Physiology and its Importance for Reference Intervals

Reference intervals are ideally defined on apparently healthy individuals and should be distinguished from clinical decision limits that are derived from known diseased patients. Knowledge of physiological changes is a prerequisite for understanding and developing reference intervals. Reference intervals may differ for various subpopulations because of differences in their physiology, most obviously between men and women, but also in childhood, pregnancy and the elderly. Changes in laboratory measurements may be due to various physiological factors starting at birth including weaning, the active toddler, immunological learning, puberty, pregnancy, menopause and ageing. The need to partition reference intervals is required when there are significant physiological changes that need to be recognised. It is important that laboratorians are aware of these changes otherwise reference intervals that attempt to cover a widened inter-individual variability may lose their usefulness. It is virtually impossible for any laboratory to directly develop reference intervals for each of the physiological changes that are currently known, however indirect techniques can be used to develop or validate reference intervals in some difficult situations such as those for children. Physiology describes our life’s journey, and it is only when we are familiar with that journey that we can appreciate a pathological departure.     

Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast

Background

It has been recognized that modular organization pervades biological complexity. Based on network analysis, ‘party hubs’ and ‘date hubs’ were proposed to understand the basic principle of module organization of biomolecular networks. However, recent study on hubs has suggested that there is no clear evidence for coexistence of ‘party hubs’ and ‘date hubs’. Thus, an open question has been raised as to whether or not ‘party hubs’ and ‘date hubs’ truly exist in yeast interactome.

Methodology

In contrast to previous studies focusing on the partners of a hub or the individual proteins around the hub, our work aims to study the network motifs of a hub or interactions among individual proteins including the hub and its neighbors. Depending on the relationship between a hub''s network motifs and protein complexes, we define two new types of hubs, ‘motif party hubs’ and ‘motif date hubs’, which have the same characteristics as the original ‘party hubs’ and ‘date hubs’ respectively. The network motifs of these two types of hubs display significantly different features in spatial distribution (or cellular localizations), co-expression in microarray data, controlling topological structure of network, and organizing modularity.

Conclusion

By virtue of network motifs, we basically solved the open question about ‘party hubs’ and ‘date hubs’ which was raised by previous studies. Specifically, at the level of network motifs instead of individual proteins, we found two types of hubs, motif party hubs (mPHs) and motif date hubs (mDHs), whose network motifs display distinct characteristics on biological functions. In addition, in this paper we studied network motifs from a different viewpoint. That is, we show that a network motif should not be merely considered as an interaction pattern but be considered as an essential function unit in organizing modules of networks.     

Evidence for over-dispersion in the distribution of clinical malaria episodes in children

Background

It may be assumed that patterns of clinical malaria in children of similar age under the same level of exposure would follow a Poisson distribution with no over-dispersion. Longitudinal studies that have been conducted over many years suggest that some children may experience more episodes of clinical malaria than would be expected. The aim of this study was to identify this group of children and investigate possible causes for this increased susceptibility.

Methodology and Principal Findings

Using Poisson regression, we chose a group of children whom we designated as ‘more susceptible’ to malaria from 373 children under 10 years of age who were followed up for between 3 to 5 years from 1998–2003. About 21% of the children were categorized as ‘more susceptible’ and although they contributed only 23% of the person-time of follow-up, they experienced 55% of total clinical malaria episodes. Children that were parasite negative at all cross-sectional survey were less likely to belong to this group [AOR = 0.09, (95% CI: 0.14–0.61), p = 0.001].

Conclusions and Significance

The pattern of clinical malaria episodes follows a negative binomial distribution. Use of lack of a clinical malaria episode in a certain time period as endpoints for intervention or immunological studies may not adequately distinguish groups who are more or less immune. It may be useful in such studies, in addition to the usual endpoint of the time to first episode, to include end points which take into account the total number of clinical episodes experienced per child.     

Ontogeny and the fossil record: what,if anything,is an adult dinosaur?

