scholarly journals Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data

Animals ◽  
2020 ◽  
Vol 10 (12) ◽  
pp. 2285
Author(s):  
Filippo Biscarini ◽  
Salvatore Mastrangelo ◽  
Gennaro Catillo ◽  
Gabriele Senczuk ◽  
Roberta Ciampolini
Keyword(s):  
Genetic Diversity ◽  
Candidate Genes ◽  
Biological Diversity ◽  
Climate Adaptation ◽  
Genetic Material ◽  
Nematode Resistance ◽  
Pedigree Data ◽  
Reproduction Traits ◽  
Regions Of Homozygosity ◽  
Detailed Picture

Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches (FIS and FROH), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds (HE=0.261, HO=0.274). Pedigree-based average inbreeding (F) was estimated at 4.9%. The correlation was low between F and genomic-based approaches (r=0.03 with FIS, r=0.21 with FROH), while it was higher between FIS and FROH (r=0.78). The low correlation between F and FROH coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like FROH may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals’ pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity.

scholarly journals Assessment of Genetic Diversity of Promising Castor Been (Ricinus communis L.) Genotypes in Nigeria

2019 ◽  
Vol 11 (3) ◽  
pp. 467-474
Author(s):  
Bolaji Zuluqurineen SALIHU ◽  
Olamide Ahmed FALUSI ◽  
Adeyinka Olufemi ADEPOJU ◽  
Ibrahim Wasiu AROLU ◽  
Oladipupo Yusuf DAUDU ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Diversity Index ◽  
Gene Diversity ◽  
Ricinus Communis ◽  
Polymorphic Information Content ◽  
Block Design ◽  
Genetic Material ◽  
Morphological Data ◽  
Research Attention ◽  
Ricinus Communis L

Castor oil plant (Ricinus communis L.) is an important oil crop with little research attention in Nigeria. In the present research, extent of genetic diversity among 20 Nigerian castor genotypes was determined using morphological descriptors and molecular markers. The genotypes were laid out on a randomized complete block design with three replicated plots. Molecular genotyping of the genotypes was carried out using genomic Simple Sequence Repeats (SSR). The genotypes revealed high divergence in seed colour, seed shape, seed mottle, seed caruncle and seed sizes. Seedling establishment varied from 70.18% (in Acc. 006) to 93.25% (Acc. 001) with average mean of 81.53%. Raceme length ranged from 15.90 cm to 29.54 cm with population mean of 20.80 cm. The highest seed yield (1222.98 kg/ha) was recorded in Acc. 001 and the least (611.46 kg/ha) was observed in Acc. 006. Seed oil content varied between 32.15% in Acc. 042 and 54.03% in Acc. 006. Agglomerative cluster dendrogram constructed from morphological data showed random distribution of the genotypes into three cluster groups irrespective of the sources/collection points. The genetic diversity based on SSR Marker Analysis revealed high average expected heterozygosity (0.74), Polymorphic information content (0.68), Nei’s gene diversity index (0.72) and Shannon's Information index (1.43). The dendrogram constructed from molecular data grouped the twenty genotypes into three groups at coefficient of 0.34. From these findings, it showed that the twenty genotypes evaluated are divergent in nature and they could serve as good genetic material for castor breeding in Nigeria.

scholarly journals Primer Binding Site (PBS) Profiling of Genetic Diversity of Natural Populations of Endemic Species Allium ledebourianum Schult.

BioTech ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 23
Author(s):  
Oxana Khapilina ◽  
Ainur Turzhanova ◽  
Alevtina Danilova ◽  
Asem Tumenbayeva ◽  
Vladislav Shevtsov ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Endemic Species ◽  
Biological Diversity ◽  
Natural Populations ◽  
Subsequent Development ◽  
Dna Profiling ◽  
Primer Binding Site ◽  
Anthropogenic Factors ◽  
Habitat Specificity ◽  
Interspersed Repeats

