Genetic analysis of kernel hardness in bread wheat using PCR-based markers

In wheat, kernel hardness is a complex genetic trait involving various directly and indirectly contributing components such as kernel hardness per se, protein content, hectolitre weight and 1,000-kernel weight. In an attempt to identify DNA markers associated with this trait, 100 recombinant inbred lines (RILs) derived from a cross between a hard grain land-race, NP4, and a soft grain variety, HB 208, were screened with 100 ISSR and 360 RAPD primers. Eighteen markers were assigned to seven linkage groups covering 223.6 cM whereas 11 markers remained unlinked. A multiple-marker model explained the percentage of phenotypic variation for kernel hardness as 20.6%, whereas that for protein content, hectolitre weight and 1,000-kernel weight was 18.8%, 13.5% and 12.1%, respectively. Our results indicate that phenotypic expression of kernel hardness is controlled by many QTLs and is interdependent on various related traits. Received: 25 July 2000 / Accepted: 24 November 2000     

Molecular evidence of hybridisation between the endemic Phoenix canariensis and the widespread P. dactylifera with Random Amplified Polymorphic DNA (RAPD) markers

We used RAPD markers to test whether morphologically intermediate individuals between the Canarian endemic Phoenix canariensis and the widespread P. dactylifera correspond to hybrids. Consistent with previous allozyme evidence, the scarcity of appropriate RAPD markers to distinguish P. dactylifera and P. canariensis indicated a close genetic relationship among these species. Only two of the 54 ten-mer primers (OPM-8 and OPK-14) tested in 221 individuals from 7 localities in different islands enabled us to unambiguously identify both species. While P. canariensis possesses two exclusive monomorphic bands of 1000 bp and 750 bp (for OPM-8 and OPM-14, respectively), dactylifera is characterised by two bands of 900 bp and 950 bp for the same primers. The additivity of these taxon-specific bands in the individuals that were morphologically intermediate provided, for the first time, firm evidence for their hybrid origin. Because these hybridisation capabilities pose clear threats to the survival of the endemic P. canariensis and some individuals that had been morphologically characterised as pure P. canariensis revealed later a hybrid nature in the RAPD analysis, we suggest that RAPD markers be used to estimate the possible incidence of introgression in the scarce extant natural populations of P. canariensis. This procedure will provide a straightforward means to select target populations to implement the in situ conservation strategies suggested previously on the basis of allozyme research.We thank Michel Ferry for providing samples of Phoenix dactylifera from the Hort del Gat Research Station on Date Palm and Arid Land Farming Systems in Elche (Spain). The authors wish to thank Jaime OShanahan for his wise comments about Phoenix canariensis. This research was funded by the Gobierno de Canarias (94-2614). A PhD Research Fellowship (Direccion General de Universidades, Gobierno de Canarias) to Gonzalez-Perez. is also acknowledged.     

Molecular identification of Todiramphus chloris subspecies on the Arabian Peninsula using three mitochondrial barcoding genes and ISSR markers

The Collared Kingfisher (Todiramphus chloris) is widely distributed across the Indian and western Pacific Oceans and consists of about 50 subspecies. Two different subspecies of T. chloris occur in the Arabian Peninsula: T. c. abyssinicus from the Red Sea coast and T. c. kalbaensis from the Arabian Sea coast in the United Arab Emirates and Oman. The aim of this study was to determine the molecular relationship between the two Arabian subspecies and to establish the first DNA barcodes from the Arabian Peninsula for this species. Three different mitochondrial genes were used: (i) cytochrome c oxidase subunit I (COI), (ii) 12S rRNA (12S) and (iii) NADH dehydrogenase-1 (ND1). The COI gene sequences of the two subspecies were 100% identical, while the 12S and ND1 gene sequences revealed a unique single nucleotide variation between the two subspecies. Thus, this single nucleotide variation can be used as a DNA barcode to discriminate between two subspecies. Furthermore, the genetic profile or fingerprint for both subspecies were compared using ten primers of the highly polymorphic nuclear markers (Inter Simple Sequence Repeat, ISSR). As expected, the DNA analysis of the ISSR markers was able to distinguish between the specimens of the two subspecies. These results suggest that T. c. abyssinicus and T. c. kalbaensis are not identical and thus belong to different subspecies. Besides, the sequences of the COI gene for T. c. abyssinicus and T. c. kalbaensis differs by only 1.28% from T. sanctus suggesting that the Arabian subspecies are closely related to the Sacred Kingfisher (T. sanctus).     

