黄牛KLF7、KLF11和KLF15基因的单核苷酸多态性及其与生长性状的关联研究
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摘要
调节能量代谢的基因具有影响家养动物生长的潜力,基因的多态性同样具有此效应。KLF家族(Kruppel-like factors)是真核生物中广泛存在的一类基础转录元件结合蛋白(BTEP),通过羧基端三个连续锌指构成的保守结构域结合靶基因启动子内富含GC的序列以调控其转录,进而调控各类细胞的增殖分化和组织发育。本研究致力于检测编码KLF转录因子家族中相关基因的单核苷酸多态性(SNPs),并分析了SNPs与黄牛生长性状的相关性。本研究采用PCR-RFLP、PCR-SSCP和DNA测序技术,检测了南阳牛、秦川牛、郏县红牛和中国荷斯坦牛共4个群体1045个个体的五个与能量代谢调控相关基因(KLF4、KLF5、KLF7、KLF11和KLF15)的遗传变异,分析了其在4个牛群体的遗传结构和遗传多样性,并对四个群体在上述基因位点的单核苷酸多态性与其生长性状进行了相关分析,以检验这些基因对4个黄牛群体生长发育的遗传效应,并对具有显著相关的候选基因进行了实时定量分析,以期发现对重要经济性状具有显著效应的遗传标记,为中国黄牛的高效选育和分子标记数据库的建立、种质资源保存与利用提供遗传学依据。
本研究共扫描了五个KLF家族基因(KLF4、KLF5、KLF7、KLF11和KLF15)的17个位点,然而仅在三个基因(KLF7、KLF11和KLF15)的五个位点有多态性,这与KLF转录因子家族在进化中的高保守性和重要功能一致。
1. KLF7基因多态性及其与南阳牛、秦川牛和郏县牛生长性状的相关分析
本研究揭示了位于KLF7基因第二外显子及其侧翼区的3个SNPs :NC_007300:g.41401C>T,42025T>C和42075A>G。其中发现了一个同义突变:苯丙氨酸/苯丙氨酸(p.F54F,C41401T)。有趣的是在同时引入三个TaqI酶切位点后这三个单核苷酸多态性可以同时被酶切和检测。在三个位点中,只有中国荷斯坦奶牛在C41401T位点偏离哈代温伯格平衡状态。连锁不平衡分析发现C41401T和T42025C在郏县红牛中强连锁,T42025C和A42075G在秦川牛、南阳牛和中国荷斯坦奶牛中强连锁(r2 > 0.33)。群体遗传指数分析发现中国荷斯坦奶牛纯合度在C41401T位点达到1,只有一个有效等位基因。χ2检验显示在P1、P2和P3位点基因型分布有显著差异,暗示这些多态性与牛品种显著相关(P<0.001)。关联分析发现在6月龄,T2T2基因型个体(T42025C)的牛比T2C2基因型个体具有更大的日增重(P = 0.009)和胸围(P = 0.009)。在12月龄,C2C2基因型个体(T42025C)比T2C2基因型个体具有更大的体重(P = 0.008)、体长(P = 0.001)和胸围(P = 0.003);A3A3基因型个体(T42075C)比A3G3基因型个体具有更大的体长(P = 0.006);单倍型C1C1C2C2A3A3(H1)个体比单倍型C1C1T2C2A3G3(H2)的个体具有更大的体长(P = 0.001)和胸围(P = 0.004);单倍型C1T1T2C2A3G3(H5)个体比单倍型C1C1T2C2A3G3(H2)的个体具有更大的坐骨端宽(P = 0.007)。
KLF7基因的三个单核苷酸多态性P1、P2和P3均与秦川牛和郏县牛的体重和体尺性状没有显著相关。
2. KLF11和KLF15基因多态性及其与南阳牛、秦川牛和郏县牛生长性状的相关分析
本研究揭示了位于KLF11和KLF15基因的2个SNPs :黄牛KLF11基因NC_007309:g.24769 C>T和KLF15基因的NC_007301:g.1230 A>G。其中KLF11基因中的C>T突变导致了异亮氨酸>缬氨酸(p.I19V)的错义突变。群体遗传分析发现检测群体中的遗传多样性不高,χ2检验发现KLF11和KLF15位点的基因型分布与黄牛品种显著相关。相关分析结果显示位于KLF11基因3'非翻译区的C/T SNP在南阳牛6月龄的体重(P = 0.002)、日增重(P = 0.006)和体长(P = 0.001),12月龄的日增重(P = 0.005)效应显著。但KLF15基因的SNP在P < 0.05水平与检测的生长性状没有显示任何相关性。尽管KLF11基因的C/T没有引起氨基酸的改变,但它可能与其它可能还未检测到的SNP或它附近的数量性状基因座(QTL)紧密连锁。
KLF11和KLF15基因的两个单核苷酸多态性均与秦川牛和郏县牛的体重和体尺性状没有显著相关。
3. KLF7和KLF11基因在秦川牛12个组织的表达谱
本试验采集3头18月龄纯种秦川牛的心、肝、脾、肺、肾、卵巢、小肠、胃、肌肉、皮下脂肪、腹部脂肪、垂体共12个组织样,采用SYBR Green I荧光染料法检测了KLF7和KLF11基因在秦川牛12个组织的相对表达量。结果显示KLF7基因在胃中表达量最高,在皮下脂肪和腹脂中也有较高的表达量。KLF11基因在胃中的表达量最高,在腹脂、肺、乳腺和皮下脂肪中也有较高表达。脂肪、胃和乳腺均是参与能量代谢的主要器官,提示KLF7和KLF11基因可能在能量代谢中具有重要作用。
Genes that regulate metabolism and energy partitioning have the potential to influence growth traits in farm animals, as do polymorphisms within these genes. KLFs (Kruppel-like factors) are highly conserved basic transcription element binding protein (BTEP). There are conserved zinc finger domains at their C-termini that can bind specifically to the GC-rich promoter sequences of target genes, thus activating or repressing their expression, and then regulate the proliferation and differentiation of kinds of cells as well as the development of tissues. This study was conducted to identify single nucleotide polymorphisms (SNPs) in genes encoding Kruppel-like factors family and assess the associations of polymorphisms identified with cattle growth traits. Genetic variations of energy homeostasis related genes (KLF4, KLF5, KLF7, KLF11 and KLF15) were detected by PCR-RFLP, PCR-SSCP and DNA sequencing techniques in 1045 individuals of four populations (Nanyang cattle, Qinchuan cattle, Jiaxian cattle and Chinese Holstein), and association analysis were carried out to evaluate the effects of genotypes of candidate genes on growth traits of four Chinese cattle populations. The objects were to discovery the hereditary characteristics and to explore molecular markers with significant effects on economic important traits for efficient selection and improvement of Chinese cattle, and to provide genetic information for foundation of molecular marker database, protection and usage of breed resource of Chinese cattle.
In current study, 17 loci of five KLFs (KLF4, KLF5, KLF7, KLF11 and KLF15 genes) were scanned, but only 5 SNPs were found in three genes (KLF7, KLF11 and KLF15 genes), this were consisted with the highly conserved and essential functions of KLF transcriptional factors.
1. Polymorphisms identification and associations of Kruppel-like factor KLF7 gene with cattle growth traits
In the current study, three SNPs of exon 2 and its flanking region of KLF7 gene were revealed: NC_007300:g.41401C>T (p.F54F), 42025T>C and 42075A>G. Interestingly, the three SNPs can be detected simultaneously after created restriction recognized sites. It was found all the breeds were in Hardy-Weinberg equilibrium except Chinese Holstein at C41401T locus (P > 0.05). The statistical results indicated there was a strong linkage not only between C41401T and T42025C in Jiaxian, but also between T42025C and A42075G in Qinchuan, Nanyang and Chinese Holstein respectively (r2 > 0.33). Significant statistical differences in genotypic frequencies at the three loci displayed that the polymorphisms were remarkably correlated with cattle breeds byχ2 test (P < 0.001). In addition, The cattle with genotype T2T2 (T42025C) had greater average daily gain (P = 0.009) and heart girth (P = 0.009) than those with genotype T2C2 at 6 months. The cattle with genotype C2C2 (T42025C) had greater body weight (P = 0.008), body length (P = 0.001), and heart girth (P = 0.003) than those with genotype T2C2 at 12 months. The cattle with genotype A3A3 (T42075C) had greater body length (P = 0.006) than those with genotype A3G3 at 12 months. the cattle with haplotype C1C1C2C2A3A3 (H1) had greater body length (P = 0.001) and heart girth (P = 0.004) than those with haplotype C1C1T2C2A3G3 (H2) at 12 months. The cattle with haplotype C1T1T2C2A3G3 (H5) had greater hucklebone width (P = 0.007) than those with haplotype C1C1T2C2A3G3 (H2) at 12 months.
