Genetic resources in breeding for adaptation

Summary A crop's ability to productively exploit its environment depends on many adaptive features which are controlled by multiple genes, interacting among themselves and with the environment in complex ways.To promote widespread adoption, breeders frequently seek to develop broad adaptation in their varieties, often through the use of genes having a large effect on a single adaptive feature. Such genes may occur within the crop, its wild relatives, or unrelated taxa. Genes for many adaptive features (e.g. temperature tolerance) may be found in extreme environments. Others (e.g. photoperiod insensitivity) may have evolved away from primary centres of origin.Well characterized and documented ex situ germplasm collections aim to serve plant breeders' need for genes. Molecular marker and geographic information system (GIS) techniques are proving useful for locating and characterizing genetic diversity. New techniques (e.g. core collections and electronic information systems) are adding to the value of collections. Ex situ and in situ conservation of wild crop relatives are receiving increased attention. With all organisms becoming a potential source of genes for breeding, in situ ecosystem conservation is assuming added significance.Farmers, particularly in diverse, marginal environments in developing countries, continue to breed landraces adapted to their specific circumstances. In areas of high ecological diversity, a multitude of adaptive gene complexes have been selected within small geographic areas. Conventional breeding frequently neglects such farmers, and participatory methods based on locally adapted diversity, coupled with appropriate technical and policy support, may prove more effective in meeting their needs. Such dynamic, on-farm conservation and management systems would also enable genetic diversity to continue to evolve as a resource for conventional breeding.For genetic resources to remain a foundation for future sustainable agricultural development, complementary conservation and breeding strategies are needed.     

On-farm Conservation Strategy to Ensure Crop Genetic Diversity in Changing Agro-ecosystems in the Republic of Korea

With the recognition of certain limitations of ex situ methods for conservation of plant genetic resources the Convention on Biological Diversity (CBD) at the ‘Earth Summit’ in 1992 highlighted the importance of traditional knowledge of indigenous and local communities that are relevant for the conservation and sustainable use of biological diversity and gave considerable attention to on‐farm and other forms of in situ conservation. Unlike semi‐static nature of ex situ conservation the in situ or on‐farm conservation (OFC) is a dynamic evolutionary process. In developing countries like Republic of Korea, where there is a continuum between the use of traditional and modern cultivars, integration of OFC with already existing gene‐bank activities in the country will be an effective approach for conservation and sustainable use of the country's crop genetic resources. However, very little efforts have been made so far in developing strategies for OFC, therefore, in this paper we describe the importance of OFC and strategies for its development in Republic of Korea. Surveys over the last 20 years have shown that the landraces of major crops have been almost replaced by newly bred varieties in the country. But some vegetatively propagated or minor crop species are still being maintained in the farmers’ fields. We have identified crop landraces, which can be classified into four different categories from the OFC point of view. These are vegetatively propagated landraces, sexually reproduced landraces, landraces with improved varieties and landraces cultivated for the reasons of personal preference. The related issues on OFC including implementation methods from the point of national cooperative system in designated specific condition are also discussed to ensure the genetic diversity in the fast changing agro‐ecosystem of the country.     

Value of permanent grassland habitats as reservoirs of Festuca pratensis Huds. and Lolium multiflorum Lam. populations for breeding and conservation

European natural and semi-natural grassland form reservoirs of genetic resources containing highly adapted and variable ecotype populations of forage plants. Variation within these reservoirs is stimulated by variation in natural and anthropogenic site-related factors. Changes in agricultural practices lead to the loss of many characteristic habitats. In order to preserve resources for breeding, targeted conservation strategies for germplasm in gene banks (ex-situ) or on site (in-situ) are needed. In order to define site-related criteria for the potential of habitats to preserve valuable resources for breeding and conservation, 38 different habitats across Switzerland were selected to collect Festuca pratensis Huds. and Lolium multiflorum Lam. ecotype populations. Phenotypic variation and population differentiation of 60 single plants were evaluated in a field experiment using 16 morpho-physiological traits. For F. pratensis, ecotype populations and cultivars were clearly separated and there was a significant correlation between diversity of morphological traits and geographic location of sampling sites. For L. multiflorum no clear separation of ecotype populations and cultivars was observed suggesting gene flow from adjacent temporary leys into permanent grassland. Several ecotype populations were superior to cultivars in important traits such as early heading or resistance to winter damage, indicating the importance of natural habitats as a reservoir of genetic resources for breeding. In conclusion, maintenance of permanent grassland in contrasting environments appears to be a promising strategy for preserving valuable genetic variation of forage grasses. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Variation in Rauvolfia serpentina genetic resources in India

