scholarly journals Genetic diversity in passion fruit plants at different altitudes

2019 ◽  
pp. 1083-1093
Author(s):  
Khétrin Silva Maciel ◽  
Paula Aparecida Muniz de Lima ◽  
Fernando Zanotti Madalon ◽  
Márcia Flores da Silva Ferreira ◽  
Rodrigo Sobreira Alexandre ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Passion Fruit ◽  
Similar Species ◽  
Passiflora Edulis ◽  
Espírito Santo ◽  
Espirito Santo ◽  
Different Altitudes

Passion fruit belongs to the Passifloraceae family and to the genus Passiflora, which is economically relevant. This genus is originated from Brazil, which has the greatest genetic diversity. The altitudinal gradient may influence the distribution of genetic variation in and between plant populations and genetic diversity may change according to the altitude. The objective of this study was to evaluate the genetic diversity in passion fruit in different altitudes of Espírito Santo, using microsatellite markers (SSR) and inter simple sequence repeat (ISSR). Five matrixes plants of each species of Passiflora edulis Sims f. flavicarpa Degener, P. edulis Sims and P. alata Curtis were studied at three altitudes (low, medium and high) in the state of Espírito Santo. For each sample, 13 microsatellite markers developed for Passiflora edulis and 14 ISSR primers were amplified according to the greatest number of polymorphic fragments and amplification quality. Low values of alleles were found (1-3), and low heterozygosity was expected and slight PIC values were found, while for the ISSR analysis a large number of bands per primer were detected and high polymorphism. The P. alata Curtis species was the most divergent to P. edulis Sims f. flavicarpa Deg. and P. edulis Sims. The SSR and ISSR markers enabled us to indicate differences among the species, but they did not always show variation between and within similar species. The populations of low altitude are different from the others, independent of the species and the marker used. The habitat has a highly important influence on genetic diversity.

scholarly journals Physical and chemical characterization of sweet passion fruits genotypes in Sao Mateus, Espírito Santo State, Brazil

2018 ◽  
Vol 9 (3) ◽  
pp. 363-371
Author(s):  
Rodrigo Sobreira Alexandre ◽  
Kleber Rogeres Monteiro Junior ◽  
Kristhiano Chagas ◽  
André Lucas Siqueira ◽  
Edilson Romais Schmildt ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Block Design ◽  
Passion Fruit ◽  
Soluble Solids ◽  
Pulp Yield ◽  
Fresh Market ◽  
Passiflora Edulis ◽  
Espírito Santo ◽  
Espirito Santo ◽  
Physical And Chemical

In Brazil 95% of the passion fruit marketed comes from the species Passiflora edulis f. flavicarpa (yellow passion fruit), the remainder are Passiflora edulis f. edulis (purple passion fruit) and Passiflora alata (sweet passion fruit), considered market niches. Because of the wide genetic variability the genus Passiflora, it is of fundamental importance to identify superior genotypes to improve the quality of fruit for the fresh market. The objective is to analyze the physical and chemical characteristics of the fruits of 33 genotypes P. alata Curtis, evaluated in a randomized complete block design with two replicates of four plants, from native matrices, located at the experimental farm of the University Center of the North of Espírito Santo, Federal University of Espírito Santo, in the Northern Region of the state of Espírito Santo, São Mateus -ES. Thirty-two mature fruits were collected in each replicate, eight per plant and the following characteristics were analyzed: fruit weight (g); equatorial and polar diameter of fruit (cm); peel thickness (mm); mass of the pulp (g); pulp volume (mL); pulp yield (%); number of seeds per fruit, pH; soluble solids (SS); titratable acidity (TA) and ratio (SS/TA). There is a wide genetic variability among P. alata genotypes as to the traits assessed. Genotypes 4, 6, 8, 11, 15, 18, 21, 25 and 26 stood out among the rest, and is therefore recommended for new plantings and future breeding programs.

scholarly journals Genetic Diversity of Purple Passion Fruit, Passiflora edulis f. edulis, Based on Single-Nucleotide Polymorphism Markers Discovered through Genotyping by Sequencing

Diversity ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 144
Author(s):  
Nohra Castillo Rodríguez ◽  
Xingbo Wu ◽  
María Isabel Chacón ◽  
Luz Marina Melgarejo ◽  
Matthew Wohlgemuth Blair
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Genotyping By Sequencing ◽  
Passion Fruit ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Passiflora Edulis ◽  
Tropical Fruit ◽  
Commercial Cultivars ◽  
Purple Passion Fruit

