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R Mago

Publications and source records attributed to R Mago.

13 recordsLinked to original sources
PubMed2025

Optimising parent selection in plant breeding: comparing metaheuristic algorithms for genotype building.

Stacking desirable haplotypes across the genome to develop superior genotypes has been implemented in several crop species. A major challenge in Optimal Haplotype Selection is identifying a set of parents that collectively contain all desirable haplotypes, a complex combinatorial problem with countless possibilities. In this study, we evaluated the performance of metaheuristic search algorithms (MSAs)-genetic algorithm (GA), differential evolution (DE), particle swarm optimisation (PSO), and simulated annealing (SA) for optimising parent selection under two genotype building (GB) objectives: Optimal Haplotype Selection (OHS) and Optimal Population Value (OPV). Using a diverse wheat population of 583 lines genotyped for 29,972 SNPs, forming 7645 haplotype blocks and phenotyped for stripe rust scores, we assessed each algorithm's performance across fitness optimisation, convergence speed, and computational efficiency. GA consistently achieved high fitness and rapid convergence, while DE showed robustness but required longer runtime and careful tuning. PSO performed well under the OHS criterion but was less effective for OPV. SA, although computationally lighter, was less consistent in finding optimal solutions. Simulation over 100 breeding cycles showed that OHS outperformed both OPV and GEBV-based selection in long-term genetic gain and diversity retention. OHS maintained heterozygosity and additive variance, which are key for sustainable improvement, while GEBV selection led to early allele fixation. Our findings underscore the potential of GB strategies that prioritise the collective performance of parent sets rather than individual ranking to enhance selection outcomes in genomic-assisted breeding programmes.

Plant Breeding↗
PubMed2005

High-resolution mapping and mutation analysis separate the rust resistance genes Sr31, Lr26 and Yr9 on the short arm of rye chromosome 1.

The stem, leaf and stripe rust resistance genes Sr31, Lr26 and Yr9, located on the short arm of rye chromosome 1, have been widely used in wheat by means of wheat-rye translocation chromosomes. Previous studies have suggested that these resistance specificities are encoded by either closely-linked genes, or by a single gene capable of recognizing all three rust species. To investigate these issues, two 1BL.1RS wheat lines, one with and one without Sr31, Lr26 and Yr9, were used as parents for a high-resolution F2 mapping family. Thirty-six recombinants were identified between two PCR markers 2.3 cM apart that flanked the resistance locus. In one recombinant, Lr26 was separated from Sr31 and Yr9. Mutation studies recovered mutants that separated all three rust resistance genes. Thus, together, the recombination and mutation studies suggest that Sr31, Lr26 and Yr9 are separate closely-linked genes. An additional 16 DNA markers were mapped in this region. Multiple RFLP markers, identified using part of the barley Mla powdery mildew resistance gene as probe, co-segregated with Sr31 and Yr9. One deletion mutant that had lost Sr31, Lr26 and Yr9 retained all Mla markers, suggesting that the family of genes on 1RS identified by the Mla probe does not contain the Sr31, Lr26 or Yr9 genes. The genetic stocks and DNA markers generated from this study should facilitate the future cloning of Sr31, Lr26 and Yr9.

Chromosome Mapping↗
PubMed2005

Development of PCR markers for the selection of wheat stem rust resistance genes Sr24 and Sr26 in diverse wheat germplasm.

The use of major resistance genes is the most cost-effective strategy for preventing stem rust epidemics in Australian wheat crops. The long-term success of this strategy is dependent on combining resistance genes that are effective against all predominant races of the pathogen, a task greatly assisted by the use of molecular markers linked to individual resistance genes. The wheat stem rust resistance genes Sr24 and Sr26 (derived from Agropyron elongatum) and SrR and Sr31 (derived from rye) are available in wheat as segments of alien chromosome translocated to wheat chromosomes. Each of these genes provides resistance to all races of wheat stem rust currently found in Australia . We have developed robust PCR markers for Sr24 and Sr26 (this study) and SrR and Sr31 (previously reported) that are applicable across a wide selection of Australian wheat germplasm. Wheat lines have recently become available in which the size of the alien segments containing Sr26, SrR and Sr31 has been reduced. Newly developed PCR-markers can be used to identify the presence of the shorter alien segment in all cases. Assuming that these genes have different gene-for-gene specificities and that the wheat industry will discourage the use of varieties carrying single genes only, the newly developed PCR markers will facilitate the incorporation of two or more of the genes Sr24, Sr26, SrR and Sr31 into wheat lines and have the potential to provide durable control to stem rust in Australia and elsewhere.