3 SNPs of KLF7 gene have no significant associations with the growth traits of Qinchuan and Jiaxian.
2. Polymorphisms identification and associations of Kruppel-like factor KLF11 and KLF15 genes with cattle growth traits
In the current study, twelve loci of KLF4, KLF5, KLF11 and KLF15 genes were scaned and two novel SNPs, NC_007309:g.24769 C>T of bovine KLF11 gene and NC_007301:g.1230 A>G of bovine KLF15 gene, were identified, in which a missense mutation was identified: p:I19V in KLF15 gene. The genetic diversities in analyzed populations were found not high. The distributions of genotypic frequencies of KLF11 and KLF15 loci were significantly associated with bovine breeds byχ2 test. Correlation analysis indicated that an C/T SNP located in 3'-UTR of the KLF11 gene had large effect on body weight (P = 0.002), average daily gain (P = 0.006), body length (P = 0.001) at 6 months and average daily gain (P = 0.005) at 12 months in Nanyang cattle. But the SNP in KLF15 gene did not showed associations at P < 0.05 with any examined traits. Although C/T in KLF11 do not cause amino acid changes, it could be linked to other yet to be detected causative mutations or nearby QTL.
2 SNPs of KLF11 and KLF15 gene have no significant associations with the growth traits of Qinchuan and Jiaxian.
3. Expression profiles of KLF7 and KLF11 genes in 12 tissues of 18 months old Qinchuan cattle
12 freezed tissues including fat in abdomen, hypophysis, small intestine, kidney, liver, muscle, heart, spleen, lung, lacteal gland, stomach, adipose layer of three Qinchuan cattle (18 months) were collected. SYBR Green I was used to detect the expression situation of KLF7 and KLF11 genes in these tissues, the results showed that the expressions of KLF7 and KLF11 were similarly abundant in stomach, adipose layer and fat in abdomen, which were major organs involving in energy metabolism. The results implied that KLF7 and KLF11 were functional important in energy metabolism.
本研究共扫描了五个KLF家族基因(KLF4、KLF5、KLF7、KLF11和KLF15)的17个位点,然而仅在三个基因(KLF7、KLF11和KLF15)的五个位点有多态性,这与KLF转录因子家族在进化中的高保守性和重要功能一致。
1. KLF7基因多态性及其与南阳牛、秦川牛和郏县牛生长性状的相关分析
本研究揭示了位于KLF7基因第二外显子及其侧翼区的3个SNPs :NC_007300:g.41401C>T,42025T>C和42075A>G。其中发现了一个同义突变:苯丙氨酸/苯丙氨酸(p.F54F,C41401T)。有趣的是在同时引入三个TaqI酶切位点后这三个单核苷酸多态性可以同时被酶切和检测。在三个位点中,只有中国荷斯坦奶牛在C41401T位点偏离哈代温伯格平衡状态。连锁不平衡分析发现C41401T和T42025C在郏县红牛中强连锁,T42025C和A42075G在秦川牛、南阳牛和中国荷斯坦奶牛中强连锁(r2 > 0.33)。群体遗传指数分析发现中国荷斯坦奶牛纯合度在C41401T位点达到1,只有一个有效等位基因。χ2检验显示在P1、P2和P3位点基因型分布有显著差异,暗示这些多态性与牛品种显著相关(P<0.001)。关联分析发现在6月龄,T2T2基因型个体(T42025C)的牛比T2C2基因型个体具有更大的日增重(P = 0.009)和胸围(P = 0.009)。在12月龄,C2C2基因型个体(T42025C)比T2C2基因型个体具有更大的体重(P = 0.008)、体长(P = 0.001)和胸围(P = 0.003);A3A3基因型个体(T42075C)比A3G3基因型个体具有更大的体长(P = 0.006);单倍型C1C1C2C2A3A3(H1)个体比单倍型C1C1T2C2A3G3(H2)的个体具有更大的体长(P = 0.001)和胸围(P = 0.004);单倍型C1T1T2C2A3G3(H5)个体比单倍型C1C1T2C2A3G3(H2)的个体具有更大的坐骨端宽(P = 0.007)。
