Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data

Mamidi, Sujan; Rossi, Mônica Lanzoni; Annam, Deepti; Moghaddam, Samira Mafi; Lee, Rian; Papa, Roberto; McClean, Phillip E.

doi:10.1071/fp11124

Cited by 81 publications

(84 citation statements)

References 112 publications

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“…Multiple domestication processes have been reported for the Phaseolus genus (Gepts and Debouck, 1991), and the domestication of common bean (Phaseolus vulgaris) occurred independently in different gene pools approximately 8000 years ago (Mamidi et al, 2011;Serrano-Serrano et al, 2012). According to the Food and Agriculture Organization (FAO, 2012), dry bean is grown in 126 countries, and the estimated global production of this legume was 25 million tons in 2012.…”

Section: Introductionmentioning

confidence: 99%

Discrimination of common bean cultivars using multiplexed microsatellite markers

Cardoso¹,

Brondani²,

Menezes³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Analysis of DNA polymorphisms allows for the genetic identification and precise discrimination of species with a narrow genetic base such as common bean. The primary objectives of the present study were to molecularly characterize commercial common bean varieties developed at various research institutions using microsatellite markers and to determine the degree of genetic diversity among the bean varieties analyzed. Fifty cultivars representing 12 grain classes and 64 genitors, i.e., accessions used to develop these cultivars, were characterized. Based on an analysis of 24 simple sequence repeats, the estimates for the average number of alleles and genetic diversity were 8.29 and 0.646, respectively. The combined probability of identity was estimated at 7.05 x 10 -17 , indicating a high individual discriminatory power. Thirtytwo percent of the cultivars exhibited heterogeneity for multiple loci that reflected either homozygosity for different alleles of a given locus in different individuals or heterozygosity for the locus. The average 1964-1978 (2014) Molecular characterization of cultivated common bean genetic diversity for the groups of cultivars and genitors was 0.605 and 0.660, respectively, with no genetic differentiation (F ST ) between these groups. Although similar estimates of expected heterozygosity were observed when the cultivars were grouped by release date, a greater number of private alleles was observed in the most recent cultivars. The genetic differentiation among cultivars originating from different institutions was not different from zero (F ST = 0.01). The molecular profile database derived from these analyses may increase the statistical power of genetic estimates and may be incorporated into breeding programs for common bean. Furthermore, the profiles obtained for the different cultivars may be used as molecular descriptors to complement traditional descriptors used in distinctiveness, uniformity and stability tests, thereby improving the traceability of samples and their derivatives and helping to protect the intellectual property rights of breeders.

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Section: Introductionmentioning

confidence: 99%

Discrimination of common bean cultivars using multiplexed microsatellite markers

Cardoso¹,

Brondani²,

Menezes³

et al. 2014

Genet. Mol. Res.

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“…Within the Mesoamerican gene pool, random amplified polymorphic DNA (59) and chloroplast data (60) have been interpreted as indicating independent domestication events. However, using coalescent simulation and ABC, Mamidi et al (57) showed that single domestication episodes for both the Mesoamerican and Andean gene pools, with strong bidirectional gene flow between domesticated and wild species, provided the best fit to data on 13 loci.…”

Section: When Where and In How Many Geographic Locations Was A Givenmentioning

confidence: 99%

“…The extraordinary phenotypic range of the common bean (Phaseolus vulgaris) has made it a particularly interesting target for domestication research (57). A range of genetic studies (e.g., ref.…”

