Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene

Background Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian $ F_{2} $ resource population. This QTL explained more than 17% of the phenotypic variance. Methods Four new markers on pig chromosome 5 were genotyped across this $ F_{2} $ population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test. Results We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the $ F_{2} $ population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size. Conclusions HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL. Ausführliche Beschreibung

Gespeichert in:

Autor*in:	Li, Pinghua [verfasserIn] Xiao, Shijun Wei, Na Zhang, Zhiyan Huang, Ruihua Gu, Yueqing Guo, Yuanmei Ren, Jun Huang, Lusheng Chen, Congying

Format:	E-Artikel
Sprache:	Englisch

Erschienen:	2012

Schlagwörter:	Quantitative Trait Locus Single Nucleotide Polymorphism Quantitative Trait Locus Region Quantitative Trait Nucleotide Standard Association Test

Anmerkung:	© Li et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (

Übergeordnetes Werk:	Enthalten in: Genetics, selection, evolution - London : BioMed Central, 1989, 44(2012), 1 vom: 15. März
Übergeordnetes Werk:	volume:44 ; year:2012 ; number:1 ; day:15 ; month:03

Links:	Volltext

DOI / URN:	10.1186/1297-9686-44-6

Katalog-ID:	SPR026806606

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520			\|a Background Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian $ F_{2} $ resource population. This QTL explained more than 17% of the phenotypic variance. Methods Four new markers on pig chromosome 5 were genotyped across this $ F_{2} $ population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test. Results We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the $ F_{2} $ population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size. Conclusions HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL.
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allfields	10.1186/1297-9686-44-6 doi (DE-627)SPR026806606 (SPR)1297-9686-44-6-e DE-627 ger DE-627 rakwb eng Li, Pinghua verfasserin aut Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Li et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian $ F_{2} $ resource population. This QTL explained more than 17% of the phenotypic variance. Methods Four new markers on pig chromosome 5 were genotyped across this $ F_{2} $ population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test. Results We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the $ F_{2} $ population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size. Conclusions HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL. Quantitative Trait Locus (dpeaa)DE-He213 Single Nucleotide Polymorphism (dpeaa)DE-He213 Quantitative Trait Locus Region (dpeaa)DE-He213 Quantitative Trait Nucleotide (dpeaa)DE-He213 Standard Association Test (dpeaa)DE-He213 Xiao, Shijun aut Wei, Na aut Zhang, Zhiyan aut Huang, Ruihua aut Gu, Yueqing aut Guo, Yuanmei aut Ren, Jun aut Huang, Lusheng aut Chen, Congying aut Enthalten in Genetics, selection, evolution London : BioMed Central, 1989 44(2012), 1 vom: 15. März (DE-627)312849052 (DE-600)2012369-3 1297-9686 nnns volume:44 year:2012 number:1 day:15 month:03 https://dx.doi.org/10.1186/1297-9686-44-6 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 44 2012 1 15 03
spelling	10.1186/1297-9686-44-6 doi (DE-627)SPR026806606 (SPR)1297-9686-44-6-e DE-627 ger DE-627 rakwb eng Li, Pinghua verfasserin aut Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Li et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian $ F_{2} $ resource population. This QTL explained more than 17% of the phenotypic variance. Methods Four new markers on pig chromosome 5 were genotyped across this $ F_{2} $ population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test. Results We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the $ F_{2} $ population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size. Conclusions HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL. Quantitative Trait Locus (dpeaa)DE-He213 Single Nucleotide Polymorphism (dpeaa)DE-He213 Quantitative Trait Locus Region (dpeaa)DE-He213 Quantitative Trait Nucleotide (dpeaa)DE-He213 Standard Association Test (dpeaa)DE-He213 Xiao, Shijun aut Wei, Na aut Zhang, Zhiyan aut Huang, Ruihua aut Gu, Yueqing aut Guo, Yuanmei aut Ren, Jun aut Huang, Lusheng aut Chen, Congying aut Enthalten in Genetics, selection, evolution London : BioMed Central, 1989 44(2012), 1 vom: 15. März (DE-627)312849052 (DE-600)2012369-3 1297-9686 nnns volume:44 year:2012 number:1 day:15 month:03 https://dx.doi.org/10.1186/1297-9686-44-6 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 44 2012 1 15 03
