猪IGF-I基因不同转录子克隆及在不同组织中表达规律研究
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摘要
IGF-Ⅰ在哺乳动物初生后的生长、发育和代谢过程中起着重要的调控作用。由于选择性拼接、不同的polyA位点以及潜在的多个启动子的使用,使它以一种极为复杂的方式进行转录,并产生多种类型的成熟mRNAs拼接变异体。本研究以松辽黑猪为研究对象,在克隆不同IGF-ⅠmRNAs的基础上,研究了不同转录子类型IGF-Ⅰ的时空表达规律;采用PCR-SSCP、序列测定并结合微卫星等方法检测了5'调控区的多态性。研究结果为进一步从基因组水平和转录水平进行该基因对猪肉质性状的决定作用研究奠定分子生物学基础,同时为将该基因用于猪的超早期选种和遗传改良提供理论依据。
采用RACE的方法,首次克隆了猪以外显子Ⅴ为结尾的两种类型转录子,利用生物信息学方法,对其编码的多肽链进行了结构分析和功能结构域比较研究。采用半定量RT-PCR方法,检测了本课题组已经获得的Ⅰ类Ea型、Ⅰ类Eb型两种IGF-Ⅰ转录子和新获得的Ⅰ类Eb型、Ⅱ类Eb型两种不同转录子的表达特性。确定四种转录子在各组织不同发育阶段中发挥生理功能的主效拼接类型。四种转录子相对表达量分别与1、3、6月龄肉质性状相关分析表明,不同转录子在6月龄时与肉质性状都有相关,而在1、3月龄时只有个别转录子与肉质性状相关,表明不同的转录子在不同的发育时期对于肌肉组织的发生和发育具有不同的作用。利用半定量RT-PCR的方法,检测了四个转录子在松辽黑猪、松野杂交猪和长白猪不同组织中的表达规律,并比较了四个转录子在同组织不同品种中的表达差异。确定了三个品种各个组织的主效转录子及其在肌肉中的表达差异。四个转录子相对表达量分别与三个品种的肉质性状分析表明,不同转录子在松辽黑猪中与肉质性状都有相关,而在松野杂交猪和长白猪中只有个别转录子与肉质性状相关。
克隆了松辽黑猪5'调控区序列并做生物信息学分析,同时对其进行PCR-SSCP和微卫星多态分析,结果只发现了一个微卫星多态性位点,序列测定结果表明,该位点具有4个等位基因(A、B、C、D),共6种基因型,遗传效应分析发现AA基因型个体具有更好的肉质,A等位基因具有提高肌内脂肪含量、改善肉质的遗传效应。可以初步推断IGF-Ⅰ基因可能是影响猪的肉质和胴体性状的一个主效基因或是一个与影响猪肉质和胴体性状的QTL连锁的基因。
IGF-Ⅰis a single copy gene,due to alternative splicing,and the use of multiple polyadenylation signals and different promoters,the IGF-Ⅰgene and its mRNAs are complicated. Spliced variants of insulin-like growth factor 1(IGF-1),a small peptide with a critical role in metabolism and growth,have been identified in various vertebrate species.IGF-Ⅰplay an important role in muscle growth and development,myoblast fusion and differentiation,and improve muscle grow and meat quality.Therefore,it has important significance for studying on pig's candidate genes of economic trait that molecular genetic construction and space-time expression of IGF-Ⅰgene is studied by modern molecular biological technology.This research applied to Songliao Black Pig as the object of studying,we cloned the pig two new IGF-ⅠmRNAs and analyzed structure and characteristics of them by bioinformatics.Levels of different spliced variants of IGF-Ⅰin different tissues,at different ages,in adipose muscle tissues of different breeds were measured by Semi Quantitative Reverse Transcription-Polymerase Chain Reaction(SQ RT-PCR),and analyzed the genetic correlation between the levels of different spliced variants of IGF-Ⅰand meat quality traits by SPSS.We detected the polymorphisms of the 5'-regulatory region of IGF-Ⅰgenes by PCR-SSCP(single-strand conformation polymorphism)、sequencing and microsatellite methods in the population of Songliao black pig,and analyzed the genetic correlation between the polymorphisms and carcass and meat quality traits by SPSS.The main results are as follows:
1.The cDNA sequences of Songliao Black pig two spliced variants of IGF-Ⅰgene,including exon five,were cloned by RACE.They were named type Eb of classⅠand type Eb of classⅡ-IGF-Ⅰgenes,type Eb of classⅠ- IGF-Ⅰgene contains a 564bp open reading frame(ORF) encoding 187 amino acids while type Eb of classⅡ- IGF-Ⅰgene contains a 516bp ORF encoding 171 amino acids.
