AFLP assessment of genetic variability in cassava accessions (Manihot esculenta) resistant and susceptible to the cassava bacterial blight (CBB)

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

Cassava (Manihot esculenta) provides calories and nutrition for more than half a billion people. It was domesticated by native Amazonian peoples through cultivation of the wild progenitor M. esculenta ssp. flabellifolia and is now grown in tropical regions worldwide. Here we provide a high-quality genome assembly for cassava with improved contiguity, linkage, and completeness; almost 97% of genes are anchored to chromosomes. We find that paleotetraploidy in cassava is shared with the related rubber tree Hevea, providing a resource for comparative studies. We also sequence a global collection of 58 Manihot accessions, including cultivated and wild cassava accessions and related species such as Ceará or India rubber (M. glaziovii), and genotype 268 African cassava varieties. We find widespread interspecific admixture, and detect the genetic signature of past cassava breeding programs. As a clonally propagated crop, cassava is especially vulnerable to pathogens and abiotic stresses. This genomic resource will inform future genome-enabled breeding efforts to improve this staple crop.

Assessment of genetic diversity in Chinese eared pheasant using fluorescent-AFLP markers

The eared pheasant consists of four species: white eared pheasant (Crossoptilon crossoptilon), Tibetan eared pheasant (Crossoptilon harmani), blue eared pheasant (Crossoptilon auritum), and brown eared pheasant (Crossoptilon mantchuricum). These species are found only in China, and are also on the list of the world's threatened species. In this paper, 74 individuals from the four eared pheasant species were assessed for population genetic diversity by means of fluorescent-AFLP markers. A total of 429 AFLP peaks were amplified by 11 pairs of fluorescent EcoRI/TaqI primer combinations. Out of all markers, 329 AFLPs were polymorphic. Each primer combination produced in reactions from 19 to 72 fragments and the polymorphic peaks percentage ranged from 53.33% to 86.11% with an average of 74.36% polymorphic bands. Genetic distance between species and genetic diversity within species were evaluated using Jaccard's similarity coefficients (SC) and the corresponding dendrogram. It was found that there was a moderate genetic distance between the four species (SC=0.674-0.832). Brown eared pheasant was genetically closely related to blue eared pheasant (SC=0.832), while white eared pheasant was more closely related to Tibetan eared pheasant (SC=0.812). Genetic diversity was lower in brown eared pheasant (SC=0.913) and Tibetan eared pheasant (SC=0.903) than in white eared pheasant (SC=0.832) and blue eared pheasant (SC=0.853).

Amplified fragment length polymorphism used for inter- and intraspecific differentiation of screwworms (Diptera: Calliphoridae)

Morphologically, early immature stages of the economically important pest called screwworms, Cochliomyia hominivorax (Coquerel) (Diptera: Calliphoridae), and non-pest secondary screwworms, Cochliomyia macellaria (Fabricius) (Diptera: Calliphoridae), are nearly indistinguishable. Correct identification is crucial to the ongoing eradication and exclusion program protecting the United States, Mexico and Central America from reinvasion of screwworms persistent in South America and the Caribbean. Amplified fragment length polymorphism (AFLP) polymerase chain reaction was used to differentiate populations of C. hominivorax and to discriminate them from C. macellaria. Ten primer pairs screened for interspecific discrimination of C. hominivorax from C. macellaria showed 52 discrete bands, allowing the two species to be readily distinguished; divergent branches on resulting dendrograms showed 100% bootstrap support. C. macellaria populations grouped at the 92% level; C. hominivorax populations grouped at the 68% level. Of the 52 bands, seven were monomorphic for both species, 22 were specific to C. macellaria, ten were present only in C. hominivorax and the remaining 13 bands differentiated C. hominivorax populations. Separate studies using ten strains of C. hominivorax showed a higher level of genetic similarity within than between populations. Analyses using 72 bands (19 monomorphic bands, 53 bands grouped all ten strains at the 58% similarity level) resolved seven mutant strains from Mexico (85% similarity level); all ten strains were resolved at the 72% similarity level. Diagnostic bands were identified for species and strain identification. We conclude that AFLP can be a valuable tool for studies of interspecific and intraspecific genetic variation in screwworm populations.

Mapping EST-derived SSRs and ESTs involved in resistance to bacterial blight in Manihot esculenta

Cassava (Manihot esculenta Crantz) is a major root crop widely grown in the tropics. Cassava bacterial blight, caused by Xanthomonas axonopodis pv. manihotis (Xam), is an important disease in Latin America and Africa resulting in significant losses. The preferred control method is the use of resistant genotypes. Mapping expressed sequence tags (ESTs) and determining their co-localization with quantitative trait loci (QTLs) may give additional evidence of the role of the corresponding genes in resistance or defense. Twenty-one EST-derived simple sequence repeats (SSRs) were mapped in 16 linkage groups. ESTs showing similarities with candidate resistance genes or defense genes were also mapped using strategies such as restriction fragment length polymorphisms, cleaved amplified polymorphic sequences, and allele-specific primers. In total, 10 defense-related genes and 2 bacterial artificial chromosomes (BACs) containing resistance gene candidates (RGCs) were mapped in 11 linkage groups. Two new QTLs associated with resistance to Xam strains CIO121 and CIO151 were detected in linkage groups A and U, respectively. The QTL in linkage group U explained 61.6% of the phenotypic variance and was associated with an RGC-containing BAC. No correlation was found between the new EST-derived SSRs or other mapped ESTs and the new or previously reported QTLs.