Identification of the ontogenetic status of an extinct organism is complex, and yet this underpins major areas of research, from taxonomy and systematics to ecology and evolution. In the case of the non-avialan dinosaurs, at least some were reproductively mature before they were skeletally mature, and a lack of consensus on how to define an ‘adult’ animal causes problems for even basic scientific investigations. Here we review the current methods available to determine the age of non-avialan dinosaurs, discuss the definitions of different ontogenetic stages, and summarize the implications of these disparate definitions for dinosaur palaeontology. Most critically, a growing body of evidence suggests that many dinosaurs that would be considered ‘adults’ in a modern-day field study are considered ‘juveniles’ or ‘subadults’ in palaeontological contexts.     

On the lack of evidence that non-human animals possess anything remotely resembling a 'theory of mind'

After decades of effort by some of our brightest human and non-human minds, there is still little consensus on whether or not non-human animals understand anything about the unobservable mental states of other animals or even what it would mean for a non-verbal animal to understand the concept of a ‘mental state’. In the present paper, we confront four related and contentious questions head-on: (i) What exactly would it mean for a non-verbal organism to have an ‘understanding’ or a ‘representation’ of another animal''s mental state? (ii) What should (and should not) count as compelling empirical evidence that a non-verbal cognitive agent has a system for understanding or forming representations about mental states in a functionally adaptive manner? (iii) Why have the kind of experimental protocols that are currently in vogue failed to produce compelling evidence that non-human animals possess anything even remotely resembling a theory of mind? (iv) What kind of experiments could, at least in principle, provide compelling evidence for such a system in a non-verbal organism?     

'Caribbean Creep' chills out: climate change and marine invasive species

Background

New marine invasions have been recorded in increasing numbers along the world''s coasts due in part to the warming of the oceans and the ability of many invasive marine species to tolerate a broader thermal range than native species. Several marine invertebrate species have invaded the U.S. southern and mid-Atlantic coast from the Caribbean and this poleward range expansion has been termed ‘Caribbean Creep’. While models have predicted the continued decline of global biodiversity over the next 100 years due to global climate change, few studies have examined the episodic impacts of prolonged cold events that could impact species range expansions.

Methodology/Principal Findings

A pronounced cold spell occurred in January 2010 in the U.S. southern and mid-Atlantic coast and resulted in the mortality of several terrestrial and marine species. To experimentally test whether cold-water temperatures may have caused the disappearance of one species of the ‘Caribbean Creep’ we exposed the non-native crab Petrolisthes armatus to different thermal treatments that mimicked abnormal and severe winter temperatures. Our findings indicate that Petrolisthes armatus cannot tolerate prolonged and extreme cold temperatures (4–6°C) and suggest that aperiodic cold winters may be a critical ‘reset’ mechanism that will limit the range expansion of other ‘Caribbean Creep’ species.

Conclusions/Significance

We suggest that temperature ‘aberrations’ such as ‘cold snaps’ are an important and overlooked part of climate change. These climate fluctuations should be accounted for in future studies and models, particularly with reference to introduced subtropical and tropical species and predictions of both rates of invasion and rates of unidirectional geographic expansion.     

Methodological Deficits in Diagnostic Research Using ‘-Omics’ Technologies: Evaluation of the QUADOMICS Tool and Quality of Recently Published Studies

Background

QUADOMICS is an adaptation of QUADAS (a quality assessment tool for use in systematic reviews of diagnostic accuracy studies), which takes into account the particular challenges presented by ‘-omics’ based technologies. Our primary objective was to evaluate the applicability and consistency of QUADOMICS. Subsequently we evaluated and describe the methodological quality of a sample of recently published studies using the tool.

