Unmanaged sexual reproduction and the dynamics of genetic diversity of a vegetatively propagated crop plant, cassava (Manihot esculenta Crantz), in a traditional farming system

Occurrence of intervarietal or interspecific natural crosses has been reported for many crop plants in traditional farming systems, underlining the potential importance of this source of genetic exchange for the dynamics of genetic diversity of crop plants. In this study, we use microsatellite loci to investigate the role of volunteer seedlings (plants originating from unmanaged sexual reproduction) in the dynamics of genetic diversity of cassava (Manihot esculenta Crantz), a vegetatively propagated crop, in a traditional farming system in Guyana. A previous field study showed that farmers incorporate such plants into the germplasm for vegetative propagation, and that many of them are likely to be assigned by farmers to recognized varieties. Under strict vegetative propagation clonality of varieties is expected. The high proportion of polyclonal varieties observed suggests that incorporation of seedlings into the germplasm for propagation is a frequent event. The molecular variability assessed with microsatellite markers shows that there is high differentiation among heterozygous varieties, whereas populations of seedlings do not depart from the proportions expected under Hardy-Weinberg assumptions. Assignment of seedlings to a recognized variety on the basis of morphological similarity greatly increases genetic diversity within the variety. We argue that recombination and gene flow play a major role in the dynamics of genetic diversity of cassava in traditional farming systems. Documenting unmanaged sexual reproduction and its genetic consequences is a prerequisite for defining strategies of in situ conservation of crop plant genetic resources.     

Informal "seed" systems and the management of gene flow in traditional agroecosystems: the case of cassava in Cauca, Colombia

Our ability to manage gene flow within traditional agroecosystems and their repercussions requires understanding the biology of crops, including farming practices' role in crop ecology. That these practices' effects on crop population genetics have not been quantified bespeaks lack of an appropriate analytical framework. We use a model that construes seed-management practices as part of a crop's demography to describe the dynamics of cassava (Manihot esculenta Crantz) in Cauca, Colombia. We quantify several management practices for cassava--the first estimates of their kind for a vegetatively-propagated crop--describe their demographic repercussions, and compare them to those of maize, a sexually-reproduced grain crop. We discuss the implications for gene flow, the conservation of cassava diversity, and the biosafety of vegetatively-propagated crops in centers of diversity. Cassava populations are surprisingly open and dynamic: farmers exchange germplasm across localities, particularly improved varieties, and distribute it among neighbors at extremely high rates vis-à-vis maize. This implies that a large portion of cassava populations consists of non-local germplasm, often grown in mixed stands with local varieties. Gene flow from this germplasm into local seed banks and gene pools via pollen has been documented, but its extent remains uncertain. In sum, cassava's biology and vegetative propagation might facilitate pre-release confinement of genetically-modified varieties, as expected, but simultaneously contribute to their diffusion across traditional agroecosystems if released. Genetically-modified cassava is unlikely to displace landraces or compromise their diversity; but rapid diffusion of improved germplasm and subsequent incorporation into cassava landraces, seed banks or wild populations could obstruct the tracking and eradication of deleterious transgenes. Attempts to regulate traditional farming practices to reduce the risks could compromise cassava populations' adaptive potential and ultimately prove ineffectual.     

Thai elite cassava genetic diversity was fortuitously conserved through farming with different sets of varieties

Many in situ conservation programs have been developed to preserve plant landrace diversity and to promote its sustainable utilization, but little is known about the effectiveness of the developed programs in conserving plant genetic diversity. We investigated the effectiveness of an unregulated (i.e., unplanned or open) conservation system maintained by Thai farmers in conserving Thai elite cassava (Manihot esculenta Crantz) varieties. Specifically, we compared genetic diversity of 266 cassava clones that were collected from 80 farms in eight provinces with 16 cassava landraces and varieties released since the 1970s through genotyping with 35 informative simple sequence repeat (SSR) markers. The SSR analysis revealed a large regional heterogeneity in cassava diversity, with a strong genetic differentiation of the assayed clones among the 80 farms (19.8 %) and across the eight provinces (11.8 %). Significant associations were also found between SSR variation and farm agro-ecological factors or some farming practices. However, there was no significant genetic differentiation (0.9 %) between the 266 farm clones and 16 reference varieties. These findings suggest that the Thai elite cassava genetic diversity was fortuitously conserved by the farmers through farming with different sets of varieties. Implications of these findings are discussed with respect to on-farm conservation of plant genetic resources.     