2.The alignment analysis of CDS sequences of type Eb of classⅠand type Eb of classⅡ-IGF-Ⅰgenes among human,sheep,cows,goats,chimpanzees,rhesus monkeys and horses shows that the consistency of type Eb of classⅠ- IGF-Ⅰgene in Songliao Black pig and other mammals is more than 91%,while the comparability of type Eb of classⅡ- IGF-Ⅰgene is more than 90%.The comparability of the protein sequences of type Eb of classⅠand type Eb of classⅡ-IGF-Ⅰgenes of Songliao Black pig with other mammals are more than 96%and 93%respectively.It verified that type Eb of classⅠand type Eb of classⅡ- IGF-Ⅰgenes are highly conserved in mammals.
3.We predicted the basic features,protein structure and molecular function of porcine type Eb of classⅠand type Eb of classⅡproteins with bioinformatics methods.The results indicate that porcine type Eb of classⅠand type Eb of classⅡ- IGF-Ⅰgenes belong to IGFs family,type Eb of classⅠand type Eb of classⅡproteins structure also contains the same IGFBPs,typeⅠandⅡreceptor domain.Bioinformatics results show that porcine type Eb of classⅠand type Eb of classⅡproteins are very conservative in the key structural and functional region.This suggests that porcine type Eb of classⅠand type Eb of classⅡproteins should have the similar function with some known proteins.
4.The expression characteristic of four spliced variants of insulin-like growth factor-Ⅰgene was investigated by RT-PCR.The results showed that the three spliced variants of insulin-like growth factor-Ⅰgene expressed in heart,liver,spleen,lung,kidney,lung,stomach,duodenum,ileum, colon,appendix,brachi -triceps,longissimus muscle of back,biceps femoris,testicle of Songliao Black Pig at the age of birth,one-month,three- month and six-month:There is much difference in the same tissue at different growing period.
5.Three spliced variants of insulin-like growth factor-Ⅰgene have the similar expression curves,which is the "S"curve or clock curve,in the same tissue at different growing period.The expression level of type Ea of classⅠ-IGF-Ⅰgene in longissimus of Songliao Black pig at one-month and six-month are significantly more than that birth and three-month.;The expression level of type Eb of classⅠ-IGF-Ⅰgene in longissimus of Songliao Black pig at one-month are significantly more than that birth,three-month and six-month;The expression level of type Eb of classⅡ-IGF-Ⅰgene in longissimus of Songliao Black pig at birth and one-month are significantly more than three-month and six-month.
6.The relationship of four spliced variants of insulin-like growth factor-Ⅰgene expression with pork quality was different at different growing stage:At one-month the type Ea of classⅠ-IGF-Ⅰgene mRNA level and meat color was negative correlation;the type Eb of classⅠ-IGF-Ⅰgene mRNA level and PH value were positive correlation.The type Ea of classⅠ-IGF-Ⅰgen mRNA level was extremely positive correlation with meat color and marbling at three-month.At six-month the type Ea of classⅠ-IGF-Ⅰgene mRNA level and the ratio of cook was positive correlation;the type Eb of classⅠ-IGF-Ⅰgen mRNA level was extremely positive correlation with meat color and marbling;the type Ea of classⅠ-IGF-Ⅰgene mRNA level was negative correlation with PH value;the type Eb of classⅡ-IGF-Ⅰgene mRNA level and drop ratio were negative correlation.
