variante específica que causa surto em humanos, sugerindo que "SARS-CoV-2" tenha se originado possivelmente de morcegos. Essas características genômicas e sua provável associação com as características do vírus, juntamente com a virulência em humanos, requerem uma consideração mais aprofundada.

Genome-Wide Association Study on Two Immune-Related Traits in Jinghai Yellow Chicken

This study was designed to discover molecular marker associated with the interferon INF-γ and avian influenza (AI) antibody titer traits in Jinghai Yellow chicken (Gallus gallus). Serum samples were taken from 400 female chickens and the INF-γ concentrations and AI antibody titer levels were measured. A genome-wide association study was carried out using specific-locus amplified fragment (SLAF) sequencing. Bioinformatics analysis was applied to detect single-nucleotide polymorphisms (SNPs) associated with the two traits. After sequencing and quality control, 103,680 SLAFs and 90,961 SNPs were obtained. The 400 samples were divided into 10 subgroups to reduce the effects of group stratification. The Bonferroni adjusted P-value of genome-wide significance was set at 1.87E−06 according to the number of independent SNP markers and linkage disequilibrium blocks. A SNP that was significantly associated with INF-γ concentration was detected in the myomesin 1 (MYOM1) gene on chromosome 2, and another SNPthat was significantly associated with the AI antibody titer level was detected in an RNA methyltransferase gene (Nsun7), which was found to have an important biological function. We propose that MYOM1 and Nsun7 are valuable candidate genes that influence the disease resistance characters of chicken. However, in-depth investigations are needed to determine the essential roles of these genes in poultry disease resistance and their possible application in breeding disease resistant poultry.(AU)

The Single Nucleotide Polymorphisms of Myostatin Gene and Their Associations with Growth and Carcass Traits in Daheng Broiler

Myostatin (MSTN) is a negative regulator of skeletal muscle growth. In order to investigate whether there is a correlation between MSTN polymorphisms and chicken production performance, in this study, single nucleotide polymorphisms (SNPs) in MSTN gene were examined across 180 Daheng broilers by direct sequencing of PCR product, and the correlations between the genotype and body weight at the age of 1-10 weeks and carcass traits at the age of 73 day were analyzed. Five SNPs (rs313622770, rs313744840, rs316247861, rs314431084, rs317126751) of MSTN gene were identified across Daheng broiler samples, and four haplotypes were reconstructed based on the five SNPs. Results of association analysis showed that four (rs313622770, rs313744840, rs316247861 and rs317126751) of these SNPs had significant association with some growth traits (p 0.05), but there were no significant effect on carcass traits and the four SNPs were strong linkage. For rs314431084, there was no significant correlation between different genotypes and growth or carcass traits. The AA genotype of rs313622770, GG genotype of rs313744840, CC genotype of rs316247861, TT genotype of rs317126751 were good for chicken growth. Diplotypes were significantly associated with chest muscle and leg muscle weight (p 0.05). Overall, these results provide evidence that polymorphisms in MSTN gene are associated with growth traits in chicken. The SNPs in MSTN gene could be utilized as potential markers for marker-assisted selection (MAS) during chicken breeding.(AU)

The Single Nucleotide Polymorphisms of Myostatin Gene and Their Associations with Growth and Carcass Traits in Daheng Broiler

Myostatin (MSTN) is a negative regulator of skeletal muscle growth. In order to investigate whether there is a correlation between MSTN polymorphisms and chicken production performance, in this study, single nucleotide polymorphisms (SNPs) in MSTN gene were examined across 180 Daheng broilers by direct sequencing of PCR product, and the correlations between the genotype and body weight at the age of 1-10 weeks and carcass traits at the age of 73 day were analyzed. Five SNPs (rs313622770, rs313744840, rs316247861, rs314431084, rs317126751) of MSTN gene were identified across Daheng broiler samples, and four haplotypes were reconstructed based on the five SNPs. Results of association analysis showed that four (rs313622770, rs313744840, rs316247861 and rs317126751) of these SNPs had significant association with some growth traits (p 0.05), but there were no significant effect on carcass traits and the four SNPs were strong linkage. For rs314431084, there was no significant correlation between different genotypes and growth or carcass traits. The AA genotype of rs313622770, GG genotype of rs313744840, CC genotype of rs316247861, TT genotype of rs317126751 were good for chicken growth. Diplotypes were significantly associated with chest muscle and leg muscle weight (p 0.05). Overall, these results provide evidence that polymorphisms in MSTN gene are associated with growth traits in chicken. The SNPs in MSTN gene could be utilized as potential markers for marker-assisted selection (MAS) during chicken breeding.

