RAPD markers of potential use in penaeid prawn (Penaeus monodon) breeding programs

The objective of this study was to verify the genetic diversity between and within seven populations of Moxotó goat (n = 264) from the States of Pernambuco, Paraíba and Rio Grande do Norte, using RAPD (Random Amplified Polymorphic DNA). Moxotó, as well as other naturalized breeds, suffers genetic losses due to the indiscriminate miscegenation with breeds raised in the Northeast Region of Brazil. The genetic characterization of these genetic resources is essential to conservation and breeding programs. DNA was extracted from lymphocytes using a non-organic protocol. The 16 primers used were selected from 120 decamer oligonucleotide primers and generated 56 polymorphic bands. The analysis of molecular variance (AMOVA) showed that the greater part of total genetic variability (71.55%) was due to differences between individuals within populations, while 21.21% was among populations. The analysis of variance among the pairs of populations demonstrated that the populations located in Floresta, PE x Angicos, RN presented a smaller value of intrapopulational differentiation (8.9%), indicating low genetic variability among them. Nei's genetic distances varied between 0.0546 and 0.1868 in the populations. The dendrogram generated showed that the Canindé breed, used as outgroup, clustered with the populations of Moxotó, indicating a possible common origin of the naturalized goat breeds.

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Genotypic diversity assessment of some durum wheat (Triticum durum) genotypes using RAPD analysis

Biodiversitas Journal of Biological Diversity ◽

10.13057/biodiv/d210643 ◽

2020 ◽

Vol 21 (6) ◽

Author(s):

RATIBA BΟUSBA ◽

SARA GUERAICHE ◽

MALIKA RACHED KANOUNI ◽

RABAH BΟUNAR ◽

ABDELHAMID DJEKΟUNE ◽

...

Keyword(s):

Durum Wheat ◽

Triticum Durum ◽

Rapd Markers ◽

Rapd Analysis ◽

Random Amplified Polymorphic Dna ◽

Genotypic Diversity ◽

Allelic Frequency ◽

Breeding Programs ◽

Diversity Assessment ◽

Local Genotypes

Abstract. Bousba R, Gueraiche S, Kanouni MR, Bounar R, Djekoune A, Khammar H, Nadia Y. 2020. Genotypic diversity assessment of some durum wheat (Triticum durum) genotypes using RAPD analysis. Biodiversitas 21: 2696-2701. Knowledge of genetic variability in durum wheat (Triticum durum Desf.) is of major importance in the development of breeding programs and the preservation of local landrace resources. The objective of this study is to highlight the molecular polymorphism among six durum wheat genotypes from different origins and characterized by different sensitivity to drought tolerance (tolerant, semi-tolerant, and non-tolerant). 15 Random Amplified Polymorphic DNA (RAPD) markers were used to assess the molecular diversity of these genotypes. Our results show a total of one hundred and sixty-nine amplicons, where one hundred and twenty-four are polymorphic bands. The number of bands per primer ranged from two (OPJ-06) to fifteen bands (primers OPE-13 and OPB-01). The values of the Allelic frequency varied from 1 (OPJ-06) to 0.20 (OPA-17) and 0.19 (OPE-13, OPO-06, B-19 and OPA-20). Also, the values of the coefficient of genetic similarity range from 0.69 to 0.80, these results indicate a large variation between tested genotypes. According to the dendrogram generated by the RAPD approach, we obtained four distinct groups: the first one (G1) contains GTADUR and KORIFFLA x SHAM, the second group (G2) contains the local genotype BIDI-17. However, the genotype WAHA was in the third group (G3), the fourth and fifth groups contained the genotypes CIRTA and TELL, respectively. A complementary analysis was done to estimate genetic differentiation, using CPA Analysis that indicated four groups among the six genotypes, where, the local genotypes BIDI-17 and CIRTA were classified together. For allele’s richness, the local genotypes show in this investigation, the highest values in comparison to the introduced genotypes, which suggested the performance of the RAPD markers (high polymorphism and fast genetic analysis). The molecular markers RAPD-PCR type, despite their non-specific characteristics, has shown a strong aptitude for genetic characterization in durum wheat and a high level of polymorphism, which makes it possible in a preliminary study to make exploitable discrimination. These results may be helpful in the improvement and varietal selection, and useful in accelerating breeding programs of durum wheat.

