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Identification of Laying-Related SNP Markers in Geese Using RAD Sequencing.

Yu S, Chu W, Zhang L, Han H, Zhao R, Wu W, Zhu J, Dodson MV, Wei W, Liu H, Chen J - PLoS ONE (2015)

Bottom Line: Recently developed restriction site-associated DNA (RAD) sequencing is a possible approach for discerning large-scale single nucleotide polymorphism (SNP) and reducing the complexity of a genome without having reference genomic information available.The result showed that 8 of 10 SNP were associated with egg numbers.Five novel genes were cloned for geese which harbored the candidate laying-related SNP, including membrane associated guanylate kinase (MAGI-1), KIAA1462, Rho GTPase activating protein 21 (ARHGAP21), acyl-CoA synthetase family member 2 (ACSF2), astrotactin 2 (ASTN2).

View Article: PubMed Central - PubMed

Affiliation: College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China.

ABSTRACT
Laying performance is an important economical trait of goose production. As laying performance is of low heritability, it is of significance to develop a marker-assisted selection (MAS) strategy for this trait. Definition of sequence variation related to the target trait is a prerequisite of quantitating MAS, but little is presently known about the goose genome, which greatly hinders the identification of genetic markers for the laying traits of geese. Recently developed restriction site-associated DNA (RAD) sequencing is a possible approach for discerning large-scale single nucleotide polymorphism (SNP) and reducing the complexity of a genome without having reference genomic information available. In the present study, we developed a pooled RAD sequencing strategy for detecting geese laying-related SNP. Two DNA pools were constructed, each consisting of equal amounts of genomic DNA from 10 individuals with either high estimated breeding value (HEBV) or low estimated breeding value (LEBV). A total of 139,013 SNP were obtained from 42,291,356 sequences, of which 18,771,943 were for LEBV and 23,519,413 were for HEBV cohorts. Fifty-five SNP which had different allelic frequencies in the two DNA pools were further validated by individual-based AS-PCR genotyping in the LEBV and HEBV cohorts. Ten out of 55 SNP exhibited distinct allele distributions in these two cohorts. These 10 SNP were further genotyped in a goose population of 492 geese to verify the association with egg numbers. The result showed that 8 of 10 SNP were associated with egg numbers. Additionally, liner regression analysis revealed that SNP Record-111407, 106975 and 112359 were involved in a multiplegene network affecting laying performance. We used IPCR to extend the unknown regions flanking the candidate RAD tags. The obtained sequences were subjected to BLAST to retrieve the orthologous genes in either ducks or chickens. Five novel genes were cloned for geese which harbored the candidate laying-related SNP, including membrane associated guanylate kinase (MAGI-1), KIAA1462, Rho GTPase activating protein 21 (ARHGAP21), acyl-CoA synthetase family member 2 (ACSF2), astrotactin 2 (ASTN2). Collectively, our data suggests that 8 SNP and 5 genes might be promising candidate markers or targets for marker-assisted selection of egg numbers in geese.

No MeSH data available.


Related in: MedlinePlus

Genotyping of the 10 SNP by allele specific PCR in geese.Electropherosis of AS-PCR revealed different genotypes of 10 SNPs. Eight individuals were randomly selected to show three genotypes of each SNP.
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pone.0131572.g001: Genotyping of the 10 SNP by allele specific PCR in geese.Electropherosis of AS-PCR revealed different genotypes of 10 SNPs. Eight individuals were randomly selected to show three genotypes of each SNP.

Mentions: The 10 SNP were subjected to genotyping in the population of 492 geese by AS-PCR (Fig 1). Genetic diversity was analyzed by software Powermarker V3.25 for each SNP. As shown in Table 4, the gene diversity (He), heterozygosity (H0), and polymorphism information content (PIC) of the 10 SNP ranged 0.4394–0.4991, 0.0830–0.5233 and 0.3161–0.3746 respectively. The SNP Record-135849 had the highest gene diversity, heterozygosity and PIC. PIC commonly used as a measure of polymorphism in genetics for a molecular marker. In the present study, the PIC values of 10 SNPs range from 0.25–0.5, indicates that these SNPs display intermediate levels of polymorphism.Seven SNP showed significant deviations from Hardy-Weinberg equilibrium (HWE) (p<0.05), while the other three SNP, including Record-135849, Record-88247 and Record-135057, were in HWE (p>0.05).


Identification of Laying-Related SNP Markers in Geese Using RAD Sequencing.

