Mitochondrial D-loop Genetic Diversity Studies of Rhinoceros unicornis in Assam, India

2020 ◽  
Author(s):  
Puranjit Das ◽  
Rita Choudhury
Keyword(s):  
Genetic Diversity ◽  
National Park ◽  
Natural Habitats ◽  
Mitochondrial Dna Control Region ◽  
Non Invasive ◽  
Rhinoceros Unicornis ◽  
Total Genetic Diversity ◽  
D Loop ◽  
High Level ◽  
Diversity Studies

In Assam wild populations of great Indian rhinoceros are found in three protected areas namely Kaziranga National Park, Orange National Park and Pobitora Wildlife Sanctuary. But it remains an area of investigation whether these three populations are homogeneous or not. To resolve this matter present genetic study was performed on mitochondrial DNA control region by using non invasive dung samples collected from the three natural habitats. The study showed a high level of genetic diversity of rhinoceros population in three habitats of Assam with 24 haplotypes from 196 samples and 21 variable sites in 413bp long nucleotide sequences was recorded. The Fst value also showed differences between the groups; and significant values obtained between Kaziranga and Pobitora with Orang groups. AMOVA analyses revealed the total genetic diversity is 91.62% and diversity between populations is only 8.38%. Thus the higher genetic variability found in Indian rhinoceros populations is important for future survivability, management and translocation to new habitat.

scholarly journals Genetic Diversity Studies in MAGIC Population of Soybean (Glycine max (L.) Merrill) Based on Mahalanobis D2 Distance

2021 ◽  
pp. 18-25
Author(s):  
Bidush Ranjan Swar ◽  
V. Swarnalatha ◽  
M. Rajendar Reddy ◽  
S. Vanisree
Keyword(s):  
Genetic Diversity ◽  
Seed Weight ◽  
Quantitative Traits ◽  
Genetic Recombination ◽  
Breeding Programs ◽  
Total Genetic Diversity ◽  
Glycine Max L ◽  
Diversity Studies ◽  
100 Seed Weight ◽  
Number Of Branches

Soybean MAGIC lines are highly variable breeding material which utilizes both recent and historic genetic recombination events. Present investigation was carried out to assess the genetic diversity present among 95 soybean MAGIC lines along with six checks for 10 different quantitative traits. All the genotypes were grouped into 16 clusters by performing Tocher’s clustering method using Mahalanobis D2 distance. Cluster I was the largest comprising of 30 genotypes followed by cluster II (23 genotypes), cluster X (15 genotypes) and cluster IX (9 genotypes). The maximum genetic distance (D2) was observed between cluster XI and XV (168.37) followed by cluster III and XV (164.3), cluster X and XV (149.64) as well as between cluster XII and cluster XVI (145.99). The cluster mean for most of the traits were high in cluster I and cluster XVI. Oil content contributed maximum (23.86%) towards total genetic diversity followed by number of pods plant-1 (18.97%), seed yield plant-1 (18.63%), 100 seed weight (11.05%) and number of branches plant-1 (10.16%) traits. The soybean MAGIC lines belong to the cluster XI (6-120) and cluster XV (6-30, 6-31, 6-5) were found to be the most divergent hence can be utilised in the recombination breeding programs to exploit maximum heterosis.

Evaluation of rice and sugarcane SSR markers for phylogenetic and genetic diversity analyses in bambooIHBT Publication No. 0732.

Genome ◽  
2008 ◽  
Vol 51 (2) ◽  
pp. 91-103 ◽  
Author(s):  
R. K. Sharma ◽  
P. Gupta ◽  
V. Sharma ◽  
A. Sood ◽  
T. Mohapatra ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Large Scale ◽  
Bamboo Species ◽  
Ssr Primers ◽  
Taxonomical Classification ◽  
High Level ◽  
The Tropics ◽  
Diversity Studies