Summary Rauvolfia serpentina (L.) Benth. ex Kurtz genetic resources from several regions of India were evaluated at New Delhi in the period 1970–76 to understand the variation pattern for root yield and associated polygenic traits. The Uttar Pradesh populations represented the wides range of diversity for most of the traits; the populations from Assam possessed high root yield potential. In other states, too, variation was evident. On the basis of variation pattern, areas in the Indian subcontinent were identified for collection and conservation of Rauvolfia germplasm.     

Diversity and adaptation in rice varieties under static (ex situ) and dynamic (in situ) management

This study compares genebank-conserved and farmer managed populations of the same farmers' varieties of rice. Seven varieties that had been collected twice, in the early 1980s and in 1991, were recollected in 1997 after having been grown continuously in farmers' fields. Since the first genebank collection, rice cultivation in the Meking delta has been intensified with a rather abrupt switch from single to double cropping, more use of chemical fertilisers, improved water management, and more market oriented production. Many farmers' varieties have been maintained as a second crop but with a considerably delayed planting time compared to previous practice. In this experiment, the ex situ materials represent adaptation to pre-intensification conditions while the in situ populations have been exposed to the intensive production system for a number of years. The materials were tested in the wet season of 1997 under current farmers' management practices in an on-farm field experiment within the area where the varieties originated. Agronomic, stress resistance and morphological traits and variation at 7 isozyme loci were observed in the field or laboratory. Analysis of variance (ANOVA) and Principal Component Analyses (PCA) were used to study differences in agronomic and morphological traits between ex and in situ populations. Isozyme variation was analyzed by Nei's diversity indices and Wright's F-statistics. Farmer-managed populations showed a general trend of later flowering and maturity time, more uniformity of grain quality, lower frequency of undesired off-types, and reduced drought stress tolerance compared with corresponding ex situ populations. There were no significant differences in grain yield or tolerance to biotic stresses. Allelic frequencies of isozymes showed no consistent differences that could be related to changes of the farming system. These results are interpreted as an adaptation to the changed farming system and include natural and farmers' selection for maturity time (all varieties are photoperiodic)and market standards. The poorer drought tolerance may reflect the fact that such stress was common before intensification but is not normally a factor under the current water management regime. For in situconservation strategies this case sheds some light on the survival of allelic diversity vs. adaptedness. Isozyme data indicate maintenance of allelic diversity. Adaptedness, however, is at risk under on-farm conservation. Natural and intentional selection will normally not remain constant over time. Consequent genetic changes include loss of adaptation to past conditions and building up of adaptation to new. In this case such changes have happened surprisingly fast. However, changes are limited to adaptation to factors of the environment and to market-relevant quality traits. Yield seems to be unaffected. Considering needs for crop improvement this case has kept the materials `updated' with respect to adaptation and unchanged with respect to yield potential. This revised version was published online in August 2006 with corrections to the Cover Date.     

Levels and distribution of genetic diversity of coconut (Cocos nucifera L., var. Typica form typica) from Sri Lanka assessed by microsatellite markers