Identification of genes associated with reproductive function in dairy cattle

The use of genomics has improved response to selection for functional traits with low heritability such as fertility traits. Much of the work on fertility traits has been performed through use of genome-wide association studies (GWAS) to identify genetic loci associated with reproductive traits. Under a GWAS approach, the assumption is that the markers on the panel are in linkage disequilibrium with causative mutations. In many cases, identification of the causative mutation is difficult because an associated genetic marker can be in intergenic regions and can be in linkage disequilibrium with variants in several nearby genes. Another approach is to identify candidate genes using knowledge of the biological pathways controlling a trait to search for single nucleotide polymorphism (SNP) in genes in those pathways. This should reveal putative causative markers responsible for genetic variation in biological function, and it is expected that the marker will be more strongly associated with a trait than one in linkage disequilibrium. An example of how a series of candidate gene studies demonstrate that identification of markers in genes involved in reproductive processes can lead to discovery of additional markers associated with genetic variation in reproductive traits is presented. In addition, the inclusion of candidate markers for fertility can improve reliability of genetic estimates for fertility traits, and the repeatability of the effects across a separate population of animals gives confidence that association elucidated by this set of markers is likely to be real. More importantly, the use of candidate genes can provide insights into the biology underpinning genetic variation in fertility, and that this understanding can lead to physiological interventions to improve reproductive function.

Identification of genes associated with reproductive function in dairy cattle

The use of genomics has improved response to selection for functional traits with low heritability such as fertility traits. Much of the work on fertility traits has been performed through use of genome-wide association studies (GWAS) to identify genetic loci associated with reproductive traits. Under a GWAS approach, the assumption is that the markers on the panel are in linkage disequilibrium with causative mutations. In many cases, identification of the causative mutation is difficult because an associated genetic marker can be in intergenic regions and can be in linkage disequilibrium with variants in several nearby genes. Another approach is to identify candidate genes using knowledge of the biological pathways controlling a trait to search for single nucleotide polymorphism (SNP) in genes in those pathways. This should reveal putative causative markers responsible for genetic variation in biological function, and it is expected that the marker will be more strongly associated with a trait than one in linkage disequilibrium. An example of how a series of candidate gene studies demonstrate that identification of markers in genes involved in reproductive processes can lead to discovery of additional markers associated with genetic variation in reproductive traits is presented. In addition, the inclusion of candidate markers for fertility can improve reliability of genetic estimates for fertility traits, and the repeatability of the effects across a separate population of animals gives confidence that association elucidated by this set of markers is likely to be real. More importantly, the use of candidate genes can provide insights into the biology underpinning genetic variation in fertility, and that this understanding can lead to physiological interventions to improve reproductive function.(AU)

Molecular identification and mapping of a novel stripe rust resistance gene in wheat resistance line CH5389 / Identificação e mapeamento de um novo gene de resistência a ferrugem linear na linhagem de trigo CH5389

Stripe rust, caused by Puccinia striiformis is one of the most destructive diseases of wheat worldwide. CH5389 is a wheat-Thinopyrum intermedium derived line conferring stripe rust resistance. Genetic analyses of seedlings of F2 populations and F2:3 families developed by crossing CH5389 and susceptible common wheat revealed that stripe rust resistance in CH5389 was controlled by a single dominant gene that was designated YrCH5389. Eight SSR and EST-PCR polymorphic markers on chromosome 3AL were identified in F2 population of CH5389/Taichung29. The YrCH5389 was flanked by EST marker BE405348 and SSR marker Xwmc388 on chromosome 3AL with genetic distances of 2.2 and 4.6 cM, respectively. Comparative genomic analysis demonstrated that the orthologous genomic region of YrCH5389 covered 990 kb in rice, 640 kb in Brachypodium, and 890 kb in sorghum. Based on the locations of the markers, the resistance gene was located to chromosome deletion bin 3AL-0.85-1.00. Because there are no officially named stripe rust resistance genes on the 3AL chromosome, the YrCH5389 should be designated as a new resistance gene. These linkage markers could be useful for marker-assisted selection in wheat resistance breeding.(AU)

