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Glenn J Bryan - One of the best experts on this subject based on the ideXlab platform.
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a single domestication for potato based on multilocus amplified fragment length polymorphism genotyping
Proceedings of the National Academy of Sciences of the United States of America, 2005Co-Authors: David M Spooner, Karen Mclean, Gavin Ramsay, Robbie Waugh, Glenn J BryanAbstract:The cultivated potato, Solanum tuberosum, ultimately traces its origin to Andean and Chilean Landraces developed by pre-Colombian cultivators. These Andean Landraces exhibit tremendous morphological and genetic diversity, and are distributed throughout the Andes, from western Venezuela to northern Argentina, and in southern Chile. The wild species progenitors of these Landraces have long been in dispute, but all hypotheses center on a group of ≈20 morphologically very similar tuber-bearing (Solanum section Petota) wild taxa referred to as the S. brevicaule complex, distributed from central Peru to northern Argentina. We present phylogenetic analyses based on the representative cladistic diversity of 362 individual wild (261) and Landrace (98) members of potato (all tuber-bearing) and three outgroup non-tuber-bearing members of Solanum section Etuberosum, genotyped with 438 robust amplified fragment length polymorphisms. Our analyses are consistent with a hypothesis of a “northern” (Peru) and “southern” (Bolivia and Argentina) cladistic split for members of the S. brevicaule complex, and with the need for considerable reduction of species in the complex. In contrast to all prior hypotheses, our data support a monophyletic origin of the Landrace cultivars from the northern component of this complex in Peru, rather than from multiple independent origins from various northern and southern members.
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A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping
Proceedings of the National Academy of Sciences of the United States of America, 2005Co-Authors: David M Spooner, Karen Mclean, Gavin Ramsay, Robbie Waugh, Glenn J BryanAbstract:The cultivated potato, Solanum tuberosum, ultimately traces its origin to Andean and Chilean Landraces developed by pre-Colombian cultivators. These Andean Landraces exhibit tremendous morphological and genetic diversity, and are distributed throughout the Andes, from western Venezuela to northern Argentina, and in southern Chile. The wild species progenitors of these Landraces have long been in dispute, but all hypotheses center on a group of approximate to 20 morphologically very similar tuber-bearing (Solanum section Petota) wild taxa referred to as the S. brevicaule complex, distributed from central Peru to northern Argentina. We present phylogenetic analyses based on the representative cladistic diversity of 362 individual wild (261) and Landrace (98) members of potato (all tuber-bearing) and three outgroup non-tuber-bearing members of Solanum section Etuberosum, genotyped with 438 robust amplified fragment length polymorphisms. Our analyses are consistent with a hypothesis of a "northern" (Peru) and "southern" (Bolivia and Argentina) cladistic split for members of the S. brevicaule complex, and with the need for considerable reduction of species in the complex. In contrast to all prior hypotheses, our data support a monophyletic origin of the Landrace cultivars from the northern component of this complex in Peru, rather than from multiple independent origins from various northern and southern members.
Kristin L Mercer - One of the best experts on this subject based on the ideXlab platform.
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genome wide genotyping of a novel mexican chile pepper collection illuminates the history of Landrace differentiation after capsicum annuum l domestication
Evolutionary Applications, 2019Co-Authors: Kristin L Mercer, Nathan Taitano, Vivian Bernau, Lev Jardonbarbolla, Brian M Leckie, Michael Mazourek, Leah K Mchale, Andrew P Michel, David J BaumlerAbstract:: Studies of genetic diversity among phenotypically distinct crop Landraces improve our understanding of fruit evolution and genome structure under domestication. Chile peppers (Capsicum spp. L.) are economically valuable and culturally important species, and extensive phenotypic variation among Landraces exists in southern Mexico, a center of C. annuum diversity. We collected 103 chile pepper seed accessions from 22 named Landraces across 27 locations in southern Mexico. We genotyped these accessions with genotyping by sequencing (GBS), yielding 32,623 filtered single-nucleotide polymorphisms. Afterward, we genotyped 32 additional C. annuum accessions from a global collection for comparison to the Mexican collection. Within the Mexican collection, genetic assignment analyses showed clear genetic differentiation between Landraces and clarified the unique nature of the Tusta Landrace. Further clustering analyses indicated that the largest fresh-use Chile de Agua and dry-use Costeno Landraces were part of separate clades, indicating that these two Landraces likely represent distinct populations. The global accessions showed considerable admixture and limited clustering, which may be due to the collapse of use-type divisions outside of Central America. The separation of the Mexican Landraces in part by fruit morphology related to use highlights the relevance of this use-type morphological diversity for plant breeders and the utility of fruit development variation for evolutionary biologists.
