Evaluation of genetic diversity and population structure of five Chinese indigenous donkey breeds using microsatellite markers

Di, Rui; Liu, Q.Y.; F, Xie; Hu, Wenping; Wang, X.-Y.; Cao, Xufeng; Pan, Z.-Y.; Chen, G.-H.; Chu, Mingxing

doi:10.17221/9/2016-cjas

Cited by 5 publications

(9 citation statements)

References 28 publications

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“…These results are comparable to the previous values reported in Balkan donkeys [35], Spanish donkeys [36] and Catalonian donkeys [37]. In terms of mean number of alleles, the genetic variability observed in the 16 Turkish donkey populations was lower than that reported in Catalonian donkey breed [37], five Spanish breeds [36], three Croatian donkey populations [38], 15 indigenous Chinese donkey breeds [39][40][41][42], Balkan donkeys [35] and Tunisian donkeys [43], but higher than that observed in the seven indigenous Italian donkey breeds [44][45][46][47].…”

Section: Discussionsupporting

confidence: 82%

“…The results of microsatellite polymorphism revealed relatively high degree of heterozygosity in the Turkish donkey populations investigated in this study. Among Turkish donkey populations, the H E ranged from 0.6294 (ISP) to 0.6983 (ANT), which showed a comparable level to the previous values reported in Spanish donkeys [ 36 ], Catalonian donkey breeds [ 37 ], Croatian coast donkey populations [ 48 ], Balkan donkey breeds [ 35 ], Tunisian donkeys [ 43 ], Chinese donkey breeds [ 39 , 40 , 41 , 42 ] and was more diversified than Italian [ 44 , 45 , 46 , 47 ] and American donkeys [ 49 ]. This finding indicates that there are appreciable differences in the level of genetic variability among 16 Turkish donkey populations.…”

Section: Discussionsupporting

confidence: 81%

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Genetic Characterization of Native Donkey (Equus asinus) Populations of Turkey Using Microsatellite Markers

Yatkın

Özdil

Ünal

et al. 2020

Animals

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This study presents the first insights to the genetic diversity and structure of the Turkish donkey populations. The primary objectives were to detect the main structural features of Turkish donkeys by microsatellite markers. A panel of 17 microsatellite markers was applied for genotyping 314 donkeys from 16 locations of Turkey. One hundred and forty-two alleles were identified and the number of alleles per locus ranged from 4 to 12. The highest number of alleles was observed in AHT05 (12) and the lowest in ASB02 and HTG06 (4), while ASB17 was monomorphic. The mean HO in the Turkish donkey was estimated to be 0.677, while mean HE was 0.675. The polymorphic information content (PIC) was calculated for each locus and ranged from 0.36 (locus ASB02) to 0.98 (locus AHT05), which has the highest number of alleles per locus in the present study. The average PIC in our populations was 0.696. The average coefficient of gene differentiation (GST) over the 17 loci was 0.020 ± 0.037 (p < 0.01). The GST values for single loci ranged from −0.004 for LEX54 to 0.162 for COR082. Nei’s gene diversity index (Ht) for loci ranged from 0.445 (ASB02) to 0.890 (AHT05), with an average of 0.696. A Bayesian clustering method, the Structure software, was used for clustering algorithms of multi-locus genotypes to identify the population structure and the pattern of admixture within the populations. When the number of ancestral populations varied from K = 1 to 20, the largest change in the log of the likelihood function (ΔK) was when K = 2. The results for K = 2 indicate a clear separation between Clade I (KIR, CAT, KAR, MAR, SAN) and Clade II (MAL, MER, TOK, KAS, KUT, KON, ISP, ANT, MUG, AYD and KAH) populations.

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Section: Discussionsupporting

confidence: 82%

Section: Discussionsupporting

confidence: 81%

Genetic Characterization of Native Donkey (Equus asinus) Populations of Turkey Using Microsatellite Markers

Yatkın

Özdil

Ünal

et al. 2020

Animals

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“…These results indicate that there are no appreciable differences in the level of genetic variability among the Croatian donkey breeds. Istrian donkey and Littoral-Dinaric donkey populations have a lower average number of alleles compared to five native Spanish breeds (range from 7.0 to 7.5) [14], four Chinese breeds (range from 6.0 to 6.80) [58], or donkey breeds from the Balkans (9.3) [19], but they are higher than two Sicilian native breeds (4.05) [59]. Comparing observed and expected heterozygosity, the values of Istrian donkey and Littoral-Dinaric donkey populations are mostly between the reported values of previous studies [20,58], with averages of H O = 0.560 and H E = 0.70, and H O = 0.63-0.71, H E = 0.93-0.70.…”

