Abstract：In China, the pigeon (Columba livia) production ranks fourth after the production of chickens (Gallus gallus), ducks (Anas platyrhynchos), and geese (Anser cygnoides orientalis). The pigeon has many valuable characters, such as high nutritional value and fast growth rate. However, little information is available about the genetic diversity of the pigeons used for agricultural production. The study on the genetic diversity and variety identification of the pigeon is of great significance for genetic conservation and inbreeding programs. The sequence of the mitochondrial cytochrome oxidase subunit Ⅰ (COI) has proven to be useful for the study of the population genetics of domestic animals. For this study, the complete COI gene sequences of 60 pigeons from three breeds (White Feather King, Thaxon, and Silver King) were analyzed. Other COI gene sequences were downloaded from GenBank, including pigeon species from other countries including the rock pigeon (Columba rupestris). No insertions or deletions were found in the COI gene. The sequence read length was 1551 bp, and encoded 517 amino acids. The average nucleotide composition was 25.6% T, 32.1% A, 26.1% C, and 16.2% G, and the content of AT (51.7%) was significantly higher than that of GC (48.3%), indicating slight base bias. Seven polymorphic sites were identified, representing 0.45% of the total analyzed sites. Six haplotypes were identified in 60 pigeons from the 3 investigated populations. The most common haplotype was Hap1, which was present in 26 out the 60 birds and had a frequency of 43.3%. The next-widespread haplotype was Hap 2 with a frequency of 25.0%. Two haplotypes were population-specific: Hap 4 for the White Feather King, Hap 5 for the Silver King pigeon. The overall haplotype diversity was 0.726±0.038. The highest haplotype diversity was found in the Silver King pigeon (0.716±0.069) whereas the lowest diversity was found in the White Feather King pigeon (0.674±0.049). The nucleotide diversity was 0.000 98±0.000 44 across the three investigated breeds, ranging from 0.000 54±0.000 27 in the White Feather King to 0.001 16±0.000 45 in the Silver King pigeon. The overall mean number of nucleotide differences was 1.518. The highest haplotype diversity was found in the Silver King Pigeon (1.795) and the lowest diversity was found in the White Feather King Pigeon (0.842). Based on the COI gene sequences of the 6 haplotypes obtained in this study, and other COI gene sequences, downloaded from GenBank, the rock pigeon (C. rupestris) was used as outgroup, and the molecular phylogenetic tree was constructed by the neighbor-joining method, based on the Kimura-2 parameter mode. Phylogenetic analysis showed that pigeons clustered into 2 cades (A and B). Only one haplotype (Hap 3) was distributed in Clade B, while all other sequences were clustered in Clade A. The median-joining network was constructed using the six haplotypes identified in this study, and the obtained haplotype network showed a star-like phylogeny. Most of the haplotypes were closely related to the common central haplotype (Hap 1), thus suggesting population expansion. The results of this study indicated that the COI gene sequence of pigeons was relatively conservative and contained few mutation sites. This was less effective for the identification of different pigeon breeds. Consequently, there was a high need to incorporate multiple molecular markers such as single nucleotide polymorphism (SNP), simple sequence repeat (SSR), and copy number variations (CNV). The COI gene could be used as a candidate molecular marker to investigate the genetic diversity and origin of pigeon species, and can thus serve as a factual and comparative basis for similar studies in the future.
陆俊贤, 贾晓旭, 付胜勇, 唐修君, 樊艳凤, 葛庆联, 卜柱, 高玉时. 基于COI基因的鸽遗传多样性和品种鉴定研究[J]. 农业生物技术学报, 2020, 28(9): 1635-1641.
LU Jun-Xian, JIA Xiao-Xu, FU Sheng-Yong, TANG Xiu-Jun, FAN Yan-Feng, GE Qing-Lian, BU Zhu, GAO Yu-Shi. Genetic Diversity and Variety Identification Study of Pigeon (Columba livia) with COI Gene. 农业生物技术学报, 2020, 28(9): 1635-1641.
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