Molecular polymorphism related to flowering trait variation in a Phaseolus vulgaris L. collection

Raggi, Lorenzo; Tissi, Carlo; Mazzucato, Andrea; Negri, Valeria

doi:10.1016/j.plantsci.2013.11.001

Cited by 12 publications

(15 citation statements)

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“…Therefore, we decided to use our germplasm collection for a medium-resolution association study, whose results might be integrated by further investigations taking into account larger samples and replicated trials. To reduce the amount of false-positives, we used a weighted mixed linear model (MLM) taking into account kinship and genetic structure (K + Q), which was proven useful in GWAS [24–27]. Moreover, to increase statistical stringency, we considered loci with high minimum allele frequency (>10%) and used the Bonferroni correction.…”

Section: Discussionmentioning

confidence: 99%

Genotyping-by-sequencing of a melon (Cucumis melo L.) germplasm collection from a secondary center of diversity highlights patterns of genetic variation and genomic features of different gene pools

et al. 2017

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BackgroundMelon (Cucumis melo L.) is one of the most important horticultural species, which includes several taxonomic groups. With the advent of next-generation sequencing, single nucleotide polymorphism (SNP) markers are widely used in the study of genetic diversity and genomics.ResultsWe report the first successful application of genotyping-by-sequencing (GBS) technology in melon. We detected 25,422 SNPs by the analysis of 72 accessions collected in Apulia, a secondary centre of diversity in Southern Italy. Analyses of genetic structure, principal components, and hierarchical clustering support the identification of three distinct subpopulations. One of them includes accessions known with the folk name of ‘carosello’, referable to the chate taxonomic group. This is one of the oldest domesticated forms of C. melo, once widespread in Europe and now exposed to the risk of genetic erosion. The second subpopulation contains landraces of ‘barattiere’, a regional vegetable production that was never characterized at the DNA level and we show was erroneously considered another form of chate melon. The third subpopulation includes genotypes of winter melon (C. melo var. inodorus). Genetic analysis within each subpopulation revealed patterns of diversity associated with fruit phenotype and geographical origin. We used SNP data to describe, for each subpopulation, the average linkage disequilibrium (LD) decay, and to highlight genomic regions possibly resulting from directional selection and associated with phenotypic variation.ConclusionsWe used GBS to characterize patterns of genetic diversity and genomic features within C. melo. We provide useful information to preserve endangered gene pools and to guide the use of germplasm in breeding. Finally, our findings lay a foundation for molecular breeding approaches and the identification of genes underlying phenotypic traits.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3429-0) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Genotyping-by-sequencing of a melon (Cucumis melo L.) germplasm collection from a secondary center of diversity highlights patterns of genetic variation and genomic features of different gene pools

et al. 2017

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“…The PCR cycle was adapted from Raggi and co-workers [62] and consisted of the following steps: 94 °C for 4 min, followed by 12 cycles of 94 °C for 30 s, x °C for 30 s, 72 °C for 30 s, 25 cycles of 94 °C for 10 s, x − 1 °C for 15 s, 72 °C for 20 s and 20 min at 72 °C for the final extension, where x is the annealing temperature (Table S5). …”

Section: Methodsmentioning

confidence: 99%

Short-Term Local Adaptation of Historical Common Bean (Phaseolus vulgaris L.) Varieties and Implications for In Situ Management of Bean Diversity

Klaedtke

Caproni

Klauck

et al. 2017

IJMS

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Recognizing both the stakes of traditional European common bean diversity and the role farmers’ and gardeners’ networks play in maintaining this diversity, the present study examines the role that local adaptation plays for the management of common bean diversity in situ. To the purpose, four historical bean varieties and one modern control were multiplied on two organic farms for three growing seasons. The fifteen resulting populations, the initial ones and two populations of each variety obtained after the three years of multiplication, were then grown in a common garden. Twenty-two Simple Sequence Repeat (SSR) markers and 13 phenotypic traits were assessed. In total, 68.2% of tested markers were polymorphic and a total of 66 different alleles were identified. FST analysis showed that the genetic composition of two varieties multiplied in different environments changed. At the phenotypic level, differences were observed in flowering date and leaf length. Results indicate that three years of multiplication suffice for local adaptation to occur. The spatial dynamics of genetic and phenotypic bean diversity imply that the maintenance of diversity should be considered at the scale of the network, rather than individual farms and gardens. The microevolution of bean populations within networks of gardens and farms emerges as a research perspective.

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“…A multidisciplinary approach is planned (i.e., genomics, population/quantitative genetics, biochemistry, plant physiology) to unraveling the genetic bases of adaptation of these crops in new agro-ecological environments. The methods here rely on previous studies that have demonstrated the effectiveness of various analysis, such as the application of: (i) population genomics, to test for signatures of selection (e.g., Bellucci et al, 2014a); (ii) evolutionary metabolomics, which appear to be a very powerful approach to characterize molecular phenotypic changes due to domestication, and to identify traits under selection in wheat (Beleggia et al, 2016); (iii) association mapping studies of complex traits, such as flowering time (Raggi et al, 2014); (iv) analysis of signatures of selection by searching for ‘unusually high’ correlations between SNPs and environmental variables at the continental scale, as successfully applied by Rodriguez et al (2016) for wild common bean from Mexico.…”

Section: Dissemination Of Phaseolus Crop Species Outside Their Centermentioning

confidence: 99%

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

et al. 2017

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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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Molecular polymorphism related to flowering trait variation in a Phaseolus vulgaris L. collection

Cited by 12 publications

References 75 publications

Genotyping-by-sequencing of a melon (Cucumis melo L.) germplasm collection from a secondary center of diversity highlights patterns of genetic variation and genomic features of different gene pools

Genotyping-by-sequencing of a melon (Cucumis melo L.) germplasm collection from a secondary center of diversity highlights patterns of genetic variation and genomic features of different gene pools

Short-Term Local Adaptation of Historical Common Bean (Phaseolus vulgaris L.) Varieties and Implications for In Situ Management of Bean Diversity

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

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