scholarly journals Genetic Diversity of 17 Autochthonous Italian Chicken Breeds and Their Extinction Risk Status

2021 ◽  
Vol 12 ◽  
Author(s):  
Dominga Soglia ◽  
Stefano Sartore ◽  
Emiliano Lasagna ◽  
Cesare Castellini ◽  
Filippo Cendron ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Extinction Risk ◽  
Low Frequency ◽  
Effective Number ◽  
Risk Of Extinction ◽  
Chicken Breeds ◽  
Inbreeding Rate ◽  
The Mean ◽  
Endangered Status

The preservation of genetic variability of autochthonous poultry breeds is crucial in global biodiversity. A recent report revealed small breed size and potential risk of extinction of all native Italian poultry breeds; therefore, a correct assessment of their genetic diversity is necessary for a suitable management of their preservation. In this work, we provided an overview of the contribution to poultry biodiversity of some Italian autochthonous breeds reared in conservation centers devoted to local biodiversity preservation. The level of genetic diversity, molecular kinship, inbreeding, contribution to overall genetic diversity, and rate of extinction of each breed were analyzed with a set of 14 microsatellite loci in 17 autochthonous chicken breeds. To evaluate genetic variability, total number (Na), and effective number (Ne) of alleles, observed (Ho) and expected (He) heterozygosity, and F (Wright’s inbreeding coefficient) index were surveyed. The contribution of each analyzed breed to genetic diversity of the whole dataset was assessed using MolKin3.0; global genetic diversity and allelic richness contributions were evaluated. All the investigated loci were polymorphic; 209 alleles were identified (94 of which private alleles). The average number of alleles per locus was 3.62, and the effective number of alleles was 2.27. The Ne resulted lower in all breeds due to the presence of low-frequency alleles that can be easily lost by genetic drift, thus reducing the genetic variability of the breeds, and increasing their risk of extinction. The global molecular kinship was 27%, the average breed molecular kinship was 53%, and the mean inbreeding rate 43%, with a self-coancestry of 78%. Wright’s statistical analysis showed a 41% excess of homozygous due to breed genetic differences (34%) and to inbreeding within the breed (9%). Genetic variability analysis showed that 11 breeds were in endangered status. The contribution to Italian poultry genetic diversity, estimated as global genetic diversity, and ranged from 30.2 to 98.5%. In conclusion, the investigated breeds maintain a unique genetic pattern and play an important role in global Italian poultry biodiversity, providing a remarkable contribution to genetic variability.

scholarly journals Population genetic variability and distribution of the endangered Greek endemic Cicer graecum under climate change scenarios

AoB Plants ◽  
2020 ◽  
Vol 12 (2) ◽  
Author(s):  
Efthalia Stathi ◽  
Konstantinos Kougioumoutzis ◽  
Eleni M Abraham ◽  
Panayiotis Trigas ◽  
Ioannis Ganopoulos ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Diversity ◽  
Genetic Variability ◽  
Hot Spot ◽  
Extinction Risk ◽  
Aflp Markers ◽  
Ex Situ ◽  
Dominant Factor ◽  
Climate Change Scenarios ◽  
Global Circulation Models

Abstract The Mediterranean hot spot includes numerous endemic and socio-economically important plant species seriously threatened by climate change and habitat loss. In this study, the genetic diversity of five populations of Cicer graecum, an endangered endemic species from northern Peloponnisos, Greece and a wild relative of the cultivated Cicer arietinum, was investigated using inter-simple sequence repeats (ISSRs) and amplified fragment length polymorphism (AFLP) markers in order to determine levels and structure of genetic variability. Nei’s gene diversity by ISSR and AFLP markers indicated medium to high genetic diversity at the population level. Moreover, AMOVA results suggest that most of the variation exists within (93 % for AFLPs and 65 % for ISSRs), rather than among populations. Furthermore, Principal Component Analysis based on ISSRs positively correlated the genetic differentiation among the populations to the geographic distances, suggesting that the gene flow among distant populations is limited. The ecological adaptation of C. graecum populations was also investigated by correlation of their genetic diversity with certain environmental variables. Aridity arose as the dominant factor positively affecting the genetic diversity of C. graecum populations. We modelled the realized climatic niche of C. graecum in an ensemble forecasting scheme under three different global circulation models and two climate change scenarios. In all cases, a severe range contraction for C. graecum is projected, highlighting the high extinction risk that is probably going to face during the coming decades. These results could be a valuable tool towards the implementation of an integrated in situ and ex situ conservation scheme approach for activating management programmes for this endemic and threatened species.

Genetic variability at allozyme markers in sycamore (Acer pseudoplatanus) populations from northwestern Italy

2007 ◽  
Vol 37 (2) ◽  
pp. 395-403 ◽  
Author(s):  
P. Belletti ◽  
I. Monteleone ◽  
D. Ferrazzini
Keyword(s):  
Genetic Variability ◽  
Single Gene ◽  
Acer Pseudoplatanus ◽  
Effective Number ◽  
Expected Heterozygosity ◽  
Slight Excess ◽  
Forest Reproductive Material ◽  
Native Populations ◽  
Reproductive Material ◽  
The Mean

Genetic diversity and differentiation of 12 native populations of sycamore ( Acer pseudoplatanus L.) from northwestern Italy were investigated by means of variation detected in 10 polymorphic isozyme systems encoded by 16 loci. The trees showed relatively large genetic variability (mean number of alleles per locus = 2.78, effective number of alleles per locus = 1.47, percentage of polymorphic loci = 96.9, expected heterozygosity = 0.280) but small interpopulational variation (FST = 0.019), suggesting the presence of a single gene pool. A slight excess of heterozygotes was found, and the overall inbreeding coefficient (FIS) was –0.038. There was a positive correlation between the age of the individuals sampled and heterozygosity, suggesting the occurrence of natural selection against homozygotes. No significant correlation was detected between genetic and geographic distances of populations, confirming the lack of any barriers to gene flow. Estimate of the mean effective number of migrants exchanged between populations was 4.399, based on the private alleles method. The contribution of the results in relation to terms of the most appropriate strategies to preserve genetic variability of sycamore and to collect forest reproductive material is discussed.

scholarly journals Genetic Diversity and Variability in Endangered Pantesco and Two Other Sicilian Donkey Breeds Assessed by Microsatellite Markers

2012 ◽  
Vol 2012 ◽  
pp. 1-6 ◽  
Author(s):  
Salvatore Bordonaro ◽  
Anna Maria Guastella ◽  
Andrea Criscione ◽  
Antonio Zuccaro ◽  
Donata Marletta
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Genetic Information ◽  
Gene Diversity ◽  
Genetic Distances ◽  
Conservation Strategies ◽  
Population Structure Analysis ◽  
The Mean ◽  
Differentiation Index

The genetic variability of Pantesco and other two Sicilian autochthonous donkey breeds (Ragusano and Grigio Siciliano) was assessed using a set of 14 microsatellites. The main goals were to describe the current differentiation among the breeds and to provide genetic information useful to safeguard the Pantesco breed as well as to manage Ragusano and Grigio Siciliano. In the whole sample, that included 108 donkeys representative of the three populations, a total of 85 alleles were detected. The mean number of alleles was lower in Pantesco (3.7), than in Grigio Siciliano and Ragusano (4.4 and 5.9, resp.). The three breeds showed a quite low level of gene diversity (He) ranging from 0.471 in Pantesco to 0.589 in Grigio. The overall genetic differentiation index (Fst) was quite high; more than 10% of the diversity was found among breeds. Reynolds’ () genetic distances, correspondence, and population structure analysis reproduced the same picture, revealing that, (a) Pantesco breed is the most differentiated in the context of the Sicilian indigenous breeds, (b) within Ragusano breed, two well-defined subgroups were observed. This information is worth of further investigation in order to provide suitable data for conservation strategies.

scholarly journals Genetic characterization of Cycas panzhihuaensis (Cycadaceae): crisis lurks behind a seemingly bright prospect

2018 ◽  
Author(s):  
Siyue Xiao ◽  
Yunheng Ji ◽  
Jian Liu ◽  
Xun Gong
Keyword(s):  
Genetic Diversity ◽  
Genetic Characterization ◽  
Extinction Risk ◽  
Demographic History ◽  
Single Copy ◽  
Jinsha River ◽  
High Genetic Diversity ◽  
Natural Reserve ◽  
Endangered Status