Orphan crops, which include many of the tropical fruit species used in the juice industry, lack genomic resources and breeding efforts. Typical of this dilemma is the lack of commercial cultivars of purple passion fruit, Passiflora edulis f. edulis, and of information on the genetic resources of its substantial semiwild gene pool. In this study, we develop single-nucleotide polymorphism (SNP) markers for the species and show that the genetic diversity of this fruit crop has been reduced because of selection for cultivated genotypes compared to the semiwild landraces in its center of diversity. A specific objective of the present study was to determine the genetic diversity of cultivars, genebank accession, and landraces through genotyping by sequencing (GBS) and to conduct molecular evaluation of a broad collection for the species P. edulis from a source country, Colombia. We included control genotypes of yellow passion fruit, P. edulis f. flavicarpa. The goal was to evaluate differences between fruit types and compare landraces and genebank accessions from in situ accessions collected from farmers. In total, 3820 SNPs were identified as informative for this diversity study. However, the majority distinguished yellow and purple passion fruit, with 966 SNPs useful in purple passion fruits alone. In the population structure analysis, purple passion fruits were very distinct from the yellow ones. The results for purple passion fruits alone showed reduced diversity for the commercial cultivars while highlighting the higher diversity found among landraces from wild or semi-wild conditions. These landraces had higher heterozygosity, polymorphism, and overall genetic diversity. The implications for genetics and breeding as well as evolution and ecology of purple passion fruits based on the extant landrace diversity are discussed with consideration of manual or pollinator-assisted hybridization of this species.

Assessment of genetic variability amongst cultivated populations of Khasi mandarin (Citrus reticulata Blanco) detected by ISSR

2021 ◽  
pp. 1-11
Author(s):  
Karishma Kashyap ◽  
Rasika M. Bhagwat ◽  
Sofia Banu
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Inter Simple Sequence Repeat ◽  
Northeast India ◽  
Issr Markers ◽  
Citrus Reticulata ◽  
Brahmaputra Valley ◽  
Indian Food ◽  
Cultivated Populations ◽  
High Level

Abstract Khasi mandarin (Citrus reticulata Blanco) is a commercial mandarin variety grown in northeast India and one of the 175 Indian food items included in the global first food atlas. The cultivated plantations of Khasi mandarin grown prominently in the lower Brahmaputra valley of Assam, northeast India, have been genetically eroded. The lack in the efforts for conservation of genetic variability in this mandarin variety prompted diversity analysis of Khasi mandarin germplasm across the region. Thus, the study aimed to investigate genetic diversity and partitioning of the genetic variations within and among 92 populations of Khasi mandarin collected from 10 cultivated sites in Kamrup and Kamrup (M) districts of Assam, India, using Inter-Simple Sequence Repeat (ISSR) markers. The amplification of genomic DNA with 17 ISSR primers yielded 216 scorable DNA amplicons of which 177 (81.94%) were polymorphic. The average polymorphism information content was 0.39 per primer. The total genetic diversity (HT = 0.28 ± 0.03) was close to the diversity within the population (HS = 0.20 ± 0.01). A high mean coefficient of gene differentiation (GST = 0.29) reflected a high level of gene flow (Nm = 1.22), indicating high genetic differentiation among the populations. Analysis of Molecular Variance (AMOVA) showed 78% of intra-population differentiation, 21% among the population and 1% among the districts. The obtained results indicate the existence of a high level of genetic diversity in the cultivated Khasi mandarin populations, indicating the need for preservation of each existing population to revive the dying out orchards in northeast India.

ISSR Marker Based Genetic Diversity in Morinda Spp. For Its Enhanced Collection, Conservation and Utilization

2021 ◽  
Author(s):  
Lalit Arya ◽  
Ramya Kossery Narayanan ◽  
Anjali Kak ◽  
Chitra Devi Pandey ◽  
Manjusha Verma ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Morinda Citrifolia ◽  
Species Differentiation ◽  
Information Index ◽  
Upgma Cluster Analysis ◽  
Simple Sequence