Molecular Clocks and Archeogenomics of a Late Period Egyptian Date Palm Leaf Reveal Introgression from Wild Relatives and Add Timestamps on the Domestication

The date palm, Phoenix dactylifera, has been a cornerstone of Middle Eastern and North African agriculture for millennia. It was first domesticated in the Persian Gulf, and its evolution appears to have been influenced by gene flow from two wild relatives, P. theophrasti, currently restricted to Crete and Turkey, and P. sylvestris, widespread from Bangladesh to the West Himalayas. Genomes of ancient date palm seeds show that gene flow from P. theophrasti to P. dactylifera may have occurred by ∼2,200 years ago, but traces of P. sylvestris could not be detected. We here integrate archeogenomics of a ∼2,100-year-old P. dactylifera leaf from Saqqara (Egypt), molecular-clock dating, and coalescence approaches with population genomic tests, to probe the hybridization between the date palm and its two closest relatives and provide minimum and maximum timestamps for its reticulated evolution. The Saqqara date palm shares a close genetic affinity with North African date palm populations, and we find clear genomic admixture from both P. theophrasti, and P. sylvestris, indicating that both had contributed to the date palm genome by 2,100 years ago. Molecular-clocks placed the divergence of P. theophrasti from P. dactylifera/P. sylvestris and that of P. dactylifera from P. sylvestris in the Upper Miocene, but strongly supported, conflicting topologies point to older gene flow between P. theophrasti and P. dactylifera, and P. sylvestris and P. dactylifera. Our work highlights the ancient hybrid origin of the date palms, and prompts the investigation of the functional significance of genetic material introgressed from both close relatives, which in turn could prove useful for modern date palm breeding.     

An examination of hybridization between the cattail species typha latifolia and typha angustifolia using random amplified polymorphic DNA and chloroplast DNA markers

Typha glauca represents a significant portion of the biomass of the wetlands surrounding the Great Lakes, USA. It is generally accepted to be a form of hybrid between T. latifolia and T. angustifolia, which itself appears to be an exotic introduction from Europe. Based on morphological and isozyme data, conflicting theories have been proposed for the hybrid nature of T. glauca: it has been described as a hybrid swarm, a distinct hybrid species and an F1 hybrid. Therefore, we developed random amplified polymorphic DNA (RAPD) and chloroplast DNA markers, specific to the parental species, to assess hybrids. Ten RAPD primers gave 17 fragments specific to T. angustifolia and 13 fragments specific to T. latifolia. All of the interspecific hybrids contained each of the species-specific markers, indicating an F1 hybrid status. Furthermore, all hybrids tested contained the T. angustifolia chloroplast haplotype, which is consistent with differential interspecific crossing success found previously. Additional confirmation of an F1 hybrid status was gained by examining seedlings from T. glauca. These progeny were expected to be advanced-generation hybrids, as opposed to the F1 hybrid parent. Analysis of the seedlings revealed segregating marker patterns consistent with patterns observed in experimental advanced-generation hybrids, although these advanced hybrids do not appear to be a significant part of mature stands. Our data do not provide support for extensive gene flow between T. latifolia and T. angustifolia. However, our results suggest that hybridization between the native and introduced Typha species has impacted the native population through the spread of the F1 hybrid, T. glauca.     

Improving the biological control of Botryodiplodia disease on some Annona cultivars using single or multi-bioagents in Egypt

