Monitoring of genetically close Tsaiya duck populations using novel microsatellite markers with high polymorphism

Abstract

Objective: A set of microsatellite markers with high polymorphism from Tsaiya duck were used for the genetic monitoring and genetic structure analysis of Brown and White Tsaiya duck populations in Taiwan.Methods: The synthetic short tandem repeated probes were used to isolate new microsatellite markers from the genomic DNA of Tsaiya ducks. Eight populations, a total of 566 samples, sourced from Ilan Branch, Livestock Research Institute were genotyped through novel and known markers. The population genetic variables were calculated using optional programs in order to describe and monitor the genetic variability and the genetic structures of these Tsaiya duck populations.Results: In total 24 primer pairs, including 17 novel microsatellite loci from this study and seven previously known loci, were constructed for the detection of genetic variations in duck populations. The average values for the allele number, the effective number of alleles, the observed heterozygosity, the expected heterozygosity, and the polymorphism information content were 11.29, 5.370, 0.591, 0.746, and 0.708, respectively. The results of analysis of molecular variance and principal component analysis indicated a contracting Brown Tsaiya duck cluster and a spreading White Tsaiya duck cluster. The Brown Tsaiya ducks and the White Tsaiya ducks with Pekin ducks were just split to six clusters and three clusters when K was set equal to 6 and 3 in the Bayesian cluster analysis. The individual phylogenetic tree revealed eight taxa, and each individual was assigned to its own population.Conclusion: According to our study, the 24 novel microsatellite markers exhibited a high capacity to analyze relationships of inter- and intra-population in those populations with a relatively limited degree of genetic diversity. We suggest that duck farms in Taiwan could use the new (novel) microsatellite set to monitor the genetic characteristics and structures of their Tsaiya duck populations at various intervals in order to ensure quality breeding and conservation strategies.

Monitoring changes in the genetic structure of Brown Tsaiya duck selected for feeding efficiency by microsatellite markers

“…All markers were highly polymorphic, except for APT001 and APT032, which were moderately polymorphic [35](unpublished). Compared to our study, the study with the newly screened markers from Brown Tsaiya duck, there was an average Na was 11.3 per locus, the mean Ne was 5.4, the mean HO was 0.591, the mean HE was 0.747, and the mean PIC was 0.708 [14]; the genetic variation was slightly higher than in this study.…”

“…The AMOVA results for the second and eighth generations (Table 6) indicate that the primary genetic variation was between individuals. The variance ratio in the eighth generation is similar to that of other study on Brown Tsaiya ducks [14]. However, because the study included several lines of Brown Tsaiya ducks, the variance among the populations was slightly higher than that in this A c c e p t e d A r t i c l e study.…”

“…The pairwise FST values of the seventh and eighth generations between the selected and control lines (i.e., Brown Tsaiya LRI 1) in this study were 0.1123 and 0.1271, respectively. Similar to the genetic analysis of Taiwan's duck breeds and lines [14] indicated that the range of FST between Brown Tsaiya duck lines (preserved Brown Tsaiya duck, Brown Tsaiya LRI 1, LRI 2, and LRI 3) separated by more than ten generations was 0.092 to 0.167. The result indicated that the differentiation between the selected and control lines has reached the level of different lines.…”

“…(7/24, 29%) [14]. The study also indicated HO is less than HE in Taiwan's duck breeds and lines, even in the germplasm-conserved Brown Tsaiya duck and White Tsaiya duck with rotational mating schemes and without selection.…”

“…Compared with the germplasm-preserved Brown Tsaiya duck (without selection), there was almost no change in genetic variations between the population separated by two generations, while RFC control line showed a decrease in the number of allele and heterozygosity [13]. Lai et al also showed that compared with germplasm-preserved Brown Tsaiya duck, the Brown Tsaiya duck lines selected for specific traits had higher values in within-population inbreeding coefficient (FIS) and more markers deviating from Hardy-Weinberg equilibrium [14]. Since the RFC selected line is still under selection, to ensure sustainable management, the aim of this study is to integrate our previous study and conduct genotyping in subsequent generations of the RFC selected and control line to evaluate the effects of continuous selection and breeding strategies on the genetic variation and differentiation over A c c e p t e d A r t i c l e time.…”