河北柴鸡MC1R基因变异研究
摘要
黑素皮质素受体1 (melanocortin 1 Receptor,MC1R)基因作为影响家禽羽色遗传的一个重要基因,本研究以MC1R基因作为影响家禽羽色的候选基因,采用PCR产物直接测序的方法,对河北柴鸡的黑羽、灰麻、黄麻和白羽四个色系,以及海兰褐和罗曼褐两个配套系红羽鸡MC1R基因的整个编码区进行了单核苷酸多态性(Single Nucleotide Polymorphism,SNP)筛查和遗传多样性分析,并采用SNPs基因型频率和单倍型等位基因频率相结合的方法分析了MC1R基因SNPs与鸡羽色的关系,以及各羽色中等位基因的分布情况,以探讨MC1R基因变异对河北柴鸡对羽色遗传的影响,从而为河北柴鸡新品系的选育提供参考依据。
结果表明,经过一个世代的提纯,主要羽色类型,即灰麻和黄麻在整个品种中的含量分别提高了7.52%和7.60%。尤其灰麻在整个品种中居于主要地位,所占比例接近60%,为今后今后的提纯扩繁打下了基础。并且这两个色系的各核苷酸多样性参数也有所降低,纯合基因型e+ (AB220303)/e+ (AB220303)和e+ (Brown Leghone)/e+ (Brown Leghone)的分布明显增多,提纯效果比较显著。
利用PCR产物直接测序法,在所有分析群体的鸡MC1R基因编码区筛查到18个SNPs,而在河北柴鸡中发现10个新SNPs,即97T>A、178G>A、207G>A、334C>T、398T>C、409G>A、486C>T、550delA、551delA和552delC(或552C>T)。然后对各群体进行遗传多样性分析,发现河北柴鸡各色系的单倍型多样性(0.727~0.905)、核苷酸多样性(0.0039~0.0052)和平均核苷酸差异数(2.551~3.381)都明显比海兰褐和罗曼褐高。
通过对MC1R基因各SNPs与羽色相关性分析,发现9个SNPs,即69C>T、212T>C、274G>A、376G>A、398T>C、427A>G、636G>A、637T>C和644A>C所形成的各种MC1R基因型与鸡羽色性状均达到了极显著或显著水平。并结合氨基酸水平的单倍型等位基因分布进行了分析,推测Val126Ile突变(376G>A)可能也会形成一个组成型活性受体,与Glu92Lys突变共同影响真黑素的分布。
根据对各单倍型等位基因在不同羽色中分布的统计,发现河北柴鸡的黑羽系以显性等位基因E (AY220304)为主;灰麻和黄麻系分别以隐性等位基因e+ (AY220303)和e+ (Brown Leghone)为主;其中e+ (Brown Leghone)是海兰褐和罗曼褐这两种红羽鸡的优势等位基因。另外,罗曼褐中Allele18的频率也较高,结合该品种的选育途径,推测该等位基因可能是eWh。
本研究结果表明,经过一个世代的选育,河北柴鸡羽色的选育均取得了一定进展,并且该品种的MC1R基因遗传多样性丰富,与其丰富的羽色相应,可以为今后的选育提供优良基因资源。某些SNPs与羽色显著或极显著相关,推测MC1R基因是鸡羽色的主要候选基因。
Melanocortin-1-receptor (MC1R), an important gene in investigation on the genetic of poultry plumage color, was used as a candidate gene affecting plumage color with the method of PCR amplication and directly sequencing in this study. The screening of Single Nucleotide Polymorphism (SNP) within the whole encoding region of MC1R gene and genetic diversity were analyzed with four color strains consisting of Hebei Domestic Chicken (black, gray plumage color with black spots, yellow plumage color with black spots and white) and two red plumage color commercial chicken (Hy-Line Variety Brown and Lohmann Brown). The correlation between SNPs of MC1R gene and poultry plumage color, and allele distribution in different plumage color were analyzed combined with SNPs genotype frequency and haplotype allele frequency, in order to discuss with the effect of MC1R gene on plumage color heridity of Hebei Domestic Chicken and provide reference to the selection of new strain in Hebei Domestic Chicken.
