Indicators for the on-farm assessment of crop cultivar and livestock breed diversity: a survey-based participatory approach

Agrobiodiversity plays a fundamental role in guaranteeing food security. However, still little is known about the diversity within crop and livestock species: the genetic diversity. In this paper we present a set of indicators of crop accession and breed diversity for different farm types at farm-level, which may potentially supply a useful tool to assess and monitor farming system agrobiodiversity in a feasible and relatively affordable way. A generic questionnaire was developed to capture the information on crops and livestock in 12 European case study regions and in Uganda by 203 on-farm interviews. Through a participatory approach, which involved a number of stakeholders, eight potential indicators were selected and tested. Five of them are recommended as potentially useful indicators for agrobiodiversity monitoring per farm: (1) crop-species richness (up to 16 crop species), (2) crop-cultivar diversity (up to 15 crop cultivars, 1–2 on average), (3) type of crop accessions (landraces accounted for 3 % of all crop cultivars in Europe, 31 % in Uganda), (4) livestock-species diversity (up to 5 livestock species), and (5) breed diversity (up to five cattle and eight sheep breeds, on average 1–2).We demonstrated that the selected indicators are able to detect differences between farms, regions and dominant farm types. Given the present rate of agrobiodiversity loss and the dramatic effects that this may have on food production and food security, extensive monitoring is urgent. A consistent survey of crop cultivars and livestock breeds on-farm will detect losses and help to improve strategies for the management and conservation of on-farm genetic resources.     

Dynamic management of crop diversity: From an experimental approach to on-farm conservation

In agricultural systems, biodiversity includes diversity within species and among species and provides many benefits for production, resilience and conservation. This article addresses the effects of a strategy of in situ conservation called dynamic management (DM) on population evolution, adaptation and diversity. Two French DM initiatives are considered, the first one corresponding to an experimental context, the second to an on-farm management. Results from a study over 26 years of experimental DM of bread wheat (Triticum aestivum L.) are first presented, including the evolution of agronomic traits and genetic diversity at neutral and fitness related loci. While this experiment greatly increased scientific knowledge of the effects of natural selection on cultivated populations, it also showed that population conservation cannot rely only on a network of experimental stations. In collaboration with a farmers' network in France, researchers have begun studying the effects of on-farm DM (conservation and selection) on diversity and adaptation. Results from these studies show that on-farm DM is a key element for the long-term conservation and use of agricultural biodiversity. This method of in situ conservation deserves more attention in industrialised countries.     

Multi-trait evolution of farmer varieties of bread wheat after cultivation in contrasting organic farming systems in Europe

Because of the lack of varieties for organic agriculture, associations of organic farmers in several European countries have begun cultivating landraces and historic varieties, effectively practicing in situ conservation of agricultural biodiversity. To promote agrobiodiversity conservation, a special list for "conservation varieties" was implemented in 2008 by the EU because for any exchange and marketing of seeds in the EU, a variety must be registered in an official catalog. Our study aimed at improving knowledge on the phenotypic diversity and evolution of such varieties when cultivated on organic farms in Europe, in order to better define their specific characteristics and the implications for the registration process. We assessed multi-trait phenotypic evolution in eight European landraces and historic varieties of bread wheat and in two pureline variety checks, each grown by eight organic farmers over 2?years and then evaluated in a common garden experiment at an organic research farm. Measurements on each farmer's version of each variety included several standard evaluation criteria for assessing distinctness, uniformity and stability for variety registration. Significant phenotypic differentiation was found among farmers' versions of each variety. Some varieties showed considerable variation among versions while others showed fewer phenotypic changes, even in comparison to the two checks. Although farmers' variety would not satisfy uniformity or stability criteria as defined in the catalog evaluation requirements, each variety remained distinct when assessed using multivariate analysis. The amount of differentiation may be related to the initial genetic diversity within landraces and historic varieties.     

Seed Systems and Farmers’ Seed Choices: The Case of Maizein the Peruvian Amazon

This paper analyzes how local seed system institutions support seed diversity, itself a requirement for agrobiodiversity maintained on-farm. The paper focuses on maize seed diversity in the central Peruvian Amazon. Using household and community level data from three different cultural groups from the central Peruvian Amazon, empirical results show the importance of collective action and the mediating role of ethnicity in the functioning of informal seed systems that in turn affect farmers’ choices regarding conservation of seed diversity. This implies that policies are needed to protect the relatively open seed exchanges of such local practices as a way to sustain on-farm agrobiodiversity.     

Influence of ethnic traditional cultures on genetic diversity of rice landraces under on-farm conservation in southwest China

Background

Crop genetic resources are important components of biodiversity. However, with the large-scale promotion of mono-cropping, genetic diversity has largely been lost. Ex-situ conservation approaches were widely used to protect traditional crop varieties worldwide. However, this method fails to maintain the dynamic evolutionary processes of crop genetic resources in their original habitats, leading to genetic diversity reduction and even loss of the capacity of resistance to new diseases and pests. Therefore, on-farm conservation has been considered a crucial complement to ex-situ conservation. This study aimed at clarifying the genetic diversity differences between ex-situ conservation and on-farm conservation and to exploring the influence of traditional cultures on genetic diversity of rice landraces under on-farm conservation.

Methods

The conservation status of rice landrace varieties, including Indica and Japonica, non-glutinous rice (Oryza sativa) and glutinous rice (Oryza sativa var. glutinosa Matsum), was obtained through ethno-biology investigation method in 12 villages of ethnic groups from Guizhou, Yunnan and Guangxi provinces of China. The genetic diversity between 24 pairs of the same rice landraces from different times were compared using simple sequence repeat (SSR) molecular markers technology. The landrace paris studied were collected in 1980 and maintained ex-situ, while 2014 samples were collected on-farm in southwest of China.

Results

The results showed that many varieties of rice landraces have been preserved on-farm by local farmers for hundreds or thousands of years. The number of alleles (Na), effective number of alleles (Ne), Nei genetic diversity index (He) and Shannon information index (I) of rice landraces were significantly higher by 12.3–30.4 % under on-farm conservation than under ex-situ conservation. Compared with the ex-situ conservation approach, rice landraces under on-farm conservation programs had more alleles and higher genetic diversity. In every site we investigated, ethnic traditional cultures play a positive influence on rice landrace variety diversity and genetic diversity.

Conclusion

Most China’s rice landraces were conserved in the ethnic areas of southwest China. On-farm conservation can effectively promote the allelic variation and increase the genetic diversity of rice landraces over the past 35 years. Moreover, ethnic traditional culture practices are a crucial foundation to increase genetic diversity of rice landraces and implement on-farm conservation.

     

Selective microenvironmental effects play a role in shaping genetic diversity and structure in a Phaseolus vulgaris L. landrace: implications for on-farm conservation

Little is known about the organization of landrace diversity and about the forces that shape and maintain within- and among-landrace population diversity. However, this knowledge is essential for conservation and breeding activities. The first aim of this study was to obtain some insight into how variation has been sculptured within a cultivated environment and to identify the loci that potentially underlie selective effects by using a Phaseolus vulgaris L. landrace case study whose natural and human environment and morpho-physiological traits are known in detail. The second aim of this study was to define an appropriate on-farm conservation strategy which can serve as a model for other populations. The farmers' populations of this threatened landrace were examined with 28 single sequence repeat molecular markers. The landrace appears to be a genetically structured population in which substantial diversity is maintained at the subpopulation level (62% of the total variance). Evidence of locus-specific selective effects was obtained for five of the 13 loci-differentiating subpopulations. Their role is discussed. Our data suggest that a complex interaction of factors (differential microenvironmental selection pressures by farmers and by biotic and abiotic conditions, migration rate and drift) explains the observed pattern of diversity. Appropriate on-farm conservation of a structured landrace requires the maintenance of the entire population.     

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.     

植物保护遗传学研究进展

保护遗传学是过用遗传学的原理和研究手段,以生物多样性尤其是遗传多样性的研究和保护为核心的一门新兴学科,近几十年来,遗传学研究在生物多样性保护的理论和实践中发挥着越来越重要的作用。本文简要回顾了保护遗传学的发展历史,研究方向和涉及的概念,着重介绍了植物保护遗传学研究所取得的一些进展,包括植物系统发育重建和保护单元的确定,遗传多样性与物种和群体适应性之间的关系,群体遗传结构与保护策略的制定以及植物遗传资源的鉴定和利用等方面的内容,并强调保护遗传学研究是未来生物多样性和保护生物学研究中一个亟待加强的研究领域。     

Identification and characterisation of traditional chestnut varieties of southern Spain using morphological and simple sequence repeat (SSRs) markers

The maintenance of plant genetic resources requires the identification of places and agroforestry systems that support high levels of genetic diversity. The aim of this work was to clarify the number and names of chestnut ( Castanea sativa ) cultivars in the south of Spain. Accordingly, 100 grafted chestnut trees corresponding to 34 traditional names were evaluated using 10 qualitative morphological traits and seven simple sequence repeat (SSRs) markers. We identified 38 varieties, 12 in the Huelva region and 26 in Malaga, and synonymies and homonymies were discussed. This work demonstrated that the joint use of morphological traits and SSR markers is an efficient method to evaluate the agrobiodiversity of chestnut in this region. It was also stated that chestnut production in the south of Spain is a traditional system using varieties developed ' in situ '. This constitutes a genuine system of on-farm conservation, which is now threatened. Consequently, adopting strategies for its safeguarding are urgently recommended.     