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Differentiated transcriptional signatures in the maize Landraces of Chiapas, Mexico
BMC Genomics, 2017Co-Authors: Matthew A. Kost, Eric Stockinger, Hugo R. Perales, Sarath Wijeratne, Asela J Wijeratne, Kristin L MercerAbstract:BackgroundLandrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and biotic change. Understanding this rich genetic resource is imperative especially since diversity can provide agricultural security as climate continues to shift.ResultsHere we employ RNA sequencing (RNA-seq) to understand the role that conditions that vary across a landscape may have played in shaping genetic diversity in the maize Landraces of Chiapas, Mexico. We collected Landraces from three distinct elevational zones and planted them in a midland common garden. Early season leaf tissue was collected for RNA-seq and we performed weighted gene co-expression network analysis (WGCNA). We then used association analysis between Landrace co-expression module expression values and environmental parameters of Landrace origin to elucidate genes and gene networks potentially shaped by environmental factors along our study gradient. Elevation of Landrace origin affected the transcriptome profiles. Two co-expression modules were highly correlated with temperature parameters of Landrace origin and queries into their ‘hub’ genes suggested that temperature may have led to differentiation among Landraces in hormone biosynthesis/signaling and abiotic and biotic stress responses. We identified several ‘hub’ transcription factors and kinases as candidates for the regulation of these responses.ConclusionsThese findings indicate that natural selection may influence the transcriptomes of crop Landraces along an elevational gradient in a major diversity center, and provide a foundation for exploring the genetic basis of local adaptation. While we cannot rule out the role of neutral evolutionary forces in the patterns we have identified, combining whole transcriptome sequencing technologies, established bioinformatics techniques, and common garden experimentation can powerfully elucidate structure of adaptive diversity across a varied landscape. Ultimately, gaining such understanding can facilitate the conservation and strategic utilization of crop genetic diversity in a time of climate change.
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Differentiated transcriptional signatures in the maize Landraces of Chiapas, Mexico
BMC Genomics, 2017Co-Authors: Matthew A. Kost, Eric Stockinger, Hugo R. Perales, Sarath Wijeratne, Asela J Wijeratne, Kristin L MercerAbstract:Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and biotic change. Understanding this rich genetic resource is imperative especially since diversity can provide agricultural security as climate continues to shift. Here we employ RNA sequencing (RNA-seq) to understand the role that conditions that vary across a landscape may have played in shaping genetic diversity in the maize Landraces of Chiapas, Mexico. We collected Landraces from three distinct elevational zones and planted them in a midland common garden. Early season leaf tissue was collected for RNA-seq and we performed weighted gene co-expression network analysis (WGCNA). We then used association analysis between Landrace co-expression module expression values and environmental parameters of Landrace origin to elucidate genes and gene networks potentially shaped by environmental factors along our study gradient. Elevation of Landrace origin affected the transcriptome profiles. Two co-expression modules were highly correlated with temperature parameters of Landrace origin and queries into their ‘hub’ genes suggested that temperature may have led to differentiation among Landraces in hormone biosynthesis/signaling and abiotic and biotic stress responses. We identified several ‘hub’ transcription factors and kinases as candidates for the regulation of these responses. These findings indicate that natural selection may influence the transcriptomes of crop Landraces along an elevational gradient in a major diversity center, and provide a foundation for exploring the genetic basis of local adaptation. While we cannot rule out the role of neutral evolutionary forces in the patterns we have identified, combining whole transcriptome sequencing technologies, established bioinformatics techniques, and common garden experimentation can powerfully elucidate structure of adaptive diversity across a varied landscape. Ultimately, gaining such understanding can facilitate the conservation and strategic utilization of crop genetic diversity in a time of climate change.
David M Spooner - One of the best experts on this subject based on the ideXlab platform.
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a single domestication for potato based on multilocus amplified fragment length polymorphism genotyping
Proceedings of the National Academy of Sciences of the United States of America, 2005Co-Authors: David M Spooner, Karen Mclean, Gavin Ramsay, Robbie Waugh, Glenn J BryanAbstract:The cultivated potato, Solanum tuberosum, ultimately traces its origin to Andean and Chilean Landraces developed by pre-Colombian cultivators. These Andean Landraces exhibit tremendous morphological and genetic diversity, and are distributed throughout the Andes, from western Venezuela to northern Argentina, and in southern Chile. The wild species progenitors of these Landraces have long been in dispute, but all hypotheses center on a group of ≈20 morphologically very similar tuber-bearing (Solanum section Petota) wild taxa referred to as the S. brevicaule complex, distributed from central Peru to northern Argentina. We present phylogenetic analyses based on the representative cladistic diversity of 362 individual wild (261) and Landrace (98) members of potato (all tuber-bearing) and three outgroup non-tuber-bearing members of Solanum section Etuberosum, genotyped with 438 robust amplified fragment length polymorphisms. Our analyses are consistent with a hypothesis of a “northern” (Peru) and “southern” (Bolivia and Argentina) cladistic split for members of the S. brevicaule complex, and with the need for considerable reduction of species in the complex. In contrast to all prior hypotheses, our data support a monophyletic origin of the Landrace cultivars from the northern component of this complex in Peru, rather than from multiple independent origins from various northern and southern members.
