A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene

We used three approaches to map the yellow rust resistance gene Yr7 and identify associated SNPs in wheat. First, we used a traditional QTL mapping approach using a double haploid (DH) population and mapped Yr7 to a low-recombination region of chromosome 2B. To fine map the QTL, we then used an association mapping panel. Both populations were SNP array genotyped allowing alignment of QTL and genome-wide association scans based on common segregating SNPs. Analysis of the association panel spanning the QTL interval, narrowed the interval down to a single haplotype block. Finally, we used mapping-by-sequencing of resistant and susceptible DH bulks to identify a candidate gene in the interval showing high homology to a previously suggested Yr7 candidate and to populate the Yr7 interval with a higher density of polymorphisms. We highlight the power of combining mapping-by-sequencing, delivering a complete list of gene-based segregating polymorphisms in the interval with the high recombination, low LD precision of the association mapping panel. Our mapping-by-sequencing methodology is applicable to any trait and our results validate the approach in wheat, where with a near complete reference genome sequence, we are able to define a small interval containing the causative gene

Genetic analysis of drought stress response in Arabidopsis thaliana and Brassica rapa

Drought is the major abiotic stress affecting plant growth and limiting crop productivity worldwide. Plants have evolved three adaptive strategies, drought escape, drought avoidance and drought tolerance, to cope with drought. Knowledge on how Quantitative Trait Loci (QTL), or genes underlying these strategies interact with their environments will significantly increase our understanding and the success of breeding for drought tolerance. This thesis focused on phenotyping shoot and root traits ofA. thaliana and B. rapa grown on sand and in greenhouses,to further understand how plants can adapt to natural drought stress. In chapter 2, an already existing ArabidopsisRIL population was selected based on the differential root drought response of the two parental lines, Sha and Col, to be evaluated under different water regimes. Chapter 3 illustrated the use of GWAS in identifying candidate genes that are associated with pant response to drought.. In order to apply the same methodology in crop breeding, chapter 4 introduces a contribution to the genetic mapping of a new B. rapa RIL population, consisting of 160 lines and genotyped with 270 different markers was achieved. The morphological and physiological responses of this population to drought was evaluated in chapter 5. The results presented in the present thesis demonstrate that QxE is an important component of the genetic variance and can play a great role in improving drought tolerance in future breeding programs. In general, several QTL and SNPs were mapped either with main effect or with interaction with environments QxE. Many of the mapped QTL showed conditional neutrality and antagonestic pleiotropy.</p

Effect of ropy and capsular exopolysaccharides producing strain of Lactobacillus plantarum 162RM on characteristics and functionality of fermented milk and soft Kareish type cheese

The contribution of selected ropy and capsular Lactobacillus plantarum 162RM on texture of fermented milk as well as on the functionality of kareish cheese was established in this study. The cell suspension of this strain was used in combination with commercial starter cultures MY900 (Lactobacillus delbrueckii ssp. Bulgaricus/I> and Streptococcus thermophilus) and MM100 (Lactococcus lactis ssp. lactis, Lactococcus lactis ssp. cremoris and Lactococcus lactis ssp. diacetyllactis) obtained from Rhodia Food to manufacture fermented milk and Kareish cheese respectively. The final pH of fermented milks manufactured with the combination of starter MY900 and different concentration of strain L. plantarum 162RM were not significantly different. Fermented milk hardness, consistency, and adhesiveness increased significantly when 8 % (V/V) of strain Lactobacillus plantarum 162RM was used. This strain produces exopolysaccharides (EPS), which by attaching to the casein matrix increases and improves the texture characteristics of fermented milk. The Experimental Kareish Cheese (EKC), made by pairing commercial starter MM100 with 8% (v/v) of L. plantarum 162RM were also compared to Control Kareich Cheese (CKC) in terms of their moisture content and textural properties. The EKC showed the greatest moisture retention and the use of ropy and capsular strain of L. plantarum 162RM affects significantly some textural properties of EKC cheese, relative to the control. The CKC samples were gummier and more chewy than the EKC fresh samples. It is therefore evident that, used in appropriate amount, this strain can increase moisture content in low fat Kareish cheese leading to improvement of textural properties. Key Words: Fermented milks, kareish cheese, ropy and capsular strain, moisture, textural properties. African Journal of Biotechnology Vol.3(10) 2004: 512-51

Evaluation of the probiotic potential of lactic acid bacteria isolated from faeces of breast-fed infants in Egypt

The probiotic-related characteristics of 55 strains of lactic acid bacteria isolated from the faeces of 3 - 6 months old breast-fed infants were determined. The API 50 CH and SDS-PAGE techniques wereemployed to ascertain the identity of the isolated strains. The predominant species among the isolated strains were Lactobacillus (Lb.) acidophilus, Lb. plantarum, Enterococcus (E.) faecium, and E. faecalis. Probiotic properties such as bile resistance, acid tolerance, and adhesion to intestinal mucous were assessed. In vitro results obtained showed that five strains, Lb. plantarum (P1 and P164), Lb. pentosus (P191), and Lb. fermentum (P10, P193) were able to meet the basic requirements for probiotic functions as they demonstrated probiotic characteristics such as tolerance to pH 3, growth in 0.4% oxgall and adhesion to intestinal mucous. The results obtained in this investigation will be used to selectpotentially probiotic strains for in vivo study