KLF7基因的三个单核苷酸多态性P1、P2和P3均与秦川牛和郏县牛的体重和体尺性状没有显著相关。
2. KLF11和KLF15基因多态性及其与南阳牛、秦川牛和郏县牛生长性状的相关分析
本研究揭示了位于KLF11和KLF15基因的2个SNPs :黄牛KLF11基因NC_007309:g.24769 C>T和KLF15基因的NC_007301:g.1230 A>G。其中KLF11基因中的C>T突变导致了异亮氨酸>缬氨酸(p.I19V)的错义突变。群体遗传分析发现检测群体中的遗传多样性不高,χ2检验发现KLF11和KLF15位点的基因型分布与黄牛品种显著相关。相关分析结果显示位于KLF11基因3'非翻译区的C/T SNP在南阳牛6月龄的体重(P = 0.002)、日增重(P = 0.006)和体长(P = 0.001),12月龄的日增重(P = 0.005)效应显著。但KLF15基因的SNP在P < 0.05水平与检测的生长性状没有显示任何相关性。尽管KLF11基因的C/T没有引起氨基酸的改变,但它可能与其它可能还未检测到的SNP或它附近的数量性状基因座(QTL)紧密连锁。
KLF11和KLF15基因的两个单核苷酸多态性均与秦川牛和郏县牛的体重和体尺性状没有显著相关。
3. KLF7和KLF11基因在秦川牛12个组织的表达谱
本试验采集3头18月龄纯种秦川牛的心、肝、脾、肺、肾、卵巢、小肠、胃、肌肉、皮下脂肪、腹部脂肪、垂体共12个组织样,采用SYBR Green I荧光染料法检测了KLF7和KLF11基因在秦川牛12个组织的相对表达量。结果显示KLF7基因在胃中表达量最高,在皮下脂肪和腹脂中也有较高的表达量。KLF11基因在胃中的表达量最高,在腹脂、肺、乳腺和皮下脂肪中也有较高表达。脂肪、胃和乳腺均是参与能量代谢的主要器官,提示KLF7和KLF11基因可能在能量代谢中具有重要作用。
Genes that regulate metabolism and energy partitioning have the potential to influence growth traits in farm animals, as do polymorphisms within these genes. KLFs (Kruppel-like factors) are highly conserved basic transcription element binding protein (BTEP). There are conserved zinc finger domains at their C-termini that can bind specifically to the GC-rich promoter sequences of target genes, thus activating or repressing their expression, and then regulate the proliferation and differentiation of kinds of cells as well as the development of tissues. This study was conducted to identify single nucleotide polymorphisms (SNPs) in genes encoding Kruppel-like factors family and assess the associations of polymorphisms identified with cattle growth traits. Genetic variations of energy homeostasis related genes (KLF4, KLF5, KLF7, KLF11 and KLF15) were detected by PCR-RFLP, PCR-SSCP and DNA sequencing techniques in 1045 individuals of four populations (Nanyang cattle, Qinchuan cattle, Jiaxian cattle and Chinese Holstein), and association analysis were carried out to evaluate the effects of genotypes of candidate genes on growth traits of four Chinese cattle populations. The objects were to discovery the hereditary characteristics and to explore molecular markers with significant effects on economic important traits for efficient selection and improvement of Chinese cattle, and to provide genetic information for foundation of molecular marker database, protection and usage of breed resource of Chinese cattle.
In current study, 17 loci of five KLFs (KLF4, KLF5, KLF7, KLF11 and KLF15 genes) were scanned, but only 5 SNPs were found in three genes (KLF7, KLF11 and KLF15 genes), this were consisted with the highly conserved and essential functions of KLF transcriptional factors.
