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MSTRAT: an algorithm for building germ plasm core collections by maximizing allelic or phenotypic richness.
- B. Gouesnard, T. Bataillon, G. Decoux, C. Rozale, D. Schoen, J. L. David
- Environmental ScienceThe Journal of heredity
An increasing number of germ plasm collections are being genotyped for marker loci such as allozymes, restriction fragment length polymorphisms (RFLPs), and random amplified polymorphic DNA (RAPD).
Grinding up wheat: a massive loss of nucleotide diversity since domestication.
Whether some of the genes departed from the empirical distribution of most loci are investigated, suggesting that they might have been selected during domestication or breeding, and a departure from the null model of demographic bottleneck for the hypothetical gene HgA is detected.
Direct estimation of mutation rate for 10 microsatellite loci in durum wheat, Triticum turgidum (L.) Thell. ssp durum desf.
A better knowledge of the mutation rate of microsatellites and of the factors that may influence the mutations would permit to improve their use in studies of population genetics and to be more relevant for the estimation of mutation.
Analysis of population structure in autotetraploid species.
In contrast to diploids, the correlation of genes between individuals within populations with respect to genes between populations (FST) may vary among loci due to the particular segregation patterns expected under tetrasomic inheritance and is consequently inappropriate for estimating demographic parameters in such populations.
Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria
The results suggest that the initial step in adaptive evolution—the production of novel beneficial mutants from which selection sorts—is very general, being characterized by an approximately exponential distribution with many mutations of small effect and few of large effect.
Nested core collections maximizing genetic diversity in Arabidopsis thaliana.
- H. Mckhann, C. Camilleri, D. Brunel
- Environmental Science, BiologyThe Plant journal : for cell and molecular…
- 1 April 2004
Nested core collections were generated based on DNA sequence data from a limited number of fragments evenly distributed in the genome and were shown to successfully capture the molecular diversity in other loci as well as the morphological diversity.
The making of a new pathogen: insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species.
A strong effect of natural selection is demonstrated in shaping the pathogen genomes with only ~3% of nonsynonymous mutations being effectively neutral, but forty percent of all fixed nonsynonym substitutions, on the other hand, are driven by positive selection.
Evidence for a large‐scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium
- Marie-France Ostrowski, J. David, T. Bataillon
- Environmental ScienceMolecular ecology
- 16 February 2006
Linkage disequilibrium analysis revealed that significant associations detected in the whole sample were mainly due to genetic differentiation among the inferred groups, and the implication of this finding for future association studies in A. thaliana is discussed.
Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula
- A. Branca, Timothy Paape, P. Tiffin
- BiologyProceedings of the National Academy of Sciences
- 26 September 2011
The authors' analyses reveal that M. truncatula harbors both higher diversity and less LD than soybean (Glycine max) and exhibits patterns of LD and recombination similar to Arabidopsis thaliana, and the population-scaled recombination rate is approximately one-third of the mutation rate, consistent with expectations for a species with a high selfing rate.
A comparative view of the evolution of grasses under domestication.
The history of domesticated grasses is reviewed and how domestication affected their phenotypic and genomic diversity is reviewed, and the role of mating systems in the domestication process is revisited.