The coconut variety Typica, form typica, commonly known as Sri Lanka tall coconuts is the most widely exploited and grown variety in Sri Lanka. Under the coconut bio-diversity conservation programme, several Typica populations have been collected by island-wide surveys and planted ex situ. Thirty-three coconut populations were subjected to microsatellite assay with eight coconut-specific microsatellite primer pairs in order to study the levels and distribution of genetic variation of the collected materials for formulating future collection strategies and selecting parents for the breeding programme. A total of 56 alleles were detected ranging from 3 to 10 alleles per primer pair with an average of 7 alleles per locus. Overall a very high level of genetic diversity was detected (0.999) for all the populations studied ranging from 0.526 for population Debarayaya to 0.683 for population Dickwella. Only four introduced coconut populations, i.e. Clovis, Margeret, Dickwella, Mirishena and an embryo-cultured population were clearly separated from the resulting dendrogram. A very high level of within population variation (99%)accounted for native populations suggests a common history and a restricted genetic base for native Sri Lankan tall coconuts. Categorization of alleles into different classes according to their frequency and distribution confirmed the results of the dedrogram and concluded the adequacy of single large collection from the entire target area to represent the total genetic diversity in Sri Lanka. This study discusses useful information regarding conservation and breeding of coconut in Sri Lanka. This revised version was published online in August 2006 with corrections to the Cover Date.     

Habitat and management affect genetic structure of Festuca pratensis but not Lolium multiflorum ecotype populations

Genetic diversity present in permanent grassland may be valuable for broadening gene pools in breeding programmes and for conservation of genetic resources. However, little is known about the amount of genetic diversity present at specific habitats and about site‐related factors affecting it. To identify valuable habitats, genetic diversity of 12 ecotype populations and four reference cultivars of both Festuca pratensis Huds. and Lolium multiflorum Lam. was analysed using Simple sequence repeat markers (SSR). Analysis of molecular variance revealed a larger within population variation for L. multiflorum (97.1%) than for F. pratensis (92.6%). F. pratensis ecotype populations were clearly separated from cultivars and formed three distinct subclusters according to the geographic regions they were sampled from. Differences between L. multiflorum ecotype populations and cultivars were small and no grouping of populations was observed. Thus, only F. pratensis ecotype populations were structured and habitat as well as management had a slight influence on genetic structure. This information may allow the design of individual strategies for targeted utilization of genetic resources in plant breeding programmes.     

Widening the genetic base of cultivated gene pool following introgression from wild Lens taxa

Wild Lens taxa are a reservoir of useful rare genes/alleles for widening the genetic base and synthesis of a new gene pool of lentil. To maximize and sustain lentil production, new gene sources are needed to be identified and incorporated into cultivated background. This needs a comprehensive approach to accumulate favourable alleles from distantly related germplasm for widening of the cultivated gene pool and would be the most appropriate strategy to solve the various problems associated with stressed crop production and plateaued yields. Furthermore, expansion of deeper understanding of lentil genomics along with extensive research undertaken in other crop species can provide suitable guidelines to cover the distribution of Lens genus and component gene pools for further remarkable progress in lentil genetic improvement. This review aims at the genus Lens distribution and gene pools, crop germplasm conserved in ex‐situ and in‐situ collection, wild species characterization and evaluation for useful traits of interest to solve production‐related problems, highlight useful gene sources present in different gene pools and the progress achieved for widening the genetic base of cultivated varieties of lentil through wide hybridization and exploring lentil genomics.     

Statistical methods for classifying genotypes

In genetic resource conservation and plant breeding, multivariate data on continuous and categorical traits are collected with the objective of selecting genotypes and accessions that best represent the entire population or gene collection with the minimum loss of genetic diversity. Therefore, the best numerical classification strategy is the one that produces the most compact and well-separated groups, that is, minimum variability within each group and maximum variability among groups. In this study, we review geometric classification techniques as well as statistical models based on mixed distribution models. The two-stage sequential clustering strategy uses all variables, continuous and categorical, and it tends to form more homogeneous groups of individuals than other clustering strategies. The sequential clustering strategy can be applied to three-way data comprising genotypes × environments × attributes. This approach groups genotypes with consistent responses for most of the continuous and categorical traits across environments. This revised version was published online in July 2006 with corrections to the Cover Date.     

大数据环境下林业资源信息云服务体系架构

为了应对林业资源信息管理在大数据时代面临的新机遇和挑战,解决智慧林业中林业资源信息服务体系架构设计与应用问题,基于云计算理论与技术,深入剖析了林业资源信息云服务的内涵及其基本特征,参照IEEE 1471 2000提出了林业资源信息云服务架构设计元模型,进而借鉴架构模式中的层架构模式设计思想,初步设计了林业资源信息云服务体系架构的总体结构和分布式协同部署模式,在国家林业局和辽宁省开展的林业资源监管服务系统构建过程中对体系架构的理论设计结果进行了实践应用和反馈修正。结果表明,林业资源信息云服务体系架构能够满足大数据环境下林业资源监管业务需求,具有良好的实用性和推广性。     

Genomic selection and enablers for agronomic traits in maize (Zea mays): A review

Maize is a commodity crop providing millions of people with food, feed, industrial raw material and economic opportunities. However, maize yields in Africa are relatively stagnant and low, at a mean of 1.7 t ha⁻¹ compared with the global average of 6 t ha⁻¹. The yield gap can be narrowed with accelerated and precision breeding strategies that are required to develop and deploy high-yielding and climate-resilient maize varieties. Genomic and phenotypic selections are complementary methods that offer opportunities for the speedy choice of contrasting parents and derived progenies for hybrid breeding and commercialization. Genomic selection (GS) will shorten the crop breeding cycle by identifying and tracking desirable genotypes and aid the timeous commercialization of market-preferred varieties. The technology, however, has not yet been fully embraced by most public and private breeding programmes, notably in Africa. This review aims to present the importance, current status, challenges and opportunities of GS to accelerate genetic gains for economic traits to speed up the breeding of high-yielding maize varieties. The first section summarizes genomic selection and the contemporary phenotypic selection and phenotyping platforms as a foundation for GS and trait integration in maize. This is followed by highlights on the reported genetic gains and progress through phenotypic selection and GS for grain yield and yield components. Training population development, genetic design and statistical models used in GS in maize breeding are discussed. Lastly, the review summarizes the challenges of GS, including prediction accuracy, and integrates GS with speed breeding, doubled haploid breeding and genome editing technologies to increase breeding efficiency and accelerate cultivar release. The paper will guide breeders in selection and trait introgression using GS to develop cultivars preferred by the marketplace.     

Breeding tepary bean (Phaseolus acutifolius) for drought adaptation: A review

Tepary bean (Phaseolus acutifolius A. Gray) is a relatively higher drought-tolerant crop than common bean (P. vulgaris), serving as genetic resource for food and genetic enhancement of related legumes. Tepary bean production is hampered by cultivation of low yielding and abiotic stress-susceptible cultivars. Targeted selection of agronomic, physiological and biochemical traits that maximizes yield gains using Phaseolus gene pool is useful to develop stress-tolerant and high-performing genotypes. The objective of this review is to provide breeding progress made regarding tepary bean improvement for drought adaptation. Agronomic, physiological and biochemical traits utilized for selection of drought-tolerant genotypes are highlighted. Genetic and genomic resources developed for tepary bean or closely related species such as common bean useful for genetic analysis and breeding are discussed. Opportunities and challenges to facilitate breeding of tepary bean genotypes with improved abiotic stress adaptation are highlighted. This will enable development of drought-tolerant tepary bean genotypes targeting selection of agronomic, physiological and biochemical traits. Use of genetically related and complementary Phaseolus species and marker-assisted selection method is key to developing drought-tolerant genotypes.     

Seeing farmers for the trees: Community forestry and the arborealisation of agriculture in northern Thailand1

Abstract: The campaign for community forestry in upland areas of northern Thailand reflects an ‘arborealised’ perspective on upland agriculture. Arborealisation – which I define as the process whereby upland livelihoods are recast as forest livelihoods – is evident in the main elements of NGO and academic advocacy for the resource rights of upland peoples. As a result of this arborealised perspective, securing rights to forest resources has come to be seen as the key to enhancing the livelihood security of upland farmers. However, the emphasis of the proposed community forest legislation on communally managed forest resources means that it will do little to enhance the tenure security of farmers in relation to agricultural land.      

