Towards a methodology for on-farm conservation of plant genetic resources

The signing of the Convention on Biological Diversity at the ``Earth Summit' in 1992, its ratification and its subsequent entering into force have highlighted the need for an approach to biodiversity conservation that employs both ex situ and in situ techniques in a complementary manner. Though much research has focused on ex situ techniques, less progress has been made in developing methodologies for the conservation of genetic diversity in situ. The definition of in situ conservation used in the Convention on Biological Diversity encompasses two distinct processes: conservation of wild species in genetic reserves and of crops on-farm. Of these two, the latter, where the genetic diversity of crop land races is conserved within traditional farming systems, has been the less studied and remains less well understood. While there are still relatively few practical examples of on-farm genetic resources conservation, most genetic diversity of immediate and potential use to plant breeders is found among land races, and there is evidence that it is being rapidly eroded. This paper attempts to set on-farm conservation within the context of plant genetic resource conservation as a whole, to introduces a possible generalised model for the conservation of genetic diversity on-farm and to promote debate around the science of on-farm conservation.     

A preliminary study of the genetic diversity of Bolivian oca (<Emphasis Type="Italic">Oxalis tuberosa</Emphasis> Mol.) varieties maintained<Emphasis Type="Italic"> in situ</Emphasis> and<Emphasis Type="Italic"> ex situ</Emphasis> through the utilization of ISSR molecular markers

ISSR molecular markers have been used to investigate genetic diversity of oca (Oxalis tuberosa Mol.), an Andean neglected tuber crop species. Sampling procedure allowed a preliminary study of the genetic diversity at the intra- and intervarietal levels. Twenty tuber lots conserved in situ in the microcentre of Candelaria and ex situ in the Toralapa Centre (Bolivia) were identified. Four ISSR primers amplified a total of 25 fragments of which 17 (68%) were polymorphic. These experiments show that the structure of oca varieties is mainly based upon vernacular names with a greater differentiation among tuber lots than within them, supporting agromorphological data. ISSR technique enlightened the existence of heterogeneous varieties in oca and divergence between in situ and ex situ conservation strategies. These observations are potentially linked to the different ways of management of tubers in these two conservation systems.     

Selecting in situ conservation sites for grape genetic resources in the USA

Previously, there has not been any in situ conservation sites for crop germplasm within the United States Department of Agriculture (USDA), Agricultural Research Service (ARS), National Plant Germplasm System (NPGS). Using morphologic and molecular (SSR markers) techniques, we assessed the genetic variation present in populations of rock grape (Vitis rupestris Scheele), a native American grape species, throughout its range. We identified seven in situ conservation sites for rock grape using a strategy based on morphologic and molecular data, taxonomic information, population size and integrity, and landholder commitment. In collaboration with federal and state landholding agencies, we have established the first NPGS in situ conservation sites for American wild relatives of a crop.     

The Dynamics of on-farm Management of Sorghum in Ethiopia: Implication for the Conservation and Improvement of Plant Genetic Resources

On-farm conservation of plant genetic resources for food and agriculture has received strong support worldwide in recent years. It has been justified on appealing assumptions: it complements ex situ conservation, allows co-evolutionary interaction of host–pathogens and crop–weed complexes, and involves local knowledge systems. This article illustrates how on-farm conservation being set for its sake is extremely difficult under farmers’ dynamic management of plant genetic resources based on sorghum. The dynamics of their management could be explained by continued introduction, displacement, loss and maintenance of aboriginal landraces that have distinct functional attributes, patch-occupancy and relative abundance profiles. Such management and hence the dynamic landrace demography has largely been triggered by co-evolving biophysical stresses, spatial and seasonal variations. The best viable alternative to support farmers’ management of genetic resources is to link conservation to crop improvement both to enhance on-farm genetic diversity and make the biophysical environment a comfortable home for the plant genotypes.     