allfields_unstemmed	10.1186/1297-9686-44-6 doi (DE-627)SPR026806606 (SPR)1297-9686-44-6-e DE-627 ger DE-627 rakwb eng Li, Pinghua verfasserin aut Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Li et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian $ F_{2} $ resource population. This QTL explained more than 17% of the phenotypic variance. Methods Four new markers on pig chromosome 5 were genotyped across this $ F_{2} $ population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test. Results We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the $ F_{2} $ population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size. Conclusions HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL. Quantitative Trait Locus (dpeaa)DE-He213 Single Nucleotide Polymorphism (dpeaa)DE-He213 Quantitative Trait Locus Region (dpeaa)DE-He213 Quantitative Trait Nucleotide (dpeaa)DE-He213 Standard Association Test (dpeaa)DE-He213 Xiao, Shijun aut Wei, Na aut Zhang, Zhiyan aut Huang, Ruihua aut Gu, Yueqing aut Guo, Yuanmei aut Ren, Jun aut Huang, Lusheng aut Chen, Congying aut Enthalten in Genetics, selection, evolution London : BioMed Central, 1989 44(2012), 1 vom: 15. März (DE-627)312849052 (DE-600)2012369-3 1297-9686 nnns volume:44 year:2012 number:1 day:15 month:03 https://dx.doi.org/10.1186/1297-9686-44-6 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 44 2012 1 15 03
allfieldsGer	10.1186/1297-9686-44-6 doi (DE-627)SPR026806606 (SPR)1297-9686-44-6-e DE-627 ger DE-627 rakwb eng Li, Pinghua verfasserin aut Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Li et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian $ F_{2} $ resource population. This QTL explained more than 17% of the phenotypic variance. Methods Four new markers on pig chromosome 5 were genotyped across this $ F_{2} $ population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test. Results We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the $ F_{2} $ population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size. Conclusions HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL. Quantitative Trait Locus (dpeaa)DE-He213 Single Nucleotide Polymorphism (dpeaa)DE-He213 Quantitative Trait Locus Region (dpeaa)DE-He213 Quantitative Trait Nucleotide (dpeaa)DE-He213 Standard Association Test (dpeaa)DE-He213 Xiao, Shijun aut Wei, Na aut Zhang, Zhiyan aut Huang, Ruihua aut Gu, Yueqing aut Guo, Yuanmei aut Ren, Jun aut Huang, Lusheng aut Chen, Congying aut Enthalten in Genetics, selection, evolution London : BioMed Central, 1989 44(2012), 1 vom: 15. März (DE-627)312849052 (DE-600)2012369-3 1297-9686 nnns volume:44 year:2012 number:1 day:15 month:03 https://dx.doi.org/10.1186/1297-9686-44-6 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 44 2012 1 15 03
allfieldsSound	10.1186/1297-9686-44-6 doi (DE-627)SPR026806606 (SPR)1297-9686-44-6-e DE-627 ger DE-627 rakwb eng Li, Pinghua verfasserin aut Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene 2012 Text txt rdacontent Computermedien c rdamedia Online-Ressource cr rdacarrier © Li et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( Background Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian $ F_{2} $ resource population. This QTL explained more than 17% of the phenotypic variance. Methods Four new markers on pig chromosome 5 were genotyped across this $ F_{2} $ population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test. Results We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the $ F_{2} $ population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size. Conclusions HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL. Quantitative Trait Locus (dpeaa)DE-He213 Single Nucleotide Polymorphism (dpeaa)DE-He213 Quantitative Trait Locus Region (dpeaa)DE-He213 Quantitative Trait Nucleotide (dpeaa)DE-He213 Standard Association Test (dpeaa)DE-He213 Xiao, Shijun aut Wei, Na aut Zhang, Zhiyan aut Huang, Ruihua aut Gu, Yueqing aut Guo, Yuanmei aut Ren, Jun aut Huang, Lusheng aut Chen, Congying aut Enthalten in Genetics, selection, evolution London : BioMed Central, 1989 44(2012), 1 vom: 15. März (DE-627)312849052 (DE-600)2012369-3 1297-9686 nnns volume:44 year:2012 number:1 day:15 month:03 https://dx.doi.org/10.1186/1297-9686-44-6 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_SPRINGER SSG-OLC-PHA GBV_ILN_11 GBV_ILN_20 GBV_ILN_22 GBV_ILN_23 GBV_ILN_24 GBV_ILN_31 GBV_ILN_39 GBV_ILN_40 GBV_ILN_60 GBV_ILN_62 GBV_ILN_63 GBV_ILN_65 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_74 GBV_ILN_95 GBV_ILN_105 GBV_ILN_110 GBV_ILN_151 GBV_ILN_161 GBV_ILN_170 GBV_ILN_213 GBV_ILN_224 GBV_ILN_230 GBV_ILN_285 GBV_ILN_293 GBV_ILN_602 GBV_ILN_2003 GBV_ILN_2014 GBV_ILN_4012 GBV_ILN_4037 GBV_ILN_4112 GBV_ILN_4125 GBV_ILN_4126 GBV_ILN_4249 GBV_ILN_4305 GBV_ILN_4306 GBV_ILN_4307 GBV_ILN_4313 GBV_ILN_4322 GBV_ILN_4323 GBV_ILN_4324 GBV_ILN_4325 GBV_ILN_4338 GBV_ILN_4367 GBV_ILN_4700 AR 44 2012 1 15 03
language	English
source	Enthalten in Genetics, selection, evolution 44(2012), 1 vom: 15. März volume:44 year:2012 number:1 day:15 month:03
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institution	findex.gbv.de
