Seed traits and genes important for translational biology--highlights from recent discoveries

Seeds provide food, feed, fiber and fuel. They are also an important delivery system of genetic information, which is essential for the survival of wild species in ecosystems and the production of agricultural crops. In this review, seed traits and genes that are potentially important for agricultural applications are discussed. Over the long period of crop domestication, seed traits have been modified through intentional or unintentional selections. While most selections have led to seed traits favorable for agricultural consumption, such as larger seeds with higher nutritional value than the wild type, other manipulations in modern breeding sometimes led to negative traits, such as vivipary, precocious germination on the maternal plant or reduced seed vigor, as a side effect during the improvement of other characteristics. Greater effort is needed to overcome these problems that have emerged as a consequence of crop improvement. Seed biology researchers have characterized the function of many genes in the last decade, including those associated with seed domestication, which may be useful in addressing critical issues in modern agriculture, such as the prevention of vivipary and seed shattering or the enhancement of yields. Recent discoveries in seed biology research are highlighted in this review, with an emphasis on their potential for translational biology.     

Assessing the Impacts of Agrobiodiversity Maintenance on Food Security Among Farming Households in Sri Lanka’s Dry Zone

Farmers’ maintenance of agrobiodiversity is fundamental to global food security, particularly in a world increasingly affected by climate change. Biodiversity helps to buffer agroecosystems from stresses like climatic variability, and the crop genetic diversity conserved with biodiverse agroecosystems is critical for plant breeding both locally and globally. Yet, despite these benefits, few studies have directly assessed the implications of household–level agrobiodiversity maintenance on household food security. Drawing on survey data collected in Sri Lanka’s Hambantota District, we evaluated the plant diversity maintained by small–scale farming households in both homegardens and crop fields and determined the relationships between this diversity and their households’ food security. We also considered how a suite of additional demographic, household, community, and farm characteristics relate to both the plant diversity maintained by a household and their food security. Similar to previous studies, the age of the agricultural decision-maker and the age and size of households’ homegardens positively correlated with the overall species richness of farming systems. Older homegardens were also identified to be more evenly distributed in their species abundance, and market–oriented households had significantly higher species richness but lower Shannon Indices. Most notably, household socioeconomic status and material wealth were important to both agrobiodiversity maintenance and household food security, while no significant relationships between species richness and food security measures were detected. These findings suggest that effort aiming to increase the food security of small–scale farming households in Sri Lanka, and elsewhere, should target those farming households with a paucity of socioeconomic assets, as these households lack both agroecological and economic resources to overcome shocks, such as those associated with climate change.     

Agricultural diversification: the potential for underutilised crops in Africa's changing climates.

Two of the greatest challenges currently facing humanity are the potential consequences of climate change and the actual consequences of reduced agricultural diversity. This paper considers the consequences of both climate change and reduced agricultural diversity on global food security and nutrition. The inextricable link between climate change and crop diversity is examined, particularly in the context of crop production in Africa where most agricultural diversity exists and where climate change will have most impact. The Green Revolution, often seen as a model for increasing global agricultural productivity, is reconsidered in terms of its failure to make a significant impact in hostile tropical environments such as those of much of Africa. An alternative or, at least, a complementary strategy, is advocated where we might better harness the huge repository of indigenous plant species cultivated and conserved by local communities for many generations across variable climates. An example is given of multidisciplinary research on bambara groundnut (Vigna subterranea), an ancient grain legume grown, cooked, processed and traded mainly by subsistence women farmers in sub-Saharan Africa. The experience gained on bambara groundnut is considered as a basis for similar efforts on many other potentially useful underutilised food crops in the climates of the future.     

Supporting crop pollinators with floral resources: network‐based phenological matching

The production of diverse and affordable agricultural crop species depends on pollination services provided by bees. Indeed, the proportion of pollinator‐dependent crops is increasing globally. Agriculture relies heavily on the domesticated honeybee; the services provided by this single species are under threat and becoming increasingly costly. Importantly, the free pollination services provided by diverse wild bee communities have been shown to be sufficient for high agricultural yields in some systems. However, stable, functional wild bee communities require floral resources, such as pollen and nectar, throughout their active season, not just when crop species are in flower. To target floral provisioning efforts to conserve and support native and managed bee species, we apply network theoretical methods incorporating plant and pollinator phenologies. Using a two‐year dataset comprising interactions between bees (superfamily Apoidea, Anthophila) and 25 native perennial plant species in floral provisioning habitat, we identify plant and bee species that provide a key and central role to the stability of the structure of this community. We also examine three specific case studies: how provisioning habitat can provide temporally continuous support for honeybees (Apis mellifera) and bumblebees (Bombus impatiens), and how resource supplementation strategies might be designed for a single genus of important orchard pollinators (Osmia). This framework could be used to provide native bee communities with additional, well‐targeted floral resources to ensure that they not only survive, but also thrive.     

The challenge of accurately documenting bee species richness in agroecosystems: bee diversity in eastern apple orchards

Bees are important pollinators of agricultural crops, and bee diversity has been shown to be closely associated with pollination, a valuable ecosystem service. Higher functional diversity and species richness of bees have been shown to lead to higher crop yield. Bees simultaneously represent a mega‐diverse taxon that is extremely challenging to sample thoroughly and an important group to understand because of pollination services. We sampled bees visiting apple blossoms in 28 orchards over 6 years. We used species rarefaction analyses to test for the completeness of sampling and the relationship between species richness and sampling effort, orchard size, and percent agriculture in the surrounding landscape. We performed more than 190 h of sampling, collecting 11,219 specimens representing 104 species. Despite the sampling intensity, we captured <75% of expected species richness at more than half of the sites. For most of these, the variation in bee community composition between years was greater than among sites. Species richness was influenced by percent agriculture, orchard size, and sampling effort, but we found no factors explaining the difference between observed and expected species richness. Competition between honeybees and wild bees did not appear to be a factor, as we found no correlation between honeybee and wild bee abundance. Our study shows that the pollinator fauna of agroecosystems can be diverse and challenging to thoroughly sample. We demonstrate that there is high temporal variation in community composition and that sites vary widely in the sampling effort required to fully describe their diversity. In order to maximize pollination services provided by wild bee species, we must first accurately estimate species richness. For researchers interested in providing this estimate, we recommend multiyear studies and rarefaction analyses to quantify the gap between observed and expected species richness.     

Using seed purity data to estimate an average pollen mediated gene flow from crops to wild relatives

Gene flow from crops to wild related species has been recently under focus in risk-assessment studies of the ecological consequences of growing transgenic crops. However, experimental studies addressing this question are usually temporally or spatially limited. Indirect population-structure approaches can provide more global estimates of gene flow, but their assumptions appear inappropriate in an agricultural context. In an attempt to help the committees providing advice on the release of transgenic crops, we present a new method to estimate the quantity of genes migrating from crops to populations of related wild plants by way of pollen dispersal. This method provides an average estimate at a landscape level. Its originality is based on the measure of the inverse gene flow, i.e. gene flow from the wild plants to the crop. Such gene flow results in an observed level of impurities from wild plants in crop seeds. This level of impurity is usually known by the seed producers and, in any case, its measure is easier than a direct screen of wild populations because crop seeds are abundant and their genetic profile is known. By assuming that wild and cultivated plants have a similar individual pollen dispersal function, we infer the level of pollen-mediated gene flow from a crop to the surrounding wild populations from this observed level of impurity. We present an example for sugar beet data. Results suggest that under conditions of seed production in France (isolation distance of 1,000 m) wild beets produce high numbers of seeds fathered by cultivated plants. Received: 5 February 2001 / Accepted: 26 March 2001     

