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      Beans ( Phaseolus ssp.) as a Model for Understanding Crop Evolution

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          Abstract

          Here, we aim to provide a comprehensive and up-to-date overview of the most significant outcomes in the literature regarding the origin of Phaseolus genus, the geographical distribution of the wild species, the domestication process, and the wide spread out of the centers of origin. Phaseolus can be considered as a unique model for the study of crop evolution, and in particular, for an understanding of the convergent phenotypic evolution that occurred under domestication. The almost unique situation that characterizes the Phaseolus genus is that five of its ∼70 species have been domesticated (i.e., Phaseolus vulgaris, P. coccineus, P. dumosus, P. acutifolius, and P. lunatus), and in addition, for P. vulgaris and P. lunatus, the wild forms are distributed in both Mesoamerica and South America, where at least two independent and isolated episodes of domestication occurred. Thus, at least seven independent domestication events occurred, which provides the possibility to unravel the genetic basis of the domestication process not only among species of the same genus, but also between gene pools within the same species. Along with this, other interesting features makes Phaseolus crops very useful in the study of evolution, including: (i) their recent divergence, and the high level of collinearity and synteny among their genomes; (ii) their different breeding systems and life history traits, from annual and autogamous, to perennial and allogamous; and (iii) their adaptation to different environments, not only in their centers of origin, but also out of the Americas, following their introduction and wide spread through different countries. In particular for P. vulgaris this resulted in the breaking of the spatial isolation of the Mesoamerican and Andean gene pools, which allowed spontaneous hybridization, thus increasing of the possibility of novel genotypes and phenotypes. This knowledge that is associated to the genetic resources that have been conserved ex situ and in situ represents a crucial tool in the hands of researchers, to preserve and evaluate this diversity, and at the same time, to identify the genetic basis of adaptation and to develop new improved varieties to tackle the challenges of climate change, and food security and sustainability.

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          Most cited references149

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          Estimation of average heterozygosity and genetic distance from a small number of individuals.

          M Nei (1978)
          The magnitudes of the systematic biases involved in sample heterozygosity and sample genetic distances are evaluated, and formulae for obtaining unbiased estimates of average heterozygosity and genetic distance are developed. It is also shown that the number of individuals to be used for estimating average heterozygosity can be very small if a large number of loci are studied and the average heterozygosity is low. The number of individuals to be used for estimating genetic distance can also be very small if the genetic distance is large and the average heterozygosity of the two species compared is low.
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            Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection.

            We report a large-scale analysis of the patterns of genome-wide genetic variation in soybeans. We re-sequenced a total of 17 wild and 14 cultivated soybean genomes to an average of approximately ×5 depth and >90% coverage using the Illumina Genome Analyzer II platform. We compared the patterns of genetic variation between wild and cultivated soybeans and identified higher allelic diversity in wild soybeans. We identified a high level of linkage disequilibrium in the soybean genome, suggesting that marker-assisted breeding of soybean will be less challenging than map-based cloning. We report linkage disequilibrium block location and distribution, and we identified a set of 205,614 tag SNPs that may be useful for QTL mapping and association studies. The data here provide a valuable resource for the analysis of wild soybeans and to facilitate future breeding and quantitative trait analysis.
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              A single domestication for maize shown by multilocus microsatellite genotyping.

              There exists extraordinary morphological and genetic diversity among the maize landraces that have been developed by pre-Columbian cultivators. To explain this high level of diversity in maize, several authors have proposed that maize landraces were the products of multiple independent domestications from their wild relative (teosinte). We present phylogenetic analyses based on 264 individual plants, each genotyped at 99 microsatellites, that challenge the multiple-origins hypothesis. Instead, our results indicate that all maize arose from a single domestication in southern Mexico about 9,000 years ago. Our analyses also indicate that the oldest surviving maize types are those of the Mexican highlands with maize spreading from this region over the Americas along two major paths. Our phylogenetic work is consistent with a model based on the archaeological record suggesting that maize diversified in the highlands of Mexico before spreading to the lowlands. We also found only modest evidence for postdomestication gene flow from teosinte into maize.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                08 May 2017
                2017
                : 8
                : 722
                Affiliations
                [1] 1Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University Ancona, Italy
                [2] 2Department of Agriculture, University of Sassari Sassari, Italy
                [3] 3School of Agricultural, Forestry, Food and Environmental Sciences, University of Basilicata Potenza, Italy
                Author notes

                Edited by: Nicolas Rispail, Consejo Superior de Investigaciones Científicas (CSIC), Spain

                Reviewed by: Zlatko Satovic, University of Zagreb, Croatia; Klaudija Carović-Stanko, University of Zagreb, Croatia

                *Correspondence: Roberto Papa, r.papa@ 123456univpm.it

                This article was submitted to Crop Science and Horticulture, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2017.00722
                5420584
                28533789
                f9b37bea-e3c9-42af-a862-192d0c837e60
                Copyright © 2017 Bitocchi, Rau, Bellucci, Rodriguez, Murgia, Gioia, Santo, Nanni, Attene and Papa.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 31 December 2016
                : 19 April 2017
                Page count
                Figures: 7, Tables: 0, Equations: 0, References: 167, Pages: 21, Words: 0
                Categories
                Plant Science
                Review

                Plant science & Botany
                domestication,genetic diversity,adaptation,population genomics,crop evolution,convergent evolution,selection signatures

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