scholarly journals Genetic Diversity and Population Genetic Structure of a Guzerá (Bos indicus) Meta-Population

Animals ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 1125
Author(s):  
Maria Gabriela C. D. Peixoto ◽  
Maria Raquel S. Carvalho ◽  
Andrea A. Egito ◽  
Raphael S. Steinberg ◽  
Frank Ângelo T. Bruneli ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Bos Indicus ◽  
Dairy Herd ◽  
Fixation Index ◽  
Population Subdivision ◽  
High Genetic Diversity ◽  
Dual Purpose ◽  
Beef Herds ◽  
Inbreeding Level ◽  
The Impact

The Brazilian Guzerá population originated from a few founders introduced from India. These animals adapted well to the harsh environments in Brazil, were selected for beef, milk, or dual-purpose (beef and milk), and were extensively used to produce crossbred animals. Here, the impact of these historical events with regard to the population structure and genetic diversity in a Guzerá meta-population was evaluated. DNA samples of 744 animals (one dairy, nine dual-purpose, and five beef herds) were genotyped for 21 microsatellite loci. Ho, He, PIC, Fis, Fit, and Fst estimates were obtained considering either farms or lineages as subpopulations. Mean Ho (0.73) and PIC (0.75) suggest that genetic diversity was efficiently conserved. Fit, Fis and Fst values (95% CI) pointed to a low fixation index, and large genetic diversity: Fit (Farms = 0.021–0.100; lineages = 0.021–0.100), Fis (Farms = –0.007–0.076; lineages = −0.014–0.070), and Fst (Farms = 0.0237–0.032; lineages = 0.029–0.038). The dual-purpose herds/selection lines are the most uniform subpopulation, while the beef one preserved larger amounts of genetic diversity among herds. In addition, the dairy herd showed to be genetically distant from other herds. Taken together, these results suggest that this Guzerá meta-population has high genetic diversity, a low degree of population subdivision, and a low inbreeding level.

scholarly journals Quantifying the effect of human practices on S. cerevisiae vineyard metapopulation diversity

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Marine Börlin ◽  
Olivier Claisse ◽  
Warren Albertin ◽  
Franck Salin ◽  
Jean-Luc Legras ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genetic Diversity ◽  
Farming System ◽  
Conventional Farming ◽  
Global Effect ◽  
High Genetic Diversity ◽  
Tight Connection ◽  
Human Practices ◽  
The Impact ◽  
Very High

Abstract Saccharomyces cerevisiae is the main actor of wine fermentation but at present, still little is known about the factors impacting its distribution in the vineyards. In this study, 23 vineyards and 7 cellars were sampled over 2 consecutive years in the Bordeaux and Bergerac regions. The impact of geography and farming system and the relation between grape and vat populations were evaluated using a collection of 1374 S. cerevisiae merlot grape isolates and 289 vat isolates analyzed at 17 microsatellites loci. A very high genetic diversity of S. cerevisiae strains was obtained from grape samples, higher in conventional farming system than in organic one. The geographic appellation and the wine estate significantly impact the S. cerevisiae population structure, whereas the type of farming system has a weak global effect. When comparing cellar and vineyard populations, we evidenced the tight connection between the two compartments, based on the high proportion of grape isolates (25%) related to the commercial starters used in the cellar and on the estimation of bidirectional geneflows between the vineyard and the cellar compartments.

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

Genome ◽  
2004 ◽  
Vol 47 (6) ◽  
pp. 1071-1081 ◽  
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.

Prevalence and Genetic Diversity of Arcobacter in Food Products in the North of Spain

2013 ◽  
Vol 76 (8) ◽  
pp. 1447-1450 ◽  
Author(s):  
BARBARA NIEVA-ECHEVARRIA ◽  
IRATI MARTINEZ-MALAXETXEBARRIA ◽  
CECILIA GIRBAU ◽  
RODRIGO ALONSO ◽  
AURORA FERNÁNDEZ-ASTORGA
Keyword(s):  
Public Health ◽  
Genetic Diversity ◽  
Basque Country ◽  
Food Products ◽  
High Genetic Diversity ◽  
The North ◽  
Arcobacter Butzleri ◽  
North Of Spain ◽  
The Impact ◽  
The Relationship

The bacterial contamination of food products can cause serious public health problems. Interest in Arcobacter contamination has increased due to the relationship between these bacteria and human enteritis. We studied the prevalence and genetic diversity of Arcobacter species at the retail level in the province of Alava in Basque Country, Spain. The results showed a high genetic diversity and indicated the regular presence of the main Arcobacter spp. associated with human enteric illness in food products. Arcobacter butzleri, Arcobacter cryaerophilus, and Arcobacter skirrowii were detected with an overall prevalence close to 40% and were isolated from 15 (42.8%) fresh cow's milk samples, 12 (73.3%) shellfish samples, 11 (55%) chicken samples, 2 (10%) pork samples, and 1 (5%) beef sample. The results indicate the need to investigate the impact of Arcobacter spp. on public health.

scholarly journals Genomic miscellany and allelic frequencies of Plasmodium falciparum msp-1, msp-2 and glurp in parasite isolates

2021 ◽  
Author(s):  
Muzafar Shah ◽  
Ibrar Ullah ◽  
Sahib Gul Afridi ◽  
Muhammad Israr ◽  
Asifullah Khan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Plasmodium Falciparum ◽  
Local Health ◽  
Multiplicity Of Infection ◽  
High Genetic Diversity ◽  
Khyber Pakhtunkhwa ◽  
Chain Reactions ◽  
Allelic Family ◽  
Allelic Frequencies ◽  
The Impact

Plasmodium falciparum, the main causative agent of malaria is an important public health vector in Khyber Pakhtunkhwa, Pakistan. Identification of the genetic diversity of malaria parasites can inform the intensity of transmission and identify potential deficiencies in malaria control programs. The aim of this study was to investigate the genetic diversity, allele frequencies and multiplicity of infection (MOI) of P. falciparum in Khyber Pakhtunkhwa, Pakistan. Methods: A total of 85 isolates from patients presenting to the local health centers with P. falciparum species were collected from 2017 to 2019. Parasite DNA was extracted from a total of 200 micro litter whole blood per patient using the Qiagen DNA extraction kit according to manufactures instructions. The polymorphic region of msp-1, msp-2 and glurp loci were genotyped by using nested polymerase chain reactions followed by gel electrophoresis for fragment analysis. Results: Genetic diversity and allelic frequencies of msp-1, msp-2 and glurp were identified in 85 blood samples. A total of 62 msp alleles were detected in which 30 for msp-1 and 32 for msp-2. For msp-1 the successful amplification occurred in (75/85) 88.23% isolates for msp-1, 78.9% (67/85) for msp-2 and 70% (60/85) for glurp. For msp-1, the K1 allelic family was predominant at 66.66% (50/75), followed by RO33 and MAD20. The frequency of samples having only K1, MAD20 and RO33 were 21.34% (16/75), 8% (6/75) and 10.67% (8/75) respectively. In msp-2, the FC27 allelic family was the most abundant with 70.14% (47/67) compared to 3D7 with 67.16% (45/67). Nine glurp RII region genotypes were identified. The overall mean multiplicity of infection was 2.6 with1.8 and 1.4 for msp-1 and msp-2 respectively while for glurp RII genes (MOI=1.03). There was no significant association between multiplicity of infection and age group (Spearman rank coefficient = 0.050; P = 0.6). There was significant correlation between MOI and parasite density for msp-2 allelic family. Conclusion: Our study showed high genetic diversity and allelic frequency with multiple clones of msp-1, msp-2 and glurp in P. falciparum isolates from malaria patients in Khyber Pakhtunkhwa Pakistan. In the present study the genotype data provided the valuable information which is essential for monitoring the impact of malaria eradication efforts in this region.

An economic assessment of the impact of new reproductive technologies on commercial dairy and beef herds

1995 ◽  
Vol 1995 ◽  
pp. 134-134 ◽  
Author(s):  
C. M. Yates ◽  
T. Rehman ◽  
A. T. Chamberlain
Keyword(s):  
Production Efficiency ◽  
Dairy Herd ◽  
Economic Assessment ◽  
Reproductive Technologies ◽  
Economic Benefits ◽  
Vital Role ◽  
Genetic Progress ◽  
Animal Reproduction ◽  
Beef Herds ◽  
The Impact

The adoption of new reproductive technologies is likely to have far reaching consequences on commercial dairy and beef herds. Within a dairy herd, milk production is influenced by the animal's genotype and its environment and their interaction. Whilst environmental factors may be manipulated in many ways, the animal's genotype is determined solely by it's parents genetic make up; therefore, animal reproduction plays a vital role in determining the genetic progress that can be made within an enterprise. Reproduction is also important within a beef enterprise as the production of a large breed calf can increase the output and thus achieve a higher production efficiency. Any reproductive technology that offers a faster rate of genetic improvement and/or an increase in production would be considered desirable if any increased costs of using that technology are compensated by the economic benefits. In order to appraise such technologies it is necessary to estimate their implications at an enterprise level in terms of production levels, efficiency and economic benefits.

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

Animals ◽  
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.

scholarly journals Genetic diversity and population structure of Alternaria species from tomato and potato in North Carolina and Wisconsin

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Tika B. Adhikari ◽  
Norman Muzhinji ◽  
Dennis Halterman ◽  
Frank J. Louws
Keyword(s):  
Genetic Diversity ◽  
North Carolina ◽  
Population Structure ◽  
Genetic Variation ◽  
Dna Sequences ◽  
Random Mating ◽  
Population Expansion ◽  
The United States ◽  
Population Subdivision ◽  
The Impact