Section: When Where and In How Many Geographic Locations Was A Givenmentioning

confidence: 99%

Storytelling and story testing in domestication

Gerbault¹,

Allaby

Boivin

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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The domestication of plants and animals marks one of the most significant transitions in human, and indeed global, history. Traditionally, study of the domestication process was the exclusive domain of archaeologists and agricultural scientists; today it is an increasingly multidisciplinary enterprise that has come to involve the skills of evolutionary biologists and geneticists. Although the application of new information sources and methodologies has dramatically transformed our ability to study and understand domestication, it has also generated increasingly large and complex datasets, the interpretation of which is not straightforward. In particular, challenges of equifinality, evolutionary variance, and emergence of unexpected or counter-intuitive patterns all face researchers attempting to infer past processes directly from patterns in data. We argue that explicit modeling approaches, drawing upon emerging methodologies in statistics and population genetics, provide a powerful means of addressing these limitations. Modeling also offers an approach to analyzing datasets that avoids conclusions steered by implicit biases, and makes possible the formal integration of different data types. Here we outline some of the modeling approaches most relevant to current problems in domestication research, and demonstrate the ways in which simulation modeling is beginning to reshape our understanding of the domestication process.T he emergence of agriculture beginning some 10,000 y ago marked more than a change in human patterns of subsistence. The beginnings of food production ushered in an era of radically new relationships between humans and other species, dramatic new evolutionary pressures, and fundamental transformations to the earth's biosphere. The evolutionary process of plant and animal domestication by humans led to morphological, physiological, behavioral, and genetic differentiation of a wide range of species from their wild progenitors (1, 2). The selection pressures that were placed on such species continue today, sometimes through direct genetic modification, and both the processes and their outcomes are accordingly of significant broader interest. Domestication is also part of a cultural evolutionary process (3, 4), and some human genes have evolved in response to cultural innovations (5-8), much as the genes of domesticated species have changed under the impact of human artificial selection. The study of domestication today is a multidisciplinary enterprise in which archaeologists and agricultural scientists have been joined by evolutionary biologists and population geneticists (2, 9).At least five major sets of questions tend to reoccur in the domestication literature. The first three are demographic: (i) When, where, and in how many geographic locations was a given species domesticated? (ii) What were the dispersal routes from the original domestication centers? (iii) To what extent did hybridization between domesticates and local wild relatives occur? The remaining questions relate to adaptation: (i...

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“…Common beans have exceptionally wide genetic variation among four gene pools and many races (Tohme et al 1996;Beebe et al 2001) two of which form the focus of sequencing work performed by Mamidi et al (2011). Reflecting this diversity, the CIAT maintains a primary gene bank with more than 36 000 accessions providing raw material for improving the crop using traditional breeding and molecular marker approaches.…”

Section: The Workhopmentioning

confidence: 99%

“…Mamidi et al (2011) have used multilocus sequence data to test models for domestication of common beans. Their data support a single domestication event in each of the MesoAmerican and Andean gene pools, and provide needed information for more precise association mapping and selection.…”

Section: The Workhopmentioning

confidence: 99%

Why not beans?

Cavalieri

Merchant

Volkenburgh

2011

Functional Plant Biol.

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Abstract. Changes in climate and urbanisation rapidly affecting human livelihood are particularly threatening to developing nations in tropical regions. Food production crises have focused the global development agenda on agricultural research, a proven approach for increasing crop yield. A few crops benefit from private investment, but improvement of most crops will rely on limited public funding that must be deployed strategically, pushing forward both proven approaches and new ideas. Why not invest in beans? More than 300 million people rely on this crop, considered to be the most important grain legume for human consumption. Yet the yield of beans, especially in poor regions or marginal soils, is reduced by abiotic stresses such as phosphorus deficiency, aluminum toxicity and especially drought. Is it possible to assemble resources, including genetic diversity in beans, breeding expertise, genomic information and tools, and physiological insight to generate rapid progress in developing new lines of beans more tolerant to abiotic stress? A workshop to address this question was held in November 2010 at the International Center for Tropical Agriculture (CIAT) in Colombia. The resulting 'call to action' is presented in this issue which also includes research papers focused on tolerance of beans to stress.

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Investigation of the domestication of common bean (Phaseolus vulgaris) using multilocus sequence data

Cited by 81 publications

References 112 publications

Discrimination of common bean cultivars using multiplexed microsatellite markers

Discrimination of common bean cultivars using multiplexed microsatellite markers

Storytelling and story testing in domestication

Why not beans?

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