Simple sequence repeat (SSR) markers are valuable tools for many purposes such as phylogenetic, fingerprinting, and molecular breeding studies. However, only a few SSR markers are known and available in bamboo species of the tropics ( Bambusa spp.). Considering that grass genomes have co-evolved and share large-scale synteny, theoretically it should be possible to use the genome sequence based SSR markers of field crops such as rice ( Oryza sativa ) and sugarcane ( Saccharum spp.) for genome analysis in bamboo. To test this, 98 mapped SSR primers representing 12 linkage groups of rice and 20 EST-derived sugarcane SSR primers were evaluated for transferability to 23 bamboo species. Of the tested markers, 44 (44.9%) rice and 15 (75%) sugarcane SSR primers showed repeatable amplification in at least one species of bamboo and thus were successfully utilized for phylogenetic and genetic diversity analyses. Transferred SSR primers revealed complex amplification patterns in bamboo, with an average of 9.62 fragments per primer, indicating a high level of polyploidy and genetic variability in bamboo. Forty-two of these primers (34 rice and 8 sugarcane SSR primers) detected an average of 2.12 unique fragments per primer and thus could be exploited for species identification. Six bamboo SSR primers exhibited cross transferability, to varying degrees, to different bamboo species. The genetic similarity coefficient indicated a high level of divergence at the species level (73%). However, a relatively low level of diversity was observed within species (25% in 20 accessions of Dendrocalamus hamiltonii ). Further, cluster analysis revealed that the major grouping was in accordance with the taxonomical classification of bamboo. Thus, the rice and sugarcane SSRs can be utilized for phylogenetic and genetic diversity studies in bamboo.

scholarly journals Genetic diversity and phylogenetic analyses of 11 cohorts of captive rhesus macaques from Chinese zoos

PeerJ ◽  
2019 ◽  
Vol 7 ◽  
pp. e6957
Author(s):  
Qian Su ◽  
Yongfang Yao ◽  
Qin Zhao ◽  
Diyan Li ◽  
Meng Xie ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Rhesus Macaques ◽  
Phylogenetic Analyses ◽  
Genetic Management ◽  
Southeastern China ◽  
Mitochondrial Dna Control Region ◽  
Clade B ◽  
In Captivity ◽  
High Level ◽  
Major Haplogroups

Rhesus macaques are raised in almost every Chinese zoo due to their likeability and ease in feeding; however, little is yet known about the genetic diversity of rhesus macaques in captivity. In this study, a 475-base pair nucleotide sequence of the mitochondrial DNA control region was obtained from the fecal DNA of 210 rhesus macaque individuals in captivity. A total of 69 haplotypes were defined, 51 of which (73.9%) were newly identified. Of all haplotypes, seven were shared between two zoos, and 62 haplotypes (89.8%) appeared only in a specific zoo, indicating a low rate of animal exchange between Chinese zoos. Moreover, there was a relatively high level of genetic diversity among the rhesus macaques (Hd = 0.0623 ± 0.0009, Pi = 0.979 ± 0.003, K = 28.974). Phylogenetic analysis demonstrated that all haplotypes were clearly clustered into two major haplogroups—Clade A (southeastern China) and Clade B (southwestern China)—and each major clade contained several small sub-haplogroups. The haplotypes of rhesus macaques from the same zoo were not clustered together for the most part, but scattered among several subclades on the phylogenetic tree. This indicates that the rhesus macaques in most Chinese zoos may originat from a diverse collection of geographical areas. Our results demonstrate that zoos play an important role in the conservation of the genetic diversity of rhesus macaques, as well as provide useful information on the genetic management of captive rhesus macaques.

scholarly journals Mitochondrial DNA-based genetic evaluation of autochthonous cattle breeds in Croatia

2014 ◽  
Vol 59 (No. 11) ◽  
pp. 519-528 ◽  
Author(s):  
A. Ivanković ◽  
S. Paprika ◽  
J. Ramljak ◽  
P. Dovč ◽  
M. Konjačić
Keyword(s):  
Genetic Diversity ◽  
Conservation Management ◽  
Large Fraction ◽  
Base Pairs ◽  
Cattle Breeds ◽  
Loop Region ◽  
D Loop ◽  
Mtdna Diversity ◽  
High Level ◽  
Relationship Of

Genetic diversity and phylogenetic relationship of three Croatian autochthonous cattle breeds was analyzed using a sequence of the mtDNA D-loop region. Among Busha, Istrian, and Slavonian Syrmian Podolian cattle 146 unrelated animals were tested. The sequencing of 780 base pairs of the mtDNA D-loop region revealed 39 polymorphic sites representing 28 different haplotypes. The highest numbers of haplotypes were observed in the Busha population and the lowest in the population of Slavonian Syrmian Podolian cattle, while the highest level of sequence diversity within a population was observed in the Istrian cattle. Our results indicate a high level of mtDNA diversity in the populations of Busha and Istrian cattle and a low level of preserved diversity in the population of Slavonian Syrmian Podolian cattle. The sequence analysis showed substantial subdivision between the breeds (F<sub>ST</sub> = 0.1434), and a large fraction of variation within the breeds. Although the dominant haplotypes are classified as the T3 haplogroup, some of the haplotypes are classified as the rarer T2 and T5 haplogroups. Genetic information based on mtDNA typing has a great importance for the future conservation management and preservation of genetic diversity in autochthonous cattle breeds. &nbsp;