Botryodiplodia disease caused by Botryodiplodia theobromae is a recently disease of some Annona cultivars in Egypt, particularly in Behera Governorate, characterized by stem purple lesions, dieback, flowers, and fruits dry and soft rot. Six fungal and bacterial bioagents, i.e., Trichoderma koningii, Trichoderma hamatum, Pseudomonas fluorescens, Pseudomonas putida, Tilletiopsis minor, and Tilletiopsis washingtonensis were tested either solely or at different amalgamations against Botryodiplodia disease, as foliar spraying using three Annona cultivars, i.e., Balady and Abd El-Razik (Annona squamosa) and Hindy (Annona cherimola). In vitro, studies revealed a significant inhibition towards the conidial germination of B. theobromae as well as on the disease incidence on artificially inoculated branches and fruits in the presence of the aforementioned bioagents. An unmistakable reduction in the disease was conspicuous under the action of multi-bioagent conduct. The bioagents were tested during 2003 and 2004 agricultural seasons under the field conditions at Nobaria, (Behera Governorate). A single application and all possible mixture of two or three of the bioagents were applied at 15 days intervals as a foliar spray. Botryodiplodia disease severity and sporulation of the pathogen were always reduced, when the multi-bioagents were applied. When Trichoderma spp. and Pseudomonads spp. were blended together, the disease was greatly abridged in the three tested cultivars compared to any of the sole bioagents. The multi-bioagents were more effective than any sole or even double treatments. The application of multi-bioagents also resulted in a significant increase of fruit yield.     

Genetic dissection of the relationship between carbon metabolism and early growth in maize,with emphasis on key-enzyme loci

The determinism of carbon metabolism traits during early growth in maize has been investigated using a marker-based quantitative genetics approach. In addition to growth traits, concentration of carbohydrates and activity of four key enzymes of their metabolism (sucrose phosphate synthase, ADP-glucose pyrophosphorylase, invertases and sucrose synthase) have been measured in leaves of individuals of a recombinant inbred line population. Using more than 100 RFLP markers, quantitative trait loci (QTLs) were mapped for each biochemical and developmental trait. Causal relationships, suggested by previous physiological studies, were reinforced by common locations of QTLs for different traits. Thus, the strong correlation between growth rate and invertase activity, which may reflect sink organ strength, could be explained to a large extent by a single region of chromosome 8. Moreover, some of the structural genes of the enzymes mapped to regions with QTLs affecting the activity of the encoded enzyme and/or concentration of its product, and sometimes growth traits. These results emphasize the possible role of the polymorphism of key-enzyme genes in physiological processes, and hence in maize growth.     

Phylogenetic relationships of Pterocarya (Juglandaceae) with an emphasis on the taxonomic status of Iranian populations using ITS and trnH-psbA sequence data

Pterocarya fraxinifolia (Lam.) Spach., a relict tree species of the Juglandaceae family, is native to the Great Caucasus, Anatolia, and to the Hyrcanian forests of the southern Azerbaijan and Northern Iran. In this study, the phylogenetic relationship of the species, sampled in selected Iranian populations, and the global biogeography of the genus Pterocarya were addressed. Leaves were collected from 8 to 10 trees from three geographically isolated habitats. The samples were analyzed with nuclear (internal transcribed spacer [ITS] regions) and chloroplast (trnH-psbA) DNA markers. The obtained results were compared and analyzed with the data registered in NCBI GenBank. It is reported that the ITS regions varied from 644 to 652 for Pterocarya genus, but we did not observe polymorphisms for Iranian Pterocarya. The phylogenetic tree divided the Pterocarya genus in three clades: clade 1 grouping exclusively the samples P. fraxinifolia, clearly separated from the East Asiatic taxa; clade 2 that includes the species P. hupehensis and P. macroptera; clade 3 clustering P. stenoptera and P. tonkinensis. Although the Iranian Pterocarya samples and P. fraxinifolia from the Caucasus were in the same clade, they presented two different secondary structures. The Iranian populations showed the maximum genetic distance with P. stenoptera and P. tonkinensis. Our analysis demonstrates that the traditional division of all the six species sampled throughout their distribution area as well as the phylogeny of the genus Pterocarya needs to be reviewed.     

A model of biocomplexity and its application to the analysis of some terrestrial and marsh eukaryotic microbial communities with an emphasis on amoeboid protists

Biocomplexity theory has become increasingly important in understanding ecosystem dynamics as we realize that the interactions among subunits in a multi-component system often produce elaborate states that are not easily explained in terms of the individual parts of the system. A Euclidean geometric model of biocomplexity is presented and illustrated using protistan communities. The model is based on three quantitative biotic dimensions (indices) for small subsamples (0.01 g) taken from each sample core of substratum: (1) richness of morphospecies expressed as mean count per 0.01 g, (2) spatial diversity of protists expressed as then umber of unique morphospecies (i.e. those occurring in only one of the 0.01-g subsamples and not in any of the other subsamples), and (3) patchiness (non-uniform aggregation) of the distribution of protists across the 0.01-g subsamples. These three indices are mapped into a three-dimensional Euclidean space model, and the position of each point and its geometric distance from the origin are used as a general index of biocomplexity. The usefulness of the model is illustrated by applying it to a range of terrestrial and marsh communities. Within the set of 15 samples examined in this study, the marsh rhizosphere samples are among the most complex.     

