scholarly journals Mango Genetic Diversity Analysis and Pedigree Inferences for Florida Cultivars using Microsatellite Markers

HortScience ◽  
2006 ◽  
Vol 41 (4) ◽  
pp. 993D-993 ◽  
Author(s):  
Raymond Schnell ◽  
J. Steven Brown ◽  
Cecile Olano ◽  
Alan Meerow ◽  
Richard Campbell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Gene Diversity ◽  
Mangifera Indica ◽  
Parentage Analysis ◽  
Southeast Asian ◽  
Land Race ◽  
Wide Range ◽  
Unbiased Gene ◽  
Primary Groups

Mangifera indica L. germplasm can be classified by origin with the primary groups being cultivars selected from the centers of diversity for the species, India and Southeast Asia, and those selected in Florida and other tropical and subtropical locations. Accessions have also been classified by horticultural type: cultivars that produce monoembryonic seed vs. cultivars that produce polyembryonic seed. In this study, we used 25 microsatellite loci to estimate genetic diversity among 203 accessions. The 25 microsatellite loci had an average of 6.96 alleles per locus and an average PIC value of 0.552. The total propagation error in the collection, i.e., plants that had been incorrectly labeled or grafted, was estimated to be 6.13%. When compared by origin, the Florida cultivars were more closely related to Indian than to Southeast Asian cultivars. Unbiased gene diversity (Hnb) of 0.600 and 0.582 was found for Indian and Southeast Asian cultivars, respectively, and both were higher than Hnb among Florida cultivars (0.538). When compared by horticultural type, Hnb was higher among the polyembryonic types (0.596) than in the monoembryonic types (0.571). Parentage analysis of the Florida cultivars was accomplished using a multistage process based on introduction dates of cultivars into Florida and selection dates of Florida cultivars. Microsatellite marker evidence suggests that as few as four Indian cultivars, and the land race known as `Turpentine', were involved in the early cultivar selections. Florida may not represent a secondary center of diversity; however, the Florida group is a unique set of cultivars selected under similar conditions offering production stability in a wide range of environments.

scholarly journals Mango Genetic Diversity Analysis and Pedigree Inferences for Florida Cultivars Using Microsatellite Markers

2006 ◽  
Vol 131 (2) ◽  
pp. 214-224 ◽  
Author(s):  
R.J. Schnell ◽  
J.S. Brown ◽  
C.T. Olano ◽  
A.W. Meerow ◽  
R.J. Campbell ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Gene Diversity ◽  
Mangifera Indica ◽  
Parentage Analysis ◽  
Southeast Asian ◽  
Land Race ◽  
Wide Range ◽  
Unbiased Gene ◽  
Primary Groups

Mango (Mangifera indica L.) germplasm can be classified by origin with the primary groups being cultivars selected from the centers of diversity for the species, India and Southeast Asia, and those selected in Florida and other tropical and subtropical locations. Accessions have also been classified by horticultural type: cultivars that produce monoembryonic seed vs. cultivars that produce polyembryonic seed. In this study we used 25 microsatellite loci to estimate genetic diversity among 203 unique mangos (M. indica), two M. griffithii Hook. f., and three M. odorata Griff. accessions maintained at the National Germplasm Repository and by Fairchild Tropical Botanic Garden in Miami, Fla. The 25 microsatellite loci had an average of 6.96 alleles per locus and an average polymorphism information content (PIC) value of 0.552 for the M. indica population. The total propagation error in the collection (i.e., plants that had been incorrectly labeled or grafted) was estimated to be 6.13%. When compared by origin, the Florida cultivars were more closely related to Indian than to Southeast Asian cultivars. Unbiased gene diversity (Hnb) of 0.600 and 0.582 was found for Indian and Southeast Asian cultivars, respectively, and both were higher than Hnb among Florida cultivars (0.538). When compared by horticultural type, Hnb was higher among the polyembryonic types (0.596) than in the monoembryonic types (0.571). Parentage analysis of the Florida cultivars was accomplished using a multistage process based on introduction dates of cultivars into Florida and selection dates of Florida cultivars. In total, 64 Florida cultivars were evaluated over four generations. Microsatellite marker evidence suggests that as few as four Indian cultivars, and the land race known as `Turpentine', were involved in the early cultivar selections. Florida may not represent a secondary center of diversity; however, the Florida group is a unique set of cultivars selected under similar conditions offering production stability in a wide range of environments.

scholarly journals Evaluation of nutraceuticals including vitamin B12 and xenobiotic degradation capacity of Pleurotus species