Cassava Trait Preferences of Men and Women Farmers in Nigeria: Implications for Breeding

Nigeria is the world’s largest cassava producer, hosting a diverse array of cassava farmers and processors. Cassava breeding programs prioritize “common denominator” traits in setting breeding agendas, to impact the largest possible number of people through improved varieties. This approach has been successful, but cassava adoption rates are less than expected, with room for improvement by integrating traits in demand by farmers and processors. This paper aims to inform breeding priority setting, by examining trait and varietal preferences of men and women cassava farmer/processors. Men and women in eight communities in Southwest and Southeast Nigeria were consulted using mixed methods. Women and men had significantly different patterns of cassava use in the Southwest. Fifty-five variety names were recorded from the communities demonstrating high genetic diversity maintained by growers, especially in the Southeast. High yield, early maturity, and root size were most important traits across both regions, while traits women and men preferred followed gender roles: women prioritized product quality/cooking traits, while men placed higher priority on agronomic traits. Trait preference patterns differed significantly between the Southeast and Southwest, and showed differentiation based on gender. Patterns of access to stem sources were determined more by region and religion than gender.     

Reconsidering the green revolution: Diversity and stability in cradle areas of crop domestication

This paper reconsiders two widely held hypotheses about the effects of the green revolution, that it led to biological simplification and instability. The hypothesis of biological simplification (genetic erosion) is tested with evidence from Andean agriculture, where farmers maintain a significant degree of crop diversity even as they adopt modern crop varieties. The hypothesis of increased instability is tested with evidence from Asia where wheat and rice yields show no general pattern of increased instability. Neither of these hypotheses is confirmed. The conventional wisdom about the green revolution should be reconsidered with emphasis on resilience and variation in modernizing farming systems.     

Factors Influencing Diversity of Farmers’ Varieties of Sweet Potato in Uganda: Implications for Conservation

Factors Influencing Diversity of Farmers’ Varieties of Sweet Potato in Uganda: Implications for Conservation. There is increasing concern that agricultural intensification is causing loss of crop biodiversity due to displacement of traditional farmers’ varieties by a small number of improved cultivars. Using ethnobotanical surveys, we assessed the implication of adoption of new sweet potato (Ipomoea batatas) cultivars on the maintenance of farmers’ varieties in Uganda. Other factors influencing varietal diversity were also assessed. A total of 102 farmer households distributed in the top three sweet potato production agro-ecological zones were interviewed. With the exception of released cultivars, very few varieties appeared in more than one region. The majority of the respondents indicated that they continue to plant some of the existing varieties when they adopt new cultivars. Loss of planting materials due to drought was a major constraint to maintaining varietal diversity for this vegetatively propagated crop. Limited land and lack of access to best management practices were also key constraints to maintenance of farmers’ varieties. The primary criteria for adopting new cultivars were higher yield, taste, and duration to maturity. Yield stability, tolerance to native biotic and abiotic stresses, and good taste were important for maintenance of currently grown varieties. Overall, criteria for variety selection varied with household characteristics including farmer age and gender, uses of the crop, micro-climatic conditions in the farmers’ fields, and level of access to agricultural extension. The observed heterogeneity in selection criteria, influence of social ties, and the role of environment in varietal maintenance have important implications for establishing breeding priorities and preservation of crop diversity.     

Farmers Drive Genetic Diversity of Thai Purple Rice (Oryza sativa L.) Landraces

Purple or black rice (Oryza sativa L.) is a culturally important germplasm in Asia with a long history of cultivation in northern Thailand. Purple rice is identified by the color of the rice pericarp, which varies from purple to black with the accumulation of phenolic acids, flavonoids, and anthocyanins. In the present study, we assessed molecular variation within and between wetland purple rice landraces germplasm from northern and northeastern Thailand using 12 microsatellite loci. All purple rice varieties surveyed showed high levels of homozygosity within varieties and strong genetic differentiation among varieties, indicating the fixation of genetic differences among them. This pattern is consistent with purple rice farming practices in northern Thailand, where a small portion of harvested seed is selected and replanted based on farmers’ preferences. The reduced genetic diversity and high homozygosity observed for purple rice is also consistent with patterns expected for this inbreeding crop. Genetic differentiation among the varieties showed some degree of structuring based on their geographical origin. Taken together, these data highlight that the genetic diversity and structure of wetland purple rice landraces is shaped by farmer utilization and cultivation through local cultural practices, and that conservation should focus on ex situ conservation across its cultivation range, along with on-farm, in situ conservation based on farmers’ seed-saving practices. In situ conservation may prove especially valuable for preserving the genetic identity of local varieties and promote adaptation to local environments.