Flowering time and elevated atmospheric CO2

Flowering is a critical milestone in the life cycle of plants, and changes in the timing of flowering may alter processes at the species, community and ecosystem levels. Therefore understanding flowering-time responses to global change drivers, such as elevated atmospheric carbon dioxide concentrations, [CO(2)], is necessary to predict the impacts of global change on natural and agricultural ecosystems. Here we summarize the results of 60 studies reporting flowering-time responses (defined as the time to first visible flower) of both crop and wild species at elevated [CO(2)]. These studies suggest that elevated [CO(2)] will influence flowering time in the future. In addition, interactions between elevated [CO(2)] and other global change factors may further complicate our ability to predict changes in flowering time. One approach to overcoming this problem is to elucidate the primary mechanisms that control flowering-time responses to elevated [CO(2)]. Unfortunately, the mechanisms controlling these responses are not known. However, past work has indicated that carbon metabolism exerts partial control on flowering time, and therefore may be involved in elevated [CO(2)]-induced changes in flowering time. This review also indicates the need for more studies addressing the effects of global change drivers on developmental processes in plants.     

Characterization of wild bee communities in apple and blueberry orchards

1. Wild bees provide invaluable ecosystem services in agricultural landscapes such as pollination. However, in recent decades, pollinator biodiversity, especially in wild bees, is declining on a global scale, with potentially far‐reaching consequences for crop production. Thus, there is an urgent need to determine whether wild bees are present in agricultural systems, such as fruit orchards.
2. In the present study, we examined the wild bee fauna at species and community levels during the period of bee activity (May to August) in apple and high‐bush blueberry orchards in New England.
3. Bee communities are crop‐specific and dominated by very few species, which fluctuate according to crop and season. The blueberry associated bee fauna was more diverse. In apple, communities were phylogenetically clustered at the genus level and dominated by solitary ground nesting bees within the genus Andrena. Species fluctuated widely in presence and abundance throughout the season, leading to differences in community composition and functional trait structure.
4. The results obtained in the present study show that apple and blueberry harbour a distinct and diverse bee fauna that performs vital pollination services in orchards. Our results provide essential baseline data for wild bees in blueberry and apple orchards and this can be used to improve management and conservation strategies for wild bee preservation in these crops.

     

城子崖遗址植硅体反映的生业经济模式

龙山文化是中国史前社会形态演进的关键阶段,亦是农业强化生产的关键时期。城子崖遗址是鲁北平原史前区域中心城址,其生业经济研究有助于理解该地区社会复杂化及文明进程。本文对城子崖遗址龙山时期不同遗迹单位的15份土样进行了系统的植硅体分析,尝试探讨了该遗址龙山文化时期的社会发展和生业经济水平、农作物生产和加工方式、野生植物资源利用情况以及各遗迹堆积及其所反映的人类行为活动信息。结果显示,该遗址龙山文化时期已形成粟、黍、稻、小麦、稗(可能)的农作物组合方式;同时,广泛采集利用聚落周边的自然植物资源,是农业与采集业并存发展的生业经济模式。先民在作物栽培中进行了锄草、灌溉等较为精细的管理,其中,黍较粟更具耐旱抗病特性,加上田间管理需求较低而被优先选择栽培。先民在收获作物时,采用类似割穗、掐穗等方法以减少作物茎秆及杂草混入,随后在户外进行小规模地脱壳、扬场工作。此外,根据灰坑中植硅体的组合特征可将其分为生活垃圾、谷物加工、蓄水淘米三个类型,水井和墓葬内的植硅体则分别与生活环境和丧葬环节等信息相关。     

Patterns and perceptions of wildlife crop raiding in and around Kerinci Seblat National Park, Sumatra

Crop raiding can reduce farmers' tolerance towards wildlife. Despite higher human population densities in rural areas, and more rapid conversion of forest to farmland, much less is known about crop raiding in Asia than in Africa. Over 14 months, we identified perceived and actual crop pests, and their patterns of crop raiding from farmland in and around Kerinci Seblat National Park, Sumatra. Farmers named either the wild boar Sus scrofa (80%) or the pig-tailed macaque Macaca nemestrina (20%) as the two most destructive crop pests. From 5125 crop raids by 11 species of mammal, most raids were indeed made by the wild boar (56%) and the pig-tailed macaque (19%). For all species combined, temporal crop raiding peaks were positively correlated with periods of high rainfall. Spatially, most crop raids occurred nearest to the forest edge and the local guarding strategies used were ineffective. However, raids by wild boars were more extensive than raids by pig-tailed macaques, which caused much greater crop damage (73%) than wild boars (26%), contrary to farmers' perceptions. Our research suggests that alternative mitigation strategies need to be trialed over dry and rainy seasons to identify the most effective strategies and that guarding effort should be increased during the rainy seasons and tailored towards specific crop raiding species based on their unique spatial patterns.     

Negative effects of pesticides on wild bee communities can be buffered by landscape context

Wild bee communities provide underappreciated but critical agricultural pollination services. Given predicted global shortages in pollination services, managing agroecosystems to support thriving wild bee communities is, therefore, central to ensuring sustainable food production. Benefits of natural (including semi-natural) habitat for wild bee abundance and diversity on farms are well documented. By contrast, few studies have examined toxicity of pesticides on wild bees, let alone effects of farm-level pesticide exposure on entire bee communities. Whether beneficial natural areas could mediate effects of harmful pesticides on wild bees is also unknown. Here, we assess the effect of conventional pesticide use on the wild bee community visiting apple (Malus domestica) within a gradient of percentage natural area in the landscape. Wild bee community abundance and species richness decreased linearly with increasing pesticide use in orchards one year after application; however, pesticide effects on wild bees were buffered by increasing proportion of natural habitat in the surrounding landscape. A significant contribution of fungicides to observed pesticide effects suggests deleterious properties of a class of pesticides that was, until recently, considered benign to bees. Our results demonstrate extended benefits of natural areas for wild pollinators and highlight the importance of considering the landscape context when weighing up the costs of pest management on crop pollination services.     

Evolutionarily inspired solutions to the crop pollination crisis

The global decline in insect diversity threatens pollination services, potentially impacting crop production and food security. Here, we argue that this looming pollination crisis is generally approached from an ecological standpoint, and that consideration of evolutionary principles offers a novel perspective. First, we outline that wild plant species have overcome ‘pollination crises’ throughout evolutionary history, and show how associated principles can be applied to crop pollination. We then highlight technological advances that can be used to adapt crop flowers for optimal pollination by local wild pollinators, especially by increasing generalization in pollination systems. Thus, synergies among fundamental evolutionary research, genetic engineering, and agro-ecological science provide a promising template for addressing a potential pollination crisis, complementing much-needed strategies focused on pollinator conservation.     

Termites and Chinese agricultural system: applications and advances in integrated termite management and chemical control

Termites are eusocial arthropod decomposers,and improve soil fertility,crop yield,and also are used by humans for their ben efits across the world.However,some species of termites are becoming a threat to the farming community as they are directly and indirectly causing major losses to the agricultural system.It is estimated that termites cost the global economy more than 40 billion USD annually,and considerable research has been done on their management.In this review,we present the available information related to sustainable and integrated termite management practices(ITM).Furthermore,we insist that the better management of this menace can be possible through:(i)improving traditional methods to keep termites away from crops;(ii)improving agricultural practices to maintain plants with more vigor and less susceptible to termite attack;and(iii)integration of available techniques to reduce termite infestation in crops and surroundings.The application of an effective combination of traditional practices with recently developed approaches is the best option for agricultural growers.Moreover,keeping in mind the beneficial nature of this pest,more innovative efforts for its management,particularly using rapidly emerging technology(e.g.,RNA interference),are needed.     

Impact of integrated pest management on food and horticultural crops in Africa

In sustainable agricultural development, integrated pest management (IPM) can play a key role in the reduction of crop losses, thereby increasing productivity while minimizing environmental contamination and health hazards. In recent years, agricultural research and development partners have pioneered outstanding contributions in IPM, notably in varietal resistance against pests, biological control of alien invasive species, substitution of inorganic pesticides with biopesticides, new export market opportunities, and new tools in biotechnology. Success stories are not limited to these areas, but are also found in the areas of human capital development, information management, and participatory approaches. The potential of IPM to contribute to poverty alleviation and food security is, however, poorly realized in Africa due to a myriad of factors, including inadequate deployment of high-yielding crop varieties, harmful pesticide regimes, political instability, conflicts in social values and civil wars, inappropriate agricultural policies, biased global trade policies, lack of market information, and poor rural infrastructures. Few African countries have adopted IPM as the official national crop protection policy and there is no framework for resource allocation to support widespread promotion of research and training in IPM. This calls for reshaping and revisiting a number of policies related to food production and agricultural development, in order to encourage partnership and participation in the identification, analysis, advocacy, and follow-up of agricultural policy issues as well as public awareness of the effect of pests and diseases on food security and the environment.     

气候变化对野生植物的影响及保护对策

以温室气体浓度持续上升、全球气候变暖为主要特征的全球气候变化对野生植物及生物多样性造成的潜在影响, 已经引起了国际学者的高度关注。本文总结了全球气候变化的现状与未来趋势, 概述了中国野生植物的保护及管理现状, 从不同侧面综述了国内外关于全球气候变暖对野生植物影响的研究进展和动态, 包括气候带北移、两极冰山退缩、高海拔山地变暖、海平面上升、早春温度提前升高、荒漠草原土壤增温、旱涝急转弯等对野生植物造成的影响以及气候变暖对种间关系和敏感植物类群的影响, 并从气候变化背景下全球生态系统敏感度、植物多样性、物种迁移与气候槽(sink areas)、物种适应与灭绝以及物候节律5个方面分析了未来全球变暖影响野生植物的总体趋势。在以后的野生植物保护与管理中, 应确定全球气候变化的植物多样性敏感区, 重点关注对气候变化敏感的植物类群以及气候要素改变植物-动物互作关系中的野生植物, 自然保护区的建设要重点考虑全球气候变化的影响, 通过在全球范围内对野生植物分布和种群变化进行长期、系统的追踪监测, 建立有效的数据库, 发展野生植物迁地保护的保育技术及信息网络, 发展有关野生植物对全球气候变化响应的量化指标及相应的模型。最后提出应将全球气候变化下野生植物保护与管理列入相关基金会的研究重点。     

Primate Crop Feeding Behavior,Crop Protection,and Conservation

Many species across a range of primate genera, irrespective of dietary and locomotory specializations, can and will incorporate agricultural crops in their diets. However, although there is little doubt that rapid, extensive conversion of natural habitats to agricultural areas is significantly impacting primate populations, primate crop foraging behaviors cannot be understood solely in terms of animals shifting to cultivated crops to compensate for reduced wild food availability. To understand fully why, how, and when primates might incorporate crops in their dietary repertoire, we need to examine primate crop foraging behavior in the context of their feeding strategies and nutritional ecology. Here I briefly outline current debates about the use of terms such as human–wildlife conflict and crop raiding and why they are misleading, summarize current knowledge about primate crop foraging behavior, and highlight some key areas for future research to support human–primate coexistence in an increasingly anthropogenic world.     

中国农业野生植物原生境保护现状及建议

中国的农业野生植物十分丰富,约有1.5万种,从2001年开始实施了农业野生植物原生境保护,目前已建成或正在建设的原生境保护区(点)共20个.然而,由于该项研究起步比较晚,势必存在不足之处,就此提出了相应的建议.     

Genome‐wide analysis of allele frequency change in sunflower crop–wild hybrid populations evolving under natural conditions

Crop‐wild hybridization occurs in numerous plant species and could alter the genetic structure and evolutionary dynamics of wild populations. Studying crop‐derived alleles in wild populations is also relevant to assessing/mitigating the risks associated with transgene escape. To date, crop‐wild hybridization has generally been examined via short‐term studies, typically within a single generation, focusing on few traits or genetic markers. Little is known about patterns of selection on crop‐derived alleles over multiple generations, particularly at a genome‐wide scale. Here, we documented patterns of natural selection in an experimental crop × wild sunflower population that was allowed to evolve under natural conditions for two generations at two locations. Allele frequencies at a genome‐wide collection of SNPs were tracked across generations, and a common garden experiment was conducted to compare trait means between generations. These data allowed us to identify instances of selection on crop‐derived alleles/traits and, in concert with QTL mapping results, test for congruence between our genotypic and phenotypic results. We found that natural selection overwhelmingly favours wild alleles and phenotypes. However, crop alleles in certain genomic regions can be favoured, and these changes often occurred in parallel across locations. We did not, however, consistently observe close agreement between our genotypic and phenotypic results. For example, when a trait evolved towards the wild phenotype, wild QTL alleles associated with that trait did not consistently increase in frequency. We discuss these results in the context of crop allele introgression into wild populations and implications for the management of GM crops.     

Genetic approaches for breeding heat stress tolerance in faba bean (<Emphasis Type="Italic">Vicia faba</Emphasis> L.)

Vicia faba L. (faba bean) is an important legume and is cultivated essentially as a cool-season crop. Changes in sowing dates and lack of precipitation expose faba bean crop to drought and heat stresses. The gradual rise in global temperatures owing to climate change is likely to exacerbate the detrimental effects of hot and dry climatic conditions on faba bean cultivation. High temperature stress is particularly damaging to faba bean during the flowering period, when the viability of pollen is critical for successful reproduction. Recent studies have shown that maintenance of protein homeostasis through synthesis of heat shock proteins plays a key role in the heat response of plants. To date, there has been no significant work linking the heat response of faba bean to the repertoire of its heat shock proteins. While quantitative trait loci have been identified for resistance against biotic stresses in faba bean, there is no parallel success with abiotic stresses in this species. Programs aiming at genetic improvement of the heat/drought resistance of this crop by both conventional breeding and molecular breeding methods are hampered because of the large and majorly ill-analyzed genome of faba bean plants. Likewise, molecular and biotechnology-related tools are poorly developed for faba bean; as a result, the fruits of transgenic research developed with model plant species are not reaching this crop. While specifically discussing the prospects for the genetic improvement of faba bean against heat and drought stresses, we highlight the areas of research which need to be strengthened on faba bean.     

Long distance pollen-mediated gene flow at a landscape level: the weed beet as a case study

Gene flow is a crucial parameter that can affect the organization of genetic diversity in plant species. It has important implications in terms of conservation of genetic resources and of gene exchanges between crop to wild relatives and within crop species complex. In the Beta vulgaris complex, hybridization between crop and wild beets in seed production areas is well documented and the role of the ensuing hybrids, weed beets, as bridges towards wild forms in sugar beet production areas have been shown. Indeed, in contrast to cultivated beets that are bi-annual, weed beets can bolt, flower and reproduce in the same crop season. Nonetheless, the extent of pollen gene dispersal through weedy lineages remains unknown. In this study, the focus is directed towards weed-to-weed gene flow, and we report the results of a pollen-dispersal analysis within an agricultural landscape composed of five sugar beet fields with different levels of infestation by weed beets. Our results, based on paternity analysis of 3240 progenies from 135 maternal plants using 10 microsatellite loci, clearly demonstrate that even if weedy plants are mostly pollinated by individuals from the same field, some mating events occur between weed beets situated several kilometres apart (up to 9.6 km), with rates of interfield-detected paternities ranging from 11.3% to 17.5%. Moreover, we show that pollen flow appears to be more restricted when individuals are aggregated as most mating events occurred only for short-distance classes. The best-fit dispersal curves were fat-tailed geometric functions for populations exhibiting low densities of weed beets and thin-tailed Weibull function for fields with weed beet high densities. Thus, weed beet populations characterized by low density with geographically isolated individuals may be difficult to detect but are likely to act as pollen traps for pollen emitted by close and remote fields. Hence, it appears evident that interfield pollen-mediated gene flow between weed beets is almost unavoidable and could contribute to the diffusion of (trans)genes in the agricultural landscape.