Evaluation of the Conservation Status of the Croatian Posavina Horse Breed Based on Pedigree and Microsatellite Data

The Croatian Posavina horse (CPH) is native Croatian breed under a conservation program and under various programs of economic use (ecosystem services, agrotourism, and meat production). The aim of this study was to analyze the status of the CPH population through an analysis of their pedigree (28,483 records), phenotype (292 licensed stallions, 255 mares), and genetic structure (292 licensed stallions). The average generation interval was 8.20 years, and the number of complete generations was 1.66. The effective number of founders and ancestors was 138 and 107, respectively, with a ratio of 1.29, and the genetic conservation index was 4.46. As for the morphometric characteristics, the average withers height of the stallions was 142.79 cm, the chest circumference was 194.28 cm, and the cannon bone circumference was 22.34. In mares, the withers height, chest, and cannon bone circumference were lower (139.71 cm, 190.30 cm, and 20.94 cm, respectively). Genetic microsatellite analysis of the 29 sire-lines showed high genetic diversity, expressed as the mean allele number (7.7), allele richness (4.0), and expected heterozygosity (0.740). There was no evidence of high inbreeding or a genetic bottleneck. The genetic and phenotypic data indicate that the CPH is an important and diverse reservoir of genetic diversity and can be conserved because of its special characteristics (adaptability).

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Diversity Analysis and Genetic Relationships among Local Brazilian Goat Breeds Using SSR Markers

Animals ◽

10.3390/ani10101842 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1842

Author(s):

Marcos Paulo Carrera Menezes ◽

Amparo Martinez Martinez ◽

Edgard Cavalcanti Pimenta Filho ◽

Jose Luis Vega-Pla ◽

Juan Vicente Delgado ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Relationships ◽

Fixation Index ◽

High Genetic Diversity ◽

Allele Number ◽

Hair Samples ◽

The Mean ◽

Polymerase Chain ◽

Single Sequence ◽

Brazilian Populations

The genetic diversity of six Brazilian native goats was reported using molecular markers. Hair samples of 332 animals were collected from different goat breeds (Moxotó, Canindé, Serrana Azul, Marota, Repartida, and Graúna) from five states of Northeast Brazil (Paraíba, Pernambuco, Rio Grande do Norte, Bahia, and Piauí). A panel of 27 microsatellites or single sequence repeats (SSRs) were selected and amplified using a polymerase chain reaction (PCR) technique. All populations showed an average allele number of over six. The mean observed heterozygosity for Brazilian breeds was superior to 0.50. These results demonstrated the high genetic diversity in the studied populations with values ranging from 0.53 (Serrana Azul) to 0.62 (Repartida). The expected average heterozygosity followed the same trend ranging from 0.58 (Serrana Azul) to 0.65 (Repartida), and the values obtained are very similar for all six breeds. The fixation index (Fis) had values under 10% except for the Moxotó breed (13%). The mean expected heterozygosity of all Brazilian populations was over 0.50. Results indicated a within-breed genetic variability in the Brazilian breeds based on the average number of alleles and the average observed heterozygosity. The interbreed genetic diversity values showed proper genetic differentiation among local Brazilian goat breeds.

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Development of microsatellite markers at the National Agrobiodiversity Center in Korea for the genetic assessment of underutilized crops

Plant Genetic Resources ◽

10.1017/s1479262114000525 ◽

2014 ◽

Vol 12 (S1) ◽

pp. S125-S129

Author(s):

Gi-An Lee ◽

Sok-Young Lee ◽

Ho-Sun Lee ◽

Kyung-Ho Ma ◽

Jae-Gyun Gwag ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Germplasm Management ◽