     

Reconfiguring Agrobiodiversity in the Amazon Estuary: Market Integration, the Açaí Trade and Smallholders’ Management Practices in Amapá, Brazil

An established body of literature documents current changes in rural livelihoods, agricultural practices, and agrobiodiversity patterns in smallholder communities across the globe. Contributing to this literature, this paper documents change in agricultural practices and agrobiodiversity patterns in a tidal floodplain settlement in Amapá, Brazil, where in recent years farmers increasingly devote their attention to the production of açaí fruits, an important regional crop with strong local, national and international markets. Research results indicate that farmers are abandoning subsistence production in annual fields to make room for açaí-dominated agroforests. At the same time, farmers are diversifying home gardens, and as a result conserve a portion of the crop diversity once maintained in annual fields in these areas. Agrobiodiversity documented in home gardens is much higher than previously recorded in the study area, and is equal or higher than previously reported in home gardens in other less-market integrated Amazonian communities. Research points to the need for innovative methods to document agrobiodiversity patterns in today’s modifying landscapes and for the historical analysis of such patterns to avoid presumptions that observed changes are unilateral and unidirectional.     

Folk taxonomy and evolutionary dynamics of cassava: A case study in Ubatuba, Brazil

A survey was conducted of Caicara farmers from Ubatuba in the Brazilian coastland between São Paulo and Rio de Janeiro States regarding the folk-taxonomy for cassava (Manihot esculenta Crantz) landraces they cultivate and cassava evolutionary dynamics in swidden cultivation. The accuracy of their folk taxonomy was assessed. Cluster analysis was used to make comparisons between names given by the farmers to sampled individuals and their isozyme phenotypes obtained with four isozyme systems. Interviews with farmers were done and ethnobiological data collected. These farmers possess a loose taxonomic system and tend to underestimate cassava genetic diversity in their gardens. However, classification skills vary considerably among them. The accuracy of their taxonomy along with the results of interviews with farmers and ethnobiological data are discussed in light of a proposed evolutionary dynamics model for cultivated cassava and its ecology in tropical swidden cultivation.     

The genomic and bioclimatic characterization of Ethiopian barley (Hordeum vulgare L.) unveils challenges and opportunities to adapt to a changing climate

The climate crisis is impacting agroecosystems and threatening food security of millions of smallholder farmers. Understanding the potential for current and future climatic adaptation of local crop agrobiodiversity may guide breeding efforts and support resilience of agriculture. Here, we combine a genomic and climatic characterization of a large collection of traditional barley varieties from Ethiopia, a staple for local smallholder farmers cropping in challenging environments. We find that the genomic diversity of barley landraces can be partially traced back to geographic and environmental diversity of the landscape. We employ a machine learning approach to model Ethiopian barley adaptation to current climate and to identify areas where its existing diversity may not be well adapted in future climate scenarios. We use this information to identify optimal trajectories of assisted migration compensating to detrimental effects of climate change, finding that Ethiopian barley diversity bears opportunities for adaptation to the climate crisis. We then characterize phenology traits in the collection in two common garden experiments in Ethiopia, using genome-wide association approaches to identify genomic loci associated with timing of flowering and maturity of the spike. We combine this information with genotype–environment associations finding that loci involved in flowering time may also explain environmental adaptation. Our data show that integrated genomic, climatic, and phenotypic characterizations of agrobiodiversity may provide breeding with actionable information to improve local adaptation in smallholder farming systems.     

Mechanisms Explaining Variety Naming by Farmers and Name Consistency of Rice Varieties in The Gambia

Mechanisms Explaining Variety Naming by Farmers and Name Consistency of Rice Varieties in The Gambia. Understanding variety naming by farmers is important for better understanding crop genetic diversity in farmer fields and its management by farmers. This paper describes variety naming of rice by farmers in The Gambia and presents mechanisms that explain naming diversity and consistency. Three types of variety names can be distinguished, referring to common old varieties, common new varieties, and uncommon varieties. Interview and plant data suggest that variety exchange affects variety naming within villages. As a result, variety names give information on the period of time a variety is used in a village, and on the flow of varieties between and within villages. Name consistency within and between villages results from and illuminates the dynamics of variety exchange within and between villages.     

