Molecular characterization of the Indian Andigena potato core collection using microsatellite markers

Twenty-four (24) microsatellite (SSR) markers of a new PGI kit were used to validate the genetic diversity of the 77 Indian Andigena potato core collections. In SSR analysis, polymorphic information content (PIC), allelic richness per locus of microsatellite loci and cluster analysis showed the high diversity of core collection. In total, 214 SSR alleles were detected in the core collection, out of which 208 alleles were polymorphic with absolute frequencies between 2 to 58. The PIC values of SSR loci ranged from 0.61 to 0.90. SSR-based dendrogram revealed eight main groups (Clusters I to VIII) including 26 single accessions at Dice similarity coefficient value of 0.37. None of the accession showed full similarity with any other accession, except that the maximum similarity (0.83) was observed between the accessions JEX/A-316 and JEX/A-317. PCA revealed 47.31% variation in the first three components. Analysis of molecular variance (AMOVA) analysis which resulted into maximum variation was due to within country origins and yield types. The genetic diversity of the core collection based on the microsatellite data appeared to have quite distinct genotypes that were formed by the morph-agronomic traits. These findings not only demonstrate the diverse core collection but are also useful for selecting genetically distinct potato materials to widen the genetic background of the potato gene pool.Keywords: Core collection, genetic diversity, potato, Solanum tuberosum subsp. andigena, SSRAfrican Journal of Biotechnology Vol. 12(10), pp. 1025-1033, 6 March, 201

High performance bdd package by exploiting memory hierarchy

Abstract The success of binary decision diagram (BDD

Chromosome Tips Damaged in Anaphase Inhibit Cytokinesis

Genome maintenance is ensured by a variety of biochemical sensors and pathways that repair accumulated damage. During mitosis, the mechanisms that sense and resolve DNA damage remain elusive. Studies have demonstrated that damage accumulated on lagging chromosomes can activate the spindle assembly checkpoint. However, there is little known regarding damage to DNA after anaphase onset. In this study, we demonstrate that laser-induced damage to chromosome tips (presumptive telomeres) in anaphase of Potorous tridactylis cells (PtK2) inhibits cytokinesis. In contrast, equivalent irradiation of non-telomeric chromosome regions or control irradiations in either the adjacent cytoplasm or adjacent to chromosome tips near the spindle midzone during anaphase caused no change in the eventual completion of cytokinesis. Damage to only one chromosome tip caused either complete absence of furrow formation, a prolonged delay in furrow formation, or furrow regression. When multiple chromosome tips were irradiated in the same cell, the cytokinesis defects increased, suggesting a potential dose-dependent mechanism. These results suggest a mechanism in which dysfunctional telomeres inhibit mitotic exit

A quantitative systems view of the spindle assembly checkpoint

The idle assembly checkpoint acts to delay chromosome segregation until all duplicated sister chromatids are captured by the mitotic spindle. This pathway ensures that each daughter cell receives a complete copy of the genome. The high fidelity and robustness of this process have made it a subject of intense study in both the experimental and computational realms. A significant number of checkpoint proteins have been identified but how they orchestrate the communication between local spindle attachment and global cytoplasmic signalling to delay segregation is not yet understood. Here, we propose a systems view of the spindle assembly checkpoint to focus attention on the key regulators of the dynamics of this pathway. These regulators in turn have been the subject of detailed cellular measurements and computational modelling to connect molecular function to the dynamics of spindle assembly checkpoint signalling. A review of these efforts reveals the insights provided by such approaches and underscores the need for further interdisciplinary studies to reveal in full the quantitative underpinnings of this cellular control pathway

Binary Decision Diagrams on Network of Workstations

The success of all binary decision diagram (BDD) based synthesis and verification algorithms depend on the ability to efficiently manipulate very large BDDs. We present algorithms for manipulation of very large Binary Decision Diagrams (BDDs) on a network of workstations (NOW). ANOW provides a collection of main memories and disks which can be used effectively to create and manipulate very large BDDs. To make efficient use of memory resources of a NOW, while completing execution in a reasonable amount of wall clock time, extension of breadth-first technique is used to manipulate BDDs. BDDs are partitioned such that nodes for a set of consecutive variables are assigned to the same workstation. We present experimental results to demonstrate the capability of such an approach and point towards the potential impact for manipulating very large BDDs. 1 Introduction The manipulation of boolean functions is one of the most important operations in several areas of computer-aided design such a..

ESPRESSO-SIGNATURE: A New Exact Minimizer for Logic Functions

We present a new algorithm for exact two-level logic optimization. We represent a set of primes by the cube of their intersection. Therefore, the unique set of sets of primes which forms the covering problem can be implicitly represented by a set of cubeswhich forms a minimum canonical cover. We obtain the minimum canonical cover starting from any initial cover and then derive the table covering problem. The method is effective; it improves on the runtime and memory usage of ESPRESSO-EXACT by average factors of 1.78 and 1.2x respectively on the 114 of 134 benchmark examples that could be completed by ESPRESSO-EXACT. Of the remaining 20 hard problems, we solve 14 exactly. For 3 of the remaining 6 we derive the covering table but the covering problem could not be solved exactly. The remaining 3 remains intractable for the moment. This research supported by Fujitsu Research y Department of Electrical Engineering and Computer Sciences, University of California Berkeley 1 Introduction..

Phytophthora infestans associated global gene expression profile in a late blight resistant Indian potato cv. Kufri Girdhari

Abstract From the past late blight is one of the most dreaded diseases of potato worldwide. In this study, microarray-based gene expression was analysed in a late blight resistant Indian potato cultivar Kufri Girdhari upon Phytophthora infestans infection. A comprehensive transcriptional analysis was performed using cDNA microarrays, containing 70,083 ESTs (expressed sequence tag libraries) from plant leaf tissues collected at two stages: pre-inoculation (0 h, water spray as control) and post-inoculation (72 h after inoculation) by challenge inoculation of P. infestans. Microarray analysis using scatter plot revealed out of total statistically significant (P≤0.01) genes (#4622), a total of 2,344 resistance genes were up-regulated at post-inoculation stage compared to pre-inoculation. These significantly genes (#2,344) were greatly expressed at post-inoculation and contribute resistance in response to the challenge inoculation of P. infestans. Further, hierarchical clustering classified the genes (#2,344) expressions into 8 different clusters. Study revealed that molecular chaperones were found to be mainly controlling resistance mechanism in Kufri Girdhari and acted as downstream signalling pathway for defense related genes response to various mechanisms (stress/harmone/signalling genes/transporter/metabolism). The selected highly up-regulated genes were further validated for their expression in the cultivar by real-time (RT) PCR analysis. Thus study provides many candidate genes/transcripts for future characterization and functionality assay as initial starting point for research work

Standard Operating Procedures (SOP?s) Potato Tissue Culture and Micropropagation

Not Availabl

Genomics Approaches for Improving Nitrogen Use Efficiency in Potato

Increasing global food production to feed rapidly growing populations where cultivable land area is limited is a serious challenge. Moreover, increasing production costs, with high fertilizer input costs, particularly using nitrogen (N), and degrading soil health are the major concerns when enhancing the sustainable agricultural food production. Potato, being the major non-cereal food crop globally, is a heavy N fertilizer feeder crop. In the past several agricultural best management practices have been discussed regarding N management in potato crop production through the intervention of agronomy and soil science. However, unlike the advances in other model plants and cereals, the application of molecular genomics tools is lacking in potato, hence it is not possible to enhance plant genetic potential with better nitrogen use efficiency (NUE). Better N-use efficient plants can be grown with less fertilizer input and also on poor soil. This chapter highlights the application of novel genomics tools to improve NUE in potato through the discovery of novel genes and markers for applications in molecular breeding methods and gene manipulation (transgenic) techniques