Genetic Characterization of the “Chusca Lojana”, a Creole Goat Reared in Ecuador, and Its Relationship with Other Goat Breeds

The largest population of goats (62%) in Ecuador is in the dry forest region in the south of the country. A Creole goat, named “Chusca Lojana”, has adapted to the dry forest region where environmental conditions are warm-dry, with sparse vegetation. Knowledge of the genetic information of the Creole goat is important to determine intra-racial diversity, the degree of genetic distance among other breeds of goats, and the possible substructure of the population, which is valuable for the conservation of such a species’ genetic resources. A total of 145 samples of the Creole goat was taken from the four biotypes previously identified. Genetic analyses were performed using 38 microsatellites recommended for studies of goat genetic diversity (FAO-ISAG). The results of within-breed genetic diversity showed a mean number of alleles per locus (MNA) of 8, an effective number of alleles (Ae) of 4.3, an expected heterozygosity (He) of 0.71, an observed heterozygosity (Ho) of 0.63, polymorphic information content (PIC) of 0.67, and an FIS value of 0.11. Between-breed genetic diversity among 43 goat populations (native of Spain, American Creole, Europeans, and Africans) showed the following values: FIS = 0.087, FIT = 0.176, and FST = 0.098. Regarding the analysis of the population structure, the results showed that the Creole Chusca Lojana goat population is homogeneous and no genetic separation was observed between the different biotypes (FST = 0.0073). In conclusion, the Chusca Lojana goat has a high genetic diversity, without exhibiting a genetic substructure. Therefore, it should be considered as a distinct population because crossbreeding with other breeds was not detected.

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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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Assessment of genetic diversity using DNA markers among Brassica rapa var. yellow sarson germplasm lines collected from Eastern Uttar Pradesh and Uttarakhand hills

Journal of Applied and Natural Science ◽

10.31018/jans.v8i3.963 ◽

2016 ◽

Vol 8 (3) ◽

pp. 1333-1340

Author(s):

Harsha Harsha ◽

Jitendra Kumar Meena ◽

Ram Bhajan ◽

Usha Pant ◽

Mohammed Talha

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Polymorphic Information Content ◽

Random Amplified Polymorphic Dna ◽

Similarity Coefficient ◽

Principal Coordinate Analysis ◽

Molecular Profile ◽

Polymorphic Band ◽

Germplasm Management ◽

High Genetic Diversity

The genetic diversity and the relatedness among thirty-one germplasm lines of yellow sarson collected from eastern UP were evaluated using morphological characters and Random Amplified Polymorphic DNA (RAPD) markers. Molecular parameters, viz. A total number of bands, average polymorphic band, average percent polymorphism, average polymorphic information content (PIC), Jaccardâ€™s similarity coefficient, Principal Coordinate Analysis (PCA) and dendrogram generated using RAPD markers. A total of 148 different polymorphic amplification products were obtained using 10 selected decamer primers. The Jaccard similarity coefficient ranged from 0.557-0.899. Maximum polymorphism detected was 100 %.The range of amplification was from 190bp to 9 kb. Some unique bands were also reported with different primers that can be used for the identification of particular accession. PYSC-11-11 and PYSC-11-36 genotypes showed a maximum number of unique loci of different size. 31 germplasm lines grouped into two major clusters I and II based on RAPD profiling. Morphological characterization was done on the basis of leaf, petal and beak characteristics. The similarity value among the germplasm lines ranged from 0.222 to 1.000 using morphological descriptors. The dendrogram generated grouped the germplasm accession into two major groups at 44% similarity value. The cluster analysis was comparable up to some extent with Principal Coordinate Analysis (PCA) of two and three-dimensional plots. The variability revealed by morphological and molecular profile were found to be non-comparable. This study indicated the presence of high genetic diversity among collected yellow sarson germplasm, which could be used for developing for breeding and germplasm management purposes.