Methodology/Principal Findings

45‘-omics’- based diagnostic studies were identified by systematic search of Pubmed using suitable MeSH terms (“Genomics”, “Sensitivity and specificity”, “Diagnosis”). Three investigators independently assessed the quality of the articles using QUADOMICS and met to compare observations and generate a consensus. Consistency and applicability was assessed by comparing each reviewer''s original rating with the consensus. Methodological quality was described using the consensus rating. Agreement was above 80% for all three reviewers. Four items presented difficulties with application, mostly due to the lack of a clearly defined gold standard. Methodological quality of our sample was poor; studies met roughly half of the applied criteria (mean ± sd, 54.7±18.4%). Few studies were carried out in a population that mirrored the clinical situation in which the test would be used in practice, (6, 13.3%); none described patient recruitment sufficiently; and less than half described clinical and physiological factors that might influence the biomarker profile (20, 44.4%).

Conclusions

The QUADOMICS tool can consistently be applied to diagnostic ‘-omics’ studies presently published in biomedical journals. A substantial proportion of reports in this research field fail to address design issues that are fundamental to make inferences relevant for patient care.     

The infection processes of Sclerotinia sclerotiorum in cotyledon tissue of a resistant and a susceptible genotype of Brassica napus

Background and Aims

Sclerotinia sclerotiorum can attack >400 plant species worldwide. Very few studies have investigated host–pathogen interactions at the plant surface and cellular level in resistant genotypes of oilseed rape/canola (Brassica napus).

Methods

Infection processes of S. sclerotiorum were examined on two B. napus genotypes, one resistant cultivar ‘Charlton’ and one susceptible ‘RQ001-02M2’ by light and scanning electron microscopy from 2 h to 8 d post-inoculation (dpi).

Key Results

The resistant ‘Charlton’ impeded fungal growth at 1, 2 and 3 dpi, suppressed formation of appresoria and infection cushions, caused extrusion of protoplast from hyphal cells and produced a hypersensitive reaction. At 8 dpi, whilst in ‘Charlton’ pathogen invasion was mainly confined to the upper epidermis, in the susceptible ‘RQ001-02M2’, colonization up to the spongy mesophyll cells was evident. Calcium oxalate crystals were found in the upper epidermis and in palisade cells in susceptible ‘RQ001-02M2’ at 6 dpi, and throughout leaf tissues at 8 dpi. In resistant ‘Charlton’, crystals were not observed at 6 dpi, whereas at 8 dpi they were mainly confined to the upper epidermis. Starch deposits were also more prevalent in ‘RQ001-02M2’.

Conclusions

This study demonstrates for the first time at the cellular level that resistance to S. sclerotiorum in B. napus is a result of retardation of pathogen development, both on the plant surface and within host tissues. The resistance mechanisms identified in this study will be useful for engineering disease-resistant genotypes and for developing markers for screening for resistance against this pathogen.     

Influence of Belonolaimus longicaudatus on Nitrate Leaching in Turf

Experiments were conducted to quantify the effects of the sting nematode (Belonolaimus longicaudatus) on root reductions and quantity of nitrate (NO₃ ⁻) leached from ‘Tifdwarf’ bermudagrass in lysimeters. Forty lysimeters were planted with ‘Tifdwarf’ bermudagrass, of which 20 were inoculated with B. longicaudatus and 20 were noninoculated. Root length was compared between treatments at six, 12, and 18 weeks after initiation of the experiments. Turf was fertilized every three weeks, and leaching events were simulated at 21 and 42-day intervals in trial one and trial two, respectively. Leachate was collected, and the quantity of NO₃ ⁻ leached was compared between treatments. Root reductions were observed in lysimeters inoculated with B. longicaudatus at all evaluation dates. Quantity of NO₃ ⁻ leached was greater in inoculated lysimeters at the 18-week evaluation during both trials. This study indicates that nematode damage to turf roots limits root vigor and N uptake, thereby increasing nitrate leaching, adding to water quality concerns.     