A ferrugem linear causada por Puccinia striiformis é uma das doenças mais destrutivas do trigo no mundo. A linhagem CH5389 é derivada do cruzamento de trigo com Thinopyrum intermedium e confere resistência a ferrugem linear. Análises genéticas de indivíduos da população F2 e família F2:3 obtida a partir do cruzamento entre CH5389 e trigo comum suscetível revelaram que a resistência à ferrugem linear na linhagem CH5389 foi controlada por um único gene dominante, designado YrCH5389. Oito marcadores polimórficos SSR e EST-PCR no cromossomo 3AL foram identificados na população F2 de CH5389/Taichung29. O gene YrCH5389 foi delimitado pelos marcadores EST BE405348 e SSR Xwmc388 no cromossomo 3AL com distâncias genéticas de 2,2 e 4,6 cM, respectivamente. Análises genômicas comparativas demonstraram que regiões genômicas ortólogas do gene YrCH5389 compreendem 990 kb em arroz, 640 kb em braquipódio e 890 kb em sorgo. Com base nas localizações dos marcadores, o gene de resistência foi localizado no cromossomo 3AL-0.85-1.00. Como não há genes oficialmente nomeados de resistência à ferrugem linear no cromossomo 3AL, o YrCH5389 deve ser designado como um gene novo de resistência. Esses marcadores de ligação podem ser úteis para a seleção assistida de genótipos de trigo resistentes a ferrugem linear.(AU)

Molecular identification and mapping of a novel stripe rust resistance gene in wheat resistance line CH5389 / Identificação e mapeamento de um novo gene de resistência a ferrugem linear na linhagem de trigo CH5389

Stripe rust, caused by Puccinia striiformis is one of the most destructive diseases of wheat worldwide. CH5389 is a wheat-Thinopyrum intermedium derived line conferring stripe rust resistance. Genetic analyses of seedlings of F2 populations and F2:3 families developed by crossing CH5389 and susceptible common wheat revealed that stripe rust resistance in CH5389 was controlled by a single dominant gene that was designated YrCH5389. Eight SSR and EST-PCR polymorphic markers on chromosome 3AL were identified in F2 population of CH5389/Taichung29. The YrCH5389 was flanked by EST marker BE405348 and SSR marker Xwmc388 on chromosome 3AL with genetic distances of 2.2 and 4.6 cM, respectively. Comparative genomic analysis demonstrated that the orthologous genomic region of YrCH5389 covered 990 kb in rice, 640 kb in Brachypodium, and 890 kb in sorghum. Based on the locations of the markers, the resistance gene was located to chromosome deletion bin 3AL-0.85-1.00. Because there are no officially named stripe rust resistance genes on the 3AL chromosome, the YrCH5389 should be designated as a new resistance gene. These linkage markers could be useful for marker-assisted selection in wheat resistance breeding.

A ferrugem linear causada por Puccinia striiformis é uma das doenças mais destrutivas do trigo no mundo. A linhagem CH5389 é derivada do cruzamento de trigo com Thinopyrum intermedium e confere resistência a ferrugem linear. Análises genéticas de indivíduos da população F2 e família F2:3 obtida a partir do cruzamento entre CH5389 e trigo comum suscetível revelaram que a resistência à ferrugem linear na linhagem CH5389 foi controlada por um único gene dominante, designado YrCH5389. Oito marcadores polimórficos SSR e EST-PCR no cromossomo 3AL foram identificados na população F2 de CH5389/Taichung29. O gene YrCH5389 foi delimitado pelos marcadores EST BE405348 e SSR Xwmc388 no cromossomo 3AL com distâncias genéticas de 2,2 e 4,6 cM, respectivamente. Análises genômicas comparativas demonstraram que regiões genômicas ortólogas do gene YrCH5389 compreendem 990 kb em arroz, 640 kb em braquipódio e 890 kb em sorgo. Com base nas localizações dos marcadores, o gene de resistência foi localizado no cromossomo 3AL-0.85-1.00. Como não há genes oficialmente nomeados de resistência à ferrugem linear no cromossomo 3AL, o YrCH5389 deve ser designado como um gene novo de resistência. Esses marcadores de ligação podem ser úteis para a seleção assistida de genótipos de trigo resistentes a ferrugem linear.