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RETRACTED ARTICLE: Comparison of traditional and new generation DNA markers declares high genetic diversity and differentiated population structure of wild almond species

Scientific Reports ◽

10.1038/s41598-017-06084-4 ◽

2017 ◽

Vol 7 (1) ◽

Cited By ~ 14

Author(s):

Karim Sorkheh ◽

Mehrana Koohi Dehkordi ◽

Sezai Ercisli ◽

Attila Hegedus ◽

Júlia Halász

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Large Scale ◽

Polymorphic Information Content ◽

Inter Simple Sequence Repeat ◽

High Genetic Diversity ◽

Hrm Analysis ◽

And Performance ◽

Wild Almond ◽

Simple Sequence

Abstract Wild almond species as sources of genetic variation may have crucial importance in breeding. A total of 389 accessions of 18 species have been analysed using inter-retrotransposon amplified polymorphism (IRAP), retrotransposon-microsatellite amplified polymorphism (REMAP), sequence-specific amplification polymorphism (S-SAP), amplified fragment length polymorphism (AFLP), inter simple sequence repeat (ISSR) and simple sequence repeats (SSR). Retrotransposon markers indicated the presence and movement of some Ty3-gypsy and Ty1-copia-elements in almond genome. Since transposable elements are associated with large-scale genome alterations, REMAP produced more reliable phylogenetic inferences than AFLP where homoplasy may affect clustering. In addition, high resolution melting (HRM) analysis was developed to detect SNPs. HRM analysis revealed 1:189 bp frequency of SNPs in exon positions, and the transition-to-transversion proportion was 1.84:1. The low transition bias suggests low methylation levels in almond genome. The polymorphic information content (PIC) was the highest for SSR markers, while SNPs had an average PIC of 0.59, which is close to the values of the rest of the markers. Huge genetic diversity, fragmented population structure and footprints of human selection was confirmed by merging information from all marker strategies. Considering time, cost and performance HRM can be a marker of choice in future studies of Prunus diversity.

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Genetic Diversity and Population Structure of Llamas (Lama glama) from the Camelid Germplasm Bank—Quimsachata

Genes ◽

10.3390/genes11050541 ◽

2020 ◽

Vol 11 (5) ◽

pp. 541

Author(s):

Gabriela F. Paredes ◽

Claudia E. Yalta-Macedo ◽

Gustavo A. Gutierrez ◽

Eudosio A. Veli-Rivera

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Genetic Variability ◽

Polymorphic Information Content ◽

South American ◽

Germplasm Bank ◽

Genetic Stock ◽

High Genetic Diversity ◽

Lama Glama ◽

Global Population

Llamas (Lama glama) are invaluable resources of Peru. Despite their importance, their population is decreasing. The Camelid Germplasm Bank—Quimsachata was created as a guardian of this South American camelid (SAC) species and established a bank of llamas from their two types, Ch’aku and Q’ara. However, these populations need to present high genetic diversity to be considered suitable conservation stocks. Thus, in the present study, 13 microsatellites specific for the SAC were used to assess the current genetic variability and differentiation of the llama population from the Bank. The global population showed high genetic diversity with a total of 157 different alleles, with an average of 12.08 alleles per microsatellite, an expected and observed heterozygosity of 0.758 and 0.707, respectively, and an average polymorphic information content (PIC) of 0.723. Although considered as two different breeds and managed separately, the genetic differentiation between Ch’aku and Q’ara was low (FST = 0.01). Accordingly, the gene flow value was high (Nm = 30.5). Overall, our results indicate the existence of high genetic variation among individuals, and thus, this llama population could be considered a suitable genetic stock for their conservation and for sustainability programs. Additionally, the 13 microsatellites can be used to study other Peruvian llama populations and monitor the genetic variability of llamas from the Camelid Germplasm Bank—Quimsachata.

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Mitochondrial DNA D-loop sequence variability reveals high haplotype diversity and multiple maternal origins in twelve indigenous goat populations from Tanzania.