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.

     

Date Palm Agrobiodiversity (<Emphasis Type="Italic">Phoenix dactylifera</Emphasis> L.) in Siwa Oasis,Egypt: Combining Ethnography,Morphometry, and Genetics

We evaluate date palm (Phoenix dactylifera L.) agrobiodiversity of Siwa oasis, Egypt, located at the crossroads of ancient Trans-Saharan routes, focusing on diversity both as expressed and maintained by the folk categorization system of Siwa inhabitants (through an ethnographic analysis) and as described by genetic sciences and a morphometric tool based on size and geometry of seeds. We verified that some named types are true cultivars, sharing not only a formal identity, important for Isiwan people, but also a genetic identity. However, we also confirm the existence of “ethnovarieties,” i.e., voluntary collections of multiple clones sharing phenotypic characteristics with the same local name, suggesting the genetic richness is higher than the apparent agrobiodiversity estimated by a superficial ethnobotanical approach. Finally, our research offers new insights on the relative importance of feral and cultivated date palms.     

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.     

Edible oil crops and their integration with the major cereals in North Shewa and South Welo,Central Highlands of Ethiopia: an ethnobotanical perspective

A total of 1050 sorghum (Sorghum bicolor) and tef (Eragrostis tef) fields distributed in six study sites within north Shewa and south Welo (Central Highlands of Ethiopia) were systematically surveyed to examine the status of integration of edible oil crops into the cereal-based farming system. Farmers' criteria for, and perception on, integration between edible oil crops and the major cereals at field level as well as integration between the cereal grains and the oilseeds in food making at home were studied and analyzed based on formal semi-structured interview and informal discussion with local expert farmers as key informants. Farmers' traditional space optimization technique has been instrumental in rightly fitting edible oil crops (as intercrops and border crops) into the cereal-based system. Six species of edible oil crops are integrated (70.3%) in various proportions in fields of sorghum and tef. At least one oil crop was significantly intercropped and/or border cropped in sorghum fields. Noog (Guizotia abyssinica) and sesame (Sesamum indicum) were the most important edible oil crops of the study area having strong integration with sorghum both at field and home level. On average, noog was more frequently intercropped with sorghum (8.3%) than with tef (4.5%), while it was more frequently border cropped with tef (32.4%) than with sorghum (19%). Sorghum was more frequently inter/border cropped with sesame (39/2%) than with tef (10.1/0.5%). The stronger the integration of a given oilseed with sorghum-based foods, the higher the companionship between sorghum fields and the oil crop in the landscape. This cultural practice by farmers has positive contributions to on-farm conservation of oil crops along with tef and specific sorghum landraces. The central theme of this paper therefore converges on the issue of on-farm in-situ agrobiodiversity conservation that was shaped by successive ancestral generations and passed on to the present.     

Diversity and structure of landraces of Agave grown for spirits under traditional agriculture: A comparison with wild populations of A. angustifolia (Agavaceae) and commercial plantations of A. tequilana

Traditional farming communities frequently maintain high levels of agrobiodiversity, so understanding their agricultural practices is a priority for biodiversity conservation. The cultural origin of agave spirits (mezcals) from west-central Mexico is in the southern part of the state of Jalisco where traditional farmers cultivate more than 20 landraces of Agave angustifolia Haw. in agroecosystems that include in situ management of wild populations. These systems, rooted in a 9000-year-old tradition of using agaves as food in Mesoamerica, are endangered by the expansion of commercial monoculture plantations of the blue agave variety (A. tequilana Weber var. Azul), the only agave certified for sale as tequila, the best-known mezcal. Using intersimple sequence repeats and Bayesian estimators of diversity and structure, we found that A. angustifolia traditional landraces had a genetic diversity (H(BT) = 0.442) similar to its wild populations (H(BT) = 0.428) and a higher genetic structure ((B) = 0.405; (B) =0. 212). In contrast, the genetic diversity in the blue agave commercial system (H(B) = 0.118) was 73% lower. Changes to agave spirits certification laws to allow the conservation of current genetic, ecological and cultural diversity can play a key role in the preservation of the traditional agroecosystems.     