Genetic Diversity in the Endangered Phebalium daviesii (Rutaceae) Compared to That in Two Widespread Congeners

1995 ◽  
Vol 43 (2) ◽  
pp. 181 ◽  
Author(s):  
AJJ Lynch ◽  
RE Vaillancourt
Keyword(s):  
Genetic Diversity ◽  
Population Bottleneck ◽  
Allozyme Data ◽  
Enzyme Systems ◽  
Total Genetic Diversity ◽  
Rare And Endangered ◽  
Ecological Habitat ◽  
Hardy Weinberg Equilibrium ◽  
High Level ◽  
Adult Plants

Genetic diversity in the rare and endangered Phebalium daviesii was compared to that in P. squamulosum subsp. squamulosum and P. glandulosum subsp. glandulosum using allozyme analysis. Phebalium daviesii was once presumed extinct, but 43 adult plants have so far been rediscovered. Phebalium squamulosum subsp. squamulosum and P. glandulosum subsp. glandulosum are widespread in the south-eastern part of the Australian mainland. Morphologically, these two taxa are the closest relatives of P. daviesii and share a similarity with P. daviesii in their ecological habitat. The level of genetic diversity and deviations from Hardy-Weinberg equiibrium were investigated using allozyme data with 18 enzyme systems. Nei's total genetic diversity, the proportion of polymorphic loci and the average number of alleles per locus were all slightly lower in P. daviesii than in P. squamulosum subsp. squamulosum and P. glandulosum subsp. glandulosum. Deviations from expected Hardy-Weinberg equilibrium were present in all three taxa and were more frequent in P. glandulosum subsp. glandulosum. This suggests that inbreeding may be occurring in all three Phebalium taxa and that P. daviesii does not suffer from increased inbreeding due to rarity. Phebalium daviesii has a high level of genetic diversity (Ht = 0.30) for such a rare species and should be able to recover from its population bottleneck with appropriate management.

Genetic diversity of mocó cotton (Gossypium hirsutum race marie-galante) from the northeast of Brazil: implications for conservation

Botany ◽  
2010 ◽  
Vol 88 (8) ◽  
pp. 765-773 ◽  
Author(s):  
Ivandilson Pessoa Pinto de Menezes ◽  
Paulo Augusto Vianna Barroso ◽  
Lúcia Vieira Hoffmann ◽  
Valeska Silva Lucena ◽  
Marc Giband
Keyword(s):  
Genetic Diversity ◽  
Gossypium Hirsutum ◽  
Geographic Origin ◽  
Rio Grande ◽  
Ex Situ ◽  
High Genetic Diversity ◽  
Breeding Programs ◽  
Extinction Process ◽  
Total Genetic Diversity ◽  
High Level

Mocó cotton ( Gossypium hirsutum  L. race marie-galante (Watt) Hutch.) is a potential source of valuable alleles for breeding programs, mainly because of its great adaptability to semi-arid conditions. With the aim of quantifying mocó cotton genetic variability, 187 plants collected in the northeast of Brazil were evaluated using 12 microsatellite markers. A total of 62 alleles were amplified, ranging from three to eight polymorphic alleles per locus. Total genetic diversity was high (0.52), and when measured on a per state basis, was of 0.37 on average. The population showed a low level of heterozygozity (HO = 0.16), reflecting a high level of endogamy (FIS = 0.67). Phylogenetic analysis using the neighbor-joining method revealed that plants sampled in different states tended to cluster according to their geographic origin, except for those collected in the states of Paraíba and Rio Grande do Norte, which grouped together. Plants from the state of Piauí formed two groups, one with an apparent allelic contribution from G. barbadense, while the second group of plants was closer to those from the states of Paraíba and Rio Grande do Norte. Despite the high genetic diversity that was observed in the remaining populations, urgent conservation efforts should be undertaken, owing to the high level of endogamy and accelerated extinction process that characterizes these populations. Such efforts should focus on the collection and ex situ maintenance of representative genetic diversity.