Background Cycas panzhihuaensis L. Zhou & S. Y. Yang (Cycadaceae) is an endangered gymnosperm species endemic in the dry-hot valley of Jinsha River basin from southwest China. Although the wild C. panzhihuaensis population from Panzhihua Cycad Natural Reserve is well protected, other known populations that fall outside the natural reserve may preserve specific genetic resources while face with larger extinction risk because of lacking essential monitoring. Methods In this study, we analyzed the genetic diversity, phylogeographical structure and demographic history of C. panzhihuaensis from seven known locations so far by sequencing three chloroplastic DNA regions (psbA-trnH, psbM-trnD, and trnS-trnG), four single-copy nuclear genes (PHYP, AC5, HSP70, and AAT) from 61 individuals, and eleven microsatellite loci (SSR) from 102 individuals. Results and Discussion We found relative high genetic diversity within populations and high genetic differentiation among the populations of C. panzhihuaensis, which is similar with the other Asian inland cycads. Despite no significant phylogeographical structure was detected, small and unprotected populations possess higher genetic diversity and more unique haplotypes, which deserve due attention. Results of demographic dynamics suggest that human activity is the key factor that leads C. panzhihuaensis to endangered status. Basing on the genetic characterization of C. panzhihuaensis, we proposed several practical guidelines for the conservation of this species, especially for its small populations.

scholarly journals Testing the breeding strategy of Hungarian Bronze turkey strains for maintaining genetic diversity with microsatellites

2011 ◽  
Vol 54 (4) ◽  
pp. 419-429
Author(s):  
S. Kusza ◽  
S. Mihók ◽  
L. Czeglédi ◽  
A. Jávor ◽  
M. Árnyasi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Mating System ◽  
Breeding Strategy ◽  
Shannon Index ◽  
Inbreeding Coefficient ◽  
Control Population ◽  
Conservation Strategies ◽  
The Mean ◽  
Two Populations

Abstract. The aim of the study was to provide information on the genetic variability of the Hungarian Bronze turkey gene reserve population and its difference from the Broad-breasted turkey, and offer guidance and proposals for its future conservation strategies. Altogether, 239 Hungarian Bronze turkeys from 10 strains and 13 Broad-breasted turkeys as a control population were genotyped for 15 microsatellites. All loci were polymorphic with the average number of alleles per locus 3.20±1.146 in the Hungarian Bronze turkey. The mean expected (Hexp) and observed heterozygosity (Hobs) were not different (0.392 and 0.376, respectively) in the overall population, and similar values were obtained for hens and bucks and among hen strains. Inbreeding coefficient (FIS) and Shannon index (I) indicated that there was low inbreeding within hens and bucks. Our results confirm that the genetic diversity in the Hungarian Bronze turkey population has been preserved by the rotational mating system. Differences between the Hungarian Bronze turkey and the Broad-breasted turkey populations were determined. Nei’s unbiased values clearly indicated that the two populations are highly genetically differentiated.

scholarly journals Genetic diversity of Ukrainian local pig breeds based on microsatellite markers

2018 ◽  
Vol 9 (2) ◽  
pp. 177-182 ◽  
Author(s):  
S. S. Kramarenko ◽  
S. I. Lugovoy ◽  
V. R. Kharzinova ◽  
V. Y. Lykhach ◽  
A. S. Kramarenko ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Microsatellite Markers ◽  
Pig Breeds ◽  
Genetic Groups ◽  
The Mean ◽  
Living Material ◽  
The Individual ◽  
High Degree ◽  
Private Alleles

Preserving the current diversity of the living material on Earth is fundamental for the survival of future generations . A study was conducted to investigate the genetic diversity of Ukrainian local pig breeds. A total of 350 pigs representing five local pig breeds from Ukraine (Mirgorod – MIR, Poltava Meat – PM, Ukrainian Meat – UM, Ukrainian White Steppe – UWS and Ukrainian Spotted Steppe – USS) and one commercial breed (Duroc, DUR) were sampled. Twelve microsatellite loci (SW24, S0155, SW72, SW951, S0386, S0355, SW240, SW857, S0101, SW936, SW911 and S0228) were selected and belong to the list of microsatellite markers recommended by ISAG. The results indicate that there exists, in general, a high degree of genetic variability within the five Ukrainian local pig breeds. However, the genetic variability in the MIR and PM breeds was significantly lower (mean Na = 2.92–3.92; Ho = 0.382–0.411; FIS = 0.178–0.184) than in the other three Ukrainian local pig breeds – UM, UWS and USS (mean Na = 5.00–8.42; Ho = 0.549–0.668; FIS = 0.027–0.066). Thirty-four private alleles were identified among the six analyzed genetic groups which were distributed between 11 of the 12 loci. A high number of alleles typical for the breed (private alleles) was observed in Duroc pigs – 9 alleles did not occur in Ukrainian local pig breeds. The HWE test showed that all of the polymorphic loci deviated from HWE (P < 0.05) in at least one population. Loci S0355 (5), S0386 (4) and SW24 (4) presented a higher number of populations in imbalance. The mean FST showed that approximately 77.8% of the genetic variation was within-population and 12.2% was across the populations. The five Ukrainian local breeds were classified into two major groups, according to the phylogenetic tree, which was based on standard genetic distance. Overall, we found that 92.6% of the individual pigs were correctly assigned (324 out of 350) to the respective breed of origin, which is likely a consequence of the well-defined breed structure. Probabilities from the allocation test of individuals for the six pig genetic groups were estimated with Structure Harvester. In cluster 1 the highest grouping probabilities were found for the MIR (0.917) and PM (0.750) breeds. Local breeds UM (0.824) and USS (0.772) were grouped in cluster 2. Cluster 3 was related to the local pig breed USW (0.873). Cluster 4 presented high allocation probabilities for the commercial pig breed Duroc (0.924). The obtained results are important for the future conservation of Ukrainian local pig breeds.

scholarly journals Pedigree analysis in four Slovak endangered horse breeds

2012 ◽  
Vol 57 (No. 2) ◽  
pp. 54-64 ◽  
Author(s):  
J. Pjontek ◽  
O. Kadlečík ◽  
R. Kasarda ◽  
M. Horný
Keyword(s):  
Genetic Diversity ◽  
Pedigree Analysis ◽  
Effective Number ◽  
Identity By Descent ◽  
Average Value ◽  
The Mean ◽  
Gene Origin

The aim of this study was to perform an analysis of genetic diversity in four endangered horse populations bred in Slovakia, describing parameters on the probability of identity by descent and gene origin. The analysed populations consisted of (reference populations in brackets) 656 (158) Hucul horses, 2052 (162) Lipizzan horses, 1951 (171) Shagya Arabian horses, and 220 (42) Slovak Sport Ponies. The equivalent complete generations ranged from 4.93 for the Slovak Sport Pony to 10.25 for the Lipizzan horses. The average value of inbreeding ranged from 2.67% for the Slovak Sport Pony to 6.26% for the Hucul. The mean average relationship coefficients varied from 3.08% for the Shagya Arabian to 9.34% for the Hucul. Individual increases in inbreeding ranged from 0.43% for the Lipizzan to 1.06% for the Hucul, while the realized effective sizes were from 117.14 to 47.67 animals. The evaluated populations were derived from 80 to 499 founders. The effective number of founders ranged from 26 to 160, while the effective number of ancestors from 7 to 32. &nbsp;

Pedigree analysis of Polish warmblood horses participating in riding performance tests

2015 ◽  
Vol 95 (1) ◽  
pp. 21-29 ◽  
Author(s):  
Alicja Borowska ◽  
Tomasz Szwaczkowski
Keyword(s):  
Genetic Diversity ◽  
Performance Test ◽  
Pedigree Analysis ◽  
Pedigree Information ◽  
Performance Tests ◽  
Effective Number ◽  
Horse Population ◽  
Inbreeding Coefficients ◽  
Discrete Generation ◽  
Inbreeding Rate

Borowska, A. and Szwaczkowski, T. 2015. Pedigree analysis of Polish warmblood horses participating in riding performance tests. Can. J. Anim. Sci. 95: 21–29. The aim of this study was to describe the population structure and genetic diversity in Polish warmblood horse population participating in the performance test. The reference population consisted of 596 stallions and 866 mares that participated in stationary performance tests conducted between 2002 and 2011 in Poland. The pedigree data contained 15 452 individuals. Completeness of pedigree information was assessed by two measures: percentage of animals with both parents known and discrete generation equivalent. Individual inbreeding coefficients, coancestry coefficient, individual increase in inbreeding, founder equivalent, founder genome equivalent, effective number of non-founders and genetic diversity loss were estimated to characterize the genetic diversity of the population. The average number of discrete generation equivalents reached 4.50 for observed stallions and 5.04 for mares, which shows good pedigree completeness. Pedigree analysis showed that 34% of the stallions and 44% of mares had inbreeding coefficients above zero. The average coancestry was 0.39% in the whole tested population. Average inbreeding rate of studied populations was very low (0.46%). The effective number of founders was 560. Generally, the inbreeding rate was low; genetic diversity was observed at a constant level for mares and only a small decrease was noticed for stallion. However, further studies are needed in this area.

