Characterisation of the complete mitochondrial genome, genetic diversity and maternal origin of Huainan Partridge chicken

1. The objectives of the present study were to investigate the complete mitochondrial genome, genetic diversity and maternal origin of Huainan Partridge chicken (HPC). 2. One complete mitochondrial genome and 37 complete D-loop regions of HPC were sequenced. Moreover, 400 mitochondrial genome D-loop sequences of Chinese native chicken were downloaded from the National Centre for Biotechnology Information database. 3. The complete HPC genome was 16,785 bp in size, including 22 tRNA genes, two rRNA genes, 13 protein-coding genes and one non-coding control region. The haplotype diversity and nucleotide diversity of HPC were 0.964, and 0.00615, respectively. Twenty-three variable sites defining 22 haplotypes were identified, and the 22 haplotypes were distributed into three haplogroups (A, B, and C). 4. In conclusion, HPC has a typical vertebrate mitochondrial genome, relatively high haplotype diversity, relatively low nucleotide diversity, and potentially three maternal lineages. HPC showed considerable genetic information exchange with Southwest Chinese chicken populations and had not admixed with European commercial breeds in the course of domestication.

1. 本研究旨在探究淮南麻黄鸡（Huainan Partridge chicken, HPC）的完整线粒体基因组、遗传多样性及母系起源。2. 本研究共测序获得1份淮南麻黄鸡的完整线粒体基因组序列与37份完整D-loop区序列；此外，从美国国家生物技术信息中心（National Centre for Biotechnology Information, NCBI）数据库下载了400条中国地方鸡的线粒体基因组D-loop区序列。3. 淮南麻黄鸡的完整线粒体基因组全长16785 bp，包含22个转运RNA（tRNA）基因、2个核糖体RNA（rRNA）基因、13个蛋白质编码基因及1个非编码控制区。该群体的单倍型多样性与核苷酸多样性分别为0.964和0.00615。本研究共鉴定出23个变异位点，可界定22种单倍型，且这22种单倍型可划分为A、B、C共3个单倍群。4. 综上，淮南麻黄鸡拥有典型的脊椎动物线粒体基因组，单倍型多样性相对较高，核苷酸多样性相对较低，且潜在存在3个母系血统。该群体与中国西南地区的鸡群存在较为显著的遗传信息交流，且在驯化过程中未与欧洲商业品种发生遗传混杂。