Fluctuating Helical Asymmetry and Morphology of Snails (Gastropoda) in Divergent Microhabitats at 'Evolution Canyons I and II,' Israel

Background

Developmental instability of shelled gastropods is measured as deviations from a perfect equiangular (logarithmic) spiral. We studied six species of gastropods at ‘Evolution Canyons I and II’ in Carmel and the Galilee Mountains, Israel, respectively. The xeric, south-facing, ‘African’ slopes and the mesic, north-facing, ‘European’ slopes have dramatically different microclimates and plant communities. Moreover, ‘Evolution Canyon II’ receives more rainfall than ‘Evolution Canyon I.’

Methodology/Principal Findings

We examined fluctuating asymmetry, rate of whorl expansion, shell height, and number of rotations of the body suture in six species of terrestrial snails from the two ‘Evolution Canyons.’ The xeric ‘African’ slope should be more stressful to land snails than the ‘European’ slope, and ‘Evolution Canyon I’ should be more stressful than ‘Evolution Canyon II.’ Only Eopolita protensa jebusitica showed marginally significant differences in fluctuating helical asymmetry between the two slopes. Contrary to expectations, asymmetry was marginally greater on the ‘European’ slope. Shells of Levantina spiriplana caesareana at ‘Evolution Canyon I,’ were smaller and more asymmetric than those at ‘Evolution Canyon II.’ Moreover, shell height and number of rotations of the suture were greater on the north-facing slopes of both canyons.

Conclusions/Significance

Our data is consistent with a trade-off between drought resistance and thermoregulation in snails; Levantina was significantly smaller on the ‘African’ slope, for increasing surface area and thermoregulation, while Eopolita was larger on the ‘African’ slope, for reducing water evaporation. In addition, ‘Evolution Canyon I’ was more stressful than Evolution Canyon II’ for Levantina.     

A canopy architectural model to study the competitive ability of chickpea with sowthistle

Background and Aims

Improving the competitive ability of crops is a sustainable method of weed management. This paper shows how a virtual plant model of competition between chickpea (Cicer arietinum) and sowthistle (Sonchus oleraceus) can be used as a framework for discovering and/or developing more competitive chickpea cultivars.

Methods

The virtual plant models were developed using the L-systems formalism, parameterized according to measurements taken on plants at intervals during their development. A quasi-Monte Carlo light-environment model was used to model the effect of chickpea canopy on the development of sowthistle. The chickpea–light environment–sowthistle model (CLES model) captured the hypothesis that the architecture of chickpea plants modifies the light environment inside the canopy and determines sowthistle growth and development pattern. The resulting CLES model was parameterized for different chickpea cultivars (viz. ‘Macarena’, ‘Bumper’, ‘Jimbour’ and ‘99071-1001’) to compare their competitive ability with sowthistle. To validate the CLES model, an experiment was conducted using the same four chickpea cultivars as different treatments with a sowthistle growing under their canopy.

Results and Conclusions

The growth of sowthistle, both in silico and in glasshouse experiments, was reduced most by ‘99071-1001’, a cultivar with a short phyllochron. The second rank of competitive ability belonged to ‘Macarena’ and ‘Bumper’, while ‘Jimbour’ was the least competitive cultivar. The architecture of virtual chickpea plants modified the light inside the canopy, which influenced the growth and development of the sowthistle plants in response to different cultivars. This is the first time that a virtual plant model of a crop–weed interaction has been developed. This virtual plant model can serve as a platform for a broad range of applications in the study of chickpea–weed interactions and their environment.Key words: Plant architecture, virtual plant modelling, L-systems formalism, crop/weed competition, integrated weed management, chickpea, Cicer arietinum, sowthistle, Sonchus oleraceus     

Accommodating ontologies to biological reality--top-level categories of cumulative-constitutively organized material entities

Background

The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and domain reference ontologies within the Open Biological and Biomedical Ontologies Foundry (OBO). BFO is important for enabling OBO ontologies to facilitate in reliably communicating and managing data and metadata within and across biomedical databases. Following its intended single inheritance policy, BFO''s three top-level categories of material entity (i.e. ‘object’, ‘fiat object part’, ‘object aggregate’) must be exhaustive and mutually disjoint. We have shown elsewhere that for accommodating all types of constitutively organized material entities, BFO must be extended by additional categories of material entity.

Methodology/Principal Findings

Unfortunately, most biomedical material entities are cumulative-constitutively organized. We show that even the extended BFO does not exhaustively cover cumulative-constitutively organized material entities. We provide examples from biology and everyday life that demonstrate the necessity for ‘portion of matter’ as another material building block. This implies the necessity for further extending BFO by ‘portion of matter’ as well as three additional categories that possess portions of matter as aggregate components. These extensions are necessary if the basic assumption that all parts that share the same granularity level exhaustively sum to the whole should also apply to cumulative-constitutively organized material entities. By suggesting a notion of granular representation we provide a way to maintain the single inheritance principle when dealing with cumulative-constitutively organized material entities.

Conclusions/Significance

We suggest to extend BFO to incorporate additional categories of material entity and to rearrange its top-level material entity taxonomy. With these additions and the notion of granular representation, BFO would exhaustively cover all top-level types of material entities that application oriented ontologies may use as templates, while still maintaining the single inheritance principle.     

Origin of the words denoting some of the most ancient old world pulse crops and their diversity in modern European languages

This preliminary research was aimed at finding the roots in various Eurasian proto-languages directly related to pulses and giving the words denoting the same in modern European languages. Six Proto-Indo-European roots were indentified, namely arnk('')- (‘a leguminous plant’), *bhabh- (‘field bean’), * (‘a kernel of leguminous plant’, ‘pea’), ghArs- (‘a leguminous plant’), *kek- (‘pea’) and *lent- (‘lentil’). No Proto-Uralic root was attested save hypothetically *kača (‘pea’), while there were two Proto-Altaic roots, *bŭkrV (‘pea’) and * (‘lentil’). The Proto-Caucasianx root * denoted pea, while another one, *hōwł(ā) (‘bean’, ‘lentil’) and the Proto-Basque root *iłha-r (‘pea’, ‘bean’, ‘vetch’) could have a common Proto-Sino-Caucasian ancestor, *hVwłV (‘bean’) within the hypothetic Dené-Caucasian language superfamily. The Modern Maltese preserved the memory of two Proto-Semitic roots, *''adaš- (‘lentil’) and *pūl- (‘field bean’). The presented results prove that the most ancient Eurasian pulse crops were well-known and extensively cultivated by the ancestors of all modern European nations. The attested lexicological continuum witnesses the existence of a millennia-long links between the peoples of Eurasia to their mutual benefit. This research is meant to encourage interdisciplinary concerted actions between plant scientists dealing with crop evolution and biodiversity, archaeobotanists and language historians.     

Source of previous treatment for re-treatment TB cases registered under the National TB control Programme, India, 2010

Background

In 2009, nearly half (289,756) of global re-treatment TB notifications are from India; no nationally-representative data on the source of previous treatment was available to inform strategies for improvement of initial TB treatment outcome.

Objectives

To assess the source of previous treatment for re-treatment TB patients registered under India''s Revised National TB control Programme (RNTCP).

Methodology

A nationally-representative cross sectional study was conducted in a sample of 36 randomly-selected districts. All consecutively registered retreatment TB patients during a defined 15-day period in these 36 districts were contacted and the information on the source of previous treatment sought.

Results

Data was collected from all 1712 retreatment TB patients registered in the identified districts during the study period. The data includes information on 595 ‘relapse’ cases, 105 ‘failure’ cases, 437 ‘treatment after default (TAD)’ cases and 575 ‘re-treatment others’ cases. The source of most recent previous anti-tuberculosis therapy for 754 [44% (95% CI, 38.2%–49.9%)] of the re-treatment TB patients was from providers outside the TB control programme. A higher proportion of patients registered as TAD (64%) and ‘retreatment others’ (59%) were likely to be treated outside the National Programme, when compared to the proportion among ‘relapse’ (22%) or ‘failure’ (6%). Extrapolated to national registration, of the 292,972 re-treatment registrations in 2010, 128,907 patients would have been most recently treated outside the national programme.