topic_facet	Quantitative Trait Locus Single Nucleotide Polymorphism Quantitative Trait Locus Region Quantitative Trait Nucleotide Standard Association Test
isfreeaccess_bool	false
container_title	Genetics, selection, evolution
authorswithroles_txt_mv	Li, Pinghua @@aut@@ Xiao, Shijun @@aut@@ Wei, Na @@aut@@ Zhang, Zhiyan @@aut@@ Huang, Ruihua @@aut@@ Gu, Yueqing @@aut@@ Guo, Yuanmei @@aut@@ Ren, Jun @@aut@@ Huang, Lusheng @@aut@@ Chen, Congying @@aut@@
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author	Li, Pinghua
spellingShingle	Li, Pinghua misc Quantitative Trait Locus misc Single Nucleotide Polymorphism misc Quantitative Trait Locus Region misc Quantitative Trait Nucleotide misc Standard Association Test Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene
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topic_title	Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene Quantitative Trait Locus (dpeaa)DE-He213 Single Nucleotide Polymorphism (dpeaa)DE-He213 Quantitative Trait Locus Region (dpeaa)DE-He213 Quantitative Trait Nucleotide (dpeaa)DE-He213 Standard Association Test (dpeaa)DE-He213
topic	misc Quantitative Trait Locus misc Single Nucleotide Polymorphism misc Quantitative Trait Locus Region misc Quantitative Trait Nucleotide misc Standard Association Test
topic_unstemmed	misc Quantitative Trait Locus misc Single Nucleotide Polymorphism misc Quantitative Trait Locus Region misc Quantitative Trait Nucleotide misc Standard Association Test
topic_browse	misc Quantitative Trait Locus misc Single Nucleotide Polymorphism misc Quantitative Trait Locus Region misc Quantitative Trait Nucleotide misc Standard Association Test
format_facet	Elektronische Aufsätze Aufsätze Elektronische Ressource
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title	Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene
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title_full	Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene
author_sort	Li, Pinghua
journal	Genetics, selection, evolution
journalStr	Genetics, selection, evolution
lang_code	eng
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author_browse	Li, Pinghua Xiao, Shijun Wei, Na Zhang, Zhiyan Huang, Ruihua Gu, Yueqing Guo, Yuanmei Ren, Jun Huang, Lusheng Chen, Congying
container_volume	44
format_se	Elektronische Aufsätze
author-letter	Li, Pinghua
doi_str_mv	10.1186/1297-9686-44-6
title_sort	fine mapping of a qtl for ear size on porcine chromosome 5 and identification of high mobility group at-hook 2 (hmga2) as a positional candidate gene
title_auth	Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene
abstract	Background Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian $ F_{2} $ resource population. This QTL explained more than 17% of the phenotypic variance. Methods Four new markers on pig chromosome 5 were genotyped across this $ F_{2} $ population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test. Results We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the $ F_{2} $ population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size. Conclusions HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL. © Li et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
abstractGer	Background Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian $ F_{2} $ resource population. This QTL explained more than 17% of the phenotypic variance. Methods Four new markers on pig chromosome 5 were genotyped across this $ F_{2} $ population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test. Results We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the $ F_{2} $ population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size. Conclusions HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL. © Li et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
abstract_unstemmed	Background Ear size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian $ F_{2} $ resource population. This QTL explained more than 17% of the phenotypic variance. Methods Four new markers on pig chromosome 5 were genotyped across this $ F_{2} $ population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test. Results We refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the $ F_{2} $ population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size. Conclusions HMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL. © Li et al; licensee BioMed Central Ltd. 2012. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (
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container_issue	1
title_short	Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene
url	https://dx.doi.org/10.1186/1297-9686-44-6
remote_bool	true
author2	Xiao, Shijun Wei, Na Zhang, Zhiyan Huang, Ruihua Gu, Yueqing Guo, Yuanmei Ren, Jun Huang, Lusheng Chen, Congying
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Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene

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