Genetic diversity of garlic (Allium sativum L.) germplasm from China by fluorescent‐based AFLP,SSR and InDel markers

Garlic (Allium sativum L.), an asexually propagated crop, is an important vegetable and medicinal plant. China is the biggest garlic producer in the world; however, the genetic background of garlic from China is not well understood. In this study, population structure and clustering analysis of garlic germplasm was performed using amplified fragment length polymorphism (AFLP), simple sequence repeat (SSR) and insertion–deletion (InDel) markers. Among 212 accessions of garlic, genetic diversity analysis identified 546 alleles amplified by AFLP, SSR and InDel primers, and 492 of these were polymorphic. All accessions were divided into five groups by structure analysis and neighbor‐joining clustering. Most traits, including allicin content, were only slightly affected by population structure, which indicated that this germplasm can be used as populations for association mapping. The results provide a molecular basis for understanding the genetic diversity of the garlic germplasm preserved in China.     

Molecular evaluation of genetic variability in wild populations of mulberry (Morus serrata Roxb.)

Sixteen populations of the wild mulberry, Morus serrata Roxb., were analysed for their genetic diversity with the aim of using them in introgressive breeding programmes with cultivated relatives. Five genets from each population were collected from different natural populations of M. serrata present in Uttaranchal and Himachal Pradesh in India, and diversity of morpho‐anatomical traits and inter‐simple sequence repeat (ISSR) markers were studied. Significant amounts of genetic diversity were observed among these populations for morpho‐anatomical as well as DNA markers. The 17 ISSR primers generated a total of 95 DNA markers, 51 of which were polymorphic, revealing 67% polymorphism among the populations. The pair‐wise genetic distance, estimated from these DNA markers varied from 0.091 between Urgam‐3 and Kathpuria to 0.258 between Dakrakao‐1 and Dunda with an average genetic distance of 0.165. Clustering analysis grouped these 16 populations into three broad groups. The grouping showed a moderate correlation with the geographical distances. Based on the morphological traits and molecular genetic variability, plants of Urgam‐1, Bhowali farm, Nainitikar, Dunda or Korwa‐2 can be selected for breeding and conservation programmes.     

Evaluation of strategies to optimize training populations for genomic prediction in oat (Avena sativa)

Genomic selection is a promising breeding methodology that could increase selection accuracy and intensity and reduce generation interval. As the cost of genotyping decreases, it will be important to optimize training populations for costly phenotypic experiments for many complex traits. The aim of this research was to evaluate different optimization strategies, by using historical data from the Norwegian oat breeding programme at Graminor. In this paper, we focus on the optimization criteria: genetic diversity, phenotypic variance and genetic similarity between the training and testing populations. The four training population strategies—prediction core, diversity core, phenotypic selection and random selection—were applied to an oat candidate population of 1124 lines. An independent testing population was used to calculate the mean prediction abilities for the traits days to heading and plant height. Moreover, the strategies were tested in three independent wheat populations. The results showed that prediction core was the most promising strategy to select training populations with high genetic similarity to the testing set, high genetic diversity, and high phenotypic variance, which resulted in higher prediction ability across population sizes and traits.     

On the colonial margins and in the global hotspot: Park–people conflicts in highland Thailand

Abstract: Forest resource management in Thailand bears the mark of its historical position on the margins of colonial power and its present position in a biodiversity hotspot. During the colonial era, British forestry in Burma and India had a fundamental influence on the knowledge and techniques used in Thai forest management. More recently, international conservation agendas and organisations have influenced the ways in which the Thai government regulates the forest within its boundaries. The treatment of forests as a national and international resource, defined in interaction with colonial neighbours and global partners, has resulted in legal constructs, spatially simplistic conservation mechanisms and a conception of nature ill‐suited to managing forests as a local resource. This paper investigates the manifestation of Thailand's historical legacy in local park‐people conflicts by drawing on research conducted in a region where the government is establishing a national park. It finds that the continued use of laws, tools and concepts derived from colonial and global influences undermines the forestry department's ability to address the contemporary challenge of managing forests as a local, as well as a national/global, commons.     

Prospects for applications of genomic tools in registration testing and seed certification of ryegrass varieties

The ryegrass (Lolium) species, perennial ryegrass (Lolium perenne L.) and Italian ryegrass (Lolium multiflorum Lam.), are the two most important pasture grass species for global temperate regions and are also useful for amenity purposes. Due to an outbreeding reproductive habit, high levels of genetic heterogeneity are present within cultivated varieties. A continual increase in delivery of new cultivars to the marketplace, along with limited capacity to discriminate on the basis of morphological characteristics in a grow‐out test, has caused difficulties for distinctness, uniformity and stability (DUS) testing in the current plant variety protection (PVP) system. A range of genomic tools and resources have been generated for ryegrasses, which provide new opportunities and challenges to the current PVP system. In this review, the currently available genomic tools and resources are described, along with prospects for applications to the PVP system and testing for seed certification and purity accreditation.     

Penetrance of creeping-rootedness in clonal progenies of lucerne and observations on underground morphology of plants differing for this character

Elaeis oleifera or ‘caiaué’, a close relative of oil palm (E. guineensis), has some agronomic traits of great interest for the oil palm genetic breeding such as slow growth, oil quality (mostly unsaturated) and disease resistance. An analysis of a Brazilian oil palm germplasm collection was carried out using RAPD (Random Amplified Polymorphic DNA) markers with the objective of understanding the genetic variation of ‘caiaué’ accessions collected in the Amazon Forest in the last two decades. A sample of 175 accessions obtained along the Amazon River Basin was analyzed and compared to 17 accessions of oil palm from Africa. Ninety-six RAPD markers were used in the analysis, of which fourteen were shown to be specific to oil palm, while twelve were specific to ‘caiaué’. Results showed that the Brazilian ‘caiaué’ accessions studied have moderate levels of genetic diversity as compared to oil palm accessions. The data allowed the establishment of similarity groups for ‘caiaué’ accessions, which is useful for selecting parental plants for population breeding. Cluster analysis showed that, in general, genetic similarities are not correlated to geographical distances, but consistent with geographical dispersal along the Amazon River network. AMOVA showed that most of the genetic variation is found within populations, as expected for anallogamous and long-lived perennial species. The study provides important information to define strategies for future collection expeditions, for germplasm conservation and for the use of E. oleifera in breeding programs. This revised version was published online in August 2006 with corrections to the Cover Date.     

Climatic adaptation of trees: rediscovering provenance tests

Summary Common garden testing of populations of different origin started with forest trees more than two hundred years ago. Since then, so-called provenance tests have been established with most commercially important species. Beyond the strictly silvicultural goals, the tests offer excellent opportunities to study intraspecific genetic variation patterns and represent probably the most powerful available tool for testing hypotheses of climatic adaptation in trees.Analysis of adaptive traits (mostly juvenile height growth) in provenance experiments indicate the existence of very effective constraints on adaptedness. The performance of populations plotted against an ecological-climatic factor exhibits a characteristic pattern and can be described by response functions. The population average of a fitness-related trait for a locally adapted population is often significantly lower than that of populations from other environments; usually the ones from milder climate perform better. The phenomenon is interpreted as adaptation lag. Suboptimal adaptation is compensated by a high level of genetic diversity. Molecular genetic studies confirm the high level of allelic and individual genetic diversity in forest trees. A consequence of individual homeostasis, phenotypic stability of populations is usually also high; the sensitivity to environmental changes is generally moderate. Phenotypically stable populations are valuable not only because of a wider range of potential cultivation but specifically because of a greater ability to adjust to unexpected changes. This trait should receive more attention in the future for obvious reasons.The maintenance of a high within-population genetic variance is favored by the genetic system of the investigated species (effective gene flow, outbreeding, high genetic load, etc.). Random events and long-lasting biotic interactions are further effects impairing the efficiency of natural selection.In view of expected climate instability, genetic adaptability of forest trees causes serious concern due to their long lifespan compared to the rapidity of expected changes in environmental conditions. The potential of provenance tests to interpret long-term adaptational processes should be utilized to analyze, model and predict response of trees to climate change. Although seldomly appreciated, provenance research might be among the most important contributions of forestry to biological sciences.