Section: Discussionmentioning

confidence: 94%

Genetic and Population Structure of Croatian Local Donkey Breeds

Ivanković

Bittante

Šubara³

et al. 2022

Diversity

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The two native Croatian donkey breeds (Littoral-Dinaric donkey and Istrian donkey) were marginalized in the second half of the 20th century and were on the verge of biological extinction. The aim of this study was to analyze the demographic and genetic status of two donkey breeds, two decades after the start of protection by analyzing their pedigrees and genetic structure. The average generation interval was higher for the Istrian donkey (7.73) than for the Littoral-Dinaric donkey (7.27). The rate of the effective number of founders compared with the effective number of ancestors in the Littoral-Dinaric donkey (1.03; 325/316) and in the Istrian donkey (1.08; 70/65) revealed no evidence of a genetic bottleneck. The inbreeding coefficient (F) and the average relatedness coefficient (AR) was lower in the Littoral-Dinaric donkey population (0.99%; 0.13%) than in the Istrian donkey population (1.77%; 1.10%). Genetic microsatellite analysis showed relatively high genetic diversity in Littoral-Dinaric donkey and Istrian donkey breeds, expressed by mean allele number (5.92; 5.85) and expected heterozygosity (0.650; 0.653). Genetic differentiation between the Littoral-Dinaric donkey and the Istrian donkey has not significantly increased in the last two decades (FST = 0.028). Genetic analysis also showed no evidence of high inbreeding or genetic bottleneck in both breeds. A total of 11 haplotypes including 28 polymorphic sites were found in 30 samples. Analysis of mtDNA has shown that the Littoral-Dinaric donkey and Istrian donkey breeds belong to the Equus asinus africanus group. The study confirms the need to use different analytical approaches to get a regular and complete insight into the situation and trends within and between breeds, so that the existing diversity can be fully preserved.

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“…The results indicated that the microsatellites of similar species are conserved and could be used to analyze the genetic diversity of donkeys. Researchers also needed to have a deeper understanding of the genetic information and genetic relationships within and among breeds to obtain more accurate and generalized conclusions, which could be more effectively applied to the conservation and further utilization of donkey breeds [ 35 , 36 , 37 ]. In terms of average allele number, the genetic variability observed in three Sicilian donkey breeds should be lower than in five Spanish and three Croatian breeds but higher than in the Italian Amiata donkey [ 38 ].…”

Section: Research On Genetic Materialsmentioning

confidence: 99%

Origin, Evolution, and Research Development of Donkeys

Wang

Hua

Shi

et al. 2022

Genes

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Lack of archaeological and whole-genome diversity data has restricted current knowledge of the evolutionary history of donkeys. With the advancement of science and technology, the discovery of archaeological evidence, the development of molecular genetics, and the improvement of whole-genome sequencing technology, the in-depth understanding of the origin and domestication of donkeys has been enhanced, however. Given the lack of systematic research, the present study carefully screened and collected multiple academic papers and books, journals, and literature on donkeys over the past 15 years. The origin and domestication of donkeys are reviewed in this paper from the aspects of basic information, cultural origin, bioarcheology, mitochondrial and chromosomal microsatellite sequences, and whole-genome sequence comparison. It also highlights and reviews genome assembly technology, by assembling the genome of an individual organism and comparing it with related sample genomes, which can be used to produce more accurate results through big data statistics, analysis, and computational correlation models. Background: The donkey industry in the world and especially in China is developing rapidly, and donkey farming is transforming gradually from the family farming model to large-scale, intensive, and integrated industrial operations, which could ensure the stability of product quality and quantity. However, theoretical research on donkey breeding and its technical development lags far behind that of other livestock, thereby limiting its industrial development. This review provides holistic information for the donkey industry and researchers, that could promote theoretical research, genomic selection (GS), and reproductive management of the donkey population.

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Evaluation of genetic diversity and population structure of five Chinese indigenous donkey breeds using microsatellite markers

Cited by 5 publications

References 28 publications

Genetic Characterization of Native Donkey (Equus asinus) Populations of Turkey Using Microsatellite Markers

Genetic Characterization of Native Donkey (Equus asinus) Populations of Turkey Using Microsatellite Markers

Genetic and Population Structure of Croatian Local Donkey Breeds

Origin, Evolution, and Research Development of Donkeys

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