A program to compare genetic differentiation statistics across loci using resampling of individuals and loci

Comparisons of genetic differentiation across populations based on different loci can provide insight into the evolutionary patterns acting on various regions of genomes. Here, we develop a program to statistically compare population genetic differentiation statistics (F(ST) or G'(ST) ) calculated from different loci. The program employs a routine that resamples either or both of individuals and loci and calculates a bootstrap confidence interval in the statistics. Resampling individuals is important when fewer than 25 individuals are sampled per population and when confidence intervals are required for individual loci. Resampling loci provides confidence intervals for sets of loci, such as a set presumed to be neutral, but can be anticonservative if fewer than 20 loci are analysed. We demonstrate the program using previously published data on the genetic differentiation at a major histocompatibility complex locus and at microsatellite loci across 10 populations of the guppy (Poecilia reticulata).     

F2breed,a New Program for Construction of Genetic Linkage Maps

This paper presents a new program F2breed for Windows and Linux operating systems, which was designed for estimation of recombination frequency between the genetic loci and construction of genetic maps based on the analysis of inheritance in a F2 population. The program implements the approach of the orientation of n points corresponding to n analyzed loci in the (n–1)-dimensional space for relative arrangement of the loci on the genetic map by consideration of various projections of this structure. The program is characterized by a convenient, intuitive interface, is easy to operate, and is suitable for working with small groups of loci (up to 100).     

A program to test linkage disequilibrium between loci in autotetraploid species

No software currently implements a test of linkage disequilibrium in autotetraploid species. We propose a program, LD4X that performs a Fisher's exact test between pairs of alleles at two loci. All combinations of alleles from two loci are treated in turn. If two alleles of a pair of loci have a nonrandom distribution, the markers are considered as linked. The program was tested on a set of microsatellite markers in synthetic alfalfa populations.     

Which genetic loci have greater population assignment power?

SUMMARY: WHICHLOCI is a program that determines the relative discriminatory power of alternate genetic loci and loci combinations for population assignment of individuals. AVAILABILITY: http://www.oregonstate.edu/dept/comes/genetics/software.htm     

A primary genetic map of markers of human chromosome 10

We have constructed a primary genetic map for human chromosome 10 from 13 polymorphic marker systems defining 11 loci, using a new gene mapping algorithm implemented in the computer program GMS. The loci form a continuous genetic map that spans approximately 116 cM in males and 170 cM in females. These loci provide regularly spaced anchor points for linkage studies, except for one interval that is 28 cM in males and 64 cM in females.     

Y-linkage and pseudoautosomal linkage.

Presently existing computer program allow for an autosomal or an X-linked mode of inheritance of loci to be analyzed for genetic linkage. They do not, however, specifically allow for more general sex-linked modes of inheritance. This study proposes methods that permit the carrying out of linkage analyses of loci following a Y-linked or a pseudoautosomal mode of inheritance.     

Epistat : a computer program for identifying and testing interactions between pairs of quantitative trait loci

 We describe a computer program, Epistat, which combines statistical methods and color-graphic displays to facilitate the analysis of interactions between pairs of quantitative trait loci (QTLs). Epistat organizes genetic-mapping data and quantitative-trait values into graphic displays which illustrate the individual effects of single loci as well as the interactions between any two loci. Keyboard commands allow the user to search the data set for individual QTLs and to test for interactions between QTLs. For a given trait, the program displays the effects of the alleles at each of two loci on the quantitative-trait value, as well as the effects of the interactions between these alleles. Loglikelihood ratios are used to compare the likelihood of explaining the effects by null, additive, or epistatic models. Examples of interactions in soybean are presented for near-infrared transmittance (NIT), seed number, and reproductive period. Epistat has been used to find numerous interactions between QTLs in soybean in which trait variation at one locus is conditional upon a specific allele at another. Received: 16 January 1996 / Accepted: 27 September 1996     

Genetic Variability Assessed by Microsatellites in a Breeding Program of Pacific White Shrimp (<Emphasis Type="Italic">Litopenaeus vannamei</Emphasis>)

Genetic diversity in a shrimp-breeding program was monitored for 2 generations by microsatellite DNA markers (Pvan1578 and Pvan1815) to establish levels of variation and proceed with a selection program. An increase in the number and frequencies of some alleles in both microsatellite loci from G₀ to G₂ was induced by foreign sire contributions. Most common alleles and high heterozygosities (around 70% in both loci) were maintained through the generations, indicating that there had not been a significant loss of genetic variability in the breeding program. However, when compared with variability in other wild and cultured stocks, the presence of 4 main alleles at both loci may be an indication that a certain reduction in variability already was present in the line used as founder stock (G₀). Therefore, it is recommended that additional genetic variability be introduced to the breeding stock by crossing it with a different line.     