Endemic species are especially vulnerable to biodiversity loss caused by isolation or habitat specificity, small population size, and anthropogenic factors. Endemic species biodiversity analysis has a critically important global value for the development of conservation strategies. The rare onion Allium ledebourianum is a narrow-lined endemic species, with natural populations located in the extreme climatic conditions of the Kazakh Altai. A. ledebourianum populations are decreasing everywhere due to anthropogenic impact, and therefore, this species requires preservation and protection. Conservation of this rare species is associated with monitoring studies to investigate the genetic diversity of natural populations. Fundamental components of eukaryote genome include multiple classes of interspersed repeats. Various PCR-based DNA fingerprinting methods are used to detect chromosomal changes related to recombination processes of these interspersed elements. These methods are based on interspersed repeat sequences and are an effective approach for assessing the biological diversity of plants and their variability. We applied DNA profiling approaches based on conservative sequences of interspersed repeats to assess the genetic diversity of natural A. ledebourianum populations located in the territory of Kazakhstan Altai. The analysis of natural A. ledebourianum populations, carried out using the DNA profiling approach, allowed the effective differentiation of the populations and assessment of their genetic diversity. We used conservative sequences of tRNA primer binding sites (PBS) of the long-terminal repeat (LTR) retrotransposons as PCR primers. Amplification using the three most effective PBS primers generated 628 PCR amplicons, with an average of 209 amplicons. The average polymorphism level varied from 34% to 40% for all studied samples. Resolution analysis of the PBS primers showed all of them to have high or medium polymorphism levels, which varied from 0.763 to 0.965. Results of the molecular analysis of variance showed that the general biodiversity of A. ledebourianum populations is due to interpopulation (67%) and intrapopulation (33%) differences. The revealed genetic diversity was higher in the most distant population of A. ledebourianum LD64, located on the Sarymsakty ridge of Southern Altai. This is the first genetic diversity study of the endemic species A. ledebourianum using DNA profiling approaches. This work allowed us to collect new genetic data on the structure of A. ledebourianum populations in the Altai for subsequent development of preservation strategies to enhance the reproduction of this relict species. The results will be useful for the conservation and exploitation of this species, serving as the basis for further studies of its evolution and ecology.

scholarly journals AUTOCHTHONOUS BREEDS OF DOMESTIC ANIMALS AND CONSERVATION MEASURES

AGROFOR ◽  
2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Zoran MALETIC
Keyword(s):  
Genetic Diversity ◽  
Biological Diversity ◽  
Domestic Animals ◽  
Conservation Strategy ◽  
Ex Situ ◽  
Animal Genetic Resources ◽  
Diversity Preservation ◽  
The Republic ◽  
International Conventions

Recently, highly productive breeds of various species of domestic animals have been used in livestock production, which has resulted in the destruction of indigenous breeds of domestic animals around the world, even in our area. This is the first reason why indigenous races and strains have been endangered. Another reason is that domestic, indigenous breeds were crossed with specialized breeds, which were imported, and in that way their genetic diversity was negatively affected. Resistance is lost, adaptation to the conditions in which they were created, the ability to survive in nature. Indigenous breeds of different species of domestic animals, which are recognized in the Republic of Srpska (BiH) are gatačko cattle and buša (cattle), Vlašić pramenka, Podveleška pramenka, Kupres pramenka (sheep), domestic Balkan horned goat (goats), Bosnian mountain horse (horses), mangulica (pigs) and pogrmuša hen or živičarka hen (poultry). By acceding to international conventions, BiH /Republic of Srpska has committed itself to establishing a system of measures that will enable the conservation of biological diversity and the protection of indigenous and endangered breeds of domestic animals. The choice of a strategy for the conservation of diversity, the establishment of an adequate conservation scheme, and the implementation of a conservation strategy are some of the key elements of any process for the conservation of genetic diversity. Preservation of autochthonous and protected breeds of domestic animals is possible through preservation in the original environment (in situ) and preservation outside the original environment (ex situ). There is a possibility of combining these models of conservation of animal genetic resources.

scholarly journals GENOMIC DETERMINATION OF THE MOST IMPORTANT FATHER LINES OF SLOVAK PINZGAU COWS

AGROFOR ◽  
2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Veronika KUKUČKOVÁ ◽  
Nina MORAVČÍKOVÁ ◽  
Radovan KASARDA
Keyword(s):  
Genetic Diversity ◽  
Genetic Structure ◽  
The State ◽  
Most Probable Number ◽  
Pedigree Data ◽  
Probable Number ◽  
Expected Heterozygosity ◽  
High Level ◽  
The Bayesian Approach

The aim of this study was to assess genetic structure of Slovak Pinzgau populationbased on polymorphism at molecular markers using statistical methods. Femaleoffspring of 12 most frequently used bulls in Slovak Pinzgau breeding programmewere investigated. Pinzgau cattle were found to have a high level of diversity,supported by the number of alleles observed across loci (average 5.31, range 2-11)and by the high within-breed expected heterozygosity (average 0.66, range 0.64-0.73). The state of genetic diversity is satisfying and standard for local populations.Detection of 12 possible subpopulation structures provided us with detailedinformation of the genetic structure. The Bayesian approach was applied, detectingthree, as the most probable number of clusters. The similarity of eachsubpopulation using microsatellites was confirmed also by high-throughputmolecular data. The observed inbreeding (FROH=2.3%) was higher than thatexpected based on pedigree data (FPED=0.4%) due to the limited number ofavailable generations in pedigree data. One of the most important steps indevelopment of efficient autochthonous breed protection programs ischaracterization of genetic variability and assessment of the population structure.The chosen set of microsatellites confirmed the suitability in determination of thesubpopulations of Pinzgau cattle in Slovakia. The state of genetic diversity at moredetailed level was successfully performed using bovineSNP50 BeadChip.

scholarly journals Vegetation period of genetic resources of flax (Linum usitatissimum L.)

2020 ◽  
Vol 66 (3) ◽  
pp. 36-47
Author(s):  
Grażyna Silska
Keyword(s):  
Medicinal Plants ◽  
Genetic Resources ◽  
Linum Usitatissimum ◽  
Biological Diversity ◽  
Cannabis Sativa ◽  
Genetic Material ◽  
Vegetation Period ◽  
Convention On Biological Diversity ◽  
Biological Features ◽  
Beginning Of Flowering

Abstract Introduction Institute of Natural Fibres and Medicinal Plants (INF&MP) is involved in gathering and evaluation of genetic resources of flax (Linum usitatissimum L.), hemp (Cannabis sativa L.) and medicinal plants, because Poland has signed the Convention on Biological Diversity. Field trials were carried out in 1990–2001 in the Experimental Station in Wojciechów located in Opolskie region. The research material was accessions of genetic resources from the collection of flax, stored at the Institute of Plant Breeding and Acclimatization Institute in Radzików near Warsaw. Objective The aim of the publication was to evaluate the following biological features of flax: time of beginning of flowering and vegetation period to yellow maturity. Methods The characteristics data for flax accessions are presented according to the methodology of development of the International Flax Database. Each flax accessions from the world collection of flax genetic resources received one of the following assessments of two vegetation periods: very short, short, medium, long and very long. Descriptors of biological features of flax were used, presented in “List of flax descriptors (L. usitatissimum L.)” edited by Janka Nozkova, published in 2011. These descriptors are used to develop the International Flax Database, which in turn helps in the rapid evaluation of the L. usitatissimum genetic resource collection. Carrying out a detailed characterization of biological features of L. usitatissimum accessions is very helpful for breeders in selecting genetic material for breeding new varieties of flax. Results The following results were obtained from the time of the beginning of flowering and the vegetation period to yellow maturity. Time of beginning of flowering was the following: very short – 0 accessions, short – 97 accessions, medium – 20 accessions, long – 2 accessions and very long – 0 accessions of flax. The genotypes tested were characterized by the following results in terms of vegetation period from sowing to yellow maturity: very short – 0, short – 37, medium – 62, long – 0 and very long – 0 accessions of flax. Conclusions Time of beginning of flowering and the vegetation period to yellow maturity shall be revalorised to the International Flax Database for those L. usitatissimum accessions that did not receive the same assessment of the biological features tested in the two or three years of the study.

scholarly journals IUCN Global Ecosystem Typology 2.0: descriptive profiles for biomes and ecosystem functional groups

2020 ◽  
Keyword(s):  
Genetic Diversity ◽  
Sustainable Development ◽  
Biological Diversity ◽  
Natural Capital ◽  
Human Life ◽  
Hierarchical Classification ◽  
Well Being ◽  
Human Influence ◽  
Ecological Traits ◽  
Ecological Functions

Ecosystems are critically important components of Earth’s biological diversity and as the natural capital that sustains human life and well-being. Yet all of the world’s ecosystems show hallmarks of human influence, and many are under acute risks of collapse, with consequences for habitats of species, genetic diversity, ecosystem services, sustainable development and human well-being. The IUCN Global Ecosystem Typology is a hierarchical classification system that, in its upper levels, defines ecosystems by their convergent ecological functions and, in its lower levels, distinguishes ecosystems with contrasting assemblages of species engaged in those functions. This report describes the three upper levels of the hierarchy, which provide a framework for understanding and comparing the key ecological traits of functionally different ecosystems and their drivers. An understanding of these traits and drivers is essential to support ecosystem management.

scholarly journals Diversity of capsaicin content, quantitative, and yield components in chili (Capsicum annuum) genotypes and their F1 hybrid