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Development of PCR-based Fingerprinting Tool in Banana (Musa sp., AAA) and Conversion of Negative to Positive DNA Marker

HortScience ◽

10.21273/hortsci.37.7.1108 ◽

2002 ◽

Vol 37 (7) ◽

pp. 1108-1111 ◽

Cited By ~ 5

Author(s):

Reynato P. Umali ◽

Nanako Kameya ◽

Ikuo Nakamura

Keyword(s):

Rapd Markers ◽

Dna Marker ◽

Plastid Dna ◽

Base Substitution ◽

Molecular Tools ◽

Arbitrary Primers ◽

Musa Sp ◽

Phylogenetic Identification ◽

The Subject ◽

Potential Use

The banana (Musa sp., AAA) genome is continuously expanding due to the high frequency of somaclonal variation. Because of this increasing diversity, numerical and morphological methods of taxonomic and phylogenetic identification of banana cultivars became laborious, difficult, and often the subject of disagreements. The aim of this study, therefore, is to develop molecular tools for DNA fingerprinting that can discriminate Musa, AAA Cavendish subgroup cultivars. In this paper, we showed that the plastid-subtype identity (PS-ID) sequence of the noncoding region between rpl16 and rpl14 genes of plastid DNA was highly conserved except for single-base substitution and deletion. These differences separated the clones into three groups (G1, G2, and G3) and suggested that clones within groups are closely related maternally. Using arbitrary primer A13, we later identified negative RAPD markers A133.0 and A131.3 specifically for S4 (selection from Giant Cavendish subgroup, AAA) and S11 (`Morado' from `Red' and `Green Red' subgroup, AAA), respectively. Fragments corresponding to the missing bands were sequenced and used as templates to design new primers with overlapping sequences. Two of these primers, Ba3.0A and Ba1.3A, successfully generated positive markers consistently amplified as Ba3.0A0.8 and Ba1.3A0.6 for S4 and S11, respectively. It is proposed that the method just described can be a better alternative over screening more arbitrary primers in generating positive markers in cases when negative ones were already identified. Results of PS-ID subtype analysis likewise suggested potential use in identifying wild maternal progenitor in polyploid bananas.

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Genetic variability of Passiflora spp. from commercial fields in the Federal District, Brazil

Ciência Rural ◽

10.1590/s0103-84782011000600013 ◽

2011 ◽

Vol 41 (6) ◽

pp. 996-1002 ◽

Cited By ~ 6

Author(s):

Ana Paula Gomes de Castro ◽

Fábio Gelape Faleiro ◽

Daniel Diego Costa Carvalho ◽

Kenia Gracielle da Fonseca ◽

Marina de Fátima Vilela ◽

...

Keyword(s):

Genetic Variability ◽

Rapd Markers ◽

Federal District ◽

Genetic Distances ◽

Passion Fruit ◽

Binary Matrix ◽

Breeding Programs ◽

Wide Range ◽

Potential Success ◽

Sour Passion Fruit

This study aimed to characterize the genetic variability in commercial accessions of passion fruit from the Federal District, Brazil, by RAPD markers. Genetic analyses were done with leaf samples of 30 accessions. DNA samples were amplified by RAPD technique, and respective markers converted into a binary matrix, from which the genetic distances between the accessions were estimated. Clustering analyis based on genetic distances allowed to detect a wide range of genetic variabillity among the accessions of sour passion fruit, and to separate them from the two sweet passion fruit. The graphical positioning of 'BRS Ouro Vermelho' confirms its potential to improve the genetic variability of commercial varieties of sour passion fruit. Dispersal of genetic distances among commercial accessions of sour passion fruit supports evidence for different genetic origins of the materials planted in the Federal District. The verified genetic variability indicates the potential success of future breeding programs for this region.

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Genetic diversity of tropical-adapted onion germplasm assessed by RAPD markers

Horticultura Brasileira ◽

10.1590/s0102-05362012000100019 ◽

2012 ◽

Vol 30 (1) ◽

pp. 112-118 ◽

Cited By ~ 1

Author(s):

Maria do Desterro M dos Santos ◽

Carlos Francisco Ragassi ◽

Maria Esther de N Fonseca ◽

Anne Gizelle R Buzar ◽

Valter R Oliveira ◽

...

