Comparative analysis of phenotypic and genotypic diversity among plantain landraces (Musa spp., AAB group)

Genetic diversity amongst 76 plantain landraces has been studied using RAPD analysis at two levels of intensity and compared with groupings based on phenotypic indices and morphotype. There was a good correlation (R²=0.78) between estimates of genetic diversity based on 76 RAPD bands and 164 RAPD bands. However, there was a poor correlation between RAPD-based estimates of genetic diversity and a phenotypic index based on agronomic characters. There was also a poor correlation between RAPD analyses and morphotype group (based on bunch type and stature). These results suggest that the traditional designations of plantain landraces based on morphotype do not provide a true reflection of overall genetic divergence. Similarly, classification systems using phenotypic indices based on agronomic characters may not provide accurate taxonomic differentiation. The level of genetic divergence within morphogroups based on bunch type suggests that True Horn plantains are derived from False Horn plantains which in turn are derived from French plantains. Genetic divergence was found to be generally quite low within the plantain landrace genepool, which is consistent with the proposed evolution of this germplasm through somatic mutation of a relatively small number of introductions. However, putative synonyms/duplicates have been shown to be genetically distinct. In contrast, a group of 12 landraces have been identified that are highly distinct from one another (showing 20–35% dissimilarity). Fertile members of this group may be useful for generating genetically diverse 2x and 4x breeding populations that can be used in breeding secondary triploid hybrid plantain varieties. Received: 8 January 2000 / Accepted: 2 March 2000     

Phenotypic Diversity and Patterns of Variation in West and Central African Plantains (Musa Spp., AAB group Musaceae)

Plantains (Musa spp., AAB group) are an important food crop and an integral component of the farming systems in the lowland humid forest zone of West and Central Africa. A group of 24 plantain cultivars, representing the major variability in West Africa, was evaluated for nine quantitative characters. The association between growth and yield parameters in this African plantain germplasm was examined to determine if the pattern of quantitative variation in inflorescence and vegetative traits agreed with taxonomic groupings based on inflorescence type and plant size. Phenotypic correlations between these traits were calculated. Giant cultivars were taller, their pseudostem thicker, and they flowered much later than medium-sized cultivars. Giant cultivars produced more foliage, resulting in heavier bunches with more hands and fruits. Groupings that resulted following principal component analysis (PCA) supported conventional taxonomic groupings of plantains. PC A was based mainly on time to flowering, pseudostem height, and number of fruits. The last two traits, in combination with the number of hermaphrodite flowers and the persistence of the male bud, sufficed to group plantain cultivars.     

The Plantain Proteome,a Focus on Allele Specific Proteins Obtained from Plantain Fruits

Proteomics has been applied with great potential to elucidate molecular mechanisms in plants. This is especially valid in the case of non‐model crops of which their genome has not been sequenced yet, or is not well annotated. Plantains are a kind of cooking bananas that are economically very important in Africa, India, and Latin America. The aim of this work was to characterize the fruit proteome of common dessert bananas and plantains and to identify proteins that are only encoded by the plantain genome. We present the first plantain fruit proteome. All data are available via ProteomeXchange with identifier PXD005589. Using our in‐house workflow, we found 37 alleles to be unique for plantain covered by 59 peptides. Although we do not have access (yet) to whole‐genome sequencing data from triploid banana cultivars, we show that proteomics is an easily accessible complementary alternative to detect different allele specific SNPs/SAAPs. These unique alleles might contribute toward the differences in the metabolism between dessert bananas and plantains. This dataset will stimulate further analysis by the scientific community, boost plantain research, and facilitate plantain breeding.     

Growth Parameters of Yield of Plantain (Musa cv. AAB)

The performance of the crop plant and the ‘ratoon’plant (lateral shoot succeeding the harvested main shoot) of65 medium-sized False Horn plantains (Musa cv. AAB) was studiedby measuring vegetative and inflorescence (bunch) parameters.From significant regressions between different parameters itappears that taller pseudostems produce leaves at a faster rate,flower earlier and produce heavier infructescences which needmore time to mature. A high yield is determined by vigorousinitial growth of the planted sucker (lateral root). Beforeflowering, there is no sink competition between ratoon and mainpseudostem growth, and fast-growing main pseudostems are accompaniedby fast-growing ratoons. After flowering, competition occursbetween the fructifying inflorescence, a preferential sink andthe ratoon. The results indicate that plantain should not beconsidered as an annual crop. Growth, development, production parameters, bananas, plantains     

