固原鸡耐寒性状微卫星标记及其相关基因遗传变异研究
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摘要
本研究以固原鸡的耐寒性状为主要研究目的，以耐寒品种一藏鸡、不耐寒的海赛克斯鸡、耐热品种一文昌鸡以及固原鸡回交产生F2作为对照群，共计766个个体为试验材料，对固原鸡的耐寒性能及相关表型性状和生产性状进了对比测试，进一步利用微卫星标记的方法对26个微卫星位点进行了扫描，并通过PCR-SSCP标记技术对耐寒性状相关的3个候选基因—TYR基因的5'调控区及第1外显子共6个位点；PPARa基因编码区共7个位点；NPY基因第2外显子共2个位点的遗传变异进行检测分析。旨在寻找与耐寒性状相连锁的微卫星标记、相关候选基因和表型性状及生产性状，为下一步精确定位固原鸡耐寒基因打下科学的理论基础，进一步为寒冷地区的家鸡选种选育工作提供科学依据。本研究获得以下研究结果：
(1)具有耐寒特性的固原鸡经过与不耐寒的海赛克斯鸡杂交，其后代----固原红鸡相对于其亲本海赛克斯鸡耐寒性明显提高(P＜0．01)。这说明固原鸡可能具有耐寒基因，并且具有一定的遗传性。通过低温下对固原鸡耐寒性能与表型及生产性状测试结果表明，固原鸡的耐寒性与羽色、肤色并无显著相关(P＞0．05)。对照组海赛克斯鸡的采食量显著低于固原鸡(P＜0．01)，产蛋量显著高于固原鸡(P＜0．01)。在固原鸡群体内乌鸡的产蛋量显著低于固原土鸡(P＜0．01)，但采食量差异不显著(P＞0．05)。固原鸡的耐寒性与体重之间相关系数为r=0．4235，但经过相关系数显著性检验差异不显著(P＞0．05)，说明体重与耐寒性无直接连锁关系。
(2)本研究通过对26个微卫星位点的扫描，结果表明，固原鸡、藏鸡和文昌鸡作为中国典型的地方品种均具有丰富的遗传变异，其中藏鸡具有极为丰富的遗传变异，杂合度达到0．8220。海赛克斯鸡群体内遗传变异较小，杂合度仅为0．4211。3个中国品种间存在极显著的遗传分化，达到45．06％。表明3个中国鸡品种间大约45％的遗传变异源自品种间的差异。固原鸡和藏鸡的遗传距离很近，可聚为一类。文昌鸡与这两个品种鸡均遗传距离均较远，单独聚为一类；海赛克斯鸡与三个中国品种均遗传距离均较远，单独聚为一类。
(3)首次发现在微卫星LEI212位点上耐寒品种固原鸡、固原鸡F2代和藏鸡所有个体均有扩增产物，而耐热品种文昌鸡和不耐寒品种海赛克斯鸡只有极个别个体有扩增产物。在MCW0141位点上各等位基因在4个品种鸡之间的分布经独立卡方检验表明，耐寒品种与耐热品种间存在极显著的差异(P＜0．01)，耐寒品种间差异不显著(P＞0．05)。通过与GenBank比对与查询，这两个位点分别位于鸡的6号和3号染色体，表明这两个位点与鸡的耐寒性存在关联，可作为鸡耐寒性标记位点。但还需进一步研究证实。通过利用最小二乘法对微卫星各位点多态与固原鸡体重的相关分析和多重比较发现，在MCW0169位点上的BE型、在MCW0351位点上的CD型、在MCW0166位点上的BB型、在MCW0073位点上的GG型和EE型体重均显著或极显著的高于其它基因型，表明这4个微卫星位点的基因型类型与固原鸡体重性状存在显著相关。
(4)采用PCR-SSCP标记技术，对TYR基因第1外显子及其5’调控区共6个位点检测表明，只有TYR1和TYR3位点具有多态性。在TYR1位点上发生C→T的单碱基同义替换，4个群体在该位点均处于Hardy-Weinberg平衡状态。在3个中国鸡品种中均检测到三种基因型(CC、CT、TT)，CC型在海赛克斯鸡中没有检测到。独立x~2检验分析表明，除文昌鸡和藏鸡间基因型和基因频率差异不显著外(P=0．883和P=0．441均＞0．05)，其它品种间频率差异均极显著(P＜0．01)。在TYR3位点上发生G→A的单碱基替换突变，在3个中国鸡品种中均检测到三种基因型(AA、AG、GG)，AA型在海赛克斯鸡中没有检测到。藏鸡和海赛克斯鸡在该位点处于极不平衡状态，固原鸡与文昌鸡均处于平衡状态。独立x~2检验分析表明，文昌鸡和固原鸡品种间频率差异不显著(P=0．678和P=0．710均大于0．05)，其余品种间频率差异极显著(P＜0．01)。
TYR基因的5’侧翼区以及第1外显子区域的变异在耐寒品种与不耐寒品种之间并无显著的差异，所以该基因多态性与鸡的耐寒性并无直接关联。
(5)采用PCR-SSCP标记技术对PPARα基因编码区共计7个位点进行单核苷酸多态检测。只有P4位点检测到多态，通过与GenBank比对(AF163809)发现1026 nt、1029 nt和1065 nt三处变异，前两处变异属于同义突变(A→G，C→T)，1065 nt处变异(缺失一个G碱基)属于移码突变。固原鸡和藏鸡均检测到3种基因型(AA，BB和AB)，文昌鸡检测到4种基因型(AA，BB，AB，CC)，而海赛克斯鸡只检测到DD和EF型，只有海赛克斯鸡在1065 nt处存在移码突变。首次发现该基因变异位点的不同与鸡不同生产用途存在关联。该位点有可能成为区分不同用途类型鸡的一个有效标记辅助选择位点。
通过对该位点基因频率和基因型频率分布进行独立卡方检验分析表明，该位点的变异在耐寒鸡品种间差异不显著(P＞0．05)，而在耐寒品种与耐热品种间显著极差异(P＜0．01)，可能与耐寒性有密切关联，但还需要进一步研究证实。