Keyword(s):

Genetic Diversity ◽

Rapd Markers ◽

Germplasm Collection ◽

Rio Grande ◽

Breeding Programs ◽

Tropical Regions ◽

Low Genetic Diversity ◽

Tropical Conditions ◽

Average Similarity ◽

Onion Germplasm

Onion is a crop of significant socioeconomic importance to Brazil. Onion germplasm with adaptation to tropical and sub-tropical conditions has played an important role in the development of this crop in the country. In this context, we studied the genetic diversity in a germplasm collection potentially useful for the development of cultivars for tropical and subtropical regions. The genetic variability of 21 accessions/cultivars that have been used as germplasm and/or were developed by onion breeding programs in Brazil was evaluated via RAPD markers. The following accessions were included in the study :'Red Creole', 'Roxa IPA-3', 'Valenciana 14', 'Beta Cristal', 'Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Alfa Tropical', 'Pêra IPA-4', 'Primavera', 'Belém IPA-9', 'Crioula Alto Vale', 'Conquista', 'Pira-Ouro', 'Vale-Ouro IPA-11', 'Franciscana IPA-10', 'Serrana', 'CNPH 6400', 'Petroline', and 'Baia Periforme'. From the 520 primers used in the initial screening only 38 displayed stable polymorphisms. They produced 624 amplicons, of which 522 (83.7%) were monomorphic and 102 (16.3%) were polymorphic. An average similarity coefficient of 0.72 was calculated among accessions based upon this subgroup of polymorphic amplicons. This allowed the discrimination of this germplasm collection into six groups with only one of them comprising more than one accession. The main group was formed by 16 accessions ('Diamante', 'Composto IPA-6', 'Aurora', 'Bojuda Rio Grande', 'Conquista', 'Pira-Ouro', 'Serrana', 'Vale-Ouro IPA-11', 'Baia Periforme', 'Primavera', 'Franciscana IPA-10', 'Belém IPA-9', 'Crioula Alto Vale', 'Petroline', 'Pêra IPA-4' and 'Alfa Tropical'), for which the genetic origin (with few exceptions) can be traced back to the variety 'Baia Periforme'. The populations 'Red Creole', 'Roxa IPA-3', 'Beta Cristal', 'CNPH 6400', and 'Valenciana 14' comprised a set of five isolated groups, showing genetic divergence among them and in relation to main 'Baia Periforme' group. This germplasm displayed a relatively low genetic diversity, with the predominance of materials originated from the base population 'Baia Periforme'. There are, however, some accessions, which can add genetic diversity to this germplasm and they can be exploited by onion breeding programs aiming to develop cultivars for tropical regions of the world.

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Selection of common bean land cultivars based on agronomic performance, cooking time, and mineral concentration

Semina Ciências Agrárias ◽

10.5433/1679-0359.2016v37n3p1255 ◽

2016 ◽

Vol 37 (3) ◽

pp. 1255 ◽

Cited By ~ 2

Author(s):

Narielen Moreira de Morais ◽

Nerinéia Dalfollo Ribeiro ◽

Lindolfo Storck ◽

Paulo Rogério Franco dos Santos ◽

Micheli Thaise Della Flora Possobom

Keyword(s):

