Analysis of the Mitochondrial COI Gene and Genetic Diversity of Endangered Goose Breeds

Abstract

The mitochondrial cytochrome c oxidase subunit I (COI) genes of six endangered goose breeds (Xupu, Yangjiang, Yan, Wuzong, Baizi, and Lingxian) were sequenced and compared to assess the genetic diversity of endangered goose breeds. By constructing phylogenetic trees and evolutionary maps of genetic relationships, the affinities and degrees of genetic variations among the six different breeds were revealed. A total of 92 polymorphic sites were detected in the 741 bp sequence of the mtDNA COI gene after shear correction, and the GC content of the processed sequence (51.11%) was higher than that of the AT content (48.89%). The polymorphic loci within the populations of five of the six breeds (Xupu, Yangjiang, Yan, Baizi, and Lingxian) were more than 10, the haplotype diversity > 0.5, and the nucleotide diversity (Pi) > 0.005, with the Baizi geese being the exception. A total of 35 haplotypes were detected based on nucleotide variation among sequences, and the goose breed haplotypes showed a central star-shaped dispersion; the FST values were -0.03781 to 0.02645, The greatest genetic differentiation (FST = 0.02645) was observed in Yan and Wuzong breeds. The most frequent genetic exchange (Nm > 15.00) was between the Wuzong and Yangjiang geese. An analysis of molecular variance showed that the population genetic variation mainly came from within the population; the base mismatch differential distribution analysis of the goose breeds and the Tajima's D and Fu's Fs neutral detection of the historical occurrence dynamics of their populations were negative (p > 0.10). The distribution curve of the base mismatches showed a multimodal peak, which indicated that the population tended to be stabilised. These results provide important genetic information for the conservation and management of endangered goose breeds and a scientific basis for the development of effective conservation strategies.

Keywords: COI gene; endangered goose; evolutionary analysis; genetic diversity.

Figure 1

Goose breeds used in the study.

Figure 2

Design of the primers.

Figure 3

Example of standard pattern obtained for the analysis of the PCR products on 1% agarose gel electrophoresis.

Figure 4

Median-joining network diagram constructed based on COI gene haplotypes. Each circle represents a unique haplotype, the colour represents endangered geese of different breeds, and the size of the circle is proportional to the number of isolates contained. The lines (shaded markers) on the branches indicate the location of the mutation, with one line for each mutation.

Figure 5

Distribution of variable loci based on haplotype control of the mtDNA COI gene. Note: “*” indicates base-identical sequences; “-” indicates a base deletion.

Figure 6

MEGA11 phylogeny (maximum-likelihood) map, constructed on the basis of mtDNA COI sequences from the six breeds of geese.

Figure 7

Distribution of base difference mismatches in the mt COI gene sequence of endangered goose breeds.