基于线粒体 DNA D-loop 全序列的麒麟鸡遗传多样性研究

李威娜 1; 2; 3; 郭美慧 1; 温锦添 1; 翁茁先 1; 2; 3; 陈洁波 3; 杜炳旺 1; 2; 3; 黄勋和 1; 2; 3

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李威娜 1,2,3，郭美慧 1，温锦添 1，翁茁先 1,2,3，陈洁波 3，杜炳旺 1,2,3，黄勋和 1,2,3.基于线粒体 DNA D-loop 全序列的麒麟鸡遗传多样性研究[J].广东农业科学,2023,50(4):100-107

查看全文 HTML 基于线粒体 DNA D-loop 全序列的麒麟鸡遗传多样性研究

Study on Genetic Diversity of Qilin Chicken Based on Complete Mitochondrial DNA D-loop Sequences

DOI：10.16768/j.issn.1004-874X.2023.04.012

中文关键词: 麒麟鸡线粒体 DNA（mtDNA） D-loop 全序列遗传多样性系统进化

英文关键词: Qilin chicken mitochondrial DNA (mtDNA) D-loop complete sequence genetic diversity phylogeny

基金项目:嘉应学院大学生创新创业训练项目（嘉院校办〔2021〕20 号）；广东省驻镇帮镇扶村农村科技特派员项目（KTP20210218）；广东省重点建设学科科研能力提升项目（2022ZDJS088）；湛江市科技计划项目（2020A04008）

作者	单位
李威娜 1,2,3，郭美慧 1，温锦添 1，翁茁先 1,2,3，陈洁波 3，杜炳旺 1,2,3，黄勋和 1,2,3	1. 嘉应学院生命科学学院，广东梅州 514015；2. 广东省山区特色农业资源保护与精准利用重点实验室，广东梅州 514015；3. 广东省五华三黄鸡科技创新中心，广东梅州 514015

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中文摘要:

【目的】从线粒体 DNA（mtDNA） D-loop 全序列角度评估麒麟鸡的遗传多样性水平，以期阐明麒麟鸡的品种形成。【方法】通过 PCR 产物直接测序法对麒麟鸡保种群的黄羽、白羽和黑羽 3 个资源群及 8 个地方鸡品种进行 mtDNA D-loop 全序列测定，分析遗传变异，并进行中性检测，构建单倍型中介网络图，探究麒麟鸡的群体历史。【结果】麒麟鸡 mtDNA D-loop 全序列为 1 231~1 232 bp，C+G 含量（39.8%）低于 T+A 含量（60.2%），总体核苷酸多样性为 0.00630±0.00054，明显高于其他 8 个地方鸡品种。3 个资源群黄羽、白羽和黑羽麒麟鸡的单倍型多样性分别为 0.777±0.076、0.816±0.060、0.710±0.057，核苷酸多样性分别为 0.00699±0.00115、0.00662 ±0.00090、0.00546±0.00062，遗传多样性水平基本上与群体规模呈正相关。麒麟鸡与 8 个地方鸡的双参数遗传距离为 0.008~0.009，净遗传距离为 0.003~0.005，均大于其他地方鸡之间的遗传距离。90 份麒麟鸡样本共检测到45 个突变位点，定义了 17 个单倍型，其中独享型单倍型 9 个，单倍型多样性为 0.773±0.039。黄羽、白羽和黑羽麒麟鸡的单倍型数量分别为 12、7、5 个。8 个地方鸡品种定义了 19 个单倍型，其中河田鸡的单倍型数量最多（8个），宁都黄鸡的最少（3 个），没有与麒麟鸡共享的单倍型。中性检测结果显示，除了黑羽麒麟鸡外，供试鸡种在品种水平上近期均未经历明显的种群扩张。麒麟鸡单倍型类群主要分布在进化枝 A、B、C 和 E，优势单倍型类群是 B（30.0%）和 E（64.4%）；8 个地方鸡单倍型类群主要为 A 和 B。【结论】独特的单倍型提示麒麟鸡具有独立的品种形成历史，相对较高的遗传多样性水平将有利于其保护和利用工作的开展。

英文摘要:

【Objective】The study was carried out to evaluate genetic diversity level of Qilin chicken inferred from complete mitochondrial DNA (mtDNA) D-loop sequences in order to clarify the bread formation of Qilin chicken.【Method】Three populations (yellow, white and black-feathered Qilin chickens) and eight indigenous chicken breeds were used for direct sequencing with PCR products of complete mtDNA D-loop region, and these sequences were then used to calculate the genetic variation and neutral test, to construct median networks of haplotypes and to investigate the breeding history of Qilin chickens.【Result】The length of mtDNA D-loop complete sequence ranged from 1 231 to 1 232 bp. The content of C+G (39.8%) was lower than that of T+A (60.2%). The total nucleotide diversity of Qilin chickens was 0.00630±0.00054, which was significantly higher than that of each of the eight indigenous chicken breeds. The haptype diversity and nucleotide diversity in yellow, white and black-feathered Qilin chickens were 0.777±0.076, 0.816±0.060, 0.710±0.057 and 0.00699±0.00115, 0.00662±0.00090, 0.00546±0.00062, respectively. The level of genetic diversity was positively correlated with population size. The K2P genetic distance and net genetic distance between Qilin chickens and eight indigenous chicken breeds ranged from 0.008 to 0.009 and 0.003 to 0.005, respectively, which were greater than those between the eight indigenous chicken breeds. A total of 45 mutation sites were detected in 90 samples of Qilin chickens. Seventeen haplotypes were defined in Qilin chickens, with eight exclusive haplotypes and haplotype diversity of 0.773±0.039. The numbers of haptypes of yellow, white and black-feathered Qilin chickens were 12, 7 and 5, respectively. Nineteen haplotypes were defined in eight adjacent indigenous chicken breeds, and no haplotype was shared with Qilin chickens. The number of haptypes of Hetian chicken (8) was greater than that of other chickens, and Ningdu yellow chicken only had three haptypes.The neutral test indicated that all chickens used in this study did not show obvious population expansion at the breed level, with the exception of black-feathered Qilin chickens. The haplotypes of Qilin chickens were distributed in clades A, B, C and E, and the dominated haplogroups were B (30.0%) and E (64.4%). The haplotypes of the eight indigenous chicken breeds were mainly distributed in clades A and B.【Conclusion】Unique haptypes indicated that Qilin chickens had an independent breed formation history, and the relatively higher level of genetic diversity of this breed will facilitate its protection and utilization.

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