Compilation of morphological and molecular data,a necessity for taxonomy: The case of Hormogaster abbatissae sp. n. (Annelida,Clitellata, Hormogastridae)

Conflict among data sources can be frequent in evolutionary biology, especially in cases where one character set poses limitations to resolution. Earthworm taxonomy, for example, remains a challenge because of the limited number of morphological characters taxonomically valuable. An explanation to this may be morphological convergence due to adaptation to a homogeneous habitat, resulting in high degrees of homoplasy. This sometimes impedes clear morphological diagnosis of species. Combination of morphology with molecular techniques has recently aided taxonomy in many groups difficult to delimit morphologically. Here we apply an integrative approach by combining morphological and molecular data, including also some ecological features, to describe a new earthworm species in the family Hormogastridae, Hormogaster abbatissae sp. n., collected in Sant Joan de les Abadesses (Girona, Spain). Its anatomical and morphological characters are discussed in relation to the most similar Hormogastridae species, which are not the closest species in a phylogenetic analysis of molecular data. Species delimitation using the GMYC method and genetic divergences with the closest species are also considered. The information supplied by the morphological and molecular sources is contradictory, and thus we discuss issues with species delimitation in other similar situations. Decisions should be based on a profound knowledge of the morphology of the studied group but results from molecular analyses should also be considered.     

Molecules and morphology: Congruence of data inColumnea (Gesneriaceae)

The cladistic analysis and comparison of molecular and morphological data has been the source of much recent debate. In this study, independent analyses of molecular and morphological data fromColumnea L. sects.Pentadenia andStygnanthe (Gesneriaceae) are compared. Comparative methods include consensus, visually comparing trees from independent analyses and combined data analysis. Consensus methods provided little resolution. Comparison of trees obtained from the independent analyses revealed some differences although the trees are highly similar. However, a combined analysis found that the level of incongruence between the two data sets was low. The tree resulting from the combined data has aspects of both the morphological and molecular trees despite the larger number of molecular characters. In addition, the combined data tree has greater resolution than either of the two data sets singly, indicating that the two types of data are congruent, and complementary to each other.     

Using Morphological,Molecular and Climatic Data to Delimitate Yews along the Hindu Kush-Himalaya and Adjacent Regions

Background

Despite the availability of several studies to clarify taxonomic problems on the highly threatened yews of the Hindu Kush-Himalaya (HKH) and adjacent regions, the total number of species and their exact distribution ranges remains controversial. We explored the use of comprehensive sets of morphological, molecular and climatic data to clarify taxonomy and distributions of yews in this region.

Methodology/Principal Findings

A total of 743 samples from 46 populations of wild yew and 47 representative herbarium specimens were analyzed. Principle component analyses on 27 morphological characters and 15 bioclimatic variables plus altitude and maximum parsimony analysis on molecular ITS and trnL-F sequences indicated the existence of three distinct species occurring in different ecological (climatic) and altitudinal gradients along the HKH and adjacent regions Taxus contorta from eastern Afghanistan to the eastern end of Central Nepal, T. wallichiana from the western end of Central Nepal to Northwest China, and the first report of the South China low to mid-elevation species T. mairei in Nepal, Bhutan, Northeast India, Myanmar and South Vietnam.

Conclusion/Significance

The detailed sampling and combination of different data sets allowed us to identify three clearly delineated species and their precise distribution ranges in the HKH and adjacent regions, which showed no overlap or no distinct hybrid zone. This might be due to differences in the ecological (climatic) requirements of the species. The analyses further provided the selection of diagnostic morphological characters for the identification of yews occurring in the HKH and adjacent regions. Our work demonstrates that extensive sampling combined with the analysis of diverse data sets can reliably address the taxonomy of morphologically challenging plant taxa.     