The Identification of SNPs in BCDO2 Gene for Skin Color in Chinese Indigenous Chicken

ABSTRACT A complete linkage disequilibrium between the SNP (SNP B) in BCDO2 gene and the yellow skin phenotype in European domestic chicken has been reported. Here, we genotyped the reported SNPs (SNP A, SNP B, and SNP C) of the BCDO2 gene in 183 Chinese Indigenous chickens from 11 breeds/populations, including 57 yellow, 17 white, and 109 black skin chickens. The frequency of all three SNPs were significantly different between yellow and white skin chickens (p 0.01). In black skin chickens, a high frequency of the heterozygous genotype (AG) in SNP A (0.51) and SNP B (0.48) was observed. A total of three haplotypes (AAA, AGA, and GAA) from these three SNPs were obtained. Frequencies of the proposed yellow skin-associated haplotype AGA in yellow skin, white skin, and black skin chickens were 0.81, 0.35, and 0.56, respectively. The results showed that the yellow skin phenotype of the evaluated birds has not been under selection, and that the BCDO2 gene in black skin chickens, evolutionally may undergo a transition phase from yellow to white skin chicken. We concluded that, the SNPs of BCDO2 gene not only can be used to determine whether the chicken was subjected to selection, but may also be used as a marker when selecting for the preferred skin color in chicken breeding programs.(AU)

The Identification of SNPs in BCDO2 Gene for Skin Color in Chinese Indigenous Chicken

ABSTRACT A complete linkage disequilibrium between the SNP (SNP B) in BCDO2 gene and the yellow skin phenotype in European domestic chicken has been reported. Here, we genotyped the reported SNPs (SNP A, SNP B, and SNP C) of the BCDO2 gene in 183 Chinese Indigenous chickens from 11 breeds/populations, including 57 yellow, 17 white, and 109 black skin chickens. The frequency of all three SNPs were significantly different between yellow and white skin chickens (p 0.01). In black skin chickens, a high frequency of the heterozygous genotype (AG) in SNP A (0.51) and SNP B (0.48) was observed. A total of three haplotypes (AAA, AGA, and GAA) from these three SNPs were obtained. Frequencies of the proposed yellow skin-associated haplotype AGA in yellow skin, white skin, and black skin chickens were 0.81, 0.35, and 0.56, respectively. The results showed that the yellow skin phenotype of the evaluated birds has not been under selection, and that the BCDO2 gene in black skin chickens, evolutionally may undergo a transition phase from yellow to white skin chicken. We concluded that, the SNPs of BCDO2 gene not only can be used to determine whether the chicken was subjected to selection, but may also be used as a marker when selecting for the preferred skin color in chicken breeding programs.

The optimal number of partial least squares components in genomic selection for pork pH / Número ótimo de componentes nos quadrados mínimos parciais aplicados à seleção genômica para pH da carne suína

The main application of genomic selection (GS) is the early identification of genetically superior animals for traits difficult-to-measure or lately evaluated, such as meat pH (measured after slaughter). Because the number of markers in GS is generally larger than the number of genotyped animals and these markers are highly correlated owing to linkage disequilibrium, statistical methods based on dimensionality reduction have been proposed. Among them, the partial least squares (PLS) technique stands out, because of its simplicity and high predictive accuracy. However, choosing the optimal number of components remains a relevant issue for PLS applications. Thus, we applied PLS (and principal component and traditional multiple regression) techniques to GS for pork pH traits (with pH measured at 45min and 24h after slaughter) and also identified the optimal number of PLS components based on the degree-of-freedom (DoF) and cross-validation (CV) methods. The PLS method out performs the principal component and traditional multiple regression techniques, enabling satisfactory predictions for pork pH traits using only genotypic data (low-density SNP panel). Furthermore, the SNP marker estimates from PLS revealed a relevant region on chromosome 4, which may affect these traits. The DoF and CV methods showed similar results for determining the optimal number of components in PLS analysis; thus, from the statistical viewpoint, the DoF method should be preferred because of its theoretical background (based on the "statistical information theory"), whereas CV is an empirical method based on computational effort.