In Situ conservation of maize in Mexico: Genetic diversity and Maize seed management in a traditional community

Results from a study of maize varieties and seed sources in a traditional community in Jalisco, Mexico, raise questions about the relationship between genetic erosion and the introduction of varieties. The relevance of models for in situ conservation of crop genetic resources based on geographical isolation of a community is discussed. The morphophenological diversity of local materials is shown to be enhanced by introductions of both improved cultivars and landraces from farmers in other communities. On the other hand, the geographical point of reference for defining “local” landrace is shown to be larger than the community itself. Farmers will classify seed obtained from other farmers in and outside the community as that of a local landrace if it resembles their own according to the phenotypic characteristics they use to distinguish varieties. Maize diversity in this community is then the result of a certain level of introduction of genetic material and not of geographical isolation.     

Genetic diversity of traditional South American Landraces of Cassava (Manihot esculenta Crantz): an analysis using microsatellites

The extent and structure of the genetic variability of traditional varieties of cassava (Manihot esculenta Crantz) have been little documented, despite considerable evidence for this crop? great varietal diversity in traditional agroecosystems. We used microsatellite markers to assess the genetic structure of traditional landraces of sweet and bitter cassava collected from five South American sites. As reference, we used a sample of 38 accessions from a world collection of cultivated cassava. For a total of 10 loci examined, we found 15 alleles that were not represented in this sample. Ten of these had been previously detected in wild Manihot species. The geographical structure of genetic variability was weak, but the genetic differentiation between bitter and sweet landraces was significant, suggesting that each form had evolved separately after domestication. Our results showed that traditional landraces form an important source of genetic diversity and merit more attention from managers of crop genetic resources.     

Resistance and resilience of root fungal communities to water limitation in a temperate agroecosystem

Understanding crop resilience to environmental stress is critical in predicting the consequences of global climate change for agricultural systems worldwide, but to date studies addressing crop resiliency have focused primarily on plant physiological and molecular responses. Arbuscular mycorrhizal fungi (AMF) form mutualisms with many crop species, and these relationships are key in mitigating the effects of abiotic stress in many agricultural systems. However, to date there is little research examining whether (1) fungal community structure in agroecosystems is resistant to changing environmental conditions, specifically water limitation and (2) resilience of fungal community structure is moderated by agricultural management systems, namely the integration of trees into cropping systems. Here, we address these uncertainties through a rainfall reduction field experiment that manipulated short‐term water availability in a soybean‐based (Glycine max L. Merr.) agroforest in Southern Ontario, Canada. We employed terminal restriction fragment length polymorphism analysis to determine the molecular diversity of both general fungal and AMF communities in soybean roots under no stress, stress (rainfall shelters added), and poststress (rainfall shelters removed). We found that general fungal and AMF communities sampled from soybean roots were resistant to rainfall reduction in a monoculture, but not in an agroforest. While AMF communities were unchanged after stress removal, general fungal communities were significantly different poststress in the agroforest, indicating a capacity for resiliency. Our study indicates that generalist fungi and AMF are responsive to changes in environmental conditions and that agroecosystem management plays a key role in the resistance and resilience of fungal communities to water limitation.     

Weed species diversity and community composition in cropping practices at two intensity levels – a six-year experiment

Alternative cropping practices can be expected to increase the diversity and change the species composition of weed communities. In a six-year field experiment we compared species diversity and species composition in the weed community of cereal fields cultivated by conventional and by low-input cropping methods. In the conventional cropping both mineral fertilizers and herbicides were applied but in the low-input cropping the fertlizer was manure and herbicides were avoided altogether. The level of nitrogen fertilization was higher in conventional cropping. A five-year crop rotation comprising rye, oat-pea, barley and two-year grasslands was used in both cropping methods. We found that the species pool was larger (42 vs 35 species) and the average number of species higher (20.2 vs 13.1 species) in low-input than in conventional cropping. This was the case both in the data pooled across crops and in each crop separately. Herbicides affected species diversity and species composition more than did nitrogen fertilization. Species susceptible to the herbicides applied declined in abundance, which resulted in more skewed dominance patterns in the communities of conventional fields than in those of low-input fields. The crop affected the species composition of weed communities more than did the cropping method. Our results suggest that weed species diversity could be promoted by using low-intensity cropping practices.     