Seed exchanges,a key to analyze crop diversity dynamics in farmer-led on-farm conservation

Sustainable management of genetic resources is a crucial issue in the global context of food security. On-farm conservation is now widely acknowledged as a relevant strategy to reach this goal because it maintains evolutionary forces within and between the different components of the agricultural system. Seed exchanges between farmers play a key role in this process but are complicated to study over different agricultural contexts. This review begins by illustrating how interdisciplinary approaches combining ethnobotany and genetics helps provide a detailed analysis of the role of social and genetic dynamic interactions related to seed exchanges in traditional farming systems with farmer-led on-farm conservation. Secondly, the evolution of crop genetic diversity management is described in the context of industrialized farming systems. We follow the evolution of crop biodiversity perception by involved actors using a socio-historical perspective. After the agricultural shift from a traditional to a productivist model, recent social developments such as citizen science and participatory research movements are emerging and are strongly concerned by the question of biodiversity. These emerging trends which recognize and value seed exchanges between farmers show similarities to farmer-to-farmer seed exchanges in traditional farming systems. To what extent are these systems comparable? To fully benefit from studies in both traditional and industrialized contexts, it will be critical to develop an interdisciplinary framework to rigorously compare seed exchange systems and more generally farmer-led on-farm conservation strategies in diverse agricultural systems.     

On-farm conservation of 12 cereal crops among 15 ethnic groups in Yunnan (PR China)

Due to the rapid diffusion of improved crop varieties, fewer and fewer landraces are being grown by farmers. The on-farm conservation of crop landraces has been proposed as means of conserving potentially important crop germplasm as an alternative to its ex situ conservation in gene banks, but the effectiveness of this approach is unproven. Particular attention is currently focused on producers sited in remote regions. Here, we report the outcomes of a survey focusing on the conservation and utilization of landraces of corn, rice, wheat, barley, buckwheat, broomcorn sorghum, Job’s tears (coix), oats and finger, foxtail, broomcorn and barnyard millets grown by 15 ethnic groups from Yunnan province (China). Many local varieties are still in existence through their utilization on-farm. The varietal richness per village sampled was estimated to be 3.5 (maximum of 17), with rice and maize being the most heterogeneous, and glutinous sorghum and barnyard millet the least. Varietal richness was significantly and positively correlated with the number of villages surveyed, the number of families and the head of population. The choice of crops and varieties maintained varied between the ethnic groups, with the more westerly and north westerly situated villages conserving the most landraces. The number of crop species used was negatively correlated with per capita annual income, while the correlation coefficient between varietal richness and per capita annual income was less pronounced. The major factors determining the level of on-farm conservation were remoteness, fragmentation of the arable area and cultural needs. The data provide baseline information for the elaboration of optimal strategies for in situ conservation and utilization of crop germplasm in China.     

Role of informal seed system in promoting landrace diversity and their on-farm conservation: a case study of rice in Indian Himalayas

Role of informal seed system in landrace diversification, in situ conservation on-farm and sustainability in production were investigated as a case study for rice diversity in Indian Himalayas. The diachronic pattern of landrace occurrence revealed substantial increase, both in landrace number and frequency, in time. The local level seed supply in Uttarakhand Himalaya revealed that about 96% seed supply originated from informal system and a mere 4% seed supply is met from formal seed supply networks. In higher elevation ranges, beyond 1200 masl, largely landrace cultivation is practiced and a greater landrace diversification in traditional production was observed. Substantial variations due to environmental adaptations in niche habitats help provide important donor germplasm for crop improvement to users. Further, the population genetic structure also indicated enough diversity being maintained on-farm. Developing pathways for strengthening local level seed system for landrace diversification linked to sustainability in food production and conserving agro-biodiversity has been emphasized.     

Development of best practices for ex situ conservation of radish germplasm in the context of the crop genebank knowledge base

Information about crop-specific best practices for ex situ conservation of plant genetic resources has been difficult to find until recently. The CGIAR, together with national and regional partners, started to fill that gap by publishing best practices on the crop genebank knowledge base (CGKB -http://cropgenebank.sgrp.cgiar.org/), a website specifically developed and officially launched in 2010 to provide easy access to knowledge about all aspects of ex situ conservation of specific crops to genebank managers and ex situ conservation researchers. A collaborative study, undertaken by Bioversity International with eight national and international genebanks, utilized the framework provided by the CGKB to develop and publish radish conservation best practices. This paper focuses on two aspects of this study: (1) Differences in procedures and practices in radish conservation currently applied in five key genebank activities, namely, acquisition of germplasm, viability testing and monitoring, seed drying, seed storage, and regeneration. While in a few cases genebanks agreed on a specific best practice to recommend, in others it was not desirable to identify one practice as superior to another, therefore a range of existing practices is described as a variety of equivalent options. The results highlight the importance of proactive genebank management aimed at meeting the standards within the specific context in which a genebank operates. (2) The framework and template provided by the CGKB in guiding the development of genebank best practices, and the CGKB as an excellent resource to widely and freely share best practices with the global community to support the effective management of crop genebanks.     

Current status of coffee (Coffea arabica L.) genetic resources in Ethiopia: implications for conservation

The aim of this article is to provide an overview of the current situation of coffee genetic resources that are dwindling at an alarming rate in Ethiopia, the centre of diversity of Coffea arabica. Firstly, we describe the coffee growing systems (forest coffee, semi-forest coffee, garden coffee and plantation coffee) and recent research on the genetic diversity of the coffee planting material associated with those systems. Whilst the maximum genetic diversity revealed by DNA-based markers is found in the forest coffees of the south-western highlands, the natural habitat of C. arabica, the taxonomy of coffee landraces is particularly rich in garden coffee systems located in ancient growing zones such as Harerge in eastern Ethiopia. After reviewing the factors involved in the genetic erosion of the Ethiopian genepool, we give an update on the status of coffee genetic resources conserved ex situ in the field genebank of the Jimma Agricultural Research Centre, with 4,780 accessions spread over 10 research stations located in the main production areas, and in the main genebank of the Institute of Biodiversity Conservation located in Choche (Limu) with 5,196 accessions conserved. Lastly, we mention the in situ conservation operations currently being implemented in Ethiopia. Improving our knowledge of the genetic structure of Ethiopian forest and garden coffee tree populations as well as genetic resources conserved ex situ will help to plan the future conservation strategy for that country. To this end, modern tools as DNA-based markers should be used to increase our understanding of coffee genetic diversity and it is proposed, with the support of the international scientific community and donor organizations, to undertake a concerted effort to rescue highly threatened Arabica coffee genetic resources in Ethiopia.

Centres of Crop Diversity and/or Origin, Genetically Modified Crops and Implications for Plant Genetic Resources Conservation

The concept of centres of crop diversity and/or origin of agriculture is briefly reviewed. The conservation status of crop genetic resources, either ex situ or in situ, cultivated or wild, has been assessed for species of the Central American and Mexican centre, demonstrating that that region is indeed one of the important centres of crop diversity for human kind. Furthermore, biotechnological developments with regard to the creation and spread of genetically modified crops have been analyzed. The likelihood of unintentional introgression of genetically modified traits into conventional seed lots, crops as well as into germplasm collections have been assessed. Related biosafety measures as well as the possible implications of intellectual property rights on transgenic crops and/or genes are being discussed vis-a-vis the possible implications they might have for germplasm management. The Central American crop genetic resources situation has been used as a “case study” to illustrate the potential impact of the spreading of GM varieties on the genetic diversity in genebanks and farmers’ fields and the need for effective and efficient conservation efforts. Conservation management strategies and practices are being proposed of mitigate the potential negative impact of GM crops on the conservation efforts.     

Characterisation of thirteen cowpea landraces from Umbria (Italy). Strategy for their conservation and promotion

Thirteen landraces of cowpea (Vigna unguiculata (L.) Walp. subsp. unguiculata cv. gr. Unguiculata) have been morphologically and agronomically characterised as part of a plan for safeguarding and protecting plant biodiversity typical of Lake Trasimeno (Umbria, central Italy). Sixty plants per accession were scored for plant vigour, growth habit, flower colour, days to flowering, days to first mature pod, pod length, total number of pods produced, seed colour pattern, 100 seed weight, total seed yield and virus susceptibility. With the exception of vigour and growth habit, all landraces appeared to be well differentiated from one another for all the characters considered. Strategies and problems related to their in situ conservation are discussed.     

Landraces in central Italy: where and why they are conserved and perspectives for their on-farm conservation

Four hundred and twenty-seven landraces belonging to different plant species (forages, cereals, pulses, garden crops and fruit trees) were found on-farm in central Italy during exploration and collecting missions carried out since 1981. Open field crops are mostly grown under modern agricultural techniques by relatively young farmers on quite large farms for Italian standards. Garden crops are mostly grown by elderly farmers, running small farms or home gardens and using traditional farming systems which include the use of mechanical tools for soil preparation and occasionally the use of chemical fertilisers. There is no unique situation in on-farm conservation and management in the investigated area: the main factors involved appear to be a fragmented habitat and the presence of relatively elderly farmers. Most landraces are directly used by farmers' families, but a part is sold at local and wider markets. The main reasons why these landraces have been maintained on-farm are: their resistance/good productivity under difficult or harsh climatic conditions, traditional reasons or organoleptic peculiarities, which make them highly valued and expensive on the local and city markets and/or simply because they are appreciated by the families. Three example cases of effective on-farm conservation are presented. Social problems seem to be the main cause of genetic erosion. Perspectives and constraints to on-farm conservation and management are briefly discussed.     

Estimating genetic erosion in landraces — two case studies

Summary The results of collecting missions in Albania in 1941 and 1993 and in South Italy in 1950 and in the eighties allowed a comparison to be made of the material cultivated. The number of landraces still cultivated recently, as compared to their former number, was the basis for the estimation of genetic erosion. Genetic erosion (GE) was calculated as GE=100%-GI (Genetic integrity). Genetic erosion was found to be 72.4% in Albania and 72.8% in South Italy, respectively. These results prove the high degree of genetic erosion in landraces from different parts of the Mediterranean area. Apart from the economic conditions, several other factors are responsible for genetic erosion, among them breeding system, crop type (i.e., garden or field crop) and crop group (e.g., cereals, vegetables and pulses).The results show that in the areas investigated there are still landraces for in situ conservation. Ex situ conservation in genebanks proved to be a possibility. An integration process is necessary to prevent losses in crops which are difficult to propagate under ex situ conditions. The complementarity of both conservation methods is stressed.     

The paradox of keystone species persecuted as pests: A call for the conservation of abundant small mammals in their native range

Small mammals, such as European rabbits (Oryctolagus cuniculus), plateau pikas (Ochotona curzoniae) and prairie dogs (Cynomys spp.), traditionally have been perceived as pests and targeted for control within their native ranges, where they perform essential ecosystem roles and are considered keystone species. These species can reach high densities, and have been subjected to eradication campaigns because of their putative negative impact on natural habitats and agriculture and their competition with livestock for forage. Eradication programmes have been a main factor causing sharp declines of these species in their natural ranges. Paradoxically, they are keystone species where they are abundant enough to be perceived as pests. The term “pest” is usually a social perception that is rarely supported by scientific data, whereas there is considerable scientific evidence of the key ecological roles played by these species. We call for the conservation of these species and present a conceptual model regarding the management of their populations. Where they occur at high numbers, and hence their effects on biodiversity are still of crucial importance, the persecution of these species should be avoided and their natural habitats preserved. In areas with high conservation value, but where these species occur at low densities, management efforts should aim to increase their density. In areas of high commercial value, managers ideally should consider changing prioritization of the area to high conservation value by purchasing the land or obtaining conservation easements. In situations with high commercial value and demonstrable low conservation concern, small mammals could be reduced humanely.     

涉县旱作梯田系统农业物种及遗传多样性保护与利用

农业生物多样性的研究和保护是全球重要农业文化遗产保护的核心要素。以王金庄为核心的涉县旱作梯田系统2014年被认定为中国重要农业文化遗产,研究其农业生物多样性,可为涉县旱作梯田系统的保护与利用提供依据,为农业文化遗产地农业生物多样性农家就地保护提供参考。本文通过对传统农家品种普查收集与入户访谈、田间调查与种植鉴定,系统研究了涉县旱作梯田系统的农业物种和传统农家品种以及由此形成的保护与利用经验与技术。研究发现涉县旱作梯田系统种植或管理的农业物种26科57属77种,其中粮食作物15种、蔬菜作物31种、油料作物5种、干鲜果14种、药用植物以及纤维烟草等12种。共有包括171个传统农家品种,其中粮食作物62个、蔬菜作物57个、干鲜果品33个、油料作物7个、药用植物和纤维烟草12个。这些农业物种及传统农家品种,通过混合种植、轮作倒茬、间作套种、优中选优等一系列保护与利用技术被活态传承和保护。但随着城镇化和现代农业的快速推进,涉县旱作梯田系统农业生物多样性保护与利用正面临着主体缺失、技术失传、传统农家品种名称混乱、种质退化以及单一化种植造成的品种多样性丧失、单一追求产量造成适应性强的品种资源丧失、农民生计方式多样化造成梯田农业的弱化、传统农家品种生产比较效益低和重要性认识不足等问题,针对这些问题提出了建立动态保护与适应性管理机制、发展特色产业、激发农民内生动力、组织开展资源普查并建立社区种子库与农民自留种相结合的传统农家品种就地活态保护机制等对策与建议。     