A principal contribuição da seleção genômica (SG) é a identificação de animais geneticamente superiores para características de difícil mensuração e/ou avaliadas tardiamente nos animais, tal como o pH da carne suína. Na SG, uma vez que o número de marcadores é geralmente maior que o número de animais genotipados, e tais marcadores são altamente correlacionados (devido ao desequilíbrio de ligação), métodos estatísticos baseados na redução de dimensionalidade têm sido propostos. Dentre estes, destaca-se o Quadrados Mínimos Parciais (PLS) pela simplicidade e alta acurácia de predição. Porém, a determinação do número ótimo de componentes a ser utilizado no PLS ainda se caracteriza como um desafio para a aplicação do método. Assim, objetivou-se aplicar o PLS (e também regressões em componentes principais e a múltipla tradicional) na SG para pH da carne suína (medido aos 45min e às 24 horas após o abate), bem como identificar o número ótimo de componentes por meio dos métodos do grau de liberdade (GL) e validação cruzada (VC). O primeiro é baseado na Teoria de Informação Estatística e VC é empírica e fundamentada em amostras independentes do arquivo original. O PLS superou os demais métodos de regressão, fornecendo predições satisfatórias quando utilizadas apenas informações genotípicas (painel de SNP de baixa densidade). Além disso, os efeitos dos SNPs estimados via PLS possibilitaram identificar uma região relevante no cromossomo 4 que pode influenciar as características estudadas. Os métodos GL e VC foram similares quanto à determinação do número ótimo de componentes na análise PLS, porém o método GL pode ser recomendado devido a sua maior fundamentação estatística.

The optimal number of partial least squares components in genomic selection for pork pH / Número ótimo de componentes nos quadrados mínimos parciais aplicados à seleção genômica para pH da carne suína

The main application of genomic selection (GS) is the early identification of genetically superior animals for traits difficult-to-measure or lately evaluated, such as meat pH (measured after slaughter). Because the number of markers in GS is generally larger than the number of genotyped animals and these markers are highly correlated owing to linkage disequilibrium, statistical methods based on dimensionality reduction have been proposed. Among them, the partial least squares (PLS) technique stands out, because of its simplicity and high predictive accuracy. However, choosing the optimal number of components remains a relevant issue for PLS applications. Thus, we applied PLS (and principal component and traditional multiple regression) techniques to GS for pork pH traits (with pH measured at 45min and 24h after slaughter) and also identified the optimal number of PLS components based on the degree-of-freedom (DoF) and cross-validation (CV) methods. The PLS method out performs the principal component and traditional multiple regression techniques, enabling satisfactory predictions for pork pH traits using only genotypic data (low-density SNP panel). Furthermore, the SNP marker estimates from PLS revealed a relevant region on chromosome 4, which may affect these traits. The DoF and CV methods showed similar results for determining the optimal number of components in PLS analysis; thus, from the statistical viewpoint, the DoF method should be preferred because of its theoretical background (based on the "statistical information theory"), whereas CV is an empirical method based on computational effort.(AU)

A principal contribuição da seleção genômica (SG) é a identificação de animais geneticamente superiores para características de difícil mensuração e/ou avaliadas tardiamente nos animais, tal como o pH da carne suína. Na SG, uma vez que o número de marcadores é geralmente maior que o número de animais genotipados, e tais marcadores são altamente correlacionados (devido ao desequilíbrio de ligação), métodos estatísticos baseados na redução de dimensionalidade têm sido propostos. Dentre estes, destaca-se o Quadrados Mínimos Parciais (PLS) pela simplicidade e alta acurácia de predição. Porém, a determinação do número ótimo de componentes a ser utilizado no PLS ainda se caracteriza como um desafio para a aplicação do método. Assim, objetivou-se aplicar o PLS (e também regressões em componentes principais e a múltipla tradicional) na SG para pH da carne suína (medido aos 45min e às 24 horas após o abate), bem como identificar o número ótimo de componentes por meio dos métodos do grau de liberdade (GL) e validação cruzada (VC). O primeiro é baseado na Teoria de Informação Estatística e VC é empírica e fundamentada em amostras independentes do arquivo original. O PLS superou os demais métodos de regressão, fornecendo predições satisfatórias quando utilizadas apenas informações genotípicas (painel de SNP de baixa densidade). Além disso, os efeitos dos SNPs estimados via PLS possibilitaram identificar uma região relevante no cromossomo 4 que pode influenciar as características estudadas. Os métodos GL e VC foram similares quanto à determinação do número ótimo de componentes na análise PLS, porém o método GL pode ser recomendado devido a sua maior fundamentação estatística.(AU)

Polymorphisms and their haplotype combinations in the lysozyme gene associated with the production traits of a chinese native chicken breed