2019 ◽  
Author(s):  
Yashvant Patel ◽  
Sanjay Kumar Vishwakarma ◽  
Kumari Sunita
Keyword(s):  
Genetic Diversity ◽  
Dye Degradation ◽  
Gene Diversity ◽  
Selection Process ◽  
Uttar Pradesh ◽  
Crude Enzyme Extract ◽  
Information Index ◽  
Wide Range ◽  
Laccase Enzyme ◽  
Average Gene

AbstractDiverse edaphic zone (namely: usar, wastelands, forest area, wetlands, flood prone area and fertile lands) were identified in the eastern part of Uttar Pradesh and collected species of Pleurotus for present study. A total of 39 purified isolates were evaluated for the presence of neutraceuticals like proteins, carbohydrates, phenolic and vitamin B12 along with xenobiotic dye degradation capacity for textile dyes (MG and BPB) and production of laccase enzyme simultaneously. Isolate no. 06, appeared most distant in dendrogram having two major clusters, which also showed highest MG degradation capacity, however, other isolates also showed excellent degradation of BPB; and the laccase activity was found in the range of 4.03 to 19.13 IU/ml of crude enzyme extract from mycelia. All the isolates used in the present study, were also mounted for their genetic diversity analysis through RAPD. Diversity study revealed gene frequency from 0.012 to 0.987 and the average gene diversity for all RAPD loci were 0.244. The Shannon Information Index was 0.397. The unbiased genetic similarity among all pairs of isolates was 0.36 to 0.93 with a mean of 0.64. Significant genetic diversity, nutraceuticals and laccase enzyme availability and dye degradation capacity within the studied genus Pleurotus was found, which makes necessary to carry out a selection process in each one for superior selection not only for human being but also many aquatic as well as other terrestrial flora and fauna. Present investigation suggest that due to wide range of variation within species, the adaptation of strains to different edaphic zones must be taken into account in selection processes.

scholarly journals Abundance and Genetic Diversity ofnifHGene Sequences in Anthropogenically Affected Brazilian Mangrove Sediments

2012 ◽  
Vol 78 (22) ◽  
pp. 7960-7967 ◽  
Author(s):  
Armando Cavalcante Franco Dias ◽  
Michele de Cassia Pereira e Silva ◽  
Simone Raposo Cotta ◽  
Francisco Dini-Andreote ◽  
Fábio Lino Soares ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Gene Diversity ◽  
Conservation Strategies ◽  
Mangrove Sediment ◽  
Nitrogen Fixing ◽  
Content Type ◽  
Sulfate Reducing ◽  
Wide Range ◽  
Gradient Gel Electrophoresis

ABSTRACTAlthough mangroves represent ecosystems of global importance, the genetic diversity and abundance of functional genes that are key to their functioning scarcely have been explored. Here, we present a survey based on thenifHgene across transects of sediments of two mangrove systems located along the coast line of São Paulo state (Brazil) which differed by degree of disturbance, i.e., an oil-spill-affected and an unaffected mangrove. The diazotrophic communities were assessed by denaturing gradient gel electrophoresis (DGGE), quantitative PCR (qPCR), and clone libraries. ThenifHgene abundance was similar across the two mangrove sediment systems, as evidenced by qPCR. However, thenifH-based PCR-DGGE profiles revealed clear differences between the mangroves. Moreover, shifts in thenifHgene diversities were noted along the land-sea transect within the previously oiled mangrove. ThenifHgene diversity depicted the presence of nitrogen-fixing bacteria affiliated with a wide range of taxa, encompassing members of theAlphaproteobacteria,Betaproteobacteria,Gammaproteobacteria,Firmicutes, and also a group of anaerobic sulfate-reducing bacteria. We also detected a unique mangrove-specific cluster of sequences denoted Mgv-nifH. Our results indicate that nitrogen-fixing bacterial guilds can be partially endemic to mangroves, and these communities are modulated by oil contamination, which has important implications for conservation strategies.

scholarly journals Genetic diversity and phylogenetic relationship of nine sheep populations based on microsatellite markers

2021 ◽  
Vol 64 (1) ◽  
pp. 7-16
Author(s):  
Qing Xia ◽  
Xiangyu Wang ◽  
Zhangyuan Pan ◽  
Rensen Zhang ◽  
Caihong Wei ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Relationship ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Group Method ◽  
Pair Group ◽  
Introduced Populations ◽  
Unbiased Gene ◽  
Relationship Of ◽  
Hu Sheep