Alleles↗
PubMed2004

Resistance genes for rye stem rust (SrR) and barley powdery mildew (Mla) are located in syntenic regions on short arm of chromosome.

Genetic stocks were developed for the localization and eventual cloning of the stem rust resistance gene SrR that occurs in wheat lines carrying the 1RS translocation from Secale cereale 'Imperial' rye. We have used a mutation-based approach for molecular analysis of the SrR region in rye. Forty-one independent mutants resulting in loss of SrR resistance were isolated: many of these were deletions of various sizes that were used to locate SrR with respect to chromosome group 1S markers. The analysis of the mutants showed that markers about 1 Mb apart flanking the barley Mla locus also flank SrR. Additionally, three of the approximately 20 closely related sequences of Mla in rye are deleted in each of six interstitial deletion mutants of SrR. The results indicate that the SrR region in rye is syntenic to the Mla region in barley or that SrR is possibly orthologous to the Mla locus.

Binding Sites↗
PubMed2001

Removal of copper by Pseudomonas putida strain S4 isolated from copper mines.

A bacterial strain, Pseudomonas putida S4, was isolated from smelter drainage of copper mines. The strain exhibited resistance to several heavy metals, like aluminium (Al), zinc (Zn), nickel (Ni), cobalt (Co) besides copper (Cu). Strain S4 could accumulate Cu from the Cu-supplemented growth medium. In the present study, we have demonstrated the Cu2+ removal capacity of this strain from various samples such as mine effluent, low-grade ore and ore-tailings, collected from the mining site. Moreover, approximately 80% of the accumulated Cu2+ could be recovered from the loaded biomass by a simple desorption procedure.

Biodegradation, Environmental↗
PubMed2000

Clinical laboratory measures in relation to depression, disability, and cognitive impairment in elderly patients.

To characterize the dimensions of physiological abnormalities that commonly occur in older individuals in a residential care setting and to evaluate their association with clinical measures, the authors conducted an exploratory factor analysis on clinical laboratory measures from a sample of 231 elderly residents (mean age: 86) living in a nursing home and congregate apartment facility. An eight-factor solution accounted for 70.2% of the variance in these measures; factors identified were interpreted as indices of renal function, protein/calorie/nutritional status, serum electrolytes/osmolarity, liver function, acute-phase processes, plasma lipids, acid/base status, and renal-tubular function. The nutritional factor was significantly associated with measures of disability and the presence of depression. The acute-phase processes factor was significantly associated with cognitive impairment.

Activities of Daily Living↗
PubMed1999

Differentiation of Asian rice gall midge, Orseolia oryzae (Wood-Mason), biotypes by sequence characterized amplified regions (SCARs).

We developed a polymerase chain reaction (PCR)-based assay that distinguished five different biotypes of the Asian gall midge (Orseolia oryzae), a major insect pest of rice. A total of 400 random primers were screened using random amplified polymorphic DNAs (RAPDs). Five diagnostic PCR products were isolated, cloned, sequenced and converted to sequence characterized amplified regions (SCARs). Primers specific to these SCARs were able to amplify specific DNA fragments from genomic DNAs of five biotypes of gall midge in a multiplexed-PCR-based assay. The amplified DNA fragments were used as diagnostic markers to identify different biotypes of gall midge. The SCAR primers were also capable of differentiating the Asian from the African rice gall midge (Orseolia oryzivora) as well as detecting a variant of biotype 5 which caused an outbreak in Kerala, India. Unlike the use of plant host differentials and midge feeding behaviour for identifying biotypes, this assay is fast, reliable and unaffected by environmental factors.

Animals↗
PubMed1994

Uptake of Zinc in Pseudomonas sp. Strain UDG26.

Zinc resistance in Pseudomonas sp. strain UDG26 was inducible. Induction led to enhanced uptake of the metal. A zinc-sensitive variant (UDG86) took up significantly less metal ion than the resistant one did. The affinity of uninduced and sensitive cells to zinc was less than that of resistant, induced cells. Metal accumulation by induced cells was not inhibited by azide, while 2,4-dinitrophenol and N-N' -dicyclohexylcarbodiimide enhanced zinc uptake because of inhibition of efflux. Transcription and translation inhibitors drastically reduced zinc accumulation, bringing it to the level found in the sensitive strain. These results suggest the involvement of protein(s) in zinc resistance.

Journal Article↗