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A single domestication for potato based on multilocus amplified fragment length polymorphism genotyping
Proceedings of the National Academy of Sciences of the United States of America, 2005Co-Authors: David M Spooner, Karen Mclean, Gavin Ramsay, Robbie Waugh, Glenn J BryanAbstract:The cultivated potato, Solanum tuberosum, ultimately traces its origin to Andean and Chilean Landraces developed by pre-Colombian cultivators. These Andean Landraces exhibit tremendous morphological and genetic diversity, and are distributed throughout the Andes, from western Venezuela to northern Argentina, and in southern Chile. The wild species progenitors of these Landraces have long been in dispute, but all hypotheses center on a group of approximate to 20 morphologically very similar tuber-bearing (Solanum section Petota) wild taxa referred to as the S. brevicaule complex, distributed from central Peru to northern Argentina. We present phylogenetic analyses based on the representative cladistic diversity of 362 individual wild (261) and Landrace (98) members of potato (all tuber-bearing) and three outgroup non-tuber-bearing members of Solanum section Etuberosum, genotyped with 438 robust amplified fragment length polymorphisms. Our analyses are consistent with a hypothesis of a "northern" (Peru) and "southern" (Bolivia and Argentina) cladistic split for members of the S. brevicaule complex, and with the need for considerable reduction of species in the complex. In contrast to all prior hypotheses, our data support a monophyletic origin of the Landrace cultivars from the northern component of this complex in Peru, rather than from multiple independent origins from various northern and southern members.
Jenny Hagenblad - One of the best experts on this subject based on the ideXlab platform.
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nineteenth century seeds reveal the population genetics of Landrace barley hordeum vulgare
Molecular Biology and Evolution, 2010Co-Authors: Matti W Leino, Jenny HagenbladAbstract:Barley (Hordeum vulgare) is a major crop, grown worldwide and in a wide range of climatic conditions. Despite its importance as a crop species, little is known about the population genetics of barley and the effects of bottlenecks, adaptation, and gene flow on genetic diversity within and between Landrace populations. In areas with highly developed agriculture, such as Northern Europe, these types of genetic studies are hampered by lack of Landraces preserved in situ or ex situ. Here, we report a genetic study of Swedish Landrace barley using 113-year-old seed samples. The results demonstrate differing levels of variation with some latitudinal effect. We also detect clear population differentiation and population structure within Sweden into a southern and a northern cluster. These results possibly reflect different introduction routes of barley into Sweden. We thus show that the study of historic material can be an important alternative for regions where no or little extant Landrace material is available.
Alexandre Dansi - One of the best experts on this subject based on the ideXlab platform.
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Folk taxonomy and traditional uses of common bean (Phaseolus vulgaris L.) Landraces by the sociolinguistic groups in the central region of the Republic of Benin
Journal of Ethnobiology and Ethnomedicine, 2018Co-Authors: Laura Estelle Yeyinou Loko, Joelle Toffa, Ahouélété Joel Akpo, A. Adjatin, Azize Orobiyi, Alexandre DansiAbstract:BackgroundCommon bean (Phaseolus vulgaris L.) is an important grain legume crop grown in the central region of the Republic of Benin. However, its production declined in recent years to the extent that its diversity is being threatened with extinction. Understanding the folk nomenclature and taxonomy, as well as use values that allow its maintenance in Beninese agricultural system, is a prerequisite to develop efficient strategies for its conservation. Knowing that each sociolinguistic group develop various uses and traditional knowledge for their crop genetic resources, we hypothesized that enhancement of farmers’ livelihood, thanks to the use values of common bean Landraces, differ from one sociolinguistic group to another and contribute to their conservation in the traditional agriculture of central Benin.MethodsHundred and one common bean producers belonging to seven sociolinguistic groups selected through 23 villages of the region under study were surveyed. Data were collected through participatory research appraisal tools and techniques (individual interviews and direct observation) using a semi-structured questionnaire. Folk nomenclature and taxonomy of common bean, local uses, and factors affecting them were investigated.ResultsAcross the seven sociolinguistic groups surveyed in the study area, five common bean generic names and 26 folk varieties corresponding to 12 Landraces have been recorded. Folk nomenclature and taxonomy were mainly based on seeds’ coat color. The present study has revealed five common bean use values in the study area (food, medicinal, commercial, fodder, and mystic-religious), which are influenced by sociolinguistic groups. Leaves, roots, and seeds of three common bean folk varieties are used by surveyed farmers for disease treatment. Nine common bean folk varieties are considered by farmers as magical plants which have supernatural properties while several taboos for deities’ followers regarding Séssé Landrace are inventoried across sociolinguistic groups. Level of education and age of respondents influence positively and significantly medicine and mystical-religious uses of common bean respectively while commercial use is positively influenced by age and negatively by gender.ConclusionsTraditional values associated with common bean Landraces in the central region of the Republic of Benin increase their chance of survival in the farming systems. Socio-demographic characteristics of respondents which influence common bean use values must be taken into account in future programs of conservation. However, an assessment of diversity and analysis of distribution of extend of common bean Landraces in the study area is a necessity for the development of an efficient strategy of conservation of this genetic resource.
