Optimizing purebred selection for crossbred performance using QTL with different degrees of dominance

A method was developed to optimize simultaneous selection for a quantitative trait with a known QTL within a male and a female line to maximize crossbred performance from a two-way cross. Strategies to maximize cumulative discounted response in crossbred performance over ten generations were derived by optimizing weights in an index of a QTL and phenotype. Strategies were compared to selection on purebred phenotype. Extra responses were limited for QTL with additive and partial dominance effects, but substantial for QTL with over-dominance, for which optimal QTL selection resulted in differential selection in male and female lines to increase the frequency of heterozygotes and polygenic responses. For over-dominant QTL, maximization of crossbred performance one generation at a time resulted in similar responses as optimization across all generations and simultaneous optimal selection in a male and female line resulted in greater response than optimal selection within a single line without crossbreeding. Results show that strategic use of information on over-dominant QTL can enhance crossbred performance without crossbred testing.     

Molecular phylogeny of Heritiera Ait on (Sterculiaceae), a tree mangrove: variations in RAPD markers and nuclear DNA content

Random amplified polymorphic DNA (RAPD) markers are used to estimate interspecific variation among mangrove and non-mangrove Heritiera fomes, H. littoralis and H. macrophylla. All the species have 2n = 38 chromosomes, with minute structural changes distinguishing the karyotype of each species. Significant variation of 4C DNA content occurs at the interspecific level. Interspecific polymorphism ranged from 14.09% between H. fomes and H. littoralis to 52.73% between H. fomes and H. macrophylla. H. macrophylla showed wide polymorphism in the RAPD marker with H. littoralis (51.23%) and H. fomes (52.73%). Two distinct RAPD products obtained from OPA-10 (1000 bp) and OPD-15 (900 bp) found characteristic molecular markers in H. macrophylla , a species from a non-mangrove habitat. H. macrophylla was more distantly related to H. fomes [genetic distance (1-F) = 0.305] than to H. littoralis [genetic distance (1-F) = 0.273]. H. littoralis was of a closer affinity to H. fomes [genetic distance (1-F) = 0.218] than to H. macrophylla.     

Unequivocal determination of sire allele origin for multiallelic microsatellites when only the sire and progeny are genotyped

The effect of a segregating economic trait locus (ETL) can be detected with the aid of a linked genetic marker, if specific alleles of each locus are in association among the individuals genotyped for the genetic marker. For dairy cattle this can be achieved by application of the ‘granddaughter design’. If only the sires and their sons are genotyped for the genetic markers, then the allele origin of sons having the same genotypes as their sires cannot be determined. Seven sires and 101 sons were genotyped for five microsatellites. The mean frequency of heterozygous sires was 77%. The mean number of alleles per locus was 8.2. Frequency of informative sons per locus ranged from 60% to 80% with a mean of 72%. With highly polymorphic microsatellites, at least 60% more grandsire families can be included in the analysis, and the number of sons assayed can be reduced by 40%, as compared to diallelic markers.     

Introducing the Multivariate Dale Model in Population‐Based Genetic Association Studies

Until recently, the most common parametric approaches to study the combined effects of several genetic polymorphisms located within a gene or in a small genomic region are, at the genotype level, logistic regressions and at the haplotype level, haplotype analyses. An alternative modeling approach, based on the case/control principle, is to regard exposures (e.g., genetic data such as derived from Single Nucleotide Polymorphisms – SNPs) as random and disease status as fixed and to use a marginal multivariate model that accounts for inter‐relationships between exposures. One such model is the multivariate Dale model. This model is based on multiple logistic regressions. That is why the model, applied in a case/control setting, leads to straightforward interpretations that are similar to those drawn in a classical logistic modeling framework. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

DNA fingerprints of dogs and cats

Human minisatellite probes consisting of tandem repeats of the 'core' sequence, a putative recombination signal in human DNA, cross-hybridize to multiple polymorphic fragments in dog and cat DNA to produce individual-specific DNA 'fingerprints'. Pedigree analysis shows that most of the DNA fragments detected in an individual are heterozygous, and that these fragments are derived from multiple dispersed autosomal loci. DNA fingerprints of cats and dogs should prove suitable for individual identification and for establishing family relationships. They are also suitable for rapid marker generation in large pedigrees and could be applied to linkage analysis in these animals.     

