Siol M, Prosperi JM, Bonnin I, Ronfort J.. How multilocus genotypic pattern helps to understand the history of selfing populations: a case study in Medicago truncatula. Heredity 100: 517-525

UMR 1097 Diversité et Adaptations des Plantes Cultivées, INRA Montpellier, Domaine de Melgueil, Mauguio, France.
Heredity (Impact Factor: 3.81). 06/2008; 100(5):517-25. DOI: 10.1038/hdy.2008.5
Source: PubMed


The occurrence of populations exhibiting high genetic diversity in predominantly selfing species remains a puzzling question, since under regular selfing genetic diversity is expected to be depleted at a faster rate than under outcrossing. Fine-scale population genetics approaches may help to answer this question. Here we study a natural population of the legume Medicago truncatula in which both the fine-scale spatial structure and the selfing rate are characterized using three different methods. Selfing rate estimates were very high ( approximately 99%) irrespective of the method used. A clear pattern of isolation by distance reflecting small seed dispersal distances was detected. Combining genotypic data over loci, we could define 34 multilocus genotypes. Among those, six highly inbred genotypes (lines) represented more than 75% of the individuals studied and harboured all the allelic variation present in the population. We also detected a large set of multilocus genotypes resembling recombinant inbred lines between the most frequent lines occurring in the population. This finding illustrates the importance of rare recombination in redistributing available allelic diversity into new genotypic combinations. This study shows how multilocus and fine-scale spatial analyses may help to understand the population history of self-fertilizing species, especially to make inferences about the relative role of foundation/migration and recombination events in such populations.

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    • "The > 70% of reads calling a variant means that no heterozygous sites were identified within individuals. This should have minor effects given high selfing rates in natural populations (> 95%; Bonnin et al., 2001; Siol et al., 2008) and ≥ 3 generations of selfing before DNA extraction. "
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    • "The >70% of reads calling a variant means that there are no heterozygous sites within individuals. This should have minor effects given high selfing rates in natural populations (>95%) [45], [46] and ≥3 generations of selfing prior to DNA extraction. Positions with >1000 (deep 26) or >500 unique reads for shallow accessions were excluded to prevent variant calling SNPs in repetitive regions that appear only once in the reference genome. "
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    • "Then, for only the MLGs shared by multiple populations, the number of each MLG was compiled per population. To gain insight into the number of independent origins of glyphosate resistance, MLGs in highly resistant populations were classified as nonrecombinant or recombinant with respect to other MLGs within the populations (Siol et al. 2008). Population structure was further investigated using the model-based Bayesian clustering program InStruct (Gao et al. 2007). "
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