scholarly journals iPBS polymorphism of rare relict and endangered Allium species growing on the territory of Kazakhstan Altai

2020 ◽  
Vol 200 (9) ◽  
pp. 63-73
Author(s):  
Olesya Rayzer ◽  
Oksana Hapilina
Keyword(s):  
Genetic Diversity ◽  
Molecular Genetic ◽  
Natural Populations ◽  
Dna Amplification ◽  
Practical Significance ◽  
Primer Binding Site ◽  
Natural Habitats ◽  
Allium Species ◽  
Different Populations ◽  
High Level

Abstract. The purpose of the study. The estimation of genetic polymorphism of Kazakhstan populations of rare relict and endemic Allium species. The novelty of the research is the use of the modern molecular genetic iPBS (Inter- Primer Binding Site Polymorphism) method of DNA amplification to assess the genetic diversity of different populations of Allium sp., collected in their natural habitats in the Kazakhstan Altai. Methods. Samples of medicinal relict and endangered species A. ledebourianum, A. altaicum, A. microdiction were collected in the places of their natural growth in the territory of the Kazakhstan Altai. DNA was isolated from 3–5 day sterile seedlings using lysis STAB buffer with RNaseA. PBS primers were used to assess the genetic diversity of different populations of Allium spp. The amplification results obtained using different PBS primers were evaluated in the GenAlex 6.5 macro program for Excel. Results. The polymorphism of 16 genotypes of the rare relict and endangered Allium sp. was analyzed using 7 PBS primers. Clearly distinguishable amplicons were obtained, the number of which varied depending on the primer used. The dendrogram, based on UPGMA analysis, grouped the studied genotypes into 2 main clusters, one of which included samples from the A. altaicum population, and the second cluster included samples from the A. ledebourianum population. A. microdiction represented by one sample did not enter any cluster, and formed a basal branch in the dendrogram. The results of the study have revealed a high degree of iPBS polymorphism and genetic diversity in rare relict and endangered Allium sp. Practical significance. The use of the molecular genetic iPBS method allows to identify a high level of polymorphism, which can serve as a basis for the identification of various genotypes of the Allium sp., which will significantly supplement traditional preservation methods of natural populations of this genus.

scholarly journals Simple Sequence Repeat Marker Analysis of Genetic Relationships within Hydrangea macrophylla

2007 ◽  
Vol 132 (3) ◽  
pp. 341-351 ◽  
Author(s):  
Sandra M. Reed ◽  
Timothy A. Rinehart
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Relationships ◽  
Allelic Diversity ◽  
Sequence Repeat ◽  
Hydrangea Macrophylla ◽  
Total Genetic Diversity ◽  
Ssr Loci ◽  
Diversity Studies ◽  
Simple Sequence

Genetic diversity studies using 39 simple-sequence repeat (SSR) markers were carried out with 114 taxa of Hydrangea macrophylla (Thunb.) Ser., including 87 H. macrophylla ssp. macrophylla cultivars and 20 members of H. macrophylla ssp. serrata (Thunb.) Makino. The SSR loci were highly variable among the taxa, producing a mean of 8.26 alleles per locus. Overall allelic richness was relatively high at 5.12 alleles per locus. H. macrophylla ssp. serrata contained nearly twice the allelic diversity of H. macrophylla ssp. macrophylla. The majority of genetic diversity was found to reside within the subspecies, with only 12% of the total genetic diversity observed occurring between subspecies. Although the elevation of H. macrophylla ssp. serrata to species level has recently been recommended by several hydrangea authorities, these data support the subspecies designation. Four cultivars (Preziosa, Pink Beauty, Tokyo Delight, and Blue Deckle) appeared to be hybrids between the two subspecies. Genetic similarities were found among five remontant cultivars (Bailmer, Oak Hill, David Ramsey, Decatur Blue, and Penny Mac) and several nonremontant cultivars, including General Vicomtesse de Vibraye, Nikko Blue, All Summer Beauty, and La France. No close genetic relationship was found between the remontant cultivar Early Sensation and other remontant cultivars. Genetic similarities were found among variegated and double-flower cultivars. Within H. macrophylla ssp. macrophylla, cultivars with mophead inflorescences clustered separately from most lacecap cultivars. This indicates the cultivars with lacecap inflorescences that were among some of the earliest introductions to Europe were not widely used in the breeding of mophead forms. Some presumed synonyms were found to be valid (‘Preziosa’ and ‘Pink Beauty’, ‘Rosalba’ and ‘Benigaku’, ‘Geoffrey Chadbund’ and ‘Mowe’), whereas others were not (‘Harlequin’ and ‘Monrey’, ‘Nigra’ and ‘Mandschurica’). This study identified potentially unexploited sources of germplasm within H. macrophylla and relationships between existing cultivars of this popular shrub. This information should be of value when selecting parents for breeding programs.