The results showed that the size percentage of gray plumage color with black spots chicken and yellow plumage color with black spots chicken, the main plumage color trait in this study, was increased by 7.52% and 7.60%, especially the population size of gray plumage color with black spots chicken prevailed with nearly 60%, which provides the basis for purification and reproduction in the future. And that the nucleotide diversity of the two plumage color strains was reduced. The distribution of homozygous genotype, e+ (AB220303)/e+ (AB220303) and e+ (Brown Leghone)/e+ (Brown Leghone) was increased significantly, which indicated that the selection had made progress.
Eighteen SNPs were detected within MC1R gene encoding region in all analyzed populatons by direct sequencing of PCR amplification product, and ten novel SNPs (97T>A, 178G>A, 207G>A, 334C>T, 398T>C, 409G>A, 486C>T, 550delA, 551delA and 552delC (or 552C>T) was found in Hebei Domestic Chicken. The genetic dversity analysis indicated that the haplotype diversity (0.727~0.905), the nucleotide diversity (0.0039~0.0052) and the average number of nucleotide differences (2.551~3.381) within each color strain of Hebei Domestic Chicken were all significantly greater than that of Hy-Line Variety Brown and Lohmann Brown.
The genotype of nine SNPs (69C>T, 212T>C, 274G>A, 376G>A, 398T>C, 427A>G, 636G>A, 637T>C and 644A>C) was significantly correlated to chicken plumage color, and then analysis combined with which and haplotype allele distribution in different different plumage color, it was deduced that the Val126Ile mutation (376G>A) might lead to a constitutive activity receptor and affect the eumelanin pigmentation together with Glu92Lys mutation.
According to the distribution of haplotype allele in different plumage color, it was found that the black strain of Hebei Domestic Chicken was characterized with the type of dominant allele E(AY220304); recessive allele e+ (AY220303) and e+ (Brown Leghone) were the predominant allele of gray plumage color with black spots and yellow plumage color with black spots, respectively; recessive allele e+ (Brown Leghone) was mainly in the two red plumage color chicken of Hy-Line Variety Brown and Lohmann Brown. Besides, it was deduced that the Allele18 might be eWh allele, in view of the higher frequency of Allele18 detected in Rohman Brwon and the selection approach of this breed.
The results of the study indicated that the selection of plumage color made progress in some way, and there were extensive variation whin MC1R gene of Hebei Domestic Chicken, corresponding to the abundant plumage color, consequently provides excellent genetic resources for further selection breeding. Some SNPs of MC1R gene significantly related to the plumage color, conferring that the MC1R gene is the candidate gene that affecting chicken plumage color.
结果表明,经过一个世代的提纯,主要羽色类型,即灰麻和黄麻在整个品种中的含量分别提高了7.52%和7.60%。尤其灰麻在整个品种中居于主要地位,所占比例接近60%,为今后今后的提纯扩繁打下了基础。并且这两个色系的各核苷酸多样性参数也有所降低,纯合基因型e+ (AB220303)/e+ (AB220303)和e+ (Brown Leghone)/e+ (Brown Leghone)的分布明显增多,提纯效果比较显著。
利用PCR产物直接测序法,在所有分析群体的鸡MC1R基因编码区筛查到18个SNPs,而在河北柴鸡中发现10个新SNPs,即97T>A、178G>A、207G>A、334C>T、398T>C、409G>A、486C>T、550delA、551delA和552delC(或552C>T)。然后对各群体进行遗传多样性分析,发现河北柴鸡各色系的单倍型多样性(0.727~0.905)、核苷酸多样性(0.0039~0.0052)和平均核苷酸差异数(2.551~3.381)都明显比海兰褐和罗曼褐高。
通过对MC1R基因各SNPs与羽色相关性分析,发现9个SNPs,即69C>T、212T>C、274G>A、376G>A、398T>C、427A>G、636G>A、637T>C和644A>C所形成的各种MC1R基因型与鸡羽色性状均达到了极显著或显著水平。并结合氨基酸水平的单倍型等位基因分布进行了分析,推测Val126Ile突变(376G>A)可能也会形成一个组成型活性受体,与Glu92Lys突变共同影响真黑素的分布。
根据对各单倍型等位基因在不同羽色中分布的统计,发现河北柴鸡的黑羽系以显性等位基因E (AY220304)为主;灰麻和黄麻系分别以隐性等位基因e+ (AY220303)和e+ (Brown Leghone)为主;其中e+ (Brown Leghone)是海兰褐和罗曼褐这两种红羽鸡的优势等位基因。另外,罗曼褐中Allele18的频率也较高,结合该品种的选育途径,推测该等位基因可能是eWh。
本研究结果表明,经过一个世代的选育,河北柴鸡羽色的选育均取得了一定进展,并且该品种的MC1R基因遗传多样性丰富,与其丰富的羽色相应,可以为今后的选育提供优良基因资源。某些SNPs与羽色显著或极显著相关,推测MC1R基因是鸡羽色的主要候选基因。