Conclusions

Nearly half of the re-treatment cases registered with the national programme were most recently treated outside the programme setting. Enhanced efforts towards extending treatment support and supervision to patients treated by private sector treatment providers are urgently required to improve the quality of treatment and reduce the numbers of patients with recurrent disease. In addition, reasons for the large number of recurrent TB cases from those already treated by the national programme require urgent detailed investigation.     

Relationships between xylem vessel characteristics, calculated axial hydraulic conductance and size-controlling capacity of peach rootstocks

Background and Aims

Previous studies indicate that the size-controlling capacity of peach rootstocks is associated with reductions of scion water potential during mid-day that are caused by the reduced hydraulic conductance of the rootstock. Thus, shoot growth appears to be reduced by decreases in stem water potential. The aim of this study was to investigate the mechanism of reduced hydraulic conductance in size-controlling peach rootstocks.

Methods

Anatomical measurements (diameter and frequency) of xylem vessels were determined in shoots, trunks and roots of three contrasting peach rootstocks grown as trees, each with different size-controlling characteristics: ‘Nemaguard’ (vigorous), ‘P30-135’ (intermediate vigour) and ‘K146-43’ (substantially dwarfing). Based on anatomical measurements, the theoretical axial xylem conductance of each tissue type and rootstock genotype was calculated via the Poiseuille–Hagen law.

Key Results

Larger vessel dimensions were found in the vigorous rootstock (‘Nemaguard’) than in the most dwarfing one (‘K146-43’) whereas vessels of ‘P30-135’ had intermediate dimensions. The density of vessels per xylem area in ‘Nemaguard’ was also less than in ‘P30-135’and ‘K146-43’. These characteristics resulted in different estimated hydraulic conductance among rootstocks: ‘Nemaguard’ had higher theoretical values followed by ‘P30-135’ and ‘K146-43’.

Conclusions

These data indicate that phenotypic differences in xylem anatomical characteristics of rootstock genotypes appear to influence hydraulic conductance capacity directly, and therefore may be the main determinant of dwarfing in these peach rootstocks.Key words: Prunus, rootstock, vessel diameter, hydraulic conductance, dwarfing, xylem anatomy, Poiseuille–Hagen     

Assessing agreement between multiple raters with missing rating information, applied to breast cancer tumour grading

Background

We consider the problem of assessing inter-rater agreement when there are missing data and a large number of raters. Previous studies have shown only ‘moderate’ agreement between pathologists in grading breast cancer tumour specimens. We analyse a large but incomplete data-set consisting of 24177 grades, on a discrete 1–3 scale, provided by 732 pathologists for 52 samples.

Methodology/Principal Findings

We review existing methods for analysing inter-rater agreement for multiple raters and demonstrate two further methods. Firstly, we examine a simple non-chance-corrected agreement score based on the observed proportion of agreements with the consensus for each sample, which makes no allowance for missing data. Secondly, treating grades as lying on a continuous scale representing tumour severity, we use a Bayesian latent trait method to model cumulative probabilities of assigning grade values as functions of the severity and clarity of the tumour and of rater-specific parameters representing boundaries between grades 1–2 and 2–3. We simulate from the fitted model to estimate, for each rater, the probability of agreement with the majority. Both methods suggest that there are differences between raters in terms of rating behaviour, most often caused by consistent over- or under-estimation of the grade boundaries, and also considerable variability in the distribution of grades assigned to many individual samples. The Bayesian model addresses the tendency of the agreement score to be biased upwards for raters who, by chance, see a relatively ‘easy’ set of samples.