Abstract Morinda (Rubiaceae) is considerably recognized for its multiple uses viz. food, medicine, dyes, firewood, tools, oil, bio-sorbent etc. The molecular characterization of such an important plant would be very useful for its multifarious enhanced utilization. In the present study, 31 Morinda genotypes belonging to two different species Morinda citrifolia and Morinda tomentosa collected from different regions of India were investigated using Inter Simple Sequence Repeat (ISSR) markers. Fifteen ISSR primers generated 176 bands with an average of 11.7 bands per primer, of which (90.34%) were polymorphic. The percentage of polymorphic bands, mean Nei’s gene diversity, mean Shannon’s information index in Morinda tomentosa and Morinda citrifolia was [(69.89%, 30.68%); (0.21 ± 0.19, 0.12 ± 0.20); (0.32 ± 0.27 0.17 ± 0.28)] respectively, revealing higher polymorphism and genetic diversity in Morinda tomentosa compared to Morinda citrifolia. Structure, and UPGMA cluster analysis placed the genotypes into well-defined separate clusters belonging to two species Morinda tomentosa and Morinda citrifolia revealing the utility of ISSR markers in species differentiation. Distinct ecotypes within a particular species could also be inferred emphasizing the collection and conservation of Morinda genotypes from different regions, in order to capture the overall diversity of respective species. Further higher diversity of M. tomentosa must be advanced for its utilization in nutraceutical, nutritional and other nonfood purposes.

scholarly journals Polymorphic microsatellites of analysis in cultivars of taro

2012 ◽  
Vol 30 (1) ◽  
pp. 106-111 ◽  
Author(s):  
Raquel SC Nunes ◽  
Fernanda R Pinhati ◽  
Luciana P Golinelli ◽  
Tiyoko Nair H Rebouças ◽  
Vânia Margaret F Paschoalin ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Local Varieties ◽  
Mato Grosso ◽  
Espírito Santo ◽  
Polymorphic Microsatellites ◽  
Espirito Santo ◽  
Microsatellite Alleles ◽  
Mato Grosso Do Sul ◽  
Simple Sequence

Taro (Colocasia esculenta) is a tuberous plant belonging to the Araceae family whose tuber is the 14th most consumed food crop in the world. Characterized as an unconventional vegetable, taro is grown in Brazil as a subsistence crop, but in recent years began to gain commercial importance, especially in the states of Espirito Santo, Minas Gerais and Rio de Janeiro. To avoid loss of genetic diversity of the local varieties traditionally grown in Brazil a core collection for taro germplasm has been developed by the Instituto Capixaba de Pesquisa, Assistência Técnica e Extensão Rural do estado do Espirito Santo (Incaper). The aim of this study was to perform a molecular characterization of the seven regional core collections. Genetic diversity of the cultivars was investigated by using SSR (Simple Sequence Repeats) polymorphisms, in seven loci (Xuqtem55, Xuqtem73, Xuqtem84, Xuqtem88, Xuqtem91, Xuqtem97 and Xuqtem110). Genetic diversity of the cultivars, based on the seven microsatellite alleles, was evaluated by using the software GelCompar II, showed that the loci Xuqtem73, Xuqtem88 and Xuqtem110 were the most informative, featuring 7, 10 and 8 alleles, respectively, a percentage of cultivars with polymorphic alleles of 85, 57 and 100% and identical PIC of 0.91. Based on Xuqtem110 locus analysis, the seven cultivars were grouped in two clusters. Chinês Regional Incaper cultivar was originated from Chinês cultivar which originated the São Bento cultivar, corroborating previous results. Macaquinho and Chinês cultivars were shown to be the primitive ones originating the allelic collections found in the states of Mato Grosso do Sul and Espirito Santo.

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.

scholarly journals Low Genetic Diversity of the Endangered Franciscana (Pontoporia blainvillei) in Its Northernmost, Isolated Population (FMAIa, Espírito Santo, Brazil)

2020 ◽  
Vol 7 ◽  
Author(s):  
Vanessa K. M. de Oliveira ◽  
Drienne M. Faria ◽  
Haydée A. Cunha ◽  
Teresa E. C. dos Santos ◽  
Adriana C. Colosio ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Control Region ◽  
Microsatellite Loci ◽  
Distribution Analysis ◽  
Sample Number ◽  
Espírito Santo ◽  
Low Genetic Diversity ◽  
Southwestern Atlantic Ocean ◽  
Espirito Santo ◽  
Pontoporia Blainvillei