Animal lysozymes, which have been studied in many of invertebrate and vertebrate species, have been characterized and demonstrated to be immune-associated molecules, digestive enzymes and multifunctional molecules. The purpose of this study was to detect the connection between lysozyme-gene polymorphism and the production traits of a Chinese native chicken breed (Langshan chicken). Four single nucleotide mutation sites were identified: G345A, C1726T, G1836A, A1838G. By the linkage disequilibrium analysis, six haplotypes and 15haplotype combinations were depicted in the studied population. The statistical analysis demonstrated that the SNPs and the haplotype combinations are related to body weight at sixteen weeks of age in Langshan chickens (p 0.05), and those with combined haplotype Hap3-Hap6 (GA-TT-GG-AA) presented higher body weight. Our study demonstrated that the SNPs and their haplotype combinations in the lysozyme gene were associated with the chicken production traits, and that SNPs can be used as a molecular marker for chicken marker-assisted selection.(AU)

Quantitative genetics theory for genomic selection and efficiency of genotypic value prediction in open-pollinated populations

Quantitative genetics theory for genomic selection has mainly focused on additive effects. This study presents quantitative genetics theory applied to genomic selection aiming to prove that prediction of genotypic value based on thousands of single nucleotide polymorphisms (SNPs) depends on linkage disequilibrium (LD) between markers and QTLs, assuming dominance and epistasis. Based on simulated data, we provided information on dominance and genotypic value prediction accuracy, assuming mass selection in an open-pollinated population, all quantitative trait loci (QTLs) of lower effect, and reduced sample size. We show that the predictor of dominance value is proportional to the square of the LD value and to the dominance deviation for each QTL that is in LD with each marker. The weighted (by the SNP frequencies) dominance value predictor has greater accuracy than the unweighted predictor. The linear × linear, linear × quadratic, quadratic × linear, and quadratic × quadratic SNP effects are proportional to the corresponding linear combinations of epistatic effects for QTLs and the LD values. LD between two markers with a common QTL causes a bias in the prediction of epistatic values. Compared to phenotypic selection, the efficiency of genomic selection for genotypic value prediction increases as trait heritability decreases. The degree of dominance did not affect the genotypic value prediction accuracy and the approach to maximum accuracy is asymptotic with increases in SNP density. The decrease in the sample size from 500 to 200 did not markedly reduce the genotypic value prediction accuracy.

Quantitative genetics theory for genomic selection and efficiency of genotypic value prediction in open-pollinated populations

Quantitative genetics theory for genomic selection has mainly focused on additive effects. This study presents quantitative genetics theory applied to genomic selection aiming to prove that prediction of genotypic value based on thousands of single nucleotide polymorphisms (SNPs) depends on linkage disequilibrium (LD) between markers and QTLs, assuming dominance and epistasis. Based on simulated data, we provided information on dominance and genotypic value prediction accuracy, assuming mass selection in an open-pollinated population, all quantitative trait loci (QTLs) of lower effect, and reduced sample size. We show that the predictor of dominance value is proportional to the square of the LD value and to the dominance deviation for each QTL that is in LD with each marker. The weighted (by the SNP frequencies) dominance value predictor has greater accuracy than the unweighted predictor. The linear × linear, linear × quadratic, quadratic × linear, and quadratic × quadratic SNP effects are proportional to the corresponding linear combinations of epistatic effects for QTLs and the LD values. LD between two markers with a common QTL causes a bias in the prediction of epistatic values. Compared to phenotypic selection, the efficiency of genomic selection for genotypic value prediction increases as trait heritability decreases. The degree of dominance did not affect the genotypic value prediction accuracy and the approach to maximum accuracy is asymptotic with increases in SNP density. The decrease in the sample size from 500 to 200 did not markedly reduce the genotypic value prediction accuracy.(AU)

Polymorphisms and their haplotype combinations in the lysozyme gene associated with the production traits of a chinese native chicken breed

Animal lysozymes, which have been studied in many of invertebrate and vertebrate species, have been characterized and demonstrated to be immune-associated molecules, digestive enzymes and multifunctional molecules. The purpose of this study was to detect the connection between lysozyme-gene polymorphism and the production traits of a Chinese native chicken breed (Langshan chicken). Four single nucleotide mutation sites were identified: G345A, C1726T, G1836A, A1838G. By the linkage disequilibrium analysis, six haplotypes and 15haplotype combinations were depicted in the studied population. The statistical analysis demonstrated that the SNPs and the haplotype combinations are related to body weight at sixteen weeks of age in Langshan chickens (p 0.05), and those with combined haplotype Hap3-Hap6 (GA-TT-GG-AA) presented higher body weight. Our study demonstrated that the SNPs and their haplotype combinations in the lysozyme gene were associated with the chicken production traits, and that SNPs can be used as a molecular marker for chicken marker-assisted selection.