Conclusions/Significance

Latent trait models can be adapted to provide novel information about the nature of inter-rater agreement when the number of raters is large and there are missing data. In this large study there is substantial variability between pathologists and uncertainty in the identity of the ‘true’ grade of many of the breast cancer tumours, a fact often ignored in clinical studies.     

基于报告基因敲入构建果生刺盘孢细胞核荧光标记菌株

运用基因敲入技术,将GFP、mCherry整合到果生刺盘孢 Colletotrichum fructicola组蛋白histone H1位点,实现融合表达,获得细胞核荧光标记菌株。基于标记菌株可以对分生孢子、营养菌丝、附着胞、侵染菌丝等结构中的细胞核进行实时活体观察。果生刺盘孢存在性亲和的“+”、“-”型菌株分化,GFP“+”型菌株和mCherry“-”型菌株接触形成明显杂交线,杂交线上单子囊内含红绿两种孢子,表明“+”、“-”型菌株间发生杂交;杂交线上子囊壳壁表达mCherry,表明由“-”型菌株发育而来。本研究构建的核荧光标记菌株将是研究果生炭疽菌细胞周期调控和有性繁殖过程的重要材料。     

High-density Integrated Linkage Map Based on SSR Markers in Soybean

A well-saturated molecular linkage map is a prerequisite for modern plant breeding. Several genetic maps have been developed for soybean with various types of molecular markers. Simple sequence repeats (SSRs) are single-locus markers with high allelic variation and are widely applicable to different genotypes. We have now mapped 1810 SSR or sequence-tagged site markers in one or more of three recombinant inbred populations of soybean (the US cultivar ‘Jack’ × the Japanese cultivar ‘Fukuyutaka’, the Chinese cultivar ‘Peking’ × the Japanese cultivar ‘Akita’, and the Japanese cultivar ‘Misuzudaizu’ × the Chinese breeding line ‘Moshidou Gong 503’) and have aligned these markers with the 20 consensus linkage groups (LGs). The total length of the integrated linkage map was 2442.9 cM, and the average number of molecular markers was 90.5 (range of 70–114) for the 20 LGs. We examined allelic diversity for 1238 of the SSR markers among 23 soybean cultivars or lines and a wild accession. The number of alleles per locus ranged from 2 to 7, with an average of 2.8. Our high-density linkage map should facilitate ongoing and future genomic research such as analysis of quantitative trait loci and positional cloning in addition to marker-assisted selection in soybean breeding.Key words: EST-derived SSR marker, integrated linkage map, microsatellite marker, polymorphism information content     

Foundation characteristics of edible Musa triploids revealed from allelic distribution of SSR markers

Background and Aims

The production of triploid banana and plantain (Musa spp.) cultivars with improved characteristics (e.g. greater disease resistance or higher yield), while still preserving the main features of current popular cultivars (e.g. taste and cooking quality), remains a major challenge for Musa breeders. In this regard, breeders require a sound knowledge of the lineage of the current sterile triploid cultivars, to select diploid parents that are able to transmit desirable traits, together with a breeding strategy ensuring final triploidization and sterility. Highly polymorphic single sequence repeats (SSRs) are valuable markers for investigating phylogenetic relationships.

Methods

Here, the allelic distribution of each of 22 SSR loci across 561 Musa accessions is analysed.

Key Results and Conclusions

We determine the closest diploid progenitors of the triploid ‘Cavendish’ and ‘Gros Michel’ subgroups, valuable information for breeding programmes. Nevertheless, in establishing the likely monoclonal origin of the main edible triploid banana subgroups (i.e. ‘Cavendish’, ‘Plantain’ and ‘Mutika-Lujugira’), we postulated that the huge phenotypic diversity observed within these subgroups did not result from gamete recombination, but rather from epigenetic regulations. This emphasizes the need to investigate the regulatory mechanisms of genome expression on a unique model in the plant kingdom. We also propose experimental standards to compare additional and independent genotyping data for reference.