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21.
Xia L Peng K Yang S Wenzl P de Vicente MC Fregene M Kilian A 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2005,110(6):1092-1098
Understanding the distribution of genetic diversity within and among individuals, populations, species and gene pools is crucial for the efficient management of germplasm collections. Molecular markers are playing an increasing role in germplasm characterization, yet their broad application is limited by the availability of markers, the costs and the low throughput of existing technologies. This is particularly true for crops of resource-poor farmers such as cassava, Manihot esculenta. Here we report on the development of Diversity Arrays Technology (DArT) for cassava. DArT uses microarrays to detect DNA polymorphism at several hundred genomic loci in a single assay without relying on DNA sequence information. We tested three complexity reduction methods and selected the two that generated genomic representations with the largest frequency of polymorphic clones (PstI/TaqI: 14.6%, PstI/BstNI: 17.2%) to produce large genotyping arrays. Nearly 1,000 candidate polymorphic clones were detected on the two arrays. The performance of the PstI/TaqI array was validated by typing a group of 38 accessions, 24 of them in duplicate. The average call rate was 98.1%, and the scoring reproducibility was 99.8%. DArT markers displayed fairly high polymorphism information content (PIC) values and revealed genetic relationships among the samples consistent with the information available on these samples. Our study suggests that DArT offers advantages over current technologies in terms of cost and speed of marker discovery and analysis. It can therefore be used to genotype large germplasm collections.Electronic Supplementary Material Supplementary material is available for this article at 相似文献
22.
M. Fregene A. Bernal M. Duque A. Dixon J. Tohme 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2000,100(5):678-685
Amplified fragment length polymophism was assessed in 20 land races and nine elite lines of cassava from Africa, resistant
and susceptible to the cassava mosaic disease (CMD). Eleven accessions from a representative core collection from Latin America,
previously studied by AFLPs, were included as a reference. AFLP data from all accessions was analyzed by both the unweighted
pair group mean average (UPGMA) and multiple cluster analysis (MCA) methods of analysis. Genetic differentiation between clusters
and the coefficient of genetic differentiation was also calculated. Results reveal a genetic divergence between African and
Latin American accessions, although some overlap was found between them. African land races resistant to CMD, were also found
to be genetically differentiated from susceptible land races and from resistant elite lines. AFLP analysis identified a considerable
number of duplicates in the African accessions, suggesting a sizeable percentage of redundancy. A unique AFLP fragment, found
in a relatively high frequency in African accessions, but absent in the Latin American accessions, was found to be associated
with branching pattern by QTL mapping in an F1 progeny derived from African and Latin American parents. The likely source
and the utility of the unique AFLP fragment in understanding the processes of genetic divergence in Africa is discussed.
Received: 15 May 1999 / Accepted: 28 July 1999 相似文献
23.
Identification and Characterization of the Cassava Core-Clock Gene EARLY FLOWERING 4 总被引:1,自引:0,他引:1
Oluwabusayo Sarah Adeyemo Elsebeth Kolmos Joe Tohme Paul Chavariaga Martin Fregene Seth J. Davis 《Tropical plant biology》2011,4(2):117-125
The angiosperm circadian clock has been well established from molecular-genetic studies in a temperate plant model. Conservation of clock function is less explored in plants from the tropics. Cassava (Manihot esculenta) is a staple crop grown in the tropics that has been of limited research interest, and more generally, research on photoperiod and clock genes has been sparse. EARLY FLOWERING 4 (AtELF4) of the temperate plant Arabidopsis thaliana (Arabidopsis) has been reported to be required for photoperiod perception and circadian function. Here, we describe our start to identify circadian and photoperiod genes in cassava with an account on the characterization of its ELF4 gene (MeELF4). After isolating MeELF4, a phylogenetic study was conducted and it was found to cluster within the ELF4 subclade of the ELF4/EFL super-family. Similar to studies in temperate plants, MeELF4 was shown to be an evening-expressed gene in cassava. This collectively suggested to us that MeELF4 could be a functional ortholog of AtELF4. To test this, complementation studies of MeELF4 were performed in the Arabidopsis elf4 mutant. Hypocotyl-length measurements and flowering-time analysis were performed. MeELF4-complementation transgenics in the elf4 background were restored to the wild-type growth habit, suggesting a total rescue of photoperiodic perception. To expand on the molecular role of MeELF4 in the resulting transgenic-complementation lines, the CCA1 and CCR2 promoter-luciferase markers where respectively introduced and bioluminescence-imaging experiments revealed a restoration of circadian-regulated gene expression. The collective results showed that the cassava gene MeELF4 is a functional clock ortholog of AtELF4. 相似文献
24.