Egg production evaluation of laying hens by multivariate analysis / Avaliação da produção de ovos de poedeiras por análise multivariada

This study aimed to verify the existence of differences between hens from the Barred Plymouth Rock (PRB) breed and White Plymouth Rock (PRW) breed by multivariate analysis of weekly egg production and cumulative during the years of 1998 and 2010, from the Laboratório de Avicultura (LAVIC) of the Departamento de Zootecnia at the Universidade Federal de Santa Maria (UFSM). For the analysis of the univariate and multivariate variance, the experimental design was completely randomized with two treatments (breed) and 299 repetitions of the PRW breed and 350 of the PRB breed. The parameters analyzed were the weekly productions of eggs per bird from the 21st to the 50th week of age (P21, P22, ..., P50) and production of eggs accumulated being from the 21st to the 25th (PA1), 21st to the 30th (PA2), 21st to the 35th (PA3), 21st to the 40th (PA4), 21st to the 45th (PA5) and 21st to 50th (PA6). Analyzes of univariate and multivariate variance were conducted and the comparison of means were made by "T" Student and Wilks respectively (P < 0, 05). Based on the results, an analysis of the principal components was performed with parameters PA1, PA2, PA4, PA5 and PA6. With the average egg production per family accumulated, a cluster analysis using Euclidean distance and single linkage method (nearest neighbors) was performed. The first two principal components meet the total variation in egg production accumulated from the 21st to 25th, 21st to 30th, 21st to 40th, 21st to 45th and 21st to 50th weeks of age. Most of the phenotypic variation of the layers can be explained by the production of eggs accumulated from the 21st until the 40th week of age, and this variable is highly correlated with total egg production. Families from the PRW and PRB breed form seven distinct groups, but homogeneous by the similarity between them. This allows direct crossings between different groups, in the pursuit for heterosis.(AU)

Objetivou-se verificar a existência de divergência entre poedeiras das raças Plymouth Rock Barrada (PRB) e Plymouth Rock Branca (PRW) por meio da análise multivariada da produção de ovos semanal e acumulada dos anos de 1998 e 2010, do Laboratório de Avicultura (Lavic) do Departamento de Zootecnia da Universidade Federal de Santa Maria (UFSM). Para as análises de variância uni e multivariada, o delineamento experimental foi inteiramente ao acaso, com dois tratamentos (raças) e 299 repetições da raça PRW e 350 da raça PRB. Os parâmetros analisados foram a produção de ovos semanal por ave da 21ª à 50ª semana de idade (P21, P22,..., P50) e a produção de ovos acumulada, sendo da 21ª à 25ª (PA1), 21ª à 30ª (PA2), 21ª à 35ª (PA3), 21ª à 40ª (PA4), 21ª à 45ª (PA5) e 21ª à 50ª (PA6). Realizaram-se as análises de variância uni e multivariada, e a comparação de médias foi feita pelos testes "T" de Student e de Wilks, respectivamente (P<0,05). Com base nos resultados, foi realizada a análise de componentes principais, com os parâmetros PA1, PA2, PA4, PA5 e PA6. E, com as médias de produção de ovos acumulada por família, foi realizada a análise de agrupamento por meio da distância euclidiana e pelo método de encadeamento único (vizinhos mais próximos). Os dois primeiros componentes principais reúnem a variação total da produção de ovos acumulada da 21ª à 25ª, 21ª à 30ª, 21ª à 40ª, 21ª à 45ª e 21ªá 50ª semanas de idade. A maior parte da variação fenotípica das poedeiras pode ser explicada pela produção de ovos acumulada da 21ª até a 40ª semana de idade, e essa variável tem alta correlação com a produção de ovos total. As famílias da raça PRW e da raça PRB formam sete grupos distintos, mas homogêneos, pela similaridade existente entre elas, o que permite direcionar cruzamentos entre os diferentes grupos, em busca da heterose.(AU)