Yu S, Chu W, Zhang L, Han H, Zhao R, Wu W, Zhu J, Dodson MV, Wei W, Liu H, Chen J - PLoS ONE (2015)

Genotyping of the 10 SNP by allele specific PCR in geese.Electropherosis of AS-PCR revealed different genotypes of 10 SNPs. Eight individuals were randomly selected to show three genotypes of each SNP.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4504669&req=5

pone.0131572.g001: Genotyping of the 10 SNP by allele specific PCR in geese.Electropherosis of AS-PCR revealed different genotypes of 10 SNPs. Eight individuals were randomly selected to show three genotypes of each SNP.
Mentions: The 10 SNP were subjected to genotyping in the population of 492 geese by AS-PCR (Fig 1). Genetic diversity was analyzed by software Powermarker V3.25 for each SNP. As shown in Table 4, the gene diversity (He), heterozygosity (H0), and polymorphism information content (PIC) of the 10 SNP ranged 0.4394–0.4991, 0.0830–0.5233 and 0.3161–0.3746 respectively. The SNP Record-135849 had the highest gene diversity, heterozygosity and PIC. PIC commonly used as a measure of polymorphism in genetics for a molecular marker. In the present study, the PIC values of 10 SNPs range from 0.25–0.5, indicates that these SNPs display intermediate levels of polymorphism.Seven SNP showed significant deviations from Hardy-Weinberg equilibrium (HWE) (p<0.05), while the other three SNP, including Record-135849, Record-88247 and Record-135057, were in HWE (p>0.05).

Bottom Line: Recently developed restriction site-associated DNA (RAD) sequencing is a possible approach for discerning large-scale single nucleotide polymorphism (SNP) and reducing the complexity of a genome without having reference genomic information available.The result showed that 8 of 10 SNP were associated with egg numbers.Five novel genes were cloned for geese which harbored the candidate laying-related SNP, including membrane associated guanylate kinase (MAGI-1), KIAA1462, Rho GTPase activating protein 21 (ARHGAP21), acyl-CoA synthetase family member 2 (ACSF2), astrotactin 2 (ASTN2).

View Article: PubMed Central - PubMed

Affiliation: College of Animal Science and Technology, Nanjing Agricultural University, Nanjing, People's Republic of China.

ABSTRACT
Laying performance is an important economical trait of goose production. As laying performance is of low heritability, it is of significance to develop a marker-assisted selection (MAS) strategy for this trait. Definition of sequence variation related to the target trait is a prerequisite of quantitating MAS, but little is presently known about the goose genome, which greatly hinders the identification of genetic markers for the laying traits of geese. Recently developed restriction site-associated DNA (RAD) sequencing is a possible approach for discerning large-scale single nucleotide polymorphism (SNP) and reducing the complexity of a genome without having reference genomic information available. In the present study, we developed a pooled RAD sequencing strategy for detecting geese laying-related SNP. Two DNA pools were constructed, each consisting of equal amounts of genomic DNA from 10 individuals with either high estimated breeding value (HEBV) or low estimated breeding value (LEBV). A total of 139,013 SNP were obtained from 42,291,356 sequences, of which 18,771,943 were for LEBV and 23,519,413 were for HEBV cohorts. Fifty-five SNP which had different allelic frequencies in the two DNA pools were further validated by individual-based AS-PCR genotyping in the LEBV and HEBV cohorts. Ten out of 55 SNP exhibited distinct allele distributions in these two cohorts. These 10 SNP were further genotyped in a goose population of 492 geese to verify the association with egg numbers. The result showed that 8 of 10 SNP were associated with egg numbers. Additionally, liner regression analysis revealed that SNP Record-111407, 106975 and 112359 were involved in a multiplegene network affecting laying performance. We used IPCR to extend the unknown regions flanking the candidate RAD tags. The obtained sequences were subjected to BLAST to retrieve the orthologous genes in either ducks or chickens. Five novel genes were cloned for geese which harbored the candidate laying-related SNP, including membrane associated guanylate kinase (MAGI-1), KIAA1462, Rho GTPase activating protein 21 (ARHGAP21), acyl-CoA synthetase family member 2 (ACSF2), astrotactin 2 (ASTN2). Collectively, our data suggests that 8 SNP and 5 genes might be promising candidate markers or targets for marker-assisted selection of egg numbers in geese.

No MeSH data available.


Related in: MedlinePlus