7.The expression characteristic of four spliced variants of insulin-like growth factor-Ⅰgene was investigated by RT-PCR.The results showed that the three spliced variants of insulin-like growth factor-Ⅰgene expressed in heart,liver,spleen,lung,kidney,lung, stomach,duodenum,ileum,colon,appendix,brachi -triceps,longissimus muscle of back,biceps femoris,testicle of Songliao Black Pig,Crossed and Landrace:There is much difference in the same tissue at different breed.
8.Class 1 IGF-ⅠmRNA(type Ea or type Eb) appeared to be much more abundant than class 2 IGF-ⅠmRNA in Songliao Black pig and Crossed.But type Eb of ClassⅡ-IGF-ⅠmRNA appeared to be much more abundant than class 1 IGF-ⅠmRNA in Landrace.
9.The relationship of four spliced variants of insulin-like growth factor-Ⅰgene expression with pork quality was different at different breeds:In Songliao Black pig:the type Ea of classⅠ-IGF-Ⅰgene mRNA level and the ratio of cook was positive correlation;the type Eb of classⅠ-IGF-Ⅰgen mRNA level was extremely positive correlation with meat color and marbling; the type Ea of classⅠ-IGF-Ⅰgene mRNA level was negative correlation with PH value:the type Eb of classⅡ-IGF-Ⅰgene mRNA level and drop ratio were negative correlation.In Crossed the type Ea of classⅠ-IGF-Ⅰgene mRNA level and cooked ratio were positive correlation;the type Eb of classⅡ-IGF-Ⅰgene mRNA level and drop ratio were negative correlation.The type Eb of classⅡ-IGF-Ⅰgen mRNA level was extremely positive correlation with PH value in Landrace.
10.The polymorphism of the 5'-regulatory region of IGF-Ⅰgene in Songliao black pig was analyzed by PCR-SSCP、sequencing and microsatellite methods.The results showed that the polymorphisms were not detected by PCR-SSCP in the 5' -regulatory region of the IGF-Ⅰgene. Four alleles and six genotypes(AA、BB、AB、CC、DD、CD) were detected in Songliao Black pig populations.The association analysis-found the individual of AA genotypes have better meat quality and allele A had positive additive effects on meat quality traits.It could be preliminarily deduced that IGF-Ⅰgene was probably a major gene or a QTL linked gene which associated with meat quality and carcass traits in pig.
采用RACE的方法,首次克隆了猪以外显子Ⅴ为结尾的两种类型转录子,利用生物信息学方法,对其编码的多肽链进行了结构分析和功能结构域比较研究。采用半定量RT-PCR方法,检测了本课题组已经获得的Ⅰ类Ea型、Ⅰ类Eb型两种IGF-Ⅰ转录子和新获得的Ⅰ类Eb型、Ⅱ类Eb型两种不同转录子的表达特性。确定四种转录子在各组织不同发育阶段中发挥生理功能的主效拼接类型。四种转录子相对表达量分别与1、3、6月龄肉质性状相关分析表明,不同转录子在6月龄时与肉质性状都有相关,而在1、3月龄时只有个别转录子与肉质性状相关,表明不同的转录子在不同的发育时期对于肌肉组织的发生和发育具有不同的作用。利用半定量RT-PCR的方法,检测了四个转录子在松辽黑猪、松野杂交猪和长白猪不同组织中的表达规律,并比较了四个转录子在同组织不同品种中的表达差异。确定了三个品种各个组织的主效转录子及其在肌肉中的表达差异。四个转录子相对表达量分别与三个品种的肉质性状分析表明,不同转录子在松辽黑猪中与肉质性状都有相关,而在松野杂交猪和长白猪中只有个别转录子与肉质性状相关。
克隆了松辽黑猪5'调控区序列并做生物信息学分析,同时对其进行PCR-SSCP和微卫星多态分析,结果只发现了一个微卫星多态性位点,序列测定结果表明,该位点具有4个等位基因(A、B、C、D),共6种基因型,遗传效应分析发现AA基因型个体具有更好的肉质,A等位基因具有提高肌内脂肪含量、改善肉质的遗传效应。可以初步推断IGF-Ⅰ基因可能是影响猪的肉质和胴体性状的一个主效基因或是一个与影响猪肉质和胴体性状的QTL连锁的基因。