1. Polymorphisms identification and associations of Kruppel-like factor KLF7 gene with cattle growth traits
In the current study, three SNPs of exon 2 and its flanking region of KLF7 gene were revealed: NC_007300:g.41401C>T (p.F54F), 42025T>C and 42075A>G. Interestingly, the three SNPs can be detected simultaneously after created restriction recognized sites. It was found all the breeds were in Hardy-Weinberg equilibrium except Chinese Holstein at C41401T locus (P > 0.05). The statistical results indicated there was a strong linkage not only between C41401T and T42025C in Jiaxian, but also between T42025C and A42075G in Qinchuan, Nanyang and Chinese Holstein respectively (r2 > 0.33). Significant statistical differences in genotypic frequencies at the three loci displayed that the polymorphisms were remarkably correlated with cattle breeds byχ2 test (P < 0.001). In addition, The cattle with genotype T2T2 (T42025C) had greater average daily gain (P = 0.009) and heart girth (P = 0.009) than those with genotype T2C2 at 6 months. The cattle with genotype C2C2 (T42025C) had greater body weight (P = 0.008), body length (P = 0.001), and heart girth (P = 0.003) than those with genotype T2C2 at 12 months. The cattle with genotype A3A3 (T42075C) had greater body length (P = 0.006) than those with genotype A3G3 at 12 months. the cattle with haplotype C1C1C2C2A3A3 (H1) had greater body length (P = 0.001) and heart girth (P = 0.004) than those with haplotype C1C1T2C2A3G3 (H2) at 12 months. The cattle with haplotype C1T1T2C2A3G3 (H5) had greater hucklebone width (P = 0.007) than those with haplotype C1C1T2C2A3G3 (H2) at 12 months.
3 SNPs of KLF7 gene have no significant associations with the growth traits of Qinchuan and Jiaxian.
2. Polymorphisms identification and associations of Kruppel-like factor KLF11 and KLF15 genes with cattle growth traits
In the current study, twelve loci of KLF4, KLF5, KLF11 and KLF15 genes were scaned and two novel SNPs, NC_007309:g.24769 C>T of bovine KLF11 gene and NC_007301:g.1230 A>G of bovine KLF15 gene, were identified, in which a missense mutation was identified: p:I19V in KLF15 gene. The genetic diversities in analyzed populations were found not high. The distributions of genotypic frequencies of KLF11 and KLF15 loci were significantly associated with bovine breeds byχ2 test. Correlation analysis indicated that an C/T SNP located in 3'-UTR of the KLF11 gene had large effect on body weight (P = 0.002), average daily gain (P = 0.006), body length (P = 0.001) at 6 months and average daily gain (P = 0.005) at 12 months in Nanyang cattle. But the SNP in KLF15 gene did not showed associations at P < 0.05 with any examined traits. Although C/T in KLF11 do not cause amino acid changes, it could be linked to other yet to be detected causative mutations or nearby QTL.
2 SNPs of KLF11 and KLF15 gene have no significant associations with the growth traits of Qinchuan and Jiaxian.
3. Expression profiles of KLF7 and KLF11 genes in 12 tissues of 18 months old Qinchuan cattle
12 freezed tissues including fat in abdomen, hypophysis, small intestine, kidney, liver, muscle, heart, spleen, lung, lacteal gland, stomach, adipose layer of three Qinchuan cattle (18 months) were collected. SYBR Green I was used to detect the expression situation of KLF7 and KLF11 genes in these tissues, the results showed that the expressions of KLF7 and KLF11 were similarly abundant in stomach, adipose layer and fat in abdomen, which were major organs involving in energy metabolism. The results implied that KLF7 and KLF11 were functional important in energy metabolism.
引文
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Kaczynski J, Cook T, Urrutia R. 2003. Sp1-and Kruppel-like transcription factors. Genome Biol, 4(2). Kanazawa A, Kawamura Y, Sekine A, et al. 2005. Single nucleotide polymorphisms in the gene encoding Kruppel-like factor 7 are associated with type 2 diabetes. Diabetologia, 48(7):1315-1322.
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Kawamura Y, Tanaka Y, Kawamori R, et al. 2006. Overexpression of Kruppel-Like factor 7 regulates adipocytokine gene expressions in human adipocytes and inhibits glucose-induced insulin secretion in pancreatic beta-cell line. Mol Endocrinol, 20(4):844-856.
Kim J J, Farnir F, Savell J, et al. 2003. Detection of quantitative trait loci for growth and beef carcass fatness traits in a cross between Bos taurus (Angus) and Bos indicus (Brahman) cattle. J Anim Sci, 81(8):1933-1942.
Knott S A, Marklund L, Haley C S, et al. 1998. Multiple marker mapping of quantitative trait loci in a cross between outbred wild boar and large white pigs. Genetics, 149(2):1069-1080.
Kuo C T, Veselits M L, Barton K P, et al. 1997. The LKLF transcription factor is required for normal tunica media formation and blood vessel stabilization during murine embryogenesis. Gene Dev, 11(22):2996-3006.
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