Reaction of some tomato cultivars to tomato leaf curl virus and evaluation of the endophytic colonisation with Beauveria bassiana on the disease incidence and its vector,Bemisia tabaci

Tomato line LA1478 and Pusa Ruby were resistant to tomato leaf curl virus (TLCV) disease. They registered higher plant height, number of branches, total phenol content and yield per plant than the other cultivars. Variety Peto 86 was tolerant to the disease while the other popular tomato cultivars, i.e. Ace, Early Pack, Money Maker, Prichard and Strain B were highly susceptible to the disease. Plant height and number of branches per plant revealed significantly positive association with fruit yield per plant. The disease index of TLCV exhibited significant negative correlations with plant height, total phenol content and fruit yield per plant – 0–4 and 5–25 adult whiteflies were observed on resistant susceptible cultivars. In the case of epiphytically colonisation by Beauveria bassiana conidia, not all developing hyphae on the leaf surface penetrated the whitefly cuticle. Many of the germ tubes elongated to a short distance before terminating its growth. On the other hand, the rapid staining of tomato tissues injected with B. bassiana conidial suspension indicates that the entomopathogenic fungus was established inside tomato tissues until the end time of the trial. The direct injection with the spore suspension yielded high post-colonisation, where the fungus was recovered from sites distant from the point of inoculation. This indicates that the fungus has the potential to move throughout the plant tissues. Laboratory bioassay of tomato whitefly feeding on tomato tissues containing B. bassiana conidial spores indicates that plant endophytic colonisation with entomopathogenic fungi may reduce insect survival on these plants. LT₅₀ values of the test diet were between three and four days. The mortality of Bemisia tabaci was high in the case of endophytically colonisation compared to epiphytically one (90.0% compared to 10.0% during three days) for whiteflies fed tomato tissues containing 1.5 × 10⁷ B. bassiana spores/ml. Application of B. bassiana as an artificial endophyte inside tomato plants can be an important component in the integrated control of tomato whiteflies. The endophytic colonising can achieve biocontrol effect based on induced disease resistance in plant tissues. According the available references, this is the first report on B. tabaci controlling by plant endophytic treatment.     

The effects of age and gender on the relationship between HMGCR promoter-911 SNP (rs33761740) and serum lipids in patients with coronary heart disease

Background

Hydroxymethylglutaryl-Coenzyme A Reductase (HMGCR) catalyzes the rate-limiting step of cholesterol biosynthesis. This enzyme is the target of the widely available cholesterol lowering statins. In this population-based case–control study, the frequencies of -911 C>A polymorphism (rs3761740) of the HMGCR gene in patients with coronary heart disease (CHD) and healthy subjects were investigated and the correlations between the different genotypes and hypercholesterolemia with cardiovascular risk factors were analyzed.

Methods

The HMGCR genotypes were determined in 365 patients with CHD and 365 controls by PCR–RFLP assay. Anthropometric measurements were measured in all participants.

Results

There was no significant difference in the genotype frequencies of the HMGCR polymorphism between the male subjects of both patient and control groups, however, the HMGCR-CC genotype was found to be more frequent in female patients with CHD than female controls (p = 0.002). The HMGCR-CC genotype showed higher total-cholesterol (TC) and LDL-cholesterol (LDL-C) levels than the CA + AA genotypes in male CHD patients (p = 0.018). Due to this significant sex interaction, a multivariate analysis was conducted on the patient group. In the multivariate logistic regression analysis, the HMGCR-CC genotype was significantly associated with age < 55 (OR = 2.837, p = 0.001) and TC ≥ 5.18 mmol/L (OR = 1.970, p = 0.027) in male subjects. However, this association was not observed in female patients (p > 0.05). This analysis confirmed that the HMGCR-CC genotype was associated with elevated TC levels in male CHD patients with age < 55 years.

Conclusion

These results suggest that age and sex modify the contribution of the HMGCR-911 polymorphism to fasting serum TC, LDL-C levels and risk of CHD.