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GENERAL ABSTRACT
Common bean (Phaseolus vulgaris L.; 2n = 2x = 22) is the most important edible
food legume and an interesting experimental crop species: the genome size,
estimated to be about 450 to 650 million base pairs (Mb)/haploid, is comparable
to rice (Bennet et al., 1995), generally considered to have the smallest genome
among major crop species. Nearly all loci are single copy (Vallejos et al., 1992 –
Freyre et al., 1998), and the traditionally large gene families, such as resistance
gene analogs (Rivkin et al., 1998) and protein kinases (Vallad et al., 2001), are of
moderate size. From a population genetics perspective, the major subdivisions of
wild common bean progenitors are known, the domesticated gene pools have
been defined and the process of its domestication has been studied in detail.
We have analyzed the DNA of 199 genotypes of Phaseolus with 418 AFLPs
fragments resulting from 14 primer combinations (chapter 2); accession from the
three known gene pool (Andean, Mesoamerican and ancestral) of P. vulgaris
were used as well as accessions from other species of Phaseolus, used as
outgroups. A Neighbor-Joining analysis was conducted to analyze relationship
among individual accessions using MEGA and a STRUCUTRE analysis was
used to validate the results. The other species of Phaseolus used in this study
resulted clearly distinguished from the P. vulgaris genotype and from the
ancestral gene pool. The structure of the dendrogram is in accord with the
previous knowledge about the origin and subdivision of P. vulgaris in the three
gene pools (Andean, Mesoamerican and ancestral); indeed the ancestral gene
pool also showed a clear separation from the other two derived gene pools
(Andean and Mesoamerica); a clear separation of the two form (wild,
domesticated) was also confirmed only for the Mesoamerican gene pool. The
diversity of the wild, for all markers, was always larger than that observed in the
domesticated forms. The molecular diversity of wild Mesoamerican was higher
than observed in the Andean gene pool, as well as for the domesticated form.
Introgression predominantly from the domesticated to the wild population in
Mesoamerica was also detected.
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We investigate also the genome of P. vulgaris using 19 AFLP primer
combinations in two recombinant inbreed populations, BJ and MG (chapter 3);
we then integrated our AFLP markers in two previously established genetic map
and finally we construct a consensus map, using 166 AFLP and framework
markers mapped in both populations. We detect a general low level of
segregation distortion, higher in the MG population (the double compared to the
BJ population); The consensus map obtained highlight a random distribution of
the markers between linkage group; we obtain a total length of 1,029 cM with an
average distance between markers is 6.2 cM. At a single linkage group level
however cluster of markers were also identified; thus out of 166 AFLP markers
mapped 22 (13.3%) were considered to represent 11 putative co-dominant loci.
To search for the signature of selection (chapter 4) we have used an approach
proposed by Beaumont and Nichols (1996) further developed by Beaumont and
Balding (2004) and implemented in the FDIST2 software; overall, show that a
consistent fraction of the genome of common bean appears to be under the
effect of selection during domestication; we indeed identified, considering the
effect of domestication (wild vs. domesticated) that about the 20% (P<0.01) of all
the markers were putatively under selection in both gene pools. When the
analysis was conducted to study the effect of the separation between gene pools
a lower fraction of markers showed the signature of selection: from 17.5% in the
wild to the 11.4% in the domesticated populations. The robustness of the outliers
detection was tested by excluding from the analysis loci that show a level of
polymorphism < 5% in each comparison and considering only loci mapped. We
also searched for additional evidence that the outliers detected were loci that
may have been affected by selection by comparing the map location of the outlier
identified. Most of the markers that were found to be potentially under the effects
of selection were indeed located in the proximity of previously mapped genes
and QTLs related to the domestication syndrome.
The initial steps of most domestication events generally included a population
bottleneck (called ‘‘domestication bottleneck’’); coalescent theory (Hudson, 1991)
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provides a population genetic framework for inferring past events, because it
utilizes the historical information accrued in DNA sequences. For this reason we
examined the impact of domestication bottleneck by sequencing 7 loci,
distributed in 4 chromosomes of the Phaseolus genome in 50 genotypes (chapter
5). We have assessed nucleotide diversity in wild, landrace and cultivars, and we
have used sequence information to explore the potential size and duration of a
domestication bottleneck. The wild genotypes are more diverse than the
landraces while landrace and cultivars have equivalent levels of diversity; in
addition, the diversity among Andean genotypes is reduced relative to the Middle
American genotypes.
We confirmed the higher level of diversity in the genes suspect to be under
selection compared to neutral genes and computer simulations of the
coalescence identified a reduction of 80% in the population size during the
bottleneck, and a value of the maximum duration of a bottleneck associated with
domestication of 500 generations, starting 3000 generations ago.
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