Unraveling the genetic complexity underlying sorghum response to water availability

Understanding the adaptation mechanisms of sorghum to drought and the underlying genetic architecture may help to improve its production in a wide range of environments. By crossing a high yielding parent (HYP) and a drought tolerant parent (DTP), we obtained 140 recombinant inbred lines (RILs), which were genotyped with 120 DArT and SSR markers covering 14 linkage groups (LGs). A subset of 100 RILs was evaluated three times in control and drought treatments to genetically dissect their response to water availability. Plants with early heading date (HD) in the drought treatment maintained yield (YLD) level by reducing seed number SN and increasing hundred seed weight (HSW). In contrast, early HD in the control treatment increased SN, HSW and YLD. In total, 133 significant QTL associated with the measured traits were detected in ten hotspot regions. Antagonistic, pleiotropic effects of a QTL cluster mapped on LG-6 may explain the observed trade-offs between SN and HSW: Alleles from DTP reduced SN and the alleles from HYP increased HSW under drought stress, but not in the control treatment. Our results illustrate the importance of considering genetic and environmental factors in QTL mapping to better understand plant responses to drought and to improve breeding programs

Enumeration and identification of lactic microflora in Algerian goats’ milk

A total of 153 strains of lactic acid bacteria were isolated from Algerian goats’ milk. The strains were identified according to morphological, biochemical and physiological criteria, as well as the use of theAPI system and SDS-PAGE technique. Identification of the isolates revealed the presence of six genera: Enterococcus (41.82%), Lactobacillus (29.40), Lactococcus (19.60%), Leuconostoc (4.57%),Streptococcus thermophilus (3.26%) and Pediococcus (1.30%). The predominant strains belong to Enterococcus faecium (24 isolates), Enterococcus durans (22 isolates), Lactococcus lactis subsp. lactis(25 isolates), Lactobacillus rhamnosus (9 isolates) and Lactobacillus delbrueckii subsp. bulgaricus (7 isolates)

Aldo–Keto Reductase 1B10 and Its Role in Proliferation Capacity of Drug-Resistant Cancers

The human aldo–keto reductase AKR1B10, originally identified as an aldose reductase-like protein and human small intestine aldose reductase, is a cytosolic NADPH-dependent reductase that metabolizes a variety of endogenous compounds, such as aromatic and aliphatic aldehydes and dicarbonyl compounds, and some drug ketones. The enzyme is highly expressed in solid tumors of several tissues including lung and liver, and as such has received considerable interest as a relevant biomarker for the development of those tumors. In addition, AKR1B10 has been recently reported to be significantly up-regulated in some cancer cell lines (medulloblastoma D341 and colon cancer HT29) acquiring resistance toward chemotherapeutic agents (cyclophosphamide and mitomycin c), suggesting the validity of the enzyme as a chemoresistance marker. Although the detailed information on the AKR1B10-mediated mechanisms leading to the drug resistance process is not well understood so far, the enzyme has been proposed to be involved in functional regulations of cell proliferation and metabolism of drugs and endogenous lipids during the development of chemoresistance. This article reviews the current literature focusing mainly on expression profile and roles of AKR1B10 in the drug resistance of cancer cells. Recent developments of AKR1B10 inhibitors and their usefulness in restoring sensitivity to anticancer drugs are also reviewed

Antimicrobial and Safety Properties of Lactobacilli Isolated from two Cameroonian Traditional Fermented Foods

Twenty-one Lactobacillus isolates from “Sha’a” (a maize – based fermented beverage) and “Kossam” (traditionally fermented cow milk) were selected in accordance with their antagonistic activities and tested for their bacteriocinogenic potential as well as safety properties. These isolates were preliminarily identified as Lactobacillus plantarum (62%), Lactobacillus rhamnosus (24%), Lactobacillus fermentum (10%) and Lactobacillus coprophilus (4%) based on phenotypic characteristics and rep-PCR genomic fingerprinting. Twelve (57.1%) out of the 21 strains tested were found to be bacteriocin producers, as revealed by the sensitivity of their antimicrobial substances to proteolytic enzymes (Trypsin, Proteinase K) and inhibition of other Lactobacillus spp. These bacteriocinogenic strains showed no positive haemolytic and gelatinase activities and proved to be sensitive to penicillin G, ampicillin, tetracycline, erythromycin, amoxicillin, chloramphenicol, co-trimoxazole and doxycyclin, but resistant to ciprofloxacin and gentamicin. The bacteriocins showed a broad inhibitory activity against Gram-positive and Gram-negative pathogenic bacteria, several of which are classified as especially dangerous by the World Health Organization, as well as Multidrug-resistant strains. These include Staphylococcus aureus, Salmonella enterica subsp. enterica serovare Typhi, Bacillus cereus, Streptococcus mutans, Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae and Shigella flexneri. These Lactobacillus strains are promising candidates for use as protective cultures in food fermentation

High-density SNP-based association mapping of seed traits in fenugreek reveals homology with clover

Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs