Crop Genetic Resources Research Articles

Maximizing genetic differentiation in core collections by PCA-based clustering of molecular marker data

Developing genetically diverse core sets is key to the effective management and use of crop genetic resources. Core selection increasingly uses molecular marker-based dissimilarity and clustering methods, under the implicit assumption that markers and genes of interest are genetically correlated. In practice, low marker densities mean that genome-wide correlations are mainly caused by genetic differentiation, rather than by physical linkage. Although of central concern, genetic differentiation per se is not specifically targeted by most commonly employed dissimilarity and clustering methods. Principal component analysis (PCA) on genotypic data is known to effectively describe the inter-locus correlations caused by differentiation, but to date there has been no evaluation of its application to core selection. Here, we explore PCA-based clustering of marker data as a basis for core selection, with the aim of demonstrating its use in capturing genetic differentiation in the data. Using simulated datasets, we show that replacing full-rank genotypic data by the subset of genetically significant PCs leads to better description of differentiation and improves assignment of genotypes to their population of origin. We test the effectiveness of differentiation as a criterion for the formation of core sets by applying a simple new PCA-based core selection method to simulated and actual data and comparing its performance to one of the best existing selection algorithms. We find that although gains in genetic diversity are generally modest, PCA-based core selection is equally effective at maximizing diversity at non-marker loci, while providing better representation of genetically differentiated groups.

Survey for The Conservation of Agrobiodiversity in Three Italian Linguistic (Occitan, Croatian and Franco-Provençal) Islands.

This study is a continuation of a research started in 1996 to study and safeguard the agrobiodiversity in Italian linguistic islands by the Institute of Plant Genetics of the C.N.R. of Bari (Italy) and the Institute of Crop Science of Kassel University (Germany). In 2011 additional three collecting missions were carried out in the Franco-Provençal, Croatian, and Occitan linguistic areas. In all 146 accessions were collected belonging mainly to landraces of cereals, pulses and vegetables. Even if these linguistic areas still conserve worthy crop genetic resources (e.g. rye and wheat in Occitan districts, common beans in Franco-Provençal villages of Apulia region), a strong genetic erosion of the most typical crops was recorded. Safeguarding these crops both ex situ and in situ is thus a matter of urgency.

Seed supply in local markets: supporting sustainable use of crop genetic resources

AbstractThis introductory paper summarizes the policy context, methodological approach, and key results from the set of papers contained in this special edition derived from a FAO-led project on seed sourcing in local markets and its farm-level impacts. The introduction provides the conceptual framework used in the papers for considering the relationship between sourcing seed from market and rural household decision-making as well as the effects this has on two key farm outcomes: on-farm diversity and household welfare. Approaches for data collection and study site selection are described, with a focus on how methodological issues were addressed in the different studies. Lastly, the paper summarizes the results of the individual papers and draws broad conclusions and policy implications for promoting the sustainable utilization of crop genetic resources through increasing market access and in a manner that supports agricultural production.

Development and storage of recalcitrant seeds of Hopea hainanensis

1 Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Germplasm Bank, Mengla, 666303 Yunnan, China (E-mail: lqy@xtbg.org.cn) 2 Department of Biology, Yunnan University, Yunnan Province 650091, PR China 3 Beijing Forestry University, Beijing 100083, China 4 Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences / Key Laboratory of Tropical Crops Germplasm Resources Utilization, Ministry of Agriculture, Hainan Danzhou 571737, P.R. China

Genetic Composition and Spatial Distribution of Farmer‐managed Phaseolus Bean Plantings: An Example from a Village in Oaxaca, Mexico

ABSTRACTIn situ conservation of crop genetic resources is an important complement to ex situ conservation, yet little is known about how small‐scale farmers perceive diversity in their own fields. In this study, we investigated the role of farmers from a community in the Sierra Juárez, Oaxaca, Mexico, in managing Phaseolus bean diversity in their fields. We collected seeds from 287 plants in 10 fields in the village of Santa María Jaltianguis and evaluated the diversity present in the collection at 10 nuclear and three chloroplast DNA (cpDNA) microsatellite markers. Following a Structure analysis, three core population clusters were identified in the collection, a finding corroborated by morphological observations, principal coordinate analysis, and neighbor‐joining tree construction using molecular data. The first two populations were identified as Phaseolus vulgaris L. ecogeographic races Mesoamerica and Jalisco and the third population as related species Phaseolus coccineus L. and Phaseolus dumosus Macfad. Each of the fields sampled consisted predominantly of a single Phaseolus species or ecogeographic race, but there was also evidence of low levels of gene flow between races Jalisco and Mesoamerica. Our data suggest farmers in Santa María Jaltianguis recognize existing inter‐ and intraspecies diversity in Phaseolus, its differential adaptation, its capacity to exploit a broad range of growing environments, and its potential to buffer the community against socioeconomic and climatic changes.

The original features of rice (Oryza sativa L.) genetic diversity and the importance of within-variety diversity in the highlands of Madagascar build a strong case for in situ conservation

In situ conservation of crop genetic resources is widely recommended but, as yet, no methods have been developed to rank the genetic entities to preserve and the social organisations to involve. The highlands of Madagascar have been identified as a key site for rice, Oryza sativa, genetic diversity. To define conservation strategies, we performed multidisciplinary analysis of rice genetic diversity and factors shaping its distribution in the target region. Along with the indica and japonica rice subspecies of O. sativa, we confirmed the presence of an atypical rice group with a preferential habitat of 1,250–1,750 m. Spatial distribution of genetic diversity was uneven. The most determining factor of this unevenness was the altitude authorising or not the presence of different rice cropping systems and the associated types of varieties. Village and individual farmer’s wealth also had a determining role on the amount of rice diversity they hosted. While molecular variance between villages in a given interval of altitude represented 16 % of the total variance, within-village variance represented more than 75 % of the total, and within-farm variance 70 % of within-village variance. This hierarchical distribution of molecular variance suggests that a small number of samples per scale (altitude interval, village and farm) could allow to capture most of the genetic diversity observed. However, within-variety diversity was also important making ex situ conservation strategies impractical and costly. Implications of the within-variety diversity are discussed in terms of adaptive advantages, evolutionary processes, and need for in situ conservation.

Collecting crop genetic resources in two Italian linguistic (Occitan and Ladin) islands and West Liguria with historical and ethnobotanical notes

A research on exploration, collecting and safeguarding plant genetic resources in Italian linguistic islands by Institute of Plant Genetics of the National Research Council of Bari (Italy) and the Institute of Crop Science of Kassel University (Germany) started in 1996. In 2010 two other linguistic areas (Occitan and Ladin) were visited with the same aim. In addition, west Liguria was covered to complete a previous exploration in that region. In all 99 accessions belonging to 51 taxa were sampled from 29 collecting sites. Rare crops for Italy were found for example Citron melon [Citrullus lanatus (Thunb.) Matsum. et Nakai subsp. lanatus var. citroides (Bailey) Mansf. ex Greb.], old landraces of root chicory (Cichorium intybus L.), Artemisia umbelliformis Lam. cultivated, ancient populations of rye selected for straw, rutabaga [Brassica napus L. var. napobrassica (L.) Rchb.], 'bleu potatoes' (Solanum sp.), etc. In conclusion the Occitan and Ladin linguistic islands still conserve worthy crop genetic resources but similar to other Italian regions inhabited by ethnic minorities, the traditional customs and language are losing importance. This phenomenon also negatively affects the cultivation of landraces causing their genetic erosion and, in many cases, extinction. A greater attention by the local government departments is desirable and necessary. Key words: Agricultural biodiversity, occitans, ladins, genetic erosion, Italy, linguistic islands.

Conservation and Management of Crop Genetic Resources in Japan

Conservation and Management of Crop Genetic Resources in Japan

An international survey on state of the art of grain legume management in gene banks

An online survey addressed to members listed the European Cooperative Programme for Crop Genetic Resources Networks Working Group Grain Legumes and Grain Legumes (GL) germplasm managers and breeders was carried out to pinpoint the current problems the management of GL germplasm, to work out the criteria and decisions involved the implementation of regeneration procedures and to identify strategic areas where further research is required. The survey was divided into three sections: (1) germplasm collection details and current status of the regeneration needs; (2) assessment over the understanding of basic information required to carry out appropriate regeneration procedures such as the breeding systems, the pollination requirements and pollinating agents, the isolation techniques and regeneration facilities; and (3) assessment of different options, addition to ex situ, such as in situ and on farm conservation. Obtaining, collating and analysing different kinds of existing data mating system of GL species, effective pollination control methods and isolation facilities by species and location is one example of a priority issue. The GL community makes a clear request for greater support for the development of well-designed methodologies of regeneration that maintain the genetic structure of populations and that the optimum regeneration strategy is most likely to be achieved through integrating pollinators with the regeneration procedures. A major concern of the GL community is the lack of empirical scientific information the most suitable pollinator agents.

Marriage exchanges, seed exchanges, and the dynamics of manioc diversity

The conservation of crop genetic resources requires understanding the different variables-cultural, social, and economic-that impinge on crop diversity. In small-scale farming systems, seed exchanges represent a key mechanism in the dynamics of crop genetic diversity, and analyzing the rules that structure social networks of seed exchange between farmer communities can help decipher patterns of crop genetic diversity. Using a combination of ethnobotanical and molecular genetic approaches, we investigated the relationships between regional patterns of manioc genetic diversity in Gabon and local networks of seed exchange. Spatially explicit Bayesian clustering methods showed that geographical discontinuities of manioc genetic diversity mirror major ethnolinguistic boundaries, with a southern matrilineal domain characterized by high levels of varietal diversity and a northern patrilineal domain characterized by low varietal diversity. Borrowing concepts from anthropology--kinship, bridewealth, and filiation--we analyzed the relationships between marriage exchanges and seed exchange networks in patrilineal and matrilineal societies. We demonstrate that, by defining marriage prohibitions, kinship systems structure social networks of exchange between farmer communities and influence the movement of seeds in metapopulations, shaping crop diversity at local and regional levels.

Predictive Association between Biotic Stress Traits and Eco‐Geographic Data for Wheat and Barley Landraces

Collections of crop genetic resources are a valuable source of new genetic variation for economically important traits, including resistance to crop diseases. New sources of useful crop traits are often identified through evaluation in field trials. The number of relevant accessions in genebank collections available to be evaluated is often substantially larger than the capacity of the evaluation project. The focused identification of germplasm strategy (FIGS) is an approach used to select subsets of germplasm from genetic resource collections in such a way as to maximize the likelihood of capturing a specific trait. This strategy uses a range of methods to link the expression of a specific trait (of a target crop) with the eco‐geographic parameters of the original collection site. This study contributes to the development of the approach by which a FIGS subset could be assembled for biotic traits. We have evaluated trait‐specific subset selection methods for two fungal