AbstractEarly blight (EB) caused by Alternaria linariae or Alternaria solani and leaf blight (LB) caused by A. alternata are economically important diseases of tomato and potato. Little is known about the genetic diversity and population structure of these pathogens in the United States. A total of 214 isolates of A. alternata (n = 61), A. linariae (n = 96), and A. solani (n = 57) were collected from tomato and potato in North Carolina and Wisconsin and grouped into populations based on geographic locations and tomato varieties. We exploited 220 single nucleotide polymorphisms derived from DNA sequences of 10 microsatellite loci to analyse the population genetic structure between species and between populations within species and infer the mode of reproduction. High genetic variation and genotypic diversity were observed in all the populations analysed. The null hypothesis of the clonality test based on the index of association $$\left( {\overline{r}_{d} } \right)$$ r ¯ d was rejected, and equal frequencies of mating types under random mating were detected in some studied populations of Alternaria spp., suggesting that recombination can play an important role in the evolution of these pathogens. Most genetic differences were found between species, and the results showed three distinct genetic clusters corresponding to the three Alternaria spp. We found no evidence for clustering of geographic location populations or tomato variety populations. Analyses of molecular variance revealed high (> 85%) genetic variation within individuals in a population, confirming a lack of population subdivision within species. Alternaria linariae populations harboured more multilocus genotypes (MLGs) than A. alternata and A. solani populations and shared the same MLG between populations within a species, which was suggestive of gene flow and population expansion. Although both A. linariae and A. solani can cause EB on tomatoes and potatoes, these two species are genetically differentiated. Our results provide new insights into the evolution and structure of Alternaria spp. and can lead to new directions in optimizing management strategies to mitigate the impact of these pathogens on tomato and potato production in North Carolina and Wisconsin.

scholarly journals The Chilean Strawberry [Fragaria chiloensis (L.) Duch.]: Genetic Diversity and Structure

2007 ◽  
Vol 132 (4) ◽  
pp. 501-506 ◽  
Author(s):  
Basilio Carrasco ◽  
Marcelo Garcés ◽  
Pamela Rojas ◽  
Guillermo Saud ◽  
Raúl Herrera ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cultural History ◽  
18Th Century ◽  
Aboriginal People ◽  
Gene Diversity ◽  
Issr Markers ◽  
High Genetic Diversity ◽  
Genetic Diversity And Structure ◽  
Abiotic And Biotic Factors ◽  
The Impact

The chilean strawberry displays high fruit quality and tolerance to abiotic and biotic factors. Additionally, this species has a rich cultural history going back for at least several thousand years in association with aboriginal people activities and continues at a reduced level today. After its introduction to Europe during the 18th century, it formed an interspecific hybrid to become the maternal species of the commercial strawberry, Fragaria ×ananassa Duch. The objectives of the current investigation were to determine the level and patterns of partitioning of intersimple sequence repeat (ISSR) diversity. ISSR markers were used to assess the genetic diversity in 216 accessions of F. chiloensis, which represented the two botanical forms present in Chile [F. chiloensis ssp. chiloensis f. chiloensis and F. chiloensis ssp. chiloensis f. patagonica (L.) Duch.]. Our results showed high genetic diversity at the species level [polymorphic ISSR loci (P) = 89.6%, gene diversity (h) = 0.24 ± 0.17, Shannon's index (S) = 0.37 ± 0.24] and a lower genetic diversity in f. chiloensis than f. patagonica. The analysis of molecular variance (AMOVA) showed a moderate genetic differentiation among accessions (φst = 14.9%). No geographic patterns for ISSR diversity were observed. AMOVA, structure, and discriminant analysis indicated that accessions tend to group by botanical form. The impact of domestication on the genetic structure of chilean strawberry and its application to breeding and conservation are discussed.

scholarly journals Changes in Genetic Diversity of Whitebark Pine (Pinus albicaulis Engelm.) Associated with Inbreeding and White Pine Blister Rust Infection

2011 ◽  
Vol 60 (1-6) ◽  
pp. 113-123 ◽  
Author(s):  
A. D. Bower ◽  
S. N. Aitken
Keyword(s):  
Genetic Diversity ◽  
Fixation Index ◽  
Pinus Albicaulis ◽  
Whitebark Pine ◽  
White Pine Blister Rust ◽  
White Pine ◽  
Age Cohorts ◽  
Rust Infection ◽  
Blister Rust ◽  
The Impact

AbstractWe investigated the association of inbreeding and infection by the introduced disease white pine blister rust (caused by the fungusCronartium ribicolaJ. C. Fisch) with genetic diversity of whitebark pine (Pinus albicaulisEngelm.) by genetically comparing cohorts of different ages in natural stands. Isozyme analysis of bud tissue was used to estimate expected and observed heterozygosity (Heand Ho), and Wright’s fixation index (Fis) for three age cohorts (seedling, young, and mature), sampled from 14 sites in British Columbia, Oregon, Idaho, and Montana. Comparison of genetic diversity parameters among cohorts within a site was used to assess the extent and persistence of inbreeding with age, while comparisons of parameters among sites within a cohort were used to assess the impact of the disease on genetic diversity. Significant evidence of inbreeding (Fis>0) was found in all age cohorts. When sites were stratified by level of blister rust infection, differences in Fisand Hoamong cohorts were only significant when level of infection was low. A significant negative association was found between level of blister rust infection and Hoin the mature cohort. This suggests that when differential selection due to blister rust is weak, more heterozygous individuals may be favored; however, more homozygous individuals may have higher fitness under higher blister rust levels

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