10.22541/au.161478201.16689055/v1 ◽

2021 ◽

Author(s):

Athumani Nguluma

Keyword(s):

Genetic Diversity ◽

Mitochondrial Dna ◽

Haplotype Diversity ◽

Capra Hircus ◽

Maternal Origin ◽

High Genetic Diversity ◽

Ecological Zones ◽

Goat Population ◽

D Loop ◽

Indigenous Goats

The Small East African (SEA) goat (Capra hircus) breeds are widely distributed in different agro-ecological zones of Tanzania. We report the genetic diversity, maternal origin, and phylogenetic relationship among the 12 Tanzanian indigenous goats populations, namely Fipa (n = 44), Songwe (n = 34), Tanga (n = 33), Pwani (n = 40), Newala (n = 49), Lindi (n = 46), Gogo (n = 73), Pare (n = 67), Maasai (n = 72), Sukuma (n = 67), and Ujiji (n = 67), based on the mitochondrial DNA (mtDNA) D-loop. High haplotype (Hd = 0.9619-0.9945) and nucleotide (π = 0.0120-0.0162) diversities were revealed from a total of 389 haplotypes. The majority of the haplotypes (h = 334) drawn from all the goat populations belonged to Haplogroup A which was consistent with the global scenario on the genetic pattern of maternal origin of all goat breeds in the world. Haplogroup G comprised of 45 haplotypes drawn from all populations except the Ujiji goat population while Haplogroup B with 10 haplotypes was dominated by Ujiji goats (41%). Tanzanian goats shared four haplotypes with the Kenyan goats and two with goats from South Africa, Namibia, and Mozambique. There was no sharing of haplotypes observed between individuals from Tanzanian goat populations with individuals from North or West Africa. The indigenous goats in Tanzania have high genetic diversity defined by 389 haplotypes and multiple maternal origins of haplogroup A, B and G. There is a lot of intermixing and high genetic variation within populations which represent an abundant resource for selective breeding in the different agro-ecological regions of the country.

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Assessment of molecular diversity in landraces of bread wheat (Triticum aestivum L.) held in an ex situ collection with Diversity Arrays Technology (DArT™)

Australian Journal of Agricultural Research ◽

10.1071/ar07010 ◽

2007 ◽

Vol 58 (12) ◽

pp. 1174 ◽

Cited By ~ 20

Author(s):

B. J. Stodart ◽

M. C. Mackay ◽

H. Raman

Keyword(s):

Genetic Diversity ◽

Molecular Diversity ◽

Polymorphic Information Content ◽

Ex Situ ◽

Dart Markers ◽

Strong Positive Correlation ◽

High Genetic Diversity ◽

Diversity Arrays Technology ◽

Wheat Landraces ◽

Landrace Accessions

Diversity Arrays Technology (DArT™) was evaluated as a tool for determining molecular diversity of wheat landraces held within the Australian Winter Cereals Collection (AWCC). Initially, a set of 44 wheat landraces was evaluated with 256 DArT markers. The dataset was compared with the results obtained using 16 amplified fragment length polymorphism (AFLP) primer combinations and 63 simple sequence repeat (SSR) markers, mapped on the 21 chromosomes, from a previous study. The DArT markers exhibited a strong positive correlation with AFLP and SSR, with each marker type distinguishing similar relationships among the 44 landrace accessions. The DArT markers exhibited a higher polymorphic information content than AFLP, and were comparable with that obtained with SSR. Three hundred and fifty-five DArT markers were then used to evaluate genetic diversity among 705 wheat landrace accessions from within the AWCC, chosen to represent 5 world regions. DArT analysis was capable of distinguishing accessions from different geographic regions, and suggested that accessions originating from Nepal represent a unique gene pool within the collection. A statistical resampling of DArT loci indicated that 10–20 loci were enough to distinguish the maximum molecular diversity present within the collection. This research demonstrates the efficacy of the DArT platform as a tool for efficient examination of wheat diversity. As an ex situ germplasm repository, the AWCC contains wheat accessions of high genetic diversity, from genetically differentiated collection sites, even though diversity was under-represented in some countries represented in the repository.

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Assessment of genetic diversity among wild populations of the striped catfish (Pangasianodon hypophthalmus) by 20 novel microsatellite markers

Ministry of Science and Technology, Vietnam ◽

10.31276/vjst.63(7).37-41 ◽

2021 ◽

Vol 63 (7) ◽

pp. 37-41

Author(s):

Van Sang Nguyen ◽

◽

Minh Thanh Nguyen ◽

Hoang Thong Nguyen ◽

Hoang Gia Linh Tran ◽

...

