Genetic diversity and population structure in a collection of roselle (Hibiscus sabdariffaL.) from Niger

2013 ◽  
Vol 12 (2) ◽  
pp. 207-214 ◽  
Author(s):  
Y. Bakasso ◽  
M. Zaman-Allah ◽  
C. Mariac ◽  
C. Billot ◽  
Y. Vigouroux ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Fragment Length Polymorphism ◽  
Genetic Groups ◽  
Diversity Assessment ◽  
Farmer Management ◽  
Morphological Differences ◽  
Close Relatives ◽  
The Impact ◽  
100 Seed Weight

Roselle (Hibiscus sabdariffaL.) is an economically important plant in Niger. Little is known about its genetic diversity and population structure. In this study, we performed the first diversity assessment of a collection of 124 roselle accessions and 16 accessions of its close relativesHibiscuscannabinusandAbelmoschusesculentus. Our study was based on ten agromorphological traits and 267 amplified fragment length polymorphism markers. We identified two major distinct groups inH. sabdariffausing a Bayesian method. These two genetic groups were associated with statistical differences for three phenological characteristics: number of days to flowering, 100-seed weight and calyx size. However, the calyx colour, i.e. a morphological characteristic often used to classify different local ecotypes, did not superimpose this separation. Our findings suggested that roselle diversity is genetically structured; the two different groups were clearly associated with morphological differences but were not commonly used by farmers for their classification. The impact of the perceived ecotype structure and its consequence on farmer management is discussed.

scholarly journals First insights into the genetic diversity of Mycobacterium tuberculosis strains in Salvador, Bahia State, Brazil

2011 ◽  
Vol 27 (9) ◽  
pp. 1859-1863
Author(s):  
Aída Cristina do Nascimento Silva ◽  
Lucilaine Ferrazoli ◽  
Vera Simonsen ◽  
Joice Neves Reis ◽  
Susan Martins Pereira ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Mycobacterium Tuberculosis ◽  
Population Structure ◽  
Restriction Fragment Length Polymorphism ◽  
Fragment Length Polymorphism ◽  
Genetic Population ◽  
Recent Transmission ◽  
Single Pattern ◽  
Study Population ◽  
Restriction Fragment Length

This study constitutes a first attempt to describe the genetic population structure of Mycobacterium tuberculosis circulating in Salvador, Bahia State, Brazil. A total of 56 confirmed cases of pulmonary tuberculosis, identified between March and June 2008, were analyzed using restriction fragment length polymorphism (IS6110-RFLP). The study population was characterized by a predominance of males (71.43%) over 30 years of age (68.75%). Forty-one isolates were found to belong to a single pattern (73.2%), while 15 (26.7%) were found in group patterns, forming six clusters. The higher level of diversity observed is much more suggestive of endogenous reactivation than recent transmission.

Assessing genetic variability among Brazilian strains ofXanthomonas axonopodispv.manihotisthrough restriction fragment length polymorphism and amplified fragment length polymorphism analyses

1999 ◽  
Vol 45 (9) ◽  
pp. 754-763 ◽  
Author(s):  
S Restrepo ◽  
T L Valle ◽  
M C Duque ◽  
V Verdier
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Restriction Fragment Length Polymorphism ◽  
Restriction Fragment ◽  
Length Polymorphism ◽  
Fragment Length ◽  
Bacterial Blight ◽  
Fragment Length Polymorphism ◽  
Amplified Fragment Length Polymorphism ◽  
Restriction Fragment Length