Abstract. The objective of this study was to assess the genetic diversity and phylogenetic relationship of nine sheep populations, including two famous high prolific populations and seven popular mutton populations raised in China. Overall, these sheep populations in this study exhibited a rich genetic diversity. Both the expected heterozygosity and Nei's unbiased gene diversity ranged from 0.64 to 0.75, with the lowest value found in Dorset sheep (DST) and the highest in Hu sheep (HUS) and Ba Han sheep (BAS). The polymorphic information content (PIC) varied between 0.59 in DST and 0.71 in HUS and BAS. Specifically, for individual breeds, the small-tail Han sheep (STH) and the four introduced populations did not display the expected diversity; therefore more attention should be paid to the maintenance of diversity during management of these populations. The results of un-weighted pair-group method (UPGMA) phylogenetic tree and structure analysis indicated that the nine investigated populations can be divided into two groups. Suffolk (SUF) and DST were clustered in one group, and the other group can be further divided into three clusters: German Mutton Merino (GMM)–BAS–Bamei Mutton sheep (BAM), HUS–STH and Du Han (DOS)–Dorper (DOP). This clustering result is consistent with sheep breeding history. TreeMix analysis also hinted at the possible gene flow from GMM to SUF. Together, an in-depth view of genetic diversity and genetic relationship will have important implications for breed-specific management.

Genetic Diversity and Demographic History of an Upper Hill Dipterocarp (Shorea platyclados): Implications for Conservation

2019 ◽  
Vol 110 (7) ◽  
pp. 844-856 ◽  
Author(s):  
Chin-Hong Ng ◽  
Soon-Leong Lee ◽  
Lee-Hong Tnah ◽  
Kevin K S Ng ◽  
Chai-Ting Lee ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Gene Diversity ◽  
Demographic History ◽  
Haplotype Diversity ◽  
Population History ◽  
Conservation Strategy ◽  
Ex Situ ◽  
History Of ◽  
Shorea Platyclados

Abstract Southeast Asian rainforests at upper hill elevations are increasingly vulnerable to degradation because most lowland forest areas have been converted to different land uses. As such, understanding the genetics of upper hill species is becoming more crucial for their future management and conservation. Shorea platyclados is an important, widespread upper hill dipterocarp in Malaysia. To elucidate the genetic structure of S. platyclados and ultimately provide guidelines for a conservation strategy for this species, we carried out a comprehensive study of the genetic diversity and demographic history of S. platyclados. Twenty-seven populations of S. platyclados across its range in Malaysia were genotyped at 15 polymorphic microsatellite loci and sequenced at seven noncoding chloroplast DNA (cpDNA) regions. A total of 303 alleles were derived from the microsatellite loci, and 29 haplotypes were identified based on 2892 bp of concatenated cpDNA sequences. The populations showed moderately high genetic diversity (mean HE = 0.680 for microsatellite gene diversity and HT = 0.650 for total haplotype diversity) and low genetic differentiation (FST = 0.060). Bayesian clustering divided the studied populations into two groups corresponding to western and eastern Malaysia. Bottleneck analysis did not detect any recent bottleneck events. Extended Bayesian skyline analyses showed a model of constant size for the past population history of this species. Based on our findings, priority areas for in situ and ex situ conservation and a minimum population size are recommended for the sustainable utilization of S. platyclados.

scholarly journals Genetic Variation and Population Structure in Jamunapari Goats Using Microsatellites, Mitochondrial DNA, and Milk Protein Genes

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
P. K. Rout ◽  
K. Thangraj ◽  
A. Mandal ◽  
R. Roy
Keyword(s):  
Genetic Diversity ◽  
Mitochondrial Dna ◽  
Genetic Variation ◽  
Population Size ◽  
Microsatellite Loci ◽  
Milk Protein ◽  
Gene Diversity ◽  
Population History ◽  
Dairy Goat ◽  
The Mean

Jamunapari, a dairy goat breed of India, has been gradually declining in numbers in its home tract over the years. We have analysed genetic variation and population history in Jamunapari goats based on 17 microsatellite loci, 2 milk protein loci, mitochondrial hypervariable region I (HVRI) sequencing, and three Y-chromosomal gene sequencing. We used the mitochondrial DNA (mtDNA) mismatch distribution, microsatellite data, and bottleneck tests to infer the population history and demography. The mean number of alleles per locus was 9.0 indicating that the allelic variation was high in all the loci and the mean heterozygosity was 0.769 at nuclear loci. Although the population size is smaller than 8,000 individuals, the amount of variability both in terms of allelic richness and gene diversity was high in all the microsatellite loci except ILST 005. The gene diversity and effective number of alleles at milk protein loci were higher than the 10 other Indian goat breeds that they were compared to. Mismatch analysis was carried out and the analysis revealed that the population curve was unimodal indicating the expansion of population. The genetic diversity of Y-chromosome genes was low in the present study. The observed mean M ratio in the population was above the critical significance value (Mc) and close to one indicating that it has maintained a slowly changing population size. The mode-shift test did not detect any distortion of allele frequency and the heterozygosity excess method showed that there was no significant departure from mutation-drift equilibrium detected in the population. However, the effects of genetic bottlenecks were observed in some loci due to decreased heterozygosity and lower level of M ratio. There were two observed genetic subdivisions in the population supporting the observations of farmers in different areas. This base line information on genetic diversity, bottleneck analysis, and mismatch analysis was obtained to assist the conservation decision and management of the breed.