(6)采用PCR-SSCP标记技术对NPY基因的第2外显子共2个位点的多态性进行了检测。结果表明，在NPY2位点上第1558个碱基处发生T→C突变，此突变引起第23个氨基酸—精氨酸变异为半胱氨酸。并且在该位点上BB型个体在4个群体内的检测概率均较低。基因型和基因频率独立卡方检验表明，耐热的文昌鸡与耐寒的固原鸡和藏鸡之间差异极显著(P＜0．01)，但是不耐寒的海赛克斯鸡与3个中国品种鸡之间差异均不显著(P＞0．05)。通过利用最小二乘法对NPY2位点多态与对固原鸡体重的相关分析和多重比较发现，AB型体重显著高于AA型(0．01＜P＜0．05)。
该基因位点的等位基因在品种间分布虽存在显著差异，但与耐寒性并无显著关联。
Guyuan chicken is the native populations spreading over cold region of northwestern of China. Cold - tolerance is a special character in Guyuan chicken population. In order to searching for linkage phenotype with the trait of cold tolerance, there are 766 individuals, including Tibetant chicken (cold-tolerance populations), Hesix chicken (non cold-torlerance populations), Wenchang chicken (hot-torlerance indigenous populations) and F2 population obtained from Guyuan hybrid with their parents (as the control population). The adoption of these populations stands for region-culture all in virtually cold and hot regions of China. There are 26 pairs of microsatellite primers have been employed to search for the linkage loci with cold tolerance. And the single nucleotide polymorphism and DNA sequencing were used to study on 3 candiadate genes: TYR gene, PPAR gene and NPY gene. Therefore, it could be great interest to know whether the differences in three genes of different chicken populations. So the aim of this study was to analyze the variation and polymorphism of the three genes, provide some important information to lipid metabolism regulation of cold tolerance, especially to accelerate the development of a cold tolerant strain of chicken in cold region of China, such as Guyuan and Tibet. The results were summarized as follows:
(1) In crosspopulationsing experiment, Guyuan chicken had significance cold tolerance (P<0.01). There was probably cold-tolerance gene in Guyuan chicken and it would be inheritance. In control experiment, the feed intake of Hesix chicken was significant lower than that of Guyuan chicken (P<0.01). In Guyuan population, the egg yield of the black was significant lower than that of native Guyuan chicken (P<0.01). There were no significance differences in feed intake between them. The correlation coefficient of cold-tolerance and weight was 0.4235. But there were no significant difference in different individuals. So, there were no direct relation between weight and tolerance. There was no significance correlation between the cold tolerance and skin color, feather color (P>0.05).