Underutilized Crops ◽

Crop Species ◽

Closely Related Species ◽

Polymorphic Loci ◽

Allele Number ◽

The Mean ◽

Genetic Assessment

The RDA Genebank at the National Agrobiodiversity Center (NAAS, RDA, Republic of Korea) has conserved about 182,000 accessions in 1777 species and is working at preserving agricultural genetic resources for the conservation and sustainable utilization of genetic diversity. The detection of genetic variability in conserved resources is important for germplasm management, but the molecular evaluation tools providing genetic information are insufficient for underutilized crops, unlike those for major crops. In this regard, the Korean National Agrobiodiversity Center has been developing microsatellite markers for several underutilized crops. We designed 3640 primer pairs flanking simple sequence repeat (SSR) motifs for 6310 SSR clones in 21 crop species. Polymorphic loci were revealed in each species (7–36), and the mean ratio of polymorphic loci to all the loci tested was 12%. The average allele number was 5.1 (2.8–10.3) and the expected heterozygosity 0.51 (0.31–0.74). Some SSRs were transferable to closely related species, such as within the genera Fagopyrum and Allium. These SSR markers might be used for studying the genetic diversity of conserved underutilized crops.

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Genetic Diversity among Calamus brandisii Becc. (Arecaceae) Populations in Kerala Part of Western Ghats

Indian Journal of Forestry ◽

10.54207/bsmps1000-2021-xm8ipx ◽

2021 ◽

Vol 43 (1) ◽

pp. 38-42

Author(s):

Kavungal Priya ◽

◽

Indira . ◽

Vadakkethil Balakrishnan Sreekumar ◽

Renuka . ◽

...

Keyword(s):

Genetic Diversity ◽

Western Ghats ◽

Rapd Markers ◽

Gene Diversity ◽

Issr Markers ◽

High Genetic Diversity ◽

Western Ghats Of India ◽

The Mean ◽

Two Parameters ◽

Two Populations

Calamus brandisii Becc. is one of the endemic slender rattans found in the Western Ghats of India. The genetic diversity of two main populations available in Kerala was investigated using 20 RAPD and 9 ISSR markers. Two parameters viz., gene diversity and genetic diversity within and among populations were analyzed. ISSR analysis showed quite high genetic diversity in Pandimotta compared to Bonacaud population whereas in RAPD markers both these populations were moderately diverse. The percentage of total genetic differentiation (Gst) among two populations is relatively higher than the mean Gst value indicating high genetic diversity within the populations. The genetic distance between these two populations was 0.1739 with ISSR markers and 0.1971 with RAPD markers. Because of its high genetic diversity, Pandimotta population can be treated as an important population of gene diversity with potentially useful genes. This may be included in the high priority reservoir for genetic conservation also.

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Microsatellite genotyping from faeces of Lontra longicaudis from southern Brazil

Iheringia Série Zoologia ◽

10.1590/s0073-47212009000100001 ◽

2009 ◽

Vol 99 (1) ◽

pp. 5-11 ◽

Cited By ~ 3

Author(s):

Laura I. Weber ◽

Cintia G. Hildebrand ◽

Anderson Ferreira ◽

Gustavo Pedarassi ◽

José A. Levy ◽

...

Keyword(s):