Method to estimate genotype probabilities at individual loci in farm livestock

Summary A Bayesian method to estimate genotype probabilities at a single locus using information on the individual and all its relatives and their mates has been developed. The method uses data over several generations, can deal with large numbers of individuals in large livestock families and allows for missing information. It can be extended to multiple alleles and can be used for autosomal or sex-linked loci. The allele frequencies and the form of expression (dominance, penetrance) must be specified. An algorithm using the method and involving an iterative procedure has been developed to calculate the genotype probabilities for practical use in livestock breeding. The method and algorithm were used to determine the accuracy of estimating genotype probabilities of sires for a female sex-limited trait, such as genetic variants of milk proteins. Data were similated and genotype probabilities estimated for 100 sires (20 replicates) with 3, 6 and 12 female offspring per sire, for different population frequencies, for additive and dominance gene action and for variable genotypic expression. Such simulation is useful in the design of testing systems for the use of information on specific genetic loci in selection.Prepared during a leave at Centre for Genetic Improvement of Livestock, Guelph, Canada     

Genetic diversity in Cucumis sativus L. assessed by variation at 18 allozyme coding loci

Summary The genetic diversity of the U.S. Cucumis sativus L. germplasm collection [757 plant introductions (PI) representing 45 countries] was assessed using 40 enzymes which represented 74 biochemical loci. Polymorphisms were observed at 18 loci (G2dh-1, Gpi-1, Gpi-2, Gr-1, Gr-2, Idh, Mdh-1, Mdh-2, Mdh-3, Mpi-2, Pepla-2, Peppap-2, Per-4, Pgd-1, Pgd-2, Pgm-1, Pgm-3, and Skdh). Two PIs (285606 and 215589) contained alleles [G2dh-1(1) and Per-4(2), respectively] which did not occur in any other PI. Other alleles which occurred in low frequencies (in < 1% of the PIs) included Gpi-1(3), Gpi-2(3), Gr-1(3), Gr-2(1), Idh(1), Mdh-1(2), Mdh-2(1), Peppap-2(1), and Pgd-1(1). Individual loci containing more than one allele in greater than 20% of the PIs included Mpi-2, Pepla-2, Pgd-2, and Pgm-1. Multivariate analyses aided in the reduction of data (principle components), depicted relationships among PIs (cluster), and identified the most discriminating enzyme loci (Pgm-1, Pepla-2, Gr-1, Pgd-2, Mpi-2, and Skdh) (classification and regression tree).Research partially supported by Asgrow, DeRuiter, Nickerson-Zwaan, Nunhems, and Sun Seed Companies; and the Graduate School, University of Wisconsin, Madison     

Occurrence of rye (Secale cereale) 350-family DNA sequences inAgropyron and otherTriticeae

Evidence is presented that in the R and P genomes (Secale cereale andAgropyron cristatum, respectively) of theTriticeae there exist closely related 350-family DNA sequences in the terminal heterochromatin. This observation is compared to the relationships between these two genomes derived from a comparison of theNor and5 S DNA loci as well as the available data on morphological characters, chromosome pairing, and isozyme studies. It is concluded that the R and P genomes are not closely related and that the common presence of very similar 350-family DNA sequences reflects the parallel amplification of this family of DNA sequences.     

Killing of Escherichia coli cells modulated by components of the stability system ParD of plasmid R1

Summary The proteins P10 and P12 have been shown to be gene products of a new stability system, ParD, of plasmid R1. It is now shown that an R1 miniplasmid, pAB112, carrying a trans-complementable amber mutation in the gene of the P10 protein, is lethal for the host in the absence of suppression. This lethal effect is suppressed in a supF background and also by deletions in pAB112 that affect the gene of the P12 protein. These data indicate that the P12 protein has a lethal effect on the host and that this effect is neutralized by the P10 protein. The possibility that the stabilization conferred by the ParD system could be due to a counterselection, mediated by P12, of cells that lose the plasmid at cell division, is discussed.     

Detection of linkage between marker loci and loci affecting quantitative traits in crosses between segregating populations

Summary By making use of pedigree information and information on marker-genotypes of the parent and F-1 individuals crossed to form an F-2 population, it is possible to carry out a linkage analysis between marker loci and loci affecting quantitative traits in a cross between segregating parent populations that are at fixation for alternative alleles at the QTL, but share the same alleles at the marker loci. For two-allele systems, depending on marker allele frequencies in the parent populations, 2–4 times as many F-2 offspring will have to be raised and scored for markers and quantitative traits in order to provide power equivalent to that obtained in a cross between fully inbred lines. Major savings in number of F-2 offspring raised can be achieved by scoring each parent pair for a large number of markers in each chromosomal region and scoring F-1 and F-2 offspring only for those markers for which the parents were homozygous for alternative alleles. For multiple allele systems, particularly when dealing with hypervariable loci, only 10%–20% additional F-2 offspring will have to be raised and scored to provide power equivalent to that obtained in a cross between inbred lines. When a resource population contains novel favorable alleles at quantitative trait loci that are not present (or rare) in a commercial population, analyses of this sort will enable the loci of interest to be identified, mapped and manipulated effectively in breeding programs.Contribution no. 2124-E, 1987 series from The Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel