Statistical Genomics and Bioinformatics

Some important and interesting topics in the newly emerging disciplines of Statistical genomics andbioinformatics have been discussed briefly in relation to plants with possible references to fruit crops. This paper is therefore divided into two parts relating to the two disciplines, respectively. In the first part, mapping of quantitative trait loci (QTL), association mapping, mapping of gene expression transcripts (eQTL), marker-assisted selection, and a systems approach to quantitative genetics have been dealt with. In the second part, generation of databases, annotation, annotated sequence databases, and sequence similarity search have been described

Homozygosity in a selfed population with an arbitrary number of linked loci

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On the statistical properties of the conditional equilibrium distribution under steady flux of mutations

The statistical properties of a conditional equilibrium distribution of mutant frequency resulting from the balance between the continued production of new mutants over many generations and their loss from the population because of random drift are discussed. The revised estimates of the average number of heterozygous sites in mammals are found to be lower than those given earlier in which the underlying stochastic process is not conditioned

A general model for sample size determination for collecting germplasm

The paper develops a general model for determining the minimum sample size for collecting germplasm for genetic conservation with an overall objective of retaining at least one copy of each allele with preassigned probability. It considers sampling from a large heterogeneous 2 k-ploid population under a broad range of mating systems leading to a general formula applicable to a fairly large number of populations. It is found that the sample size decreases as ploidy levels increase, but increases with the increase in inbreeding. Under exclusive selfing the sample size is the same, irrespective of the ploidy level, when other parameters are held constant. Minimum sample sizes obtained for diploids by this general formula agree with those already reported by earlier workers. The model confirms the conservative characteristics of genetic variability of polysomic inheritance under chromosomal segregation

Radar back-scattering from non-spherical scatterers

"Definition of terms" (2 l.) laid in.Includes bibliographical references (p. 56-57).Enumeration continues through succeeding title.Part 1. Cross-sections of conducting prolates and spheroidal functions – Part 2. Cross-sections from non-spherical raindrops

Sample size for collecting germplasms - a polyploid model with mixed mating system

The present paper discusses a general expression for determining the minimum sample size (plants) for a given number of seeds or vice versa for capturing multiple allelic diversity. The model considers sampling from a large 2 k-ploid population under a broad range of mating systems. Numerous expressions/results developed for germplasm collection/regeneration for diploid populations by earlier workers can be directly deduced from our general expression by assigning appropriate values of the corresponding parameters. A seed factor which influences the plant sample size has also been isolated to aid the collectors in selecting the appropriate combination of number of plants and seeds per plant. When genotypic multiplicity of seeds is taken into consideration, a sample size of even less than 172 plants can conserve diversity of 20 alleles from 50,000 polymorphic loci with a very large probability of conservation (0.9999) in most of the cases

The Kirkhouse Trust: Successes and Challenges in Twenty Years of Supporting Independent, Contemporary Grain Legume Breeding Projects in India and African Countries

This manuscript reviews two decades of projects funded by the Kirkhouse Trust (KT), a charity registered in the UK. KT was established to improve the productivity of legume crops important in African countries and in India. KT’s requirements for support are: (1) the research must be conducted by national scientists in their home institution, either a publicly funded agricultural research institute or a university; (2) the projects need to include a molecular biology component, which to date has mostly comprised the use of molecular markers for the selection of one or more target traits in a crop improvement programme; (3) the projects funded are included in consortia, to foster the creation of scientific communities and the sharing of knowledge and breeding resources. This account relates to the key achievements and challenges, reflects on the lessons learned and outlines future research priorities

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Not AvailableMost characters of economic importance in plants and animals, and complex diseases in humans, exhibit quantitative variation, the genetics of which has been a fascinating subject of study since Mendel's discovery of the laws of inheritance. The classical genetic basis of continuous variation based on the infinitesimal model of Fisher and mostly using statistical methods has since undergone major modifications. The advent of molecular markers and their extensive mapping in several species has enabled detection of genes of metric characters known as quantitative trait loci (QTL). Modeling the high-resolution mapping of QTL by association analysis at the population level as well as at the family level has indicated that incorporation of a haplotype of a pair of single-nucleotide polymorphisms (SNPs) in the model is statistically more powerful than a single marker approach. High-throughput genotyping technology coupled with micro-arrays has allowed expression of thousand of genes with known positions in the genome and has provided an intermediate step with mRNA abundance as a sub-phenotype in the mapping of genotype onto phenotype for quantitative traits. Such gene expression profiling has been combined with linkage analysis in what is known as eQTL mapping. The first study of this kind was on budding yeast. The associated genetic basis of protein abundance using mass spectrometry has also been attempted in the same population of yeast. A comparative picture of transcript vs. protein abundance levels indicates that functionally important changes in the levels of the former are not necessarily reflected in changes in the levels of the latter. Genes and proteins must therefore be considered simultaneously to unravel the complex molecular circuitry that operates within a cell. One has to take a global perspective on life processes instead of individual components of the system. The network approach connecting data on genes, transcripts, proteins, metabolites etc. indicates the emergence of a systems quantitative genetics. It seems that the interplay of the genotype-phenotype relationship for quantitative variation is not only complex but also requires a dialectical approach for its understanding in which 'parts' and 'whole' evolve as a consequence of their relationship and the relationship itself evolves.Not Availabl