Melanocortin-1-receptor (MC1R), an important gene in investigation on the genetic of poultry plumage color, was used as a candidate gene affecting plumage color with the method of PCR amplication and directly sequencing in this study. The screening of Single Nucleotide Polymorphism (SNP) within the whole encoding region of MC1R gene and genetic diversity were analyzed with four color strains consisting of Hebei Domestic Chicken (black, gray plumage color with black spots, yellow plumage color with black spots and white) and two red plumage color commercial chicken (Hy-Line Variety Brown and Lohmann Brown). The correlation between SNPs of MC1R gene and poultry plumage color, and allele distribution in different plumage color were analyzed combined with SNPs genotype frequency and haplotype allele frequency, in order to discuss with the effect of MC1R gene on plumage color heridity of Hebei Domestic Chicken and provide reference to the selection of new strain in Hebei Domestic Chicken.
The results showed that the size percentage of gray plumage color with black spots chicken and yellow plumage color with black spots chicken, the main plumage color trait in this study, was increased by 7.52% and 7.60%, especially the population size of gray plumage color with black spots chicken prevailed with nearly 60%, which provides the basis for purification and reproduction in the future. And that the nucleotide diversity of the two plumage color strains was reduced. The distribution of homozygous genotype, e+ (AB220303)/e+ (AB220303) and e+ (Brown Leghone)/e+ (Brown Leghone) was increased significantly, which indicated that the selection had made progress.
Eighteen SNPs were detected within MC1R gene encoding region in all analyzed populatons by direct sequencing of PCR amplification product, and ten novel SNPs (97T>A, 178G>A, 207G>A, 334C>T, 398T>C, 409G>A, 486C>T, 550delA, 551delA and 552delC (or 552C>T) was found in Hebei Domestic Chicken. The genetic dversity analysis indicated that the haplotype diversity (0.727~0.905), the nucleotide diversity (0.0039~0.0052) and the average number of nucleotide differences (2.551~3.381) within each color strain of Hebei Domestic Chicken were all significantly greater than that of Hy-Line Variety Brown and Lohmann Brown.
The genotype of nine SNPs (69C>T, 212T>C, 274G>A, 376G>A, 398T>C, 427A>G, 636G>A, 637T>C and 644A>C) was significantly correlated to chicken plumage color, and then analysis combined with which and haplotype allele distribution in different different plumage color, it was deduced that the Val126Ile mutation (376G>A) might lead to a constitutive activity receptor and affect the eumelanin pigmentation together with Glu92Lys mutation.
According to the distribution of haplotype allele in different plumage color, it was found that the black strain of Hebei Domestic Chicken was characterized with the type of dominant allele E(AY220304); recessive allele e+ (AY220303) and e+ (Brown Leghone) were the predominant allele of gray plumage color with black spots and yellow plumage color with black spots, respectively; recessive allele e+ (Brown Leghone) was mainly in the two red plumage color chicken of Hy-Line Variety Brown and Lohmann Brown. Besides, it was deduced that the Allele18 might be eWh allele, in view of the higher frequency of Allele18 detected in Rohman Brwon and the selection approach of this breed.
The results of the study indicated that the selection of plumage color made progress in some way, and there were extensive variation whin MC1R gene of Hebei Domestic Chicken, corresponding to the abundant plumage color, consequently provides excellent genetic resources for further selection breeding. Some SNPs of MC1R gene significantly related to the plumage color, conferring that the MC1R gene is the candidate gene that affecting chicken plumage color.
引文
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