scholarly journals Genetic diversity assessment of an indigenous horse population of Greece

2017 ◽  
Vol 33 (1) ◽  
pp. 81-90
Author(s):  
George Laliotis ◽  
Meni Avdi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Pedigree Data ◽  
Horse Population ◽  
Heterozygote Deficit ◽  
Diversity Assessment ◽  
The Mean ◽  
North Western ◽  
Insular Region ◽  
Of Greece

Highly endangered local breeds are considered important not only for the maintenance of their genetic diversity for future survival but also because they regarded as part of the cultural heritage of the local and national communities. Using pedigree data and an analysis of 18 microsatellite loci we investigated the genetic diversity of a private (commercial) indigenous Skyros horse population, reared in an insular region of North-Western of Greece. The overall average animal inbreeding value reached 24%. Concerning average inbreeding value over non founding animals, it was estimated to 0.013, while the corresponding value over inbred animals were 0.13.The mean number of alleles per locus amounted to 3.72, ranging between 1 and 7 alleles. The average observed heterozygosity was 0.57. Taking into account the inbreeding estimated index, an average heterozygote deficit (Fis) of -0.09 was noted (P<0.05). Although the population maintained reasonable levels of genetic diversity, well studied inbreeding strategies should be implemented, in order to reduce the loss of genetic variability, to avoid extinction and further genetic drift of the population.

scholarly journals Microsatellite analysis of pacu broodstocks used in the stocking program of Paranapanema River, Brazil

2011 ◽  
Vol 68 (3) ◽  
pp. 308-313 ◽  
Author(s):  
Jayme Aparecido Povh ◽  
Ricardo Pereira Ribeiro ◽  
Nelson Mauricio Lopera-Barrero ◽  
Carolina Bespalhok Jacometo ◽  
Lauro Vargas ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Null Allele ◽  
Gene Diversity ◽  
Genetic Difference ◽  
Low Frequency ◽  
Bottleneck Effect ◽  
Reproductive Management ◽  
The Mean ◽  
Positive Coefficients ◽  
Recent Bottleneck

Monitoring the genetic diversity has fundamental importance for fish stocking programs. This experiment aims to evaluate the genetic diversity in two hatchery stations (A and B) with pacu Piaractus mesopotamicus (Holmberg, 1887) in Andirá, state of Paraná, Brazil used in stocking programs of Paranapanema River. Six microsatellite loci were amplified using DNA extracted from 60 fin-clipping samples. The broodstock B had the average number of alleles and the mean heterozygosity (alleles: 3.7 and H O: 0.628) higher than the broodstock A (alleles: 3.5 and H O: 0.600). Alleles with low frequency levels were observed in the both broodstocks. The positive coefficients of endogamy in the locus Pme2 (broodstock A: F IS = 0.30 and broodstock B: F IS = 0.20), Pme5 (broodstock B: F IS = 0.15), Pme14 (broodstock A: F IS = 0.07) and Pme28 (broodstock A: F IS = 0.24 and broodstock B: F IS = 0.20) indicated deficiency of heterozygotes. Presence of null allele in the locus Pme2 was detected. The negative estimates in loci Pme4 (broodstock A: F IS = - 0.43 and broodstock B: F IS = - 0.37), Pme5 (broodstock A: F IS= - 0.11), Pme14 (broodstock B: F IS= - 0.15) and Pme32 (broodstock A: F IS = - 0.93 and broodstock B: F IS = - 0.60) were indicating the excess of heterozygotes. Evidence of linkage disequilibrium and lower allelic richness was found only in the broodstock A. Nei's gene diversity was high in both broodstocks. The genetic distance (0.085) and identity (0.918) showed similarity between broodstocks, which reflects a possible common origin. 6.05% of the total genetic variance was due to differences among broodstocks. Recent bottleneck effect in two broodstocks was observed. The results indicated a higher genetic diversity in the two broodstocks and they presented low genetic difference. This was caused by the reproductive management in both hatchery stations, reduction of population size and genetic exchange between the hatchery stations.

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