Keyword(s):

Genetic Diversity ◽

Microsatellite Markers ◽

Polymorphic Information Content ◽

Draft Genome ◽

Null Alleles ◽

Wild Populations ◽

High Genetic Diversity ◽

Pangasianodon Hypophthalmus ◽

Striped Catfish ◽

The Mean

The striped catfish, Pangasianodon hypophthalmus, is one of the most economically important aquaculture species in Vietnam. This study developed 26 novel microsatellite markers from the draft genome of the striped catfish to assess the genetic diversity of three wild populations of the striped catfish (Bien Ho, Cuu Long, and Kratie) for establishing the breeding program. The study exhibited that 6 out of 26 loci had significantly high null allele frequency and deviated from Hardy - Weinberg equilibrium; thus, they were eliminated for further analysis. Across 20 loci without null alleles, a total of 255 different alleles was identified, ranging from 7 to 21 alleles per locus, with many unique alleles for each population. The results based on 20 loci revealed the mean polymorphic information content PIC=0.783; the mean observed heterozygosity Ho=0.809; the mean expected heterozygosity He=0.812; inbreeding coefficient Fis=-0.0147 (Fis<0). The results indicated that the striped catfish populations have high genetic diversity and are suitable for selective breeding. The Analysis of Molecular Variance (AMOVA) and comparison of genetic distances showed significant genetic differentiation among three populations while the Kratie population was distant from the others.

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Diversity of West African dwarf goat in southwestern Nigeria based on allozyme Markers

Nigerian Journal of Animal Production ◽

10.51791/njap.v45i3.391 ◽

2020 ◽

Vol 45 (3) ◽

Author(s):

O.K. Awobajo ◽

O.H. Osaiyuwu ◽

A.E. Salako ◽

A.O. Odeniyi

Keyword(s):

Genetic Diversity ◽

Allele Frequency ◽

Gene Diversity ◽

Polymorphic Information Content ◽

West African ◽

Southwestern Nigeria ◽

Cellulose Acetate Electrophoresis ◽

West African Dwarf ◽

Goat Population ◽

West African Dwarf Goat

Effective conservation, rational management and inadequate information on genetic diversity are the major challenges in livestock production. Genetic diversity has been used to reveal the extent of differentiation within livestock species. However, information on the use of allozymes in genetic diversity of the West African Dwarf (WAD) goat is insufficient. Therefore, genetic diversity of the WAD goat populations in southwestern Nigeria was investigated in this study. Three protein loci markers were used. Blood (5 mL each) samples were randomly collected from20, 20, 40 and 60 goats from Ondo ,Oyo, Ogun andOsun States respectively. The samples were subjected to cellulose acetate electrophoresis to determine the genetic variants at Haemoglobin (Hb), Carbonic Anhydrase (CA) and Transferrin (Tf) loci. Another set of blood (5 mL) from 20 different individual animals were randomly obtained from each of Ondo, Oyo, Ogun, and Osun States. Allele frequency, observed heterozygosity (H ), Polymorphic Information Content (PIC), F-statistic (F F and F ), gene flow (Nm), gene diversity (D), number of alleles per loci (A ), effective number of allele (AE) Mean Number of Allele (MNA) were generated from the data obtained. Data were analysed using Hardy-Weinberg equilibrium (HWE) at α0.05. The allele frequency ranged between 0.11 (Hb ) and 0.58 (Hb ), 0.17 (CA ) and 0.44 (CA ) and 0.08 (Tf ) to 0.60 (Tf ). Deviation from HWE was not significant in all populations except at Tf locus (0.00). The H ranged from 0.43 to 0.62 andNm and D ranged between 3.68 and 32.40 and 0.34 to 0.50 respectively. TheMNAwas 0.67 butA ranged from 1.52 to 2.00. The allozymes revealed some level of genetic diversity and a genetic differentiation indicative of the amount of genetic differences among individualswithin theWestAfricanDwarf goat population.