Evaluation of genetic diversity and relationships within an on-farm collection of Perilla frutescens (L.) Britt. using microsatellite markers

The present study demonstrates utilization of 11 microsatellite markers to explore genetic diversity held in Perilla frutescens (L.) Britt. landrace accessions growing on farms in different parts of Korea and Japan and to assess their genetic relationships. All microsatellite loci were polymorphic and produced a total of 96 alleles ranging from 4 to 20, with an average of 8.7 alleles per locus. Of the 96 alleles found, a total of 15 unique landrace-specific alleles were observed at 9 different loci. The locus GBPFM203 provided the highest number of alleles (20), of which five were unique and each specific to a particular landrace accession. The occurrence of unique, accession-specific alleles presented molecular evidence for the generation of new alleles within on-farm collection of Perilla. The mean values of observed (H _O) and expected heterozygosity (H _E) were 0.39 and 0.68, respectively, indicating a considerable amount of polymorphism within this collection. A genetic distance-based phylogeny grouped the two Perilla varieties, var. frutescens and var. crispa (Thunb.) Decne into two distinct groups. Accessions belonging to var. frutescens could also be divided into two subgroups at a close genetic distance (GD = 0.432). The overall clustering pattern did not strictly follow the grouping of accessions according to their geographic origins. These observations are indicative of extensive germplasm exchange among farms from different geographical regions. The genetic similarity observed among the Perilla landraces may be useful for future Perilla crop variety identification, conservation, and improvement programs.     

Genetic erosion and in situ conservation of Lima bean (Phaseolus lunatus L.) landraces in its Mesoamerican diversity center

Lima bean (Phaseolus lunatus L.) is an important crop in traditional Mayan agriculture of the Yucatan Peninsula, Mexico, its Mesoamerican center of diversity. Genetic erosion in this species is currently a threat in this region out of 3 of 21 landraces dominate 71.24% of the cultivated area, and 12 are rare landraces grown only in 6.29%. Using 90 ISSR loci, we estimated the diversity and genetic relationships for 21 landraces to analyzing their risk of genetic erosion, and generate data for their in situ conservation. Total genetic diversity was high (h = 0.29), however it was lower than wild gene pool reported (h = 0.69). The abundant landraces had genetic diversity values lower (h = 0.13, I = 0.17) than the common (h = 0.26, I = 0.33) and rare landraces (h = 0.24, I = 0.27). However, the rare landraces are in a higher risk of genetic erosion due to local extinction. The cluster analysis showed no groups corresponding to morpho-phenological characteristics, geographic origin or traditional classification, which resulted from high inter-landraces gene flow levels. The molecular data confirmed that the domesticated Lima bean pool of the Yucatan Peninsula has a high risk of genetic erosion. If current tendencies in landrace cultivation continue, many will no longer be planted within two to three generations, with a consequent loss of their alleles. Programs urgently need to be established for in situ conservation of Lima bean landraces in this region.     

A case study of seed exchange networks and gene flow for barley (Hordeum vulgare subsp. vulgare) in Morocco

Local patterns of seed regeneration and trade that occur outside the formal breeding sector (seed exchange networks) can have a strong influence on the genetic diversity and evolution of traditional crop varieties. Despite this, little is known about the extent to which seed exchange networks influence gene flow and genetic structure in traditional crop varieties. Here we study barley (Hordeum vulgare subsp. vulgare) in rural communes of Northern Morocco in 2008 and 2009. We quantified seed regeneration and exchange by farmers within the seed exchange network using structured interviews. Using SSR markers, we also quantified the neutral genetic diversity and structure of a complex of traditional varieties referred to as Beldi that is managed in this exchange network. The majority of farmers (>88 %) report cultivating Beldi. Most seeds of Beldi (70–90 %) are maintained on-farm, while the remainder of seeds are obtained from local markets within the commune. Beldi has high genetic diversity and there is weak but significant genetic structure between communes (F_ST = 0.031). From SSR marker data there is evidence of a high level of gene flow between communes not reported in interviews. Seeds purchased in local markets likely represent seeds from a larger geographic region, leading to lower genetic structure among communes than expected based on the reported level of on-farm seed regeneration and local sourcing of seed. We discuss the implications of this seed exchange network for the conservation of traditional barley varieties in the study region.