The franciscana, Pontoporia blainvillei, is the most endangered small cetacean in the Southwestern Atlantic Ocean, occurring from Itaúnas, Espírito Santo, Brazil to Chubut province, Argentina. This area is divided into four Franciscana Management Areas (FMA). The northern portion of this species distribution is not continuous and a previous genetic study using mitochondrial DNA (mtDNA) separated it into FMAIa (Espírito Santo state) and FMAIb (North of Rio de Janeiro state). In order to increase the information about this population we expanded the sample number and evaluated mitochondrial and nuclear DNA diversity. Samples of 68 franciscanas found stranded on beaches from 2005 to 2020 were analyzed. Analyses included 350 bp of the mtDNA control region (D-loop) and 12 microsatellite loci. We identified three control region haplotypes in FMAIa, two of them not previously observed in this population, one being a new haplotype. Haplotype and nucleotide diversities were 0.0408 and 0.00012 respectively, the lowest reported for all FMAs analyzed until now. The Neutrality tests were not significant and Mismatch Distribution analysis did not reject the hypothesis of population expansion. One of the microsatellite loci was monomorphic, and for the other loci, two to nine alleles were identified, with expected heterozygosities ranging from 0.306 to 0.801. No substructure was revealed and effective population size (Ne) was estimated in 117.9 individuals. Even with an increased sample size, the high mitochondrial genetic homogeneity suggested for the population in a previous study was confirmed. Among six loci previously analyzed in other franciscana populations, five showed the lowest observed heterozygosities for the Espírito Santo population. The novel microsatellite data also showed low genetic diversity and could not reject the hypothesis of a single, panmitic population along the coast of Espírito Santo. This species has been intensively impacted in the last years by incidental capture during fishing activities and habitat degradation, caused by pollution, coastal development and environmental disasters in FMAIa. Considering that this population is small, isolated, and with low levels of genetic diversity, we reinforce the necessity of different conservation actions, focusing mainly on the reduction of bycatch of this species in the region.

scholarly journals Genetic diversity and interspecific relationships of some Allium species using inter simple sequence repeat markers

2015 ◽  
Vol 22 (2) ◽  
pp. 67-75 ◽  
Author(s):  
Leila Samiei ◽  
Mahnaz Kiani ◽  
Homa Zarghami ◽  
Farshid Memariani ◽  
Mohammad Reza Joharchi
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Gene Diversity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Allium Species ◽  
Interspecific Relationships ◽  
Simple Sequence

In this study genetic diversity and interspecific relationships of 11 Allium L. species from Khorassan province of Iran including 32 accessions were investigated by inter simple sequence repeat (ISSR) markers. Nine ISSR primers produced a total of 80 polymorphic markers and revealed high polymorphism among the studied species. The average gene diversity, effective number of alleles and Shannon’s information index were 0.2, 1.28 and 0.3, respectively. Allium kuhsorkhense exhibited the greatest level of variation (He: 0.18), whereas A. stipitatum demonstrated the lowest level of variability (He: 0.05). UPGMA (Unweighted Pair Group Method with Arithmetic mean) analysis showed that Allium accessions have a similarity range of 0.60 to 0.95. Allium scapriscapum composed the most distant group in the dendrogram. The clustered groups of Allium species clearly reflect the recent taxonomic concept of the genus at the subgenus and section levels. The present study showed that the ISSR technique is an effective molecular approach for analyzing genetic diversity and relationship in Allium species.Bangladesh J. Plant Taxon. 22(2): 67-75, 2015 (December)

Inter Simple Sequence Repeat (ISSR) markers to assess genetic diversity and relatedness within strawberry genotypes

2008 ◽  
Vol 88 (2) ◽  
pp. 313-322 ◽  
Author(s):  
S. C. Debnath ◽  
S. Khanizadeh ◽  
A. R. Jamieson ◽  
C. Kempler
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Genetic Similarity ◽  
Inter Simple Sequence Repeat ◽  
Issr Markers ◽  
Group Method ◽  
Sequence Repeat ◽  
Breeding Lines ◽  
Pair Group ◽  
Simple Sequence

The goal of this study was to determine the level of genetic diversity and relatedness among 16 strawberry (Fragaria H ananassa Duch.) cultivars and 11 breeding lines developed in Canada, using Inter Simple Sequence Repeat (ISSR) markers. Seventeen primers generated 225 polymorphic ISSR-PCR bands. Cluster analysis by the unweighted pair-group method with arithmetic averages (UPGMA) revealed a substantial degree of genetic similarity among the genotypes ranging from 63 to 77% that were in agreement with the principal coordinate (PCO) analysis. Geographical distribution for the place of breeding program explained only 1.4% of total variation as revealed by analysis of molecular variance (AMOVA). The ISSR markers detected a sufficient degree of polymorphism to differentiate among strawberry genotypes, making this technology valuable for cultivar identification and for the more efficient choice of parents in current strawberry breeding programs. Key words: Fragaria × ananassa, DNA fingerprinting, multivariate analysis, breeding, genetic similarity

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