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Genetic diversity and fragmentation of Aspidosperma quebracho-blanco (Apocynaceae) natural habitats, conservation issues in Chaco forest and savanna biomes

Darwiniana nueva serie ◽

10.14522/darwiniana.2021.91.932 ◽

2021 ◽

Vol 9 (1) ◽

pp. 115-129

Author(s):

Thomáz S. Guerreiro Botelho ◽

Gecele Matos Paggi ◽

Maria Ana Farinaccio

Keyword(s):

Genetic Diversity ◽

Polymorphic Information Content ◽

Natural Habitat ◽

Mantel Test ◽

Shannon Index ◽

Conservation Strategies ◽

Conservation Units ◽

Natural Habitats ◽

High Genetic Diversity ◽

Genetic Diversity And Structure

The present study analyses the first data on genetic diversity of A. quebracho-blanco with the fragmentation of its natural habitat, supporting conservation strategies such as the definition of priority areas for conservation. DNA was extracted from 25 individuals of five populations of A. quebracho-blanco from Argentina, Paraguay, and Brazil. Six ISSR primers were used to characterize the genetic diversity and structure of this species. The genotypes were grouped according to a distance matrix, considering the genetic diversity indices of Nei (He), Shannon (H’), polymorphic information content (PIC), and heterozygosis (H). The populations showed an average genetic diversity that ranged from 0.09 to 0.15 for the Shannon index and from 0.19 to 0.31 for the Nei index; the Mantel test was not significant (r2 = 0.25, P = 0.106). The results obteined for the sampled populations reveal that conservation units are indispensable for conserving the species genetic resources. In addition, it would be essential to construct a germplasm bank for the Cordoba (Argentina) population, which is a population with high genetic diversity in a region of lower fragmentation compared to other regions evaluated, to ensure the conservation of A. quebracho-blanco.

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Genetic Diversity and Population Assessment of Musa L. (Musaceae) Employing CDDP Markers

Plant Molecular Biology Reporter ◽

10.1007/s11105-021-01290-x ◽

2021 ◽

Author(s):

David Okeh Igwe ◽

Onyinye Constance Ihearahu ◽

Anne Adhiambo Osano ◽

George Acquaah ◽

George Nkem Ude

Keyword(s):

Genetic Diversity ◽

Polymorphic Information Content ◽

Similarity Index ◽

High Genetic Diversity ◽

Population Assessment ◽

Polymorphic Loci ◽

Information Index ◽

Gene Based Markers ◽

Population Indices ◽

Estimate Gene Flow

AbstractSixty-six accessions of Musa genus with different genomic groups that consisted of wild relatives and cultivated lines were obtained from the International Transit Center, Belgium, for DNA extraction using Cetyl trimethylammonium bromide method, followed by amplification with Conserved DNA-derived Polymorphism (CDDP) markers for genetic diversity and population assessment. A total of 421 alleles with major allele frequency of 2.051 were detected from the reproducible markers. High genetic diversity (GD, 11.093) and polymorphic information content (0.918) were revealed. The number of polymorphic loci and percentage of polymorphic loci ranged from 59 to 66 and 89.34 to 100, respectively. Using the potential genetic indicators including effective number of alleles, Nei’s genetic diversity, and Shannon’s information index, the AS genomic group was identified to have the highest GD, while the AAA accessions had the lowest GD indices. The GD parameters identified in the accessions were ranked as AS > AAB > AAAA > AA > ABB > wild diploidy > BB > AB > AAA from high to low based on polymorphic loci of the markers. Total intraspecific GD, interspecific GD, and estimate gene flow identified were 0.433, 0.404, and 7.113, respectively. The coefficient of gene differentiation of 0.066 was obtained, indicating 6.57% among the population and 93.43% within the population. Dendrogram analysis produced nine major groups with subgroups at similarity index of 0.814. These CDDP functional gene-based markers were informative and very efficient in resolving GD, and population indices among the banana and plantain accessions of different genomes. The identified CDDP markers might serve as potential tools for selecting suitable training populations for breeding and conservation of Musa species.

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