Recent progress in the characterization of molecular determinants in the Xanthomonas axonopodis pv. manihotis-cassava interaction

Cassava bacterial blight, caused by Xanthomonas axonopodis pv. manihotis (Xam), is a widespread disease that affects cassava (Manihot esculenta Crantz). Studies on the pathogen population structure, pathogen diagnosis, identification and expression of plant genes involved in resistance have been carried out. Different molecular techniques were developed to assess the genetic diversity among the Xampopulations. Characterization of Xam population dynamics over time had enable us to determine the different factors that are associated with resistance breakdown and those that influence the genetic structure or virulence phenotypes of the pathogen's population. Methods for detecting the pathogen in vegetative planting materials and true seeds were developed and contributed to reduce the impact of the disease. To better understand the genetics of resistance a quantitative trait loci (QTLs) approach was developed. Using a PCR-based strategy with degenerate primers we isolated two resistance gene candidates in cassava. We also characterized a region of a chromosome rich in R-gene like sequence. In this review we also report the main results obtained by transcript profiling methodologies, cDNA-AFLP and ESTs developed by the authors to characterize the genes involved in disease resistance. All together these techniques allowed the identification of molecular markers either associated to CBB resistance or that may represent putative genes involved in disease resistance. This article reviews current knowledge on the molecular cassava-Xam interactions.

A unigene catalogue of 5700 expressed genes in cassava

Two economically important characters, starch content and cassava bacterial blight resistance, were targeted to generate a large collection of cassava ESTs. Two libraries were constructed from cassava root tissues of varieties with high and low starch contents. Other libraries were constructed from plant tissues challenged by the pathogen Xanthomonas axonopodis pv.manihotis. We report here the single pass sequencing of 11,954 cDNA clones from the 5' ends, including 111 from the 3' ends. Cluster analysis permitted the identification of a unigene set of 5,700 sequences. Sequence analyses permitted the assignment of a putative functional category for 37% of sequences whereas approximately 16% sequences did not show any significant similarity with other proteins present in the database and therefore can be considered as cassava specific genes. A group of genes belonging to a large multigene family was identified. We characterize a set of genes detected only in infected libraries putatively involved in the defense response to pathogen infection. By comparing two libraries obtained from cultivars contrasting in their starch content a group of genes associated to starch biosynthesis and differentially expressed was identified. This is the first large cassava EST resource developed today and publicly available thus making a significant contribution to genomic knowledge of cassava.

Identification of genes in cassava that are differentially expressed during infection with Xanthomonas axonopodis pv. manihotis

SUMMARY The cDNA-amplified fragment length polymorphism approach was used to identify differentially expressed transcripts from cassava infected by Xanthomonas axonopodis pv. manihotis (Xam). Approximately 3600 transcript-derived fragments (TDFs) were screened of which 340 were isolated. The nucleotide sequences of 250 TDFs were analysed and assembled into contigs and singletons. The amino acid sequences of their predicted products were compared with entries in databases and 63 of these clones showed homology to known plant genes. Of these, 32 showed similarity to plant defence proteins. Fifty-one TDFs corresponded to proteins of unknown function and 106 did not match any sequence in the public databases. Quantitative reverse transcription PCR was carried out with a selected set of gene transcripts that demonstrated an increase of expression during the infection. These results point out candidate genes that are associated with cassava resistance to Xam and reinforce the idea of a complex process occurring during this plant-pathogen interaction.

Genetic introgression as a potential to widen a species' niche: insights from alpine Carex curvula

Understanding what causes the decreasing abundance of species at the margins of their distributions along environmental gradients has drawn considerable interest, especially because of the recent need to predict shifts in species distribution patterns in response to climatic changes. Here, we address the ecological range limit problem by focusing on the sedge, Carex curvula, a dominant plant of high-elevation grasslands in Europe, for which two ecologically differentiated but crosscompatible taxa have been described in the Alps. Our study heuristically combines an extensive phytoecological survey of alpine plant communities to set the niche attributes of each taxon and a population genetic study to assess the multilocus genotypes of 177 individuals sampled in typical and marginal habitats. We found that ecological variation strongly correlates with genetic differentiation. Our data strongly suggest that ecologically marginal populations of each taxon are mainly composed of individuals with genotypes resulting from introgressive hybridization. Conversely, no hybrids were found in typical habitats, even though the two taxa were close enough to crossbreed. Thus, our results indicate that genotype integrity is maintained in optimal habitats, whereas introgressed individuals are favored in marginal habitats. We conclude that gene flow between closely related taxa might be an important, although underestimated, mechanism shaping species distribution along gradients.

AFLP analysis of genetic polymorphism and evolutionary relationships among cultivated and wild Nicotiana species

Amplified fragment length polymorphism (AFLP) analysis was used to determine the degree of intra- and inter-specific genetic variation in the genus Nicotiana. Forty-six lines of cultivated tobacco (Nicotiana tabacum L.) and seven wild Nicotiana species, including N. sylvestris, N. tomentosiformis, N. otophora, N. glutinosa, N. suaveolens, N. rustica, and N. longiflora, were analyzed, using at least eight different oligonucleotide primer combinations capable of detecting a minimum of 50 polymorphic bands per primer pair. The amount of genetic polymorphism present among cultivated tobacco lines (N. tabacum) was limited, as evidenced by the high degree of similarity in the AFLP profiles of cultivars collected worldwide. Six major clusters were found within cultivated tobacco that were primarily based upon geographic origin and manufacturing quality traits. A greater amount of genetic polymorphism exists among wild species of Nicotiana than among cultivated forms. Pairwise comparisons of the AFLP profiles of wild and cultivated Nicotiana species show that polymorphic bands present in N. tabacum can be found in at least one of three proposed wild progenitor species (i.e., N. sylvestris, N. tomentosiformis, and N. otophora). This observation provides additional support for these species contributing to the origin of N. tabacum.Key words: AFLP, evolution, genetic diversity, Nicotiana, tobacco, wild relatives of tobacco.

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

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.