IGF-Ⅰis a single copy gene,due to alternative splicing,and the use of multiple polyadenylation signals and different promoters,the IGF-Ⅰgene and its mRNAs are complicated. Spliced variants of insulin-like growth factor 1(IGF-1),a small peptide with a critical role in metabolism and growth,have been identified in various vertebrate species.IGF-Ⅰplay an important role in muscle growth and development,myoblast fusion and differentiation,and improve muscle grow and meat quality.Therefore,it has important significance for studying on pig's candidate genes of economic trait that molecular genetic construction and space-time expression of IGF-Ⅰgene is studied by modern molecular biological technology.This research applied to Songliao Black Pig as the object of studying,we cloned the pig two new IGF-ⅠmRNAs and analyzed structure and characteristics of them by bioinformatics.Levels of different spliced variants of IGF-Ⅰin different tissues,at different ages,in adipose muscle tissues of different breeds were measured by Semi Quantitative Reverse Transcription-Polymerase Chain Reaction(SQ RT-PCR),and analyzed the genetic correlation between the levels of different spliced variants of IGF-Ⅰand meat quality traits by SPSS.We detected the polymorphisms of the 5'-regulatory region of IGF-Ⅰgenes by PCR-SSCP(single-strand conformation polymorphism)、sequencing and microsatellite methods in the population of Songliao black pig,and analyzed the genetic correlation between the polymorphisms and carcass and meat quality traits by SPSS.The main results are as follows:
1.The cDNA sequences of Songliao Black pig two spliced variants of IGF-Ⅰgene,including exon five,were cloned by RACE.They were named type Eb of classⅠand type Eb of classⅡ-IGF-Ⅰgenes,type Eb of classⅠ- IGF-Ⅰgene contains a 564bp open reading frame(ORF) encoding 187 amino acids while type Eb of classⅡ- IGF-Ⅰgene contains a 516bp ORF encoding 171 amino acids.
2.The alignment analysis of CDS sequences of type Eb of classⅠand type Eb of classⅡ-IGF-Ⅰgenes among human,sheep,cows,goats,chimpanzees,rhesus monkeys and horses shows that the consistency of type Eb of classⅠ- IGF-Ⅰgene in Songliao Black pig and other mammals is more than 91%,while the comparability of type Eb of classⅡ- IGF-Ⅰgene is more than 90%.The comparability of the protein sequences of type Eb of classⅠand type Eb of classⅡ-IGF-Ⅰgenes of Songliao Black pig with other mammals are more than 96%and 93%respectively.It verified that type Eb of classⅠand type Eb of classⅡ- IGF-Ⅰgenes are highly conserved in mammals.
3.We predicted the basic features,protein structure and molecular function of porcine type Eb of classⅠand type Eb of classⅡproteins with bioinformatics methods.The results indicate that porcine type Eb of classⅠand type Eb of classⅡ- IGF-Ⅰgenes belong to IGFs family,type Eb of classⅠand type Eb of classⅡproteins structure also contains the same IGFBPs,typeⅠandⅡreceptor domain.Bioinformatics results show that porcine type Eb of classⅠand type Eb of classⅡproteins are very conservative in the key structural and functional region.This suggests that porcine type Eb of classⅠand type Eb of classⅡproteins should have the similar function with some known proteins.
4.The expression characteristic of four spliced variants of insulin-like growth factor-Ⅰgene was investigated by RT-PCR.The results showed that the three spliced variants of insulin-like growth factor-Ⅰgene expressed in heart,liver,spleen,lung,kidney,lung,stomach,duodenum,ileum, colon,appendix,brachi -triceps,longissimus muscle of back,biceps femoris,testicle of Songliao Black Pig at the age of birth,one-month,three- month and six-month:There is much difference in the same tissue at different growing period.
