Funding information:
Program for Young Outstanding Scientists of University (gxyqZD2022017)
Anhui Poultry-Industry Technology Research System (AHCYJSTX-06-10)
Municipal Science and Technology Cooperation Project (KJ2021564)
Municipal Science and Technology Cooperation Project (KJ20200323)
The Science and Technology Major Project of Anhui Province
(201903a06020018)
Abstract: To investigate
the conservation and phylogenetic relationship with other breeds of the
local Anhui Province Huaibei Grey donkey (HGD), the complete
mitochondrial DNA (mtDNA) was
sequenced and de novo assembled using
deep sequencing data from total genomic DNA. The final size of mtDNA was
16 670 bp (NCBI submission number: MZ911746), including 22 tRNA genes,
two rRNA genes, 13 protein-coding genes (PCGs), and one non-coding
control region. The PCGs region consisted of 5 559 codons. Most of the
PCGs had ATG and TAA as the start and stop codons, respectively. Then we
analyzed the proximal part of the D-loop region (418 bp, between 15 419
bp to 15 836 bp) from HGDs, using DNAsp v6 software. We identified 23
polymorphic nucleotide sites and found that the A, C, G, and T bases
comprised 30.4%, 34.9%, 13.1%, 21.6%, respectively, of the mtDNA
D-loop sequence. The haplotype and nucleotide diversity were 0.87000 and
0.02115, correspondingly. Altogether, the 60 sequences displayed 11
different haplotypes, the most frequent haplotype was H9 (23.33%),
followed by H4 (21.67%). MJ network analysis indicated that all
haplotypes were clearly divided into
Clade Ⅰ and Ⅱ lineages, which indicates that HGD may have two maternal
lineages. Phylogeographic analysis
indicates that the Somali lineage could be the most probable
domestication center for HGD. Our study provides an empirical basis for
the characterization, conservation, and management of HGD genetic
resources.
KEYWORDS: Huaibei grey donkey, mtDNA, D-loop, haplotype,
genetic diversity, maternal origin