Grain Yield ◽

Common Bean ◽

Nutritional Quality ◽

Cooking Time ◽

Agronomic Performance ◽

Mineral Concentration ◽

Breeding Programs ◽

Calcium Iron ◽

Santa Maria ◽

Potential Use

The potential use of common bean land cultivars with respect to their agronomic performance, cooking time and nutritional quality has scarcely been evaluated in breeding programs. The objective of the present study was to evaluate 19 common bean land cultivars for their agronomic traits, cooking time, and mineral concentration in grains to identify cultivars for potential use by a higher number of farmers or even breeding programs. Two field experiments were conducted in Alegrete and Santa Maria, Rio Grande do Sul (RS), Brazil, in the 2012/2013 season. The experimental design consisted of randomized blocks with three replications. A total of 23 cultivars were evaluated; 19 land cultivars were obtained from smallholder farmers from RS, and there were four control cultivars (Carioca, Pérola, Valente, and Guapo Brilhante). The traits evaluated included the cycle, insertion of the first pod, grain yield, cooking time, and concentrations of calcium, iron, zinc, and copper in the grains. The data were subjected to joint variance analysis, Pearson correlation analysis, and the Z index. The common bean cultivars showed differences in the cycle, insertion of the first pod, grain yield, cooking time, calcium, iron, zinc, and copper concentrations in grains, and the Z index. The cultivars Preto Miúdo and Cavalo Rajado had a high grain yield, i.e., greater than 2,900 kg ha-1. The land cultivars were classified as having early and intermediate cycles, and all had cooking times less than 30 min. Palha Roxa, Carioca Vermelho, and Perdiz had high concentrations of calcium, iron, zinc, and copper in the grains, an intermediate cycle, and low grain yield. Positive correlations of moderate magnitude were observed between the calcium and iron (r= 0.597), iron and zinc (r= 0.570), and zinc and copper (r= 0.548) concentrations. Indirect selection for high iron or zinc concentrations in grains will be effective for obtaining common bean cultivars with a higher nutritional quality. A cross between Carioca Santa Maria and Guapo Brilhante cultivar is recommended to obtain segregants with high agronomic performance, fast cooking, and high minerals concentration of in the grains.

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Gene-for-gene interactions are required for disease resistance mediated by virus transgene

Plant Protection Science ◽

10.17221/10349-pps ◽

2002 ◽

Vol 38 (SI 1 - 6th Conf EFPP 2002) ◽

pp. 177-179

Author(s):

M. Ravelonandro

Keyword(s):

Disease Resistance ◽

Rna Interference ◽

Molecular Mechanisms ◽

Plant Viruses ◽

Economic Losses ◽

Gene Interactions ◽

Severe Damage ◽

Breeding Programs ◽

Pathogen Derived Resistance ◽

Potential Use

Plant viruses cause severe damage and significant economic losses to agriculture. Control of virus usually consist of the elimination of virus vectors (insects, nematodes, fungi, etc), improvement of the sanitary status of the propagation material, the use of resistance sources in breeding programs. The application of the pathogen-derived resistance strategy has opened new avenues to protect plants against viruses. Two molecular mechanisms seem to underlie the engineered protection, the virus transgene-derived protein and the transgene-RNA interference. A few examples that support the efficiencies of these two molecular mechanisms are reviewed here and discussed in light of the potential use of virusresistant transgenic plants in agriculture.

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Genetic analysis of species in the Genus Catasetum (ORCHIDACEAE) using RAPD Markers

Brazilian Archives of Biology and Technology ◽

10.1590/s1516-89132010000200017 ◽

2010 ◽

Vol 53 (2) ◽

pp. 375-387 ◽

Cited By ~ 8

Author(s):

Luciana do Valle Rego Oliveira ◽

Ricardo Tadeu de Faria ◽

Claudete de Fátima Ruas ◽

Paulo Maurício Ruas ◽

Melissa de Oliveira Santos ◽

...

Keyword(s):

Molecular Markers ◽

Genetic Variability ◽

Genetic Analysis ◽

Genetic Relationship ◽

Genetic Similarity ◽

Core Collection ◽

Rapd Markers ◽

Dna Amplification ◽

Breeding Programs

In this work, RAPD molecular markers were used to access the genetic variability and to study the inter and intraespecifc relationship in a group of 37 species, including 56 individuals. A total of 15 RAPD primers were selected for DNA amplification. From a total of 221 bands analyzed, 209 (95%) were polymorphics. The level of interespecifc genetic similarity ranged from 37% between Catasetum complanatum and Catasetum laminatum to 83% between Catasetum triodon and Catasetum uncatum. The intraspecifc genetic similarity varied 88% for the individuals of Catasetum triodon to 93% between the individuals of Catasetum atratum and Catasetum macrocarpum. These results would contribute to understand the genetic relationship in Catasetum, to define the strategies to establish a germplasm core collection for the genus and to provide support for breeding programs.

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