scholarly journals Scot molecular markers and population differentiation in Hedera helix L.

Genetika ◽  
2021 ◽  
Vol 53 (2) ◽  
pp. 739-756
Author(s):  
Haiying Li ◽  
Yingxue Wang ◽  
Rabia Iqbal
Keyword(s):  
Genetic Diversity ◽  
Biochemical Characterization ◽  
Gene Diversity ◽  
Polymorphic Information Content ◽  
Shannon Index ◽  
Start Codon ◽  
Hedera Helix ◽  
Allele Number ◽  
Unbiased Gene ◽  
Reliable Marker

Hedera helix L. is a specie that is used for its ornamental and medicinal properties widely. In spite of its very good biochemical characterization, the knowledge about the DNA variability is very limited and no DNA markers were used to analyses the genomic variability of the populations, up to date. In the present study, genetic diversity of 56 Hedera helix, individuals nine populations were studied using 10 Start Codon Targeted (SCoT) markers. High polymorphic bands (95.78%), polymorphic information content (0.25) and allele number (1.34) showed SCoT as a reliable marker system for genetic analysis in Hedera helix. At the species, the percentage of polymorphic loci [P] was 66.20%, Nei?s gene diversity [H] was 0.159, Shannon index [I] was 0.148 and unbiased gene diversity [UHe] was 0.56. Genetic variation within populations (70%) was higher than among populations (30%) based on analysis of molecular variance (AMOVA). We used SCoT molecular marker for our genetic investigation with the following aims: 1- Investigate genetic diversity both among and with date Hedera helix, 2-Identify genetic groups within these nine populations ivy, and 3-produce data on the genetic structure of date ivy populations. The results obtained revealed a high within-population genetic variability.

scholarly journals Evaluation of Avocado Germplasm Using Microsatellite Markers

2003 ◽  
Vol 128 (6) ◽  
pp. 881-889 ◽  
Author(s):  
R.J. Schnell ◽  
J.S. Brown ◽  
C.T. Olano ◽  
E.J. Power ◽  
C.A. Krol ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci ◽  
Gene Diversity ◽  
West Indian ◽  
Molecular Data ◽  
Persea Americana ◽  
The West ◽  
Phytophthora Root Rot ◽  
Field Station ◽  
Major Cluster

Three horticultural races of avocado (Persea americana Mill.) are known: Guatemalan, Mexican, and West Indian. Each race has unique characteristics and current commercial varieties have been selected from within the races or from interracial hybrids. Using 14 microsatellite loci we investigated the genetic variation among 224 accessions (394 plants) maintained at the National Germplasm Repository (NGR) in Miami, Fla., and a set of 34 clones from the University of California South Coast Field Station (SCFS) located in Irvine, Calif. The 14 microsatellite loci had an average of 18.8 alleles per locus and average unbiased genetic diversity was 0.83. The total propagation error in the collection, i.e., plants that had been incorrectly labeled or grafted, was estimated to be 7.0%. Although many unique alleles did exist, no useful race-specific markers were found. A general concordance between the horticultural race and the clusters obtained from molecular data was observed. Principal Coordinate Analysis (PCA) grouped the Guatemalan and Mexican races into two distinct clusters. The West Indian also grouped into a unique major cluster but with an outlying group. Using the PCA a change in the racial designation or interracial hybrid status for 50 accessions (19.7%) is proposed. The unbiased gene diversity estimate was highest in the Mexican and Guatemalan races and lower in the West Indian group. This demonstrates the need to collect more of the West Indian germplasm to broaden the genetic diversity and to emphasize the identification of individuals conferring resistance to Phytophthora Root Rot (PRR).

Assessment of the genetic diversity of microsatellite loci of horses of Heavy Draft breeds

2018 ◽  
pp. 39-44
Author(s):  
N. Blohina ◽  
◽  
L. Khrabrova ◽  
A. Zaitcev ◽  
I. Gavrilicheva ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Loci
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