2020 ◽  
Vol 21 (5) ◽  
Author(s):  
Zulfikar D Sahid ◽  
MUHAMAD SYUKUR ◽  
AWANG MAHARIJAYA
Keyword(s):  
Genetic Diversity ◽  
Capsicum Annuum ◽  
Block Design ◽  
Genetic Material ◽  
Morphological Characters ◽  
Fruit Weight ◽  
Yield Component ◽  
Quantitative Yield ◽  
F1 Hybrid ◽  
Randomized Complete Block Design

Abstract. Sahid ZD, Syukur M, Maharijaya A. 2020. Genetic diversity of capsaicin content, quantitative, and yield component in chili (Capsicum annuum) and their F1 hybrid. Biodiversitas 21: 2251-2257. Chili (Capsicum annuum L.) is one of the horticultural plants that have many benefits. The benefit of chili was determined by pungency level of its fruit. Pungency level of the chili is due to the capsaicin content in fruit. Information about the genetic diversity of capsaicin is still rarely available. The aims of this study were to obtain diversity information on quantitative, yield component, and capsaicin content, and to analyze the correlation among chili genotypes based on their morphological characters. This study used Randomized Complete Block Design with three replications. The genetic material used in this study consisted of 21 genotypes consisting of 6 genotypes of chili elders and 15 hybrid F1 genotypes resulting from their crossing. Six genotypes of the chili parents are C5, F6074, F9160291, Yuni, Bara, and Giant. 15 hybrid F1 genotypes used in this study are C5 x Bara, C5 x F6074, C5 x Yuni, C5 x Giant, C5 x F9160291, Bara x F6074, Bara x Yuni, Bara x Giant, Bara x F9160291, F6074 x Yuni, F6074 x Giant, F6074 x F9160291, Yuni x Giant, Yuni x F9160291, and Giant x F9160291. The observation was made on the variables of quantitative, yield, and capsaicin components on chili. The results showed that the highest capsaicin content only was found in Bara x F9160291. The results of scatterplot analysis showed that the highest capsaicin and yield component was found in BaraxF6074 and C5 x Yuni genotype. The results of cluster analysis showed that chili was clustered into three color groups. The character of capsaicin content is negatively correlated and very different from fruit weight, fruit diameter, fruit length, thick fruit flesh, total amount of fruit per plant, and fruit weight per plant.

scholarly journals The pattern of genetic diversity of different breeds of pigs based on microsatellite analysis

2020 ◽  
Vol 24 (7) ◽  
pp. 747-754
Author(s):  
V. R. Kharzinova ◽  
N. A. Zinovieva
Keyword(s):  
Genetic Diversity ◽  
Genetic Relationships ◽  
Molecular Genetic ◽  
Genetic Material ◽  
Animal Husbandry ◽  
Molecular Genetic Analysis ◽  
Fixation Index ◽  
Large White ◽  
Black And White ◽  
The Republic

One of the main tasks of genetics and animal breeding is the assessment of genetic diversity and the study of genetic relationships between different breeds and populations using molecular genetic analysis methods. We analysed the polymorphism of microsatellites and the information on the state of genetic diversity and the population structure of local breeds in Russia: the Kemerovo, the Berkshire, the Liven, the Mangalitsa, and the Civilian; in the Republic of Belarus: the Large White and the Black-and-White; and in Ukraine: the White Steppe, as well as commercial breeds of imported origin of domestic reproduction: the Large White, the Landrace, and the Duroc. The materials used for this study were the tissue and DNA samples extracted from 1,194 pigs and DNA of the UNU “Genetic material bank of domestic and wild animal species and birds” of the L.K. Ernst Federal Research Center for Animal Husbandry. Polymorphisms of 10 microsatellites (S0155, S0355, S0386, SW24, SO005, SW72, SW951, S0101, SW240, and SW857) were determined according to the previously developed technique using DNA analyser ABI3130xl. To estimate the allele pool of each population, the average number of alleles (NA), the effective number of alleles (NE ) based on the locus, the rarified allelic richness (AR), the observed (HO ) and expected (HE ) heterozygosity, and the fixation index (FIS) were calculated. The degree of genetic differentiation of the breeds was assessed based on the pairwise values of FST and D. The analysis of the allelic and genetic diversity parameters of the local breeds showed that the maximum and minimum levels of polymorphism were observed in pigs of the Ukrainian White Steppe breed (NA = 6.500, NE = 3.709, and AR = 6.020) and in pigs of the Duroc breed (NA = 4.875, NE = 2.119, and AR = 3.821), respectively. The highest level of genetic diversity was found in the Large White breed of the Republic of Belarus (HO = 0.707 and NE = 0.702). The minimum level of genetic diversity was found in pigs of the imported breeds – the Landrace (HO = 0.459, HE = 0.400) and the Duroc (HO = 0.480, HE = 0.469) – indicating a high selection pressure in these breeds. Based on the results of phylogenetic analysis, the genetic origin of Large White pigs, the breeds, from which the Berkshire pigs originated, and the genetic detachment of the Landrace from the Mangalitsa breeds were revealed. The cluster analysis showed a genetic consolidation of the Black-and-White, the Berkshire, and the Mangalitsa pigs. Additionally, the imported breeds with clustering depending on the origin were characterised by a genetic structure different from that of the other breeds. The information obtained from these studies can serve as a guide for the management and breeding strategies of the pig breeds studied, to allow their better use and conservation.

scholarly journals Research Concerning Cucumber (Cucumis Sativus L. Mill) Genetic Diversity

2011 ◽  
Vol 68 (2) ◽  
Author(s):  
Aurel MAXIM ◽  
Mignon ŞANDOR ◽  
Lucia MIHALESCU ◽  
Ovidiu MAXIM ◽  
Oana MARE ROŞCA
Keyword(s):  
Genetic Diversity ◽  
Biological Diversity ◽  
Genetic Erosion ◽  
Farming Systems ◽  
Convention On Biological Diversity ◽  
Cultivated Plants ◽  
Cucumis Sativus L ◽  
Local Varieties ◽  
Industrial Farming ◽  
The University

During the second part of the twentieth century the cultivated plants have been faced with genetic erosion, because of the expandinding industrial farming systems. The sustainable agriculture can not exist without a rich genetic diversity. After the United Nations Conference from Rio de Janeiro (1992), when the Convention on Biological Diversity was adopted, a series of acts and european references that protect agrobiodiversity had emerged. Between 2007 and 2010, at the University of Agricultural Sciences and Veterinary Medicine a program which aims to identify and conserve local vegetable varieties was conducted. Out of 290 cultivars, 171 (58.9%) were genuine local varieties. There were collected 12 cucumber cultivars from the following counties: Salaj (7), Cluj (3), Bistrita-Nasaud (1) and Satu-Mare (1). The morphologic caractheristics proved that all this 12 cultivars were authentic and valuable local varieties. The local varieties were agronomical, biological and biochemical characterized, both in field and laboratory. The seeds achieved from those 12 local varieties were preserved in the Suceava Gene Bank, from where stakeholders (farmers, agronomists, researchers) can obtain seeds.

Genetic diversity assessment and gene expression analysis of prolonged shelf-life genes in Mangalore melon (Cucumis melo ssp. agrestis var. acidulus)

2021 ◽  
Author(s):  
Raghavendra Gunnaiah ◽  
Ratnakar M. Shet ◽  
Ashwini Lamani ◽  
Dattatraya H. Radhika ◽  
Rudrappa C. Jagadeesha
Keyword(s):  
Genetic Diversity ◽  
Shelf Life ◽  
Candidate Genes ◽  
Cucumis Melo ◽  
South India ◽  
Ethylene Biosynthesis ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Tree Construction ◽  
Diversity Assessment

Abstract Mangalore melon (Cucumis melo ssp. agrestis var. acidulus) is a non-dessert melon, extensively grown in the coastal districts of South India, but hardly known to the rest of the World. Immature or mature fruits of Mangalore melon are used in preparation of delicious dishes such as vegetable stew, chutneys and curries. They are appreciated for nutritional values, long shelf life and biotic stress resistance. Seventy-nine accessions of Mangalore melon were collected from five states of South India and their genetic diversity was assessed using inter simple sequence repeat (ISSR) markers. Putative candidate genes of extended shelf life in Mangalore melon were studied by quantitative reverse transcription polymerase chain reaction in comparison with cantaloupe (Cucumis melo L.). Shelf life varied from 65 days to 300 days at room temperature. Six ISSR primers amplified 142 fragments ranging from 80 bp to 2380 bp with an average of 23.66 bands per marker on a high-resolution capillary electrophoresis system. Neighbor joining phylogenetic tree construction from the ISSR allele similarity based genetic distance revealed two major clusters with 46 and 33 accessions in each cluster. Expression of fruit ripening related genes of ethylene biosynthesis (1-aminocyclopropane-1-carboxylate synthase, 1-aminocyclopropane-1-carboxylate oxidase) and cell wall metabolism (polygalacturonase, xyloglucan endotransglucosylase/hydrolase and expansin) in Mangalore melons was significantly lower than the cantaloupe melon at 180 days after harvest. Mangalore melon is a promising genetic resource for enhancing the shelf life of melons and the putative candidate genes are useful in enhancing shelf life of cantaloupe following validation and conformation.

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