木薯SYP基因的序列特征及表达分析

植物突触融合蛋白(SYP)是一类与植物细胞内囊泡介导转运有关的蛋白。部分SYP基因与植物对生物和非生物胁迫的响应有关。该文利用生物信息学工具分析了木薯(Manihot esculenta)SYP基因及其蛋白结构、核苷酸多态性和系统进化关系, 并利用RT-PCR技术检测了木薯不同组织中SYP基因的表达。结果表明, 木薯SYP基因及其蛋白结构均具有明显的规律性和家族成员间的保守性; SYP基因的cDNA在基因间以及不同品种间具高度一致性, 核苷酸变异以同义替换为主。进化分析表明, 植物SYP基因可分为2个亚家族, 木薯SYP基因倾向于与蓖麻(Ricinus communis)SYP基因聚在进化树同一分支的末端。半定量RT-PCR分析表明, 5个木薯SYP家族成员具有组织特异性。上述研究结果为木薯SYP基因功能研究和功能单核苷酸标记的开发奠定了重要基础。     

Glutinous Rice and Its Importance for Hill Farmers in Laos

Glutinous Rice and Its Importance for Hill Farmers in Laos. Economic Botany, 50(4): 401-408. 1996. Glutinous or waxy rice is the most important crop for subsistence farming economies in the hills of Northern Laos. Hill farmers continue to use traditional varieties only. Geographical and political isolation have contributed towards their preservation. Traditional varieties are mainly of the japonica type, have a good yield potential, are well adapted to the local conditions, and represent a wide genetic diversity. Farmers interviewed prefer varieties with large panicles, planted 2.7 varieties on average, with 17, 30 and 53% of the area planted to early, medium and late varieties, respectively. Out of 544 traditional cultivars 95% flowered within 88–120 days after planting. Crops planted together with rice in order of importance are: maize, cucumber, chili, taro, and sesame. Farmers reported annual milled rice production of 125 kg per capita and rice self-sufficiency for 8 months for 1992 and 1993. Maize, cassava, and products from the forest are major rice substitutes and food security in remote areas could best be improved by increasing production of maize and cassava in combination with livestock production systems.     

Landraces of maize in Central Mexico: an altitudinal transect

Conservation of crop genetic resources is now considered an important component of sustainable agricultural development. If conservation of genetic resources for agriculture is to be successful, a more complete understanding of the dynamics affecting traditional (landrace) crop populations is needed. We conducted a study of maize-based agriculture in the Central Highlands of Mexico in communities at 2400, 1700, 1400, and 1200 masl to assess the status of traditional varieties in an area characterized by thorough integration into the national economy. Our research contradicts the view that modern varieties persist because of marginal conditions, deficient infrastructure, weaker markets, or traditional attitudes. One or two landraces dominated highland maize populations and farmers appeared to be more conservative in terms of their emphasis on traditional maize varieties than at lower elevations. The dominance of traditional varieties in the highlands is well known but poorly explained, and the coexistence of traditional and modern varieties in the mid-elevations was unexpected. Our highland study area has good roads, is near Mexico City, and is less than 50 km away from four major crop research institutes that have done maize breeding since 1950’s. We suggest that in situ conservation of maize genetic resources in the highlands is sustained because the landraces there have good agronomic performance and are highly valued by farmers for their end-use qualities. At the mid-elevations, competition between local and modern maize was sharpest, and farmers have found that both landraces and improved varieties suit their needs, hence enhancing genetic diversity. Interventions and incentives would appropriately be carried out here to assure in situ conservation of locally adapted landraces of maize.     

Integrating gene flow, crop biology, and farm management in on-farm conservation of avocado (Persea americana, Lauraceae)

Maintaining crop diversity on farms where cultivars can evolve is a conservation goal, but few tools are available to assess the long-term maintenance of genetic diversity on farms. One important issue for on-farm conservation is gene flow from crops with a narrow genetic base into related populations that are genetically diverse. In a case study of avocado (Persea americana var. americana) in one of its centers of diversity (San Jerónimo, Costa Rica), we used 10 DNA microsatellite markers in a parentage analysis to estimate gene flow from commercialized varieties into a traditional crop population. Five commercialized genotypes comprised nearly 40% of orchard trees, but they contributed only about 14.5% of the gametes to the youngest cohort of trees. Although commercialized varieties and the diverse population were often planted on the same farm, planting patterns appeared to keep the two types of trees separated on small scales, possibly explaining the limited gene flow. In a simulation that combined gene flow estimates, crop biology, and graft tree management, loss of allelic diversity was less than 10% over 150 yr, and selection was effective in retaining desirable alleles in the diverse subpopulation. Simulations also showed that, in addition to gene flow, managing the genetic makeup and life history traits of the invasive commercialized varieties could have a significant impact on genetic diversity in the target population. The results support the feasibility of on-farm crop conservation, but simulations also showed that higher levels of gene flow could lead to severe losses of genetic diversity even if farmers continue to plant diverse varieties.