Xanthomonas axonopodis pv.manihotis (Xam) causes bacterial blight, a major disease of cassava, which is a starchy root crop that feeds about 500 million people throughout the world. To better select resistant cassava germplasm, we examined the population structure of Xam in Brazil, Latin America's largest producer of cassava, and a major center of diversity for the crop. The 79 strains collected between 1941 and 1996 from three edaphoclimatic zones were analyzed by restriction fragment length polymorphism (RFLP), using a probe linked to a Xam pathogenicity gene (pthB). Thirty-eight haplotypes were identified, and geographical differentiation for the Xam strains was demonstrated. Strains from subtropical zone (ECZ 6) showed high genetic diversity in most of the sites from which they were collected. They also showed migration from site to site. RFLP and amplified fragment length polymorphism (AFLP) analyses were carried out on 37 Xam strains and compared; the AFLP assays were performed using eight primer combinations. A multiple correspondence analysis, used to assess genetic relatedness among strains and estimate genetic diversity, indicated that the Brazilian Xam population showed high diversity. No correlation was found between AFLP and RFLP data, but the two techniques provided complementary information on the genetic diversity of Xam. Most strains were highly aggressive on a susceptible cultivar. The genetic analysis presented here contributes to a better understanding of the Xam population structure in Brazil and will help select strains of the pathogen for screening cassava germplasm resistant to the disease.Key words: cassava bacterial blight, resistance, genetic diversity, molecular characterization.

Sequence homology of polymorphic AFLP markers in garlic (Allium sativum L.)

Genome ◽  
2006 ◽  
Vol 49 (10) ◽  
pp. 1246-1255 ◽  
Author(s):  
Meryem Ipek ◽  
Ahmet Ipek ◽  
Philipp W. Simon
Keyword(s):  
Genetic Diversity ◽  
Linkage Mapping ◽  
Allium Sativum ◽  
Fragment Length Polymorphism ◽  
Aflp Markers ◽  
Homologous Sequences ◽  
Diversity Assessment ◽  
Band Sequence ◽  
Diversity Studies ◽  
Sequence Identities

Linkage mapping and genetic diversity studies with DNA markers in plant species assume that comigrating bands are identical, or at least that they have homologous sequences. To test this assumption in a plant with a large genome, sequence identities of 7 polymorphic amplified fragment length polymorphism (AFLP) markers of garlic, previously used to estimate similarity in genetic diversity studies, were characterized. Among 37 diverse garlic clones, 87 bands from these 7 polymorphisms were excised, amplicons were cloned, and 2 to 6 colonies were sequenced from each band, to yield a total of 191 DNA amplicons. Of these 87 bands, 83 bands (95.4%) contained AFLP amplicons that were identical or highly homologous to the typical marker of that band; only 4 bands contained amplicons with little homology to the same-sized amplicons of other garlic clones. Of these 83 bands, 64 (73.6%) contained only highly homologous amplicons (>90% sequence identity), whereas 19 (21.8%) contained both homologous and nonhomologous amplicons, with sequence identities less than 60%. Of the 37 nonhomologous amplicons identified, 25 (67.5%) differed in length from other amplicons in the band. Sequence conservation of AFLP amplicons followed patterns similar to phylogenetic relationships among garlic clones, making them useful for developing simple PCR-based markers in genetic mapping and diversity assessment.

scholarly journals Is the Murciano-Granadina a single goat breed? A molecular genetics approach

2010 ◽  
Vol 62 (5) ◽  
pp. 1191-1198 ◽  
Author(s):  
A.M. Martínez ◽  
J.L. Vega-Pla ◽  
J.M. León ◽  
M.E. Camacho ◽  
J.V. Delgado ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Multivariate Analysis ◽  
Population Structure ◽  
Genetic Differentiation ◽  
Success Rate ◽  
Molecular Genetics ◽  
Clustering Analysis ◽  
Genetic Evaluation ◽  
Goat Breed ◽  
Genetic Groups

The population structure of the Murciano-Granadina breed was determined using 25 microsatellites from 266 goats of seven populations. The results of the genetic differentiation analysis showed that it is possible to differentiate the Murciana and Granadina populations even though a low F ST value (0.0432) had been obtained. Individuals could be assigned to their populations with a success rate of more than 80%. Bayesian-based clustering analysis of allele frequencies and multivariate analysis revealed that Murciana and Granadina populations were grouped in different clusters since K=3. The results demonstrate that Murciana and Granadina are still two different genetic groups included into Murciano-Granadina denomination. There is the opportunity to the genetically manage these populations, under a single herd-book but adding the necessary modifications to respect the conservation of the genetic diversity based on the use of multibreed models of genetic evaluation.

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