5.Three spliced variants of insulin-like growth factor-Ⅰgene have the similar expression curves,which is the "S"curve or clock curve,in the same tissue at different growing period.The expression level of type Ea of classⅠ-IGF-Ⅰgene in longissimus of Songliao Black pig at one-month and six-month are significantly more than that birth and three-month.;The expression level of type Eb of classⅠ-IGF-Ⅰgene in longissimus of Songliao Black pig at one-month are significantly more than that birth,three-month and six-month;The expression level of type Eb of classⅡ-IGF-Ⅰgene in longissimus of Songliao Black pig at birth and one-month are significantly more than three-month and six-month.
6.The relationship of four spliced variants of insulin-like growth factor-Ⅰgene expression with pork quality was different at different growing stage:At one-month the type Ea of classⅠ-IGF-Ⅰgene mRNA level and meat color was negative correlation;the type Eb of classⅠ-IGF-Ⅰgene mRNA level and PH value were positive correlation.The type Ea of classⅠ-IGF-Ⅰgen mRNA level was extremely positive correlation with meat color and marbling at three-month.At six-month the type Ea of classⅠ-IGF-Ⅰgene mRNA level and the ratio of cook was positive correlation;the type Eb of classⅠ-IGF-Ⅰgen mRNA level was extremely positive correlation with meat color and marbling;the type Ea of classⅠ-IGF-Ⅰgene mRNA level was negative correlation with PH value;the type Eb of classⅡ-IGF-Ⅰgene mRNA level and drop ratio were negative correlation.
7.The expression characteristic of four spliced variants of insulin-like growth factor-Ⅰgene was investigated by RT-PCR.The results showed that the three spliced variants of insulin-like growth factor-Ⅰgene expressed in heart,liver,spleen,lung,kidney,lung, stomach,duodenum,ileum,colon,appendix,brachi -triceps,longissimus muscle of back,biceps femoris,testicle of Songliao Black Pig,Crossed and Landrace:There is much difference in the same tissue at different breed.
8.Class 1 IGF-ⅠmRNA(type Ea or type Eb) appeared to be much more abundant than class 2 IGF-ⅠmRNA in Songliao Black pig and Crossed.But type Eb of ClassⅡ-IGF-ⅠmRNA appeared to be much more abundant than class 1 IGF-ⅠmRNA in Landrace.
9.The relationship of four spliced variants of insulin-like growth factor-Ⅰgene expression with pork quality was different at different breeds:In Songliao Black pig:the type Ea of classⅠ-IGF-Ⅰgene mRNA level and the ratio of cook was positive correlation;the type Eb of classⅠ-IGF-Ⅰgen mRNA level was extremely positive correlation with meat color and marbling; the type Ea of classⅠ-IGF-Ⅰgene mRNA level was negative correlation with PH value:the type Eb of classⅡ-IGF-Ⅰgene mRNA level and drop ratio were negative correlation.In Crossed the type Ea of classⅠ-IGF-Ⅰgene mRNA level and cooked ratio were positive correlation;the type Eb of classⅡ-IGF-Ⅰgene mRNA level and drop ratio were negative correlation.The type Eb of classⅡ-IGF-Ⅰgen mRNA level was extremely positive correlation with PH value in Landrace.
10.The polymorphism of the 5'-regulatory region of IGF-Ⅰgene in Songliao black pig was analyzed by PCR-SSCP、sequencing and microsatellite methods.The results showed that the polymorphisms were not detected by PCR-SSCP in the 5' -regulatory region of the IGF-Ⅰgene. Four alleles and six genotypes(AA、BB、AB、CC、DD、CD) were detected in Songliao Black pig populations.The association analysis-found the individual of AA genotypes have better meat quality and allele A had positive additive effects on meat quality traits.It could be preliminarily deduced that IGF-Ⅰgene was probably a major gene or a QTL linked gene which associated with meat quality and carcass traits in pig.
引文
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