(2) Geneticstructure and diversity of five chicken populations were evaluated with 26 microsatellite loci. The result showed that there was abundant genetic diversity in three Chinese chicken populations. The average heterozygos value of Tibetant was the highest (0.822). Considerable population differentiation was observed and there was 45.5 % of the total genetic variation came from populations differences. The genetic distance of Guyuan chicken and Tibetant chicken was the most nearly. And they contained in one group. The Wenchang chicken and Hesix chicken contained to other group separately. Association analysis between the polymorphisms and body weight growth trait of Guyuan, at MCW169, MCW166, MCW351 and MCW073 locus, individuals with genotype BE, CD, BB and GG had higher body weight compared to individuals with other genotype, AD, DD and GK.
(3) Two special microsatellite loci were found. At LEI212 locus, every individuals of Guyuan and Tibetant as cold torlerance populations had PCR products. But there were not products in Wenchang and Hesix populations. The chi-square of allelic analysis revealed that there was no significant difference between Guyuan and Wenchang populations (P>0.05). At MCW141 locus, the chi-square analysis revealed that there was no significant difference between Guyuan and Wenchang populations (P>0.05), but there was significant statistical difference between cold-tolerance and hot-tolerance populations (P<0.01). Aligned them with the sequence of GenBank, the two loci were located at Chromosomes 6 and 3, respectively. And the two loci were possibly related with cold-tolerance and hot-tolerance, which could be considered as the candidate loci and might be the effective loci for further study.
(4) In this study, six loci of the gene exonl and one locus of 5' flanking region were analyzed by PCR-SSCP and DNA sequencing. The results indicated that there were polymorphisms only at TYR1 and TYR3 locus. At TYR1 locus, there was one silent mutation site: C to T, three genotypes (TT, CC and TC) was detected in three Chinese chicken populations respectively. Genotype CC wasn't detected in Hisex chicken. The chi-square analysis revealed that there was only significant difference between Wenchang and Tibent populations (P<0.01). At TYR3 locus, there was one mutation site: G to A, three genotypes (GG, AA and GA) was detected in Chinese local chicken populations and genotype AA wasn't detected in Hisex chicken populations. The chi-square analysis revealed that there was only significant difference between Wenchang and Guyuan populations (P<0.01). It was concluded that there was abundant variation of TYR gene in Chinese local chicken populations. It showed that there was no direct relation between cold tolerance and the variation of regions of exon1 and one locus of 5' flanking region of TYR gene.
(5) In this study, the genetic variations of PPARA gene in 4 chicken populations (Guyuan, Wenchang, Tibetan and Hisex) were detected by PCR-SSCP and DNA sequencing. The results indicated that 6 different genotypes (namely, AA-EF) were detected in four chicken populations at P4 locus. Aligned them with the sequence AF163809, the nucleotide sequences of genotype AA, BB, AB and CC all revealed silent mutations in three Chinese populations. The nucleotide sequences of genotype DD and EF in Hisex showed several frame-shift mutations. It was implied that there were abundant variations of PPARαgene in chicken populations. Moreover, distribution of genotype frequency within PPARαgene was significant difference in 4 populations selected for special purpose in special region. It was implied that this locus could be probably utilized as an effective marker in marker assisted selection for layer, meat and egg concurrent and broiler populations.
It showed that there was direct relation between cold tolerance and the variation of PPARA gene, but which needed to be confirmed further.