Morphological and genetic diversity of the family Azollaceae inferred from vegetative characters and RAPD markers

Family Azollaceae has seven species with a controversial taxonomy. The identification of species without reproductive structures relies on vegetative characters but some are variable, leading to misinterpretations. The molecular methods may be helpful, but until now, they did not provide a conclusive Azolla taxonomy. Therefore, we studied the family Azollaceae at vegetative and molecular levels. Analysis of vegetative, random amplified polymorphic DNA (RAPD) and combined data showed a comparable grouping of the Azolla species in two main clusters: cluster I, referred to as section Rhizosperma (A. pinnata and A. nilotica) and cluster II, referred to as section Azolla (A. filiculoides, A. microphylla, A. caroliniana and A. mexicana), with the exception of A. rubra, which clustered differently depending on the method. All the Azolla species were distinguished by the 13 polymorphic vegetative characters, the 211 RAPD markers or the combined data, with the latest showing the highest discrimination. The Shannon Index diversity was greater with RAPD (2.276) than with vegetative characters (0.054), highlighting the higher discriminating power of the molecular data. The partitioning of diversity was, as expected, high among species for all the types of data and low within species, with the lowest diversity obtained for morphological data. Both data sets (vegetative and RAPD) allowed the distinction of all the species and their clustering into sections Rhizosperma and Azolla, suggesting this as the most correct for this family. The dendrogram from the combined data was the most accurate, highlighting the benefit of integrating different types of data to study the family Azollaceae.     

Components of morphological variation in Baikalian endemial cyclopid Acanthocyclops signifer complex from different localities

Use of traditional methods for morphological studies only permits the analysis of a small part of the information embodied in morphological structures. Besides comparing populations using the mean values of characters which allows one to estimate their morphological similarity, analysis of variation among individuals within a population can be informative. Variation among individuals consists of factorial and stochastic components. The factorial component is an upper estimate of genetic heterogeneity and thus permits one to evaluate the population's adaptability. The stochastic component (estimated by fluctuating asymmetry, i.e. random deviations from perfect bilateral symmetry), being a measure of developmental stability, is an indicator of a population's fitness. Assessment of measurement error is necessary for assessment of the true value of the stochastic component and for selection of the most informative characters. Such analysis allows one to extract additional information from morphological data in comparison with methods traditionally used on copepods. This approach was applied to an analysis of morphological variation in the study of the Baikalian endemic cyclopoid Acanthocyclops signifer (Mazepova) from three different isolated localities. Characters typically used in studies of taxonomy of this group are considered here. Measurement error was rather high (more than 50% of the stochastic component), which can be explained by technical difficulties of measuring the characters. All populations differ in the mean values of the characters. This shows the taxonomic heterogeneity of this group and reveals the necessity of its taxonomic revision. Populations also differ in the level of stochastic and factorial components of the total variance. The data are interpreted from the point of view of taxonomy and the possible evolution of the group.     

A Duplex PCR Assay for the Detection of Ralstonia solanacearum Phylotype II Strains in Musa spp.

Banana wilt outbreaks that are attributable to Moko disease-causing strains of the pathogen Ralstonia solanacearum (Rs) remain a social and economic burden for both multinational corporations and subsistence farmers. All known Moko strains belong to the phylotype II lineage, which has been previously recognized for its broad genetic basis. Moko strains are paraphyletic and are distributed among seven related but distinct phylogenetic clusters (sequevars) that are potentially major threats to Musaceae, Solanaceae, and ornamental crops in many countries. Although clustered within the Moko IIB-4 sequevar, strains of the epidemiologically variant IIB-4NPB do not cause wilt on Cavendish or plantain bananas; instead, they establish a latent infection in the vascular tissues of plantains and demonstrate an expanded host range and high aggressiveness toward Solanaceae and Cucurbitaceae. Although most molecular diagnostic methods focus on strains that wilt Solanaceae (particularly potato), no relevant protocol has been described that universally detects strains of the Musaceae-infecting Rs phylotype II. Thus, a duplex PCR assay targeting Moko and IIB-4NPB variant strains was developed, and its performance was assessed using an extensive collection of 111 strains representing the known diversity of Rs Moko-related strains and IIB-4NPB variant strains along with certain related strains and families. The proposed diagnostic protocol demonstrated both high accuracy (inclusivity and exclusivity) and high repeatability, detected targets on either pure culture or spiked plant extracts. Although they did not belong to the Moko clusters described at the time of the study, recently discovered banana-infecting strains from Brazil were also detected. According to our comprehensive evaluation, this duplex PCR assay appears suitable for both research and diagnostic laboratories and provides reliable detection of phylotype II Rs strains that infect Musaceae.