Evaluation of the genetic diversity of some rare geese breeds based on microsatellite markers

Microsatellites were utilized to determine the genetic diversity and estimate the relationship between 9 goose populations. A total of 58 unique alleles were found in all 9 populations, and the allele frequency ranged from 0.71% (Toulouse breed: TOU) to 18.33% (local Egyptian breed of grey colour: LB1). The effective number of alleles ranged from 2.04 (Wanxi breed: WX) to 5.36 (Emden breed: EMED), observed heterozygosity ranged from 0.37 (WX) to 0.62 (EMED), and expected heterozygosity was reported in the range of 0.43 (WX) to 0.7 (EMED). The results revealed highly polymorphic content of the tested loci, with three populations [WX, Sichuan breed (SC), Zhejiang breed (ZHE)] reported to be slightly polymorphous. Within the 9 populations, breeding coefficient (Fis) ranged from 0.03 (EMED) to 0.26 (WX). The phylogenetic tree showed two clades: the first clade contained LB1 and the three Chinese breeds (ZHE, WX, SC), while the second clade contained the local Egyptian breed of white colour (LB2) and Pilgrim breed (PIL) and the three western breeds [Roman tufted breed (ROT), TOU, EMED]. Only three populations showed distinct boundaries at clustering (SC, ZHE, WX), which was found by structure analysis. Principal coordinates analysis 2D and 3D scatter plots were constructed for distinct population structure distribution results, confirming the geographical distribution of the breeds. The deviation of the principal coordinates' analysis from the F-1 axis was 54.01% and from F-2 was 15.37%. Finally, self-organised map node arrangements represented the relationship and the interaction between different populations, providing an idea about the population structure of rare and indigenous goose breeds, especially the two Egyptian local breeds LB1 and LB2. The aim of this study was to determine genetic diversity and genetic correlation using 9 microsatellite markers in order to explore the breeding history of the investigated rare goose breeds, to provide data on changes in population structure, and to provide the basis for the development of appropriate plans to improve population growth for respective environmental needs with some emphasis on the conservation of genetic resources.