(6) In this study, two loci of the gene exon2 and intron 2 of NPY (Neuropeptide Y) gene were analyzed by PCR-SSCP and DNA sequencing. The results indicated that there was significient polymorphism only at NPY2 locous. There was one mutation site: T to C at 1558 nt (Aligned them with GenBank accession No: 3JJM87298), which caused the 23th amino acid variation (Arg to Cys). And only a few genotypes BB were detected in four chicken populations. The chi-square analysis revealed that there was significant difference between cold tolerance populations and Wenchang populations (P<0.01). There was no significant difference between Hesix and other three populations (P>0.05). It showed that there was no direct relation between cold tolerance and the variation of NPY gene. Association analysis between the polymorphisms and body weight growth trait of Guyuan, at NPY2 locus, individuals with genotype AB had higher body weight compared to individuals with genotype AA.
(1)具有耐寒特性的固原鸡经过与不耐寒的海赛克斯鸡杂交，其后代----固原红鸡相对于其亲本海赛克斯鸡耐寒性明显提高(P＜0．01)。这说明固原鸡可能具有耐寒基因，并且具有一定的遗传性。通过低温下对固原鸡耐寒性能与表型及生产性状测试结果表明，固原鸡的耐寒性与羽色、肤色并无显著相关(P＞0．05)。对照组海赛克斯鸡的采食量显著低于固原鸡(P＜0．01)，产蛋量显著高于固原鸡(P＜0．01)。在固原鸡群体内乌鸡的产蛋量显著低于固原土鸡(P＜0．01)，但采食量差异不显著(P＞0．05)。固原鸡的耐寒性与体重之间相关系数为r=0．4235，但经过相关系数显著性检验差异不显著(P＞0．05)，说明体重与耐寒性无直接连锁关系。
(2)本研究通过对26个微卫星位点的扫描，结果表明，固原鸡、藏鸡和文昌鸡作为中国典型的地方品种均具有丰富的遗传变异，其中藏鸡具有极为丰富的遗传变异，杂合度达到0．8220。海赛克斯鸡群体内遗传变异较小，杂合度仅为0．4211。3个中国品种间存在极显著的遗传分化，达到45．06％。表明3个中国鸡品种间大约45％的遗传变异源自品种间的差异。固原鸡和藏鸡的遗传距离很近，可聚为一类。文昌鸡与这两个品种鸡均遗传距离均较远，单独聚为一类；海赛克斯鸡与三个中国品种均遗传距离均较远，单独聚为一类。
(3)首次发现在微卫星LEI212位点上耐寒品种固原鸡、固原鸡F2代和藏鸡所有个体均有扩增产物，而耐热品种文昌鸡和不耐寒品种海赛克斯鸡只有极个别个体有扩增产物。在MCW0141位点上各等位基因在4个品种鸡之间的分布经独立卡方检验表明，耐寒品种与耐热品种间存在极显著的差异(P＜0．01)，耐寒品种间差异不显著(P＞0．05)。通过与GenBank比对与查询，这两个位点分别位于鸡的6号和3号染色体，表明这两个位点与鸡的耐寒性存在关联，可作为鸡耐寒性标记位点。但还需进一步研究证实。通过利用最小二乘法对微卫星各位点多态与固原鸡体重的相关分析和多重比较发现，在MCW0169位点上的BE型、在MCW0351位点上的CD型、在MCW0166位点上的BB型、在MCW0073位点上的GG型和EE型体重均显著或极显著的高于其它基因型，表明这4个微卫星位点的基因型类型与固原鸡体重性状存在显著相关。
(4)采用PCR-SSCP标记技术，对TYR基因第1外显子及其5’调控区共6个位点检测表明，只有TYR1和TYR3位点具有多态性。在TYR1位点上发生C→T的单碱基同义替换，4个群体在该位点均处于Hardy-Weinberg平衡状态。在3个中国鸡品种中均检测到三种基因型(CC、CT、TT)，CC型在海赛克斯鸡中没有检测到。独立x~2检验分析表明，除文昌鸡和藏鸡间基因型和基因频率差异不显著外(P=0．883和P=0．441均＞0．05)，其它品种间频率差异均极显著(P＜0．01)。在TYR3位点上发生G→A的单碱基替换突变，在3个中国鸡品种中均检测到三种基因型(AA、AG、GG)，AA型在海赛克斯鸡中没有检测到。藏鸡和海赛克斯鸡在该位点处于极不平衡状态，固原鸡与文昌鸡均处于平衡状态。独立x~2检验分析表明，文昌鸡和固原鸡品种间频率差异不显著(P=0．678和P=0．710均大于0．05)，其余品种间频率差异极显著(P＜0．01)。
TYR基因的5’侧翼区以及第1外显子区域的变异在耐寒品种与不耐寒品种之间并无显著的差异，所以该基因多态性与鸡的耐寒性并无直接关联。
(5)采用PCR-SSCP标记技术对PPARα基因编码区共计7个位点进行单核苷酸多态检测。只有P4位点检测到多态，通过与GenBank比对(AF163809)发现1026 nt、1029 nt和1065 nt三处变异，前两处变异属于同义突变(A→G，C→T)，1065 nt处变异(缺失一个G碱基)属于移码突变。固原鸡和藏鸡均检测到3种基因型(AA，BB和AB)，文昌鸡检测到4种基因型(AA，BB，AB，CC)，而海赛克斯鸡只检测到DD和EF型，只有海赛克斯鸡在1065 nt处存在移码突变。首次发现该基因变异位点的不同与鸡不同生产用途存在关联。该位点有可能成为区分不同用途类型鸡的一个有效标记辅助选择位点。