scholarly journals Evaluating genetic diversity and identifying priority conservation for seven Tibetan pig populations in China based on the mtDNA D-loop

2020 ◽  
Vol 33 (12) ◽  
pp. 1905-1911
Author(s):  
Qianyun Ge ◽  
Caixia Gao ◽  
Yuan Cai ◽  
Ting Jiao ◽  
Jinqiang Quan ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Resource ◽  
Genetic Contribution ◽  
Contribution Rate ◽  
Mitochondrial Dna Control Region ◽  
Pig Breeds ◽  
Tibetan Pig ◽  
Tibetan Pigs ◽  
D Loop ◽  
Development And Utilization

Objective: Tibetan pigs, an excellent species unique to China, face serious threats, which in turn affects the development and utilization of the outstanding advantages of plateau hypoxia adaptability and reduces their genetic diversity. Therefore, a discussion of measures to conserve this genetic resource is necessary. The method, based on genetic diversity, genetic divergence and total genetic contribution rate of population, reflects the priority conservation order and varies depending on the three different purposes of conservation.Methods: We analyzed mitochondrial DNA control region (D-loop) variation in 1,201 individuals from nine Tibetan pig populations across five provinces and downloaded 564 mtDNA D-loop sequences from three indigenous pig breeds in Qinghai, Sichuan, and Yunnan Provinces distributed near the Tibetan pigs.Results: We analyzed three different aspects: Changdu Tibetan pigs have the highest genetic diversity, and from the perspective of genetic diversity, the priority conservation is Changdu Tibetan pigs. Hezuo Tibetan pigs have the highest genetic contribution, so the priority conservation is Hezuo Tibetan pigs in the genetic contribution aspect. Rkaze Tibetan pigs were severely affected by indigenous pig breeds, so if considering from the perspective of introgression, the priority conservation is Rkaze Tibetan pigs.Conclusion: This study evaluated genetic diversity and comprehensively assessed conservation priority from three different aspects in nine Tibetan pig populations.

Genetic Relationships between Tropical Sprangletop (Leptochloa virgata) Populations from Mexico: Understanding Glyphosate Resistance Spread

Weed Science ◽  
2016 ◽  
Vol 64 (4) ◽  
pp. 579-587 ◽  
Author(s):  
Ricardo Alcántara-de la Cruz ◽  
Yolanda Romano ◽  
María Dolores Osuna-Ruíz ◽  
José Alfredo Domínguez-Valenzuela ◽  
Julio Menéndez ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Shikimic Acid ◽  
Genetic Relationships ◽  
Glyphosate Resistance ◽  
Long Distance ◽  
Whole Plant ◽  
Total Genetic Diversity ◽  
Susceptible Populations ◽  
High Level

The susceptibility to glyphosate and genetic diversity based on intersimple sequence repeat markers were characterized for 17 tropical sprangletop populations collected from two separate regions mainly in Persian lime groves in Veracruz, Mexico. The whole-plant dose response together with shikimic acid assays indicated different levels of glyphosate resistance in those populations. Genetic diversity values (h) estimated using POPGENE ranged from 0.119 to 0.198 and 0.117 to 0.214 within susceptible and resistant populations, respectively. The average genetic diversity (HS) within the susceptible populations was 0.157, and the total genetic diversity (HT) was 0.218. TheHSof the resistant populations was 0.144, and theHTwas 0.186. The analysis of molecular variance based on the response to glyphosate indicated that most of the genetic variation was found within groups of susceptible and resistant populations (90% of the genetic variation), whereas 10% or less was among groups. The high level of genetic diversity between glyphosate-resistant tropical sprangletop populations from distant and adjacent locations is likely due to both short- and long-distance seed dispersal and independent evolutionary events in tropical sprangletop populations among Persian lime groves in Veracruz.

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