Computer program for calculating recombination values from electrophoretic data

A FORTRAN computer program was developed to calculate recombination values from F2 data. The input to the program is data on codominant alleles in any number of F2 families segregating for any number of loci, the limit being applied by the computer's memory capacity. For each pair of loci, regardless of the number of segregating progenies used, one recombination value is estimated by the method of maximum likelihood and reported with its standard error. In cases in which more than one family is used for the estimation, the chi-square for the homogeneity of the data also is reported.     

豌豆种质表型性状SSR标记关联分析

关联分析是以连锁不平衡原理为基础,鉴定某一群体内表型性状与遗传标记或候选基因间关系的遗传分析方法。本研究利用59个多态性SSR标记,对192份豌豆种质进行全基因组扫描,以分析SSR位点遗传多样性,寻找其连锁不平衡位点;采用TASSEL软件的一般线性模型,利用59个SSR标记对19个形态性状进行关联分析。结果显示SSR位点间有较高的多态性和一定程度的连锁不平衡,共检测出32个SSR标记位点与14个表形性状相关联,一些SSR标记与2个或多个形态性状相关联。     

jMHC: software assistant for multilocus genotyping of gene families using next-generation amplicon sequencing

Genotyping of multilocus gene families, such as the major histocompatibility complex (MHC), may be challenging because of problems with assigning alleles to loci and copy number variation among individuals. Simultaneous amplification and genotyping of multiple loci may be necessary, and in such cases, next-generation deep amplicon sequencing offers a great promise as a genotyping method of choice. Here, we describe jMHC, a computer program developed for analysing and assisting in the visualization of deep amplicon sequencing data. Software operates on FASTA files; therefore, output from any sequencing technology may be used. jMHC was designed specifically for MHC studies but it may be useful for analysing amplicons derived from other multigene families or for genotyping other polymorphic systems. The program is written in Java with user-friendly graphical interface (GUI) and can be run on Microsoft Windows, Linux OS and Mac OS.     

Accounting for epistasis in linkage analysis of general pedigrees

Complex traits are generally believed to be influenced by multiple loci. Identification of loci involved in complex traits is more difficult for interacting than for additive loci. Here we describe an extension of the program lm_twoqtl in the package MORGAN to handle two quantitative trait loci (QTLs) with gene-gene interaction. We investigate whether parametric linkage analysis that accounts for such epistasis improves prospects for linkage detection and accuracy of localization of QTLs. Through use of simulated data we show that analysis that accounts for epistasis provides higher lod scores and better localization than does analysis without epistasis. In addition, we demonstrate that the difference between lod scores in the presence vs. absence of use of an interaction model in analysis is greater in extended than in nuclear pedigrees.     

构建分子标记连锁图谱的图论构图方法

结合统计学、遗传学和图论原理,建立了一种新的分子标记连锁图谱构建的方法,即图论构图法．应用这种方法,从７７个家蚕ＲＡＰＤ标记位点中构建了７个标记位点的两个连锁群．与ＭＡＰＭＡＲＫＥＲ程序所构建的结果相比表明,图论构图法具有更为可靠的构图效果．     

GIbPSs: a toolkit for fast and accurate analyses of genotyping‐by‐sequencing data without a reference genome

Genotyping‐by‐sequencing (GBS) and related methods are increasingly used for studies of non‐model organisms from population genetic to phylogenetic scales. We present GIbPSs, a new genotyping toolkit for the analysis of data from various protocols such as RAD, double‐digest RAD, GBS, and two‐enzyme GBS without a reference genome. GIbPSs can handle paired‐end GBS data and is able to assign reads from both strands of a restriction fragment to the same locus. GIbPSs is most suitable for population genetic and phylogeographic analyses. It avoids genotyping errors due to indel variation by identifying and discarding affected loci. GIbPSs creates a genotype database that offers rich functionality for data filtering and export in numerous formats. We performed comparative analyses of simulated and real GBS data with GIbPSs and another program, pyRAD. This program accounts for indel variation by aligning homologous sequences. GIbPSs performed better than pyRAD in several aspects. It required much less computation time and displayed higher genotyping accuracy. GIbPSs retained smaller numbers of loci overall in analyses of real GBS data. It nevertheless delivered more complete genotype matrices with greater locus overlap between individuals and greater numbers of loci sampled in all individuals.     

Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach.

A new method for the estimation of migration rates and effective population sizes is described. It uses a maximum-likelihood framework based on coalescence theory. The parameters are estimated by Metropolis-Hastings importance sampling. In a two-population model this method estimates four parameters: the effective population size and the immigration rate for each population relative to the mutation rate. Summarizing over loci can be done by assuming either that the mutation rate is the same for all loci or that the mutation rates are gamma distributed among loci but the same for all sites of a locus. The estimates are as good as or better than those from an optimized FST-based measure. The program is available on the World Wide Web at http://evolution.genetics. washington.edu/lamarc.html/.     

ldne: a program for estimating effective population size from data on linkage disequilibrium

ldne is a program with a Visual Basic interface that implements a recently developed bias correction for estimates of effective population size (N(e) ) based on linkage disequilibrium data. The program reads genotypic data in standard formats and can accommodate an arbitrary number of samples, individuals, loci, and alleles, as well as two mating systems: random and lifetime monogamy. ldne calculates separate estimates using different criteria for excluding rare alleles, which facilitates evaluation of data for highly polymorphic markers such as microsatellites. The program also introduces a jackknife method for obtaining confidence intervals that appears to perform better than parametric methods currently in use.     

miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data

MicroRNAs (miRs) have been broadly implicated in animal development and disease. We developed a novel computational strategy for the systematic, whole-genome identification of miRs from high throughput sequencing information. This method, miRTRAP, incorporates the mechanisms of miR biogenesis and includes additional criteria regarding the prevalence and quality of small RNAs arising from the antisense strand and neighboring loci. This program was applied to the simple chordate Ciona intestinalis and identified nearly 400 putative miR loci.     

A recoding scheme for X-linked and pseudoautosomal loci to be used with computer programs for autosomal LOD-score analysis

We present a recoding scheme that allows for a parametric multipoint X-chromosomal linkage analysis of dichotomous traits in the context of a computer program for autosomes that can use trait models with imprinting. Furthermore, with this scheme, it is possible to perform a joint multipoint analysis of X-linked and pseudoautosomal loci. It is required that (1) the marker genotypes of all female nonfounders are available and that (2) there are no male nonfounders who have daughters in the pedigree. The second requirement does not apply if the trait locus is pseudoautosomal. The X-linked marker loci are recorded by adding a dummy allele to the males' hemizygous genotypes. For modelling an X-linked trait locus, five different liability classes are defined, in conjunction with a paternal imprinting model for male nonfounders. The formulation aims at the mapping of a diallelic trait locus relative to an arbitrary number of codominant markers with known genetic distances, in cases where a program for a genuine X-chromosomal analysis is not available.     

The Inheritance of Enzyme Variants for Tyrosine Aminotransferase, Nadp-Dependent Malate Dehydrogenase, Nadp-Dependent Isocitrate Dehydrogenase, and Tetrazolium Oxidase in TETRAHYMENA PYRIFORMIS, Syngen 1

The isozymic patterns of tyrosine aminotransferase, NADP malate dehydrogenase, NADP isocitrate dehydrogenase, and tetrazolium oxidase were examined by starch-gel electrophoresis in Tetrahymena pyriformis, syngen 1. The genetics of the alleles controlling these enzymes was studied through a breeding program. Each enzyme locus was shown to assort vegetatively, as do other loci in this organism. A detailed analysis of the assortment process for the tyrosine aminotransferase locus indicated that the rate of stabilization of heterozygotes into pure types was essentially identical to previously-reported rates for other loci.     

PERMANENT GENETIC RESOURCES: Characterization of microsatellite markers for the almendro (Dipteryx panamensis), a tetraploid rainforest tree

The almendro (Dipteryx panamensis, Fabaceae) is a tetraploid tree native to the Atlantic lowland rainforests of Central America. We present nine microsatellite primer pairs amplified in three multiplexed reactions for 549 individuals from four sites in Costa Rica. All loci were polymorphic, ranging from three to 13 alleles per locus. Expected heterozygosity was estimated with the program tetrasat, and ranged from 0.21 to 0.74 across loci. These markers will be used for estimating pollen dispersal, seed dispersal, genetic structure and genetic diversity in fragmented landscapes.