通过对该位点基因频率和基因型频率分布进行独立卡方检验分析表明，该位点的变异在耐寒鸡品种间差异不显著(P＞0．05)，而在耐寒品种与耐热品种间显著极差异(P＜0．01)，可能与耐寒性有密切关联，但还需要进一步研究证实。
(6)采用PCR-SSCP标记技术对NPY基因的第2外显子共2个位点的多态性进行了检测。结果表明，在NPY2位点上第1558个碱基处发生T→C突变，此突变引起第23个氨基酸—精氨酸变异为半胱氨酸。并且在该位点上BB型个体在4个群体内的检测概率均较低。基因型和基因频率独立卡方检验表明，耐热的文昌鸡与耐寒的固原鸡和藏鸡之间差异极显著(P＜0．01)，但是不耐寒的海赛克斯鸡与3个中国品种鸡之间差异均不显著(P＞0．05)。通过利用最小二乘法对NPY2位点多态与对固原鸡体重的相关分析和多重比较发现，AB型体重显著高于AA型(0．01＜P＜0．05)。
该基因位点的等位基因在品种间分布虽存在显著差异，但与耐寒性并无显著关联。
Guyuan chicken is the native populations spreading over cold region of northwestern of China. Cold - tolerance is a special character in Guyuan chicken population. In order to searching for linkage phenotype with the trait of cold tolerance, there are 766 individuals, including Tibetant chicken (cold-tolerance populations), Hesix chicken (non cold-torlerance populations), Wenchang chicken (hot-torlerance indigenous populations) and F2 population obtained from Guyuan hybrid with their parents (as the control population). The adoption of these populations stands for region-culture all in virtually cold and hot regions of China. There are 26 pairs of microsatellite primers have been employed to search for the linkage loci with cold tolerance. And the single nucleotide polymorphism and DNA sequencing were used to study on 3 candiadate genes: TYR gene, PPAR gene and NPY gene. Therefore, it could be great interest to know whether the differences in three genes of different chicken populations. So the aim of this study was to analyze the variation and polymorphism of the three genes, provide some important information to lipid metabolism regulation of cold tolerance, especially to accelerate the development of a cold tolerant strain of chicken in cold region of China, such as Guyuan and Tibet. The results were summarized as follows:
(1) In crosspopulationsing experiment, Guyuan chicken had significance cold tolerance (P<0.01). There was probably cold-tolerance gene in Guyuan chicken and it would be inheritance. In control experiment, the feed intake of Hesix chicken was significant lower than that of Guyuan chicken (P<0.01). In Guyuan population, the egg yield of the black was significant lower than that of native Guyuan chicken (P<0.01). There were no significance differences in feed intake between them. The correlation coefficient of cold-tolerance and weight was 0.4235. But there were no significant difference in different individuals. So, there were no direct relation between weight and tolerance. There was no significance correlation between the cold tolerance and skin color, feather color (P>0.05).
(2) Geneticstructure and diversity of five chicken populations were evaluated with 26 microsatellite loci. The result showed that there was abundant genetic diversity in three Chinese chicken populations. The average heterozygos value of Tibetant was the highest (0.822). Considerable population differentiation was observed and there was 45.5 % of the total genetic variation came from populations differences. The genetic distance of Guyuan chicken and Tibetant chicken was the most nearly. And they contained in one group. The Wenchang chicken and Hesix chicken contained to other group separately. Association analysis between the polymorphisms and body weight growth trait of Guyuan, at MCW169, MCW166, MCW351 and MCW073 locus, individuals with genotype BE, CD, BB and GG had higher body weight compared to individuals with other genotype, AD, DD and GK.
(3) Two special microsatellite loci were found. At LEI212 locus, every individuals of Guyuan and Tibetant as cold torlerance populations had PCR products. But there were not products in Wenchang and Hesix populations. The chi-square of allelic analysis revealed that there was no significant difference between Guyuan and Wenchang populations (P>0.05). At MCW141 locus, the chi-square analysis revealed that there was no significant difference between Guyuan and Wenchang populations (P>0.05), but there was significant statistical difference between cold-tolerance and hot-tolerance populations (P<0.01). Aligned them with the sequence of GenBank, the two loci were located at Chromosomes 6 and 3, respectively. And the two loci were possibly related with cold-tolerance and hot-tolerance, which could be considered as the candidate loci and might be the effective loci for further study.
(4) In this study, six loci of the gene exonl and one locus of 5' flanking region were analyzed by PCR-SSCP and DNA sequencing. The results indicated that there were polymorphisms only at TYR1 and TYR3 locus. At TYR1 locus, there was one silent mutation site: C to T, three genotypes (TT, CC and TC) was detected in three Chinese chicken populations respectively. Genotype CC wasn't detected in Hisex chicken. The chi-square analysis revealed that there was only significant difference between Wenchang and Tibent populations (P<0.01). At TYR3 locus, there was one mutation site: G to A, three genotypes (GG, AA and GA) was detected in Chinese local chicken populations and genotype AA wasn't detected in Hisex chicken populations. The chi-square analysis revealed that there was only significant difference between Wenchang and Guyuan populations (P<0.01). It was concluded that there was abundant variation of TYR gene in Chinese local chicken populations. It showed that there was no direct relation between cold tolerance and the variation of regions of exon1 and one locus of 5' flanking region of TYR gene.
(5) In this study, the genetic variations of PPARA gene in 4 chicken populations (Guyuan, Wenchang, Tibetan and Hisex) were detected by PCR-SSCP and DNA sequencing. The results indicated that 6 different genotypes (namely, AA-EF) were detected in four chicken populations at P4 locus. Aligned them with the sequence AF163809, the nucleotide sequences of genotype AA, BB, AB and CC all revealed silent mutations in three Chinese populations. The nucleotide sequences of genotype DD and EF in Hisex showed several frame-shift mutations. It was implied that there were abundant variations of PPARαgene in chicken populations. Moreover, distribution of genotype frequency within PPARαgene was significant difference in 4 populations selected for special purpose in special region. It was implied that this locus could be probably utilized as an effective marker in marker assisted selection for layer, meat and egg concurrent and broiler populations.
It showed that there was direct relation between cold tolerance and the variation of PPARA gene, but which needed to be confirmed further.
(6) In this study, two loci of the gene exon2 and intron 2 of NPY (Neuropeptide Y) gene were analyzed by PCR-SSCP and DNA sequencing. The results indicated that there was significient polymorphism only at NPY2 locous. There was one mutation site: T to C at 1558 nt (Aligned them with GenBank accession No: 3JJM87298), which caused the 23th amino acid variation (Arg to Cys). And only a few genotypes BB were detected in four chicken populations. The chi-square analysis revealed that there was significant difference between cold tolerance populations and Wenchang populations (P<0.01). There was no significant difference between Hesix and other three populations (P>0.05). It showed that there was no direct relation between cold tolerance and the variation of NPY gene. Association analysis between the polymorphisms and body weight growth trait of Guyuan, at NPY2 locus, individuals with genotype AB had higher body weight compared to individuals with genotype AA.
引文
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