B Utete C Phiri SS Mlambo N Maringapasi N Muboko TB Fregene 《African Journal of Aquatic Science》2018,43(1):1-15
Concentrations of aluminium, cadmium, chromium, cobalt, copper, iron, lead, nickel and zinc were determined in surface water, benthic sediments, and the gills, liver and stomach muscle tissues of Oreochromis niloticus and Clarias gariepinus in peri-urban lakes Chivero and Manyame, Zimbabwe. Five sites were sampled in each lake once per month in November 2015, February, May, August and November 2016. Pollution load index detected no metal contamination, whereas the geo-accumulation index reflected heavy to extreme sediment pollution, with Fe, Cd, Zn, Cr, Ni and Cu present in both lakes. Significant spatial temporal variations were detected for Al, Cr, Cu and Pb across sites within and between the two lakes. High Fe, Al and Cr concentrations in water and sediments in lakes Chivero and Manyame derive from geogenic background sources in addition to anthropogenic loads and intensity. Elevated concentrations of Al, Pb, Cu, Cd, Fe and Zn detected in gills, liver and stomach tissue of catfish corroborate concentrations in water and sediments, and pose the highest ecological and health risk for hydrobionts in lakes Chivero and Manyame. Contiguity of peri-urban lakes exposes them to similar threats, necessitating creative water management strategies, which ensure ecological continuity. 相似文献
25.
Dan TA Eisenberg Benjamin Campbell Peter B Gray Michael D Sorenson 《BMC evolutionary biology》2008,8(1):173
Background
Minor alleles of the human dopamine receptor polymorphisms, DRD2/TaqI A and DRD4/48 bp, are related to decreased functioning and/or numbers of their respective receptors and have been shown to be correlated with body mass, height and food craving. In addition, the 7R minor allele of the DRD4 gene is at a higher frequency in nomadic compared to sedentary populations. Here we examine polymorphisms in the DRD2 and DRD4 genes with respect to body mass index (BMI) and height among men in two populations of Ariaal pastoralists, one recently settled (n = 87) and the other still nomadic (n = 65). The Ariaal live in northern Kenya, are chronically undernourished and are divided socially among age-sets. 相似文献26.
27.
Background
The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways. 相似文献28.
29.
V. Jorge M. Fregene C. M. Vélez M. C. Duque J. Tohme V. Verdier 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》2001,102(4):564-571
We evaluated cassava bacterial blight (CBB) infection in an pair-cross population of 150 individuals derived from an intra-specific
cross between two non-inbred cassava (Manihot esculenta Crantz) lines. The replicated trials were carried out in the field under high disease pressure over two consecutive crop
cycles. Evaluations were conducted at 4 and 7 months after planting for the two cycles. Simple regression analysis and the
nonparametric Kruskal-Wallis rank-sum test revealed that eight quantitative trait loci (QTLs) were involved in resistance.
We detected changes in QTLs from crop cycle to crop cycle. The pathogen population (Xanthomonas axonopodis pv. manihotis) was also monitored over the period, using a restriction fragment length polymorphism probe and pathogenic tests. Changes
in QTL detection over the 2 years could be correlated with changes in pathogen population structure. One QTL, located in linkage
group D, was conserved over the two crop cycles, and in field to greenhouse evaluations. This study thus identified molecular
markers useful for marker assisted-selection, a technique that can accelerate the long, multiple-season process of breeding
for CBB resistance.
Received: 1 January 2000 / Accepted: 25 June 2000 相似文献
30.
Cassava bacterial blight (CBB) is caused by Xanthomonas axonopodis pv. manihotis (Xam). Resistance is found in Manihot esculenta and, in addition, has been introgressed from a wild relative, M. glaziovii. The resistance is thought to be polygenic and additively inherited. Ninety-three varieties of M. esculenta (Crantz) were assessed by AFLPs for genetic diversity and for resistance to CBB. AFLP analysis was performed using two primer combinations and a 79.2% level of polymorphism was found. The phenogram obtained showed between 74% and 96% genetic similarity among all cassava accessions analysed. The analysis permitted the unique identification of each individual. Two Xam strains were used for resistance screening. Variation in the reaction of cassava varieties to Xam strains was observed for all plant accessions. The correlation of resistance to both strains, had a coefficient of 0.53, suggesting the independence of resistance to each strain. Multiple correspondence analysis showed a random distribution of the resistance/susceptibility response with respect to overall genetic diversity as measured by AFLP analysis. A total heterozygosity index was calculated to determine the diversity within clusters as well as among them. Our results demonstrate that resistance to CBB is broadly distributed in cassava germplasm and that AFLP analysis is an effective and efficient means of providing quantitative estimates of genetic similarities among cassava accessions. 相似文献