Origins and genetic conservation of tropical trees in agroforestry systems: a case study from the Peruvian Amazon

Hundreds of native tree species are currently found in extensive agroforestry ecosystems in the Peruvian Amazon, forming an important reservoir of biodiversity. To further promote conservation, farmers are encouraged to supplement intra-specific genetic diversity in these populations with seed collected from local forests. For some tree species, however, this approach may be inappropriate, as stands of these taxa already found on-farm may not be of local origin. Despite this issue being of importance for conservation, little information is available on the history of cultivated trees in the region, a situation that we here rectify for the important fruit tree Inga edulis. Based on nuclear SSR and chloroplast DHPLC analyses of closely geographically matched natural and planted stands at five sites, it appears that cultivated material of I. edulis is primarily of non-local origin, indicating that conservation based on new wide-scale infusions from local wild stands into farms may be inappropriate in the region. Although nuclear and chloroplast diversity were both lower in planted stands, values were still relatively high (∼80 and 70% of natural stands, respectively), indicating that when farmers plant trees, good collection practice of seed from already cultivated I. edulis should be an effective means for ensuring long-term conservation on farms.     

西双版纳社区旱稻品种多样性与就地保护初探

应用户级水平农业生物多样性评价方法,对云南省西双版纳州3个少数民族村寨(哈尼族大卡老寨、基诺族巴卡小寨和傣族曼那龙寨)的旱稻(Oryza sativa)品种进行收集,就旱稻品种的管理和利用等问题进行了问卷调查和农户访谈,并基于农艺性状的统计分析,初步探讨了社区旱稻品种多样性的就地保护措施。结果如下：(1)在3个调查村寨共记载收集到31个旱稻品种,多样的旱稻品种满足了人们的不同需求;(2)主成分分析结果表明,旱稻品种农艺性状多样性主要表现在产量性状和剑叶形态两个方面,其中巴卡小寨和大卡老寨的品种多样性均高于曼那龙寨,并且这些早稻品种中存在具优良性状的稻种资源;(3)3个少数民族村寨具有不同的民族文化背景,不同民族间或不同村寨农户间自发的种子交换以及他们传统的轮作、间作耕作方式,维持和提高了旱稻品种多样性;(4)通过保护民族文化和传统习俗,充分利用当地民族的旱稻种植管理知识,促进民间自发的种子交换,由政府、科研机构和农户共同参与,通过示范和培训加强科学指导,是对西双版纳社区旱稻品种资源多样性进行就地保护的有效措施。     

Old Crop,New Society: Persistence and Change of Tartary Buckwheat Farming in Yunnan,China

Traditional agricultural systems are important for crop genetic resources conservation. Many scholars have addressed the problem of traditional cultivar replacement by modern varieties, but few have investigated the entire loss of traditional crops from farming systems. Our prior research suggested that tartary buckwheat (Fagopyrum tataricum (L.) Gaertn.) agriculture is rapidly decreasing in Yunnan China, the center of the crop’s origin and an important repository of on-farm genetic diversity. Using interdisciplinary methodology to determine whether the crop is indeed in decline and evaluate reasons behind planting trends, we found a combination of interacting agroecological, socio-cultural, and institutional factors influence tartary buckwheat planting in Yunnan. Farmer ethnicity, presence of a commercial market for the crop, and government agricultural policy were particularly important. Low commercial value of the crop compared to other alternatives, reduction of available farmland, and labor shortages were major reasons cited for crop abandonment. Despite an overall reduction in tartary buckwheat planting across a wide spectrum of farms, we also found the crop retains subsistence, rotational and cultural value for many Yunnan farmers. We conclude that although Yunnan farms are increasingly managed commercially rather than for subsistence, tartary buckwheat will continue to occupy a niche in the agricultural landscape.     

Farmers' use of wild relative and sexual reproduction in a vegetatively propagated crop. The case of yam in Benin

The impact of traditional farmers' management on genetic diversity of vegetatively propagated crops is poorly documented. In this study, we analysed the impact of ennoblement of spontaneous yams, an original traditional farmers' practice, on the genetic diversity of yam (Dioscorea sp.) in Benin. We used 11 microsatellite markers on yam tubers from a small village in northern Benin and demonstrated that wild x cultivated hybrids are spontaneously formed. Many of the spontaneous yams collected by farmers from surrounding savannah areas for ennoblement were shown to be of wild and hybrid genotypes. Moreover, we demonstrated that some yam varieties have a wild or hybrid signature. Lastly, we performed a broader ranging genetic analysis on yam material from throughout Benin and showed that this practice is used in different ecological and ethno-linguistic regions. Through this practice, farmers create new varieties with new genetic combinations via sexual reproduction of wild and cultivated yams. This system, whereby a sexual cycle and asexual propagation are mixed, ensures potential large-scale cultivation of the best genotypes while preserving the potential for future adaptation.     

大豆种质资源遗传多样性研究进展

我国拥有丰富的大豆种质资源,大豆种质资源遗传多样性研究也取得了较大进展。总结了近年来大豆种质资源组成、保存、研究、利用等几方面的研究进展,讨论了大豆遗传多样性的重要性和发展方向,以期为大豆优良品种培育相关研究提供参考。