Genetic dissection of grain iron and zinc concentrations in lentil (Lens culinaris Medik.)

Iron (Fe) and zinc (Zn) deficiencies are wide spread in South Asia and Africa. Biofortification of food crops is a viable means of addressing micronutrient deficiencies. Lentil is an important pulse crop that provides affordable source of proteins, minerals, fibre and carbohydrates for micronutrient deficient countries. An association mapping (AM) panel of 96 diverse lentil genotypes fromIndia and Mediterranean region was evaluated for three seasons and genotyped using 80 polymorphic simple-sequence repeat (SSR) markers for identification of the markers associated with grain Fe and Zn concentrations. A Bayesian model based clustering identified five subpopulations, adequately explaining the genetic structure of the AM panel. The linkage disequilibrium (LD) analysis usingmixed linear model (MLM) identified two SSR markers, GLLC106 and GLLC108, associated with grain Fe concentration explaining 17% and 6% phenotypic variation, respectively and three SSR markers (PBALC 364, PBALC 92 and GLLC592) associated with grain Zn concentration, explaining 6%, 8% and 13% phenotypic variation, respectively. The identified SSRs exhibited consistentperformance across three seasons and have potential for utilization in lentil molecular breeding programme.

Introgression of LTP2 gene through marker assisted backcross in barley (Hordeum vulgare L. )

Background: Marker-assisted introgression currently represents the most widely spread application of DNA markers as an aid to selection in plant breeding. New barley germplasm should be supplemented by genes that facilitate growth and development under stressful conditions. The homology search against known genes is a fundamental approach to identify genes among the generated sequences. This procedure can be utilized for SNP search in genes of predicted function of interest and associated gene ontology (GO). Results: Backcross breeding enhanced by marker selection may become a powerful method to transfer one or a few genes controlling a specific trait. In the study, the integrated approach of combining phenotypic selection with marker assisted backcross breeding for introgression of LTP2 gene, in the background of semi-dwarf spring barley cultivar, was employed. This study discusses the efficiency of molecular marker application in backcrossing targeted on the selected gene. Conclusions: BC6 lines developed in this study can serve as a unique and adequate plant material to dissect the role of LTP2 gene. Due to its role in lipid transfer, the LTP2 may be crucial in lipidome modification in response to abiotic stress.

Identification and genetic diversity analysis of Memecylon species using ISSR, RAPD and Gene-Based DNA barcoding tools

Background: Memecylon species are commonly used in Indian ethnomedical practices. The accurate identification is vital to enhance the drug's efficacy and biosafety. In the present study, PCR based techniques like RAPD, ISSR and DNA barcoding regions, such as 5s, psbA-trnH, rpoC1, ndh and atpF-atpH, were used to authenticate and analyze the diversity of five Memecylon species collected from Western Ghats of India. Results: Phylogenetic analysis clearly distinguished Memecylon malabaricum from Memecylon wightii and Memecylon umbellatum from Memecylon edule and clades formed are in accordance with morphological keys. In the RAPD and ISSR analyses, 27 accessions representing five Memecylon species were distinctly separated into three different clades. M. malabaricum and M. wightii grouped together and M. umbellatum, M. edule and Memecylon talbotianum grouped in the same clade with high Jaccard dissimilarity coefficient and bootstrap support between each node, indicating that these grouped species are phylogenetically similar. Conclusion: Data from the present study reveals that chloroplast psbA-trnH region could be used as a potential candidate region for identifying Memecylon species, and ISSR marker system could be used for estimating genetic diversity since it has high percent polymorphism compared to RAPD marker.

DNA alterations in the tumor genome and their associations with clinical outcome in prostate cancer / 亚洲男科学杂志(英文版)

Although most prostate cancer (PCa) cases are not life-threatening, approximately 293 000 men worldwide die annually due to PCa. These lethal cases are thought to be caused by coordinated genomic alterations that accumulate over time. Recent genome-wide analyses of DNA from subjects with PCa have revealed most, if not all, genetic changes in both germline and PCa tumor genomes. In this article, I first review the major, somatically acquired genomic characteristics of various subtypes of PCa. I then recap key findings on the relationships between genomic alterations and clinical parameters, such as biochemical recurrence or clinical relapse, metastasis and cancer-specific mortality. Finally, I outline the need for, and challenges with, validation of recent findings in prospective studies for clinical utility. It is clearer now than ever before that the landscape of somatically acquired aberrations in PCa is highlighted by DNA copy number alterations (CNAs) and TMPRSS2-ERG fusion derived from complex rearrangements, numerous single nucleotide variations or mutations, tremendous heterogeneity, and continuously punctuated evolution. Genome-wide CNAs, PTEN loss, MYC gain in primary tumors, and TP53 loss/mutation and AR amplification/mutation in advanced metastatic PCa have consistently been associated with worse cancer prognosis. With this recently gained knowledge, it is now an opportune time to develop DNA-based tests that provide more accurate patient stratification for prediction of clinical outcome, which will ultimately lead to more personalized cancer care than is possible at present.

Candidate gene markers for Candidatus Liberibacter asiaticus for detecting citrus greening disease.

Citrus Huanglongbing (HLB) also known as citrus greening is one of the most devastating diseases of citrus worldwide. The disease is caused by Candidatus Liberibacter bacterium, vectored by the psyllid Diaphorina citri Kuwayama and Trioza erytreae Del Guercio. Citrus plants infected by the HLB bacterium may not show visible symptoms sometimes for years following infection. The aim of this study was to develop effective gene-specific primer pairs for polymerase chain reaction based method for quick screening of HLB disease. Thirty-two different gene-specific primer pairs, across the Ca. Liberibacter asiaticus genome, were successfully developed. The possibility of these primer pairs for cross-genome amplification across ‘Ca. Liberibacter africanus’ and ‘Ca. Liberibacter americanus’ were tested. The applicability of these primer pairs for detection and differentiation of Ca Liberibacter spp. is discussed.

Application of large-scale sequencing to marker discovery in plants.

Advances in DNA sequencing provide tools for efficient large-scale discovery of markers for use in plants. Discovery options include large-scale amplicon sequencing, transcriptome sequencing, gene-enriched genome sequencing and whole genome sequencing. Examples of each of these approaches and their potential to generate molecular markers for specific applications have been described. Sequencing the whole genome of parents identifies all the polymorphisms available for analysis in their progeny. Sequencing PCR amplicons of sets of candidate genes from DNA bulks can be used to define the available variation in these genes that might be exploited in a population or germplasm collection. Sequencing of the transcriptomes of genotypes varying for the trait of interest may identify genes with patterns of expression that could explain the phenotypic variation. Sequencing genomic DNA enriched for genes by hybridization with probes for all or some of the known genes simplifies sequencing and analysis of differences in gene sequences between large numbers of genotypes and genes especially when working with complex genomes. Examples of application of the above-mentioned techniques have been described.

Estudios preliminares de la estructura genética del perro cimarrón uruguayo usando microsatélites / Preliminary studies of the genetic structure of cimarron uruguayo dog using microsatellite markers

Objetive. To analyze the population structure, using microsatellite markers in a sample of “Cimarron Uruguayo” dogs. Materials and methods. Thirty dogs were analyzed in different areas of Uruguay with a set of nine molecular microsatellite markers using PCR. The population structure was analyzed using the free distribution software “Structure’’. Results. According to our data, the preliminary results show that it is not possible to establish a subdivision among the animals in the sample. Conclusions. The study supports the hypothesis that the currently existing canines derive from a founding nucleus that took refuge in the Northeastern region of the country. The distribution of the breed among the different areas of Uruguay continues nowadays, so there is no isolation among the different groups of animals, and the exchange is constant.

Diversity among Stylosanthes species: Habitat, edaphic and agro-climatic affinities leading to cultivar development.

Since the introduction of Stylosanthes, a range legume, in India in early seventies extensive efforts have been made for its evaluation and adaptation. However, limited germplasm and narrow genetic base were major impediments in its wider adaptations. Of late, introduction of several new improved germplasm including newly identified species, cultivars and bred materials from Australia, Colombia, Brazil and Ethiopia and their evaluation at selected centers under different agro-climatic conditions improved the existing scenario as many lines including S. scabra RRR as well as newly introduced species S. seabrana has shown great promise for diverse agro-climatic zones. Because of concerted efforts which was largely generated from the recently concluded Austrialian Centre for International Agricultural Research (ACIAR) stylo project and background study during the period of early eighties Stylosanthes has been considered as the most important tropical legume which not only improve the soil fertility but also provide nutritive forage. Two species namely S. hamata and S. scabra largely contribute to the supply of forages for cattle, buffalo, goats and sheep. As a nitrogen fixing legume, the plant helps replenish soil nutrients when used in ley farming, mixed and inter-cropping systems. The scenario has largely changed due to the better performance of newly introduced S. seabrana species which possessed high seedling vigour, high nutritional parameters and better adaptation under rainfed situations in heavy clay and cracking soil types. It provides good foliage and being erect and low sticky in nature showed compatibility for mixed cropping. Results also demonstrated reasonable yield in first year by all four major species which ultimately geared up in second year of growth. This was stable in S. hamata and S. viscosa for another two years whereas other two species namely S. scabra and S. seabrana indicated enhanced yield in consecutive years.