Genetic Diversity ◽

Conservation Status ◽

Significant Degree ◽

Southern Brazil ◽

High Genetic Diversity ◽

Low Degree ◽

Faecal Samples ◽

High Level ◽

Degree Of Differentiation ◽

Lontra Longicaudis

A genetic study of the neotropical river otter Lontra longicaudis (Olfers, 1818), which has an unknown conservation status, was carried out at the Taim Ecological Station and the margins of the Vargas stream, Rio Grande do Sul, southern Brazil. Faecal samples were collected, and DNA was extracted using a silica-guanidine method. Five microsatellite loci were amplified using PCR with heterologous primers previously described for Lutra lutra (Linnaeus, 1758). Sixteen faecal samples out of 29 from Taim and 11 out of 14 from Vargas stream margins contained enough DNA for genetic analysis. A total of 49 different alleles were found at both localities, from which 18 were exclusively found in individuals from Taim and 17 were exclusives from Vargas individuals. The most common allele was the same at both locations for three loci (Lut715, Lut733, and Lut818). A high level of genetic diversity was found at both sites (NeTaim=4.1, HoTaim=0.299, HeTaim=0.681; NeVargas=4.9, HoVargas=0.355, HeVargas=0.724), being higher at the Vargas stream site. A high and significant level of heterozygote deficiency was observed at most loci according to the χ2 test. The homogeneity χ2 test (P<0.001) showed that there were significant differences in the allele frequencies between the two locations. Genotyping for more than one locus was possible in 81.5% of samples, from which only 37% were possible to genotype for more than three loci. A low degree of relatedness was found among individuals from Taim (R=0.055±0.310), but an even lower value of relatedness was found at the Vargas site (R= -0.285±0.440). The significant degree of differentiation (I=0.890; F ST=0.059) found between Taim and Vargas individuals suggests that there is more than one population of otters in the southern extreme of Brazil, which probably are associated with the water body systems found in this region, the Mirim and the Caiuvá/Flores/Mangueira Lagoons. The high genetic diversity and low relatedness found at the Vargas stream, lead us to believe that the Vargas stream may be acting as a corridor between these water bodies for otter dispersion.

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SSR cross-amplification and variation within coffee trees (Coffea spp.)

Genome ◽

10.1139/g04-064 ◽

2004 ◽

Vol 47 (6) ◽

pp. 1071-1081 ◽

Cited By ~ 42

Author(s):

V Poncet ◽

P Hamon ◽

J Minier ◽

C Carasco ◽

S Hamon ◽

...

Keyword(s):

Genetic Diversity ◽

Null Allele ◽

Polymorphic Locus ◽

Coffea Canephora ◽

Fixation Index ◽

High Genetic Diversity ◽

Allele Number ◽

Primer Sets ◽

Polymorphism Level ◽

Potential Use

Primer sets were developed from 85 Coffea arabica sequences in addition to 25 already published primer sets. They were subsequently used for amplification in six African Coffea species: Coffea canephora (CAN), Coffea eugenioides (EUG), Coffea heterocalyx (HET), Coffea liberica (LIB), Coffea sp. Moloundou (MOL) and Coffea pseudozanguebariae (PSE). The amplification percentages for these 110 primer pairs ranged from 72.7% for LIB to 86.4% for PSE. Good transferability was thus obtained within the Coffea genus. When focusing on the two species CAN and PSE, high genetic diversity, high polymorphic locus rates (above 80%) and a mean allele number per polymorphic locus of more than 3 were noted. The estimated null allele percentage was –11% for PSE and –9% for CAN. Sixty three percent (CAN) and 79.5% (PSE) of the fixation index (Fis) values were positive. The within-species polymorphism information content (PIC) distribution showed two modes for both species. Although the two species shared 30 polymorphic loci, no correlation between CAN and PSE PIC values was obtained. All of these data are discussed in relation to the polymorphism level and the potential use of these SSRs for subsequent analysis of genetic diversity or genetic mapping.Key words: microsatellite, Coffea, transferability, genetic diversity.

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Is it possible to obtain zero estimates of genetic diversity? A case study of the Nigerian indigeneous goat breeds at the β-lactoglobulin gene locus

Biotechnology in Animal Husbandry ◽

10.2298/bah1704375e ◽

2017 ◽

Vol 33 (4) ◽

pp. 375-388

Author(s):

Emeka Ezewudo ◽

Geka Abubakar ◽

Sunday Egena ◽

Olushola Alabi

Keyword(s):

Genetic Diversity ◽

Genetic Distance ◽

Gene Locus ◽

Polymorphic Locus ◽

Information Index ◽

Expected Heterozygosity ◽

Goat Population ◽

The Mean ◽

Β Lactoglobulin

The current investigation was conducted to appraise the genetic diversity and genetic distance of three goat populations namely; Red Sokoto, Sahel and West African Dwarf (WAD), in Nigeria, making use of blood samples collected from 20, 20 and 20 individual from which blood DNAs were extraction, respectively. The DNAs extracted were used to study polymorphism at the ?-lactoglobulin gene locus using RLFP-PCR process. Results revealed that the mean total number of alleles was 1 while the effective number of alleles was also 1. The percentage of polymorphic locus was 0% while Shannon?s information index, observed homozygousity, expected heterozygosity, unbiased expected heterozygosity and inbreeding coefficient (F) were all observed to be 0.000. The pairwise Fst was 0.000 between all the breeds of goats. Variation within and between the populations of goats was 0% at p>0.05. The genetic distance between the goat breeds was 0.000. The present study revealed that RLFP-PCR may not be a powerful tool for the study of the ?-lactoglobulin gene locus and hence other methodologies should be employed for a broader judgment on the genetic status of the goat population at the locus.

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Genetic diversity and conservation of the endemic tuco-tuco Ctenomys ibicuiensis (Rodentia: Ctenomyidae)

Journal of Mammalogy ◽

10.1093/jmammal/gyaa119 ◽

2020 ◽

Author(s):

Mayara Delagnelo Medeiros ◽

Daniel Galiano ◽

Bruno Busnello Kubiak ◽

Paula Angélica Roratto ◽

Thales Renato Ochotorena de Freitas

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Environmental Changes ◽

Isolation By Distance ◽

Conservation Status ◽

Significant Risk ◽

Structured Populations ◽

Small Range ◽

High Genetic Diversity ◽

Landscape Modification

Abstract Endemic, small range species are susceptible to environmental changes and landscape modification. Understanding genetic diversity and distributional patterns is important for implementation of effective conservation measures. In this context, genetic diversity was evaluated to update the conservation status of an endemic tuco-tuco, Ctenomys ibicuiensis. Phylogeographic and population genetic analyses of mitochondrial DNA and microsatellite loci were carried out using 46 individuals sampled across the species’ distribution. Ctenomys ibicuiensis presented moderate to high genetic diversity and highly structured populations with low levels of gene flow and isolation by distance. Anthropogenic landscape changes threaten this restricted-range tuco-tuco. Considering its limited geographic distribution and highly structured populations with low gene flow, we consider C. ibicuiensis to be at significant risk of extinction.

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Exploring the Genetic Diversity of Some Squash (Cucurbita Maxima L.) Germplasm Using Morphological and Molecular Markers in Erzincan

10.21203/rs.3.rs-848708/v1 ◽

2021 ◽

Author(s):

HALIL IBRAHIM OZTURK ◽

Veysel Dönderalp ◽

Hüseyin Bulut ◽

Recep Korkut ◽

Arash HOSSEINPOUR ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Resources ◽

Ssr Markers ◽

Molecular Level ◽

Polymorphic Information Content ◽

Plant Genetic Resources ◽

Molecular Characteristics ◽

Cucurbita Maxima ◽

High Genetic Diversity ◽

The Mean

Abstract Background Plant genetic resources constitute the most valuable assets of countries. It is of great importance to determine the genetic variation among these resources and to use the data in breeding studies. Cucurbita maxima species in the cucurbitaceae family have high genetic diversity, but its genetic diversity at the molecular level is inadequately characterized. Methods and Results To determine the genetic diversity among genotypes of Cucurbita maxima species of squash, which is widely grown in Erzincan, 14 different squash genotypes collected were examined based on the morphological parameters and molecular characteristics. SSR (Simple sequence repeat) markers were used to determine genetic diversity at the molecular level. The analysis of morphological characterization within genotypes showed a wide variability in morphological traits of plant, flower, fruit, and leaf. Seven SSR markers yielded a total of 23 polymorphic bands, the number of alleles per marker ranged from 2 to 5, and the mean number of alleles was 3.286. Polymorphic information content (PIC) ranged from 0.00 (GMT-M61) to 0.202 (GMT-P25), and the mean PIC value per marker was 0.130. Cluster analysis using Nei's genetic distance determined that 14 genotypes were divided into 3 major groups. Conclusions The SSR markers used were effective in distinguish among similar winter squash or pumpkin and therefore can be beneficial for consideration of Cucurbita maxima species diversity, screening of genetic resources and their selection.

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Genetic Diversity of Cambuci (Campomanesia Phaea) Revealed by Microsatellite Markers

10.21203/rs.3.rs-669769/v1 ◽

2021 ◽

Author(s):

Rafael Oliveira Moreira ◽

Eduardo de Andrade Bressan ◽

Horst Bremer Neto ◽

Angelo Pedro Jacomino ◽

Antonio Figueira ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Microsatellite Markers ◽

Native Species ◽

Genetic Parameters ◽

Genomic Library ◽

Conservation Strategies ◽

Paulo State ◽

Allele Number ◽

Expected Heterozygosity

Abstract Campomanesia phaea (Myrtaceae), known as cambuci, is a native species from the Brazilian Atlantic Forest with great potential to be developed as a new fruit crop. Microsatellite markers were developed for cambuci to characterize the genetic diversity and to investigate the genetic structure of a group of accessions originally collected at the presumed center of diversity of the species. The work involved the collection of 145 accessions from five regional groups (Juquitiba, Paraibuna, Mogi das Cruzes, Ribeirão Pires, and Salesópolis) in São Paulo state, Brazil. Fourteen loci were identified in an enriched genomic library developed from one of these accessions. Six out of 14 loci revealed to be polymorphic, disclosing 26 alleles. Based on the allele frequencies, the calculated genetic parameters of the five groups indicated an average allele number per loci (A) of 3.83, with the expected heterozygosity (He) of 0.57 and the observed heterozygosity (Ho) of 0.54. The analysis of the genetic structure indicated that most of the genetic diversity is found within each population (HS = 0.57), whereas the genetic diversity among populations was low (GST = 0.19). The genetic diversity parameter of Nei was considered low for the cambuci analyzed populations, with no evidence of inbreeding. Based on Darwin analysis, we chose 18 accessions from the five regional populations to compose a core collection that includes most of the genetic diversity found in this study. Our findings may contribute to define better conservation strategies and genetic breeding approaches for this native species in Brazil.

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Microsatellite variability reveals high genetic diversity and low genetic differentiation in a critical giant panda population

Current Zoology ◽

10.1093/czoolo/57.6.717 ◽

2011 ◽

Vol 57 (6) ◽

pp. 717-724 ◽

Cited By ~ 2

Author(s):

Jiandong Yang ◽

Zhihe Zhang ◽

Fujun Shen ◽

Xuyu Yang ◽

Liang Zhang ◽

...

Keyword(s):

Genetic Diversity ◽

Genetic Differentiation ◽

Giant Panda ◽

Population Decline ◽

Management Strategies ◽

Ailuropoda Melanoleuca ◽

High Genetic Diversity ◽

Giant Pandas ◽

Allele Number ◽

High Level

Abstract Understanding present patterns of genetic diversity is critical in order to design effective conservation and management strategies for endangered species. Tangjiahe Nature Reserve (NR) is one of the most important national reserves for giant pandas Ailuropoda melanoleuca in China. Previous studies have shown that giant pandas in Tangjiahe NR may be threatened by population decline and fragmentation. Here we used 10 microsatellite DNA markers to assess the genetic variability in the Tangjiahe population. The results indicate a low level of genetic differentiation between the Hongshihe and Motianling subpopulations in the reserve. Assignment tests using the Bayesian clustering method in STRUCTURE identified one genetic cluster from 42 individuals of the two subpopulations. All individuals from the same subpopulation were assigned to one cluster. This indicates high gene flow between subpopulations. F statistic analyses revealed a low FIS-value of 0.024 in the total population and implies a randomly mating population in Tangjiahe NR. Additionally, our data show a high level of genetic diversity for the Tangjiahe population. Mean allele number (A), Allelic richness (AR) and mean expected heterozygosity (HE) for the Tangjiahe population was 5.9, 5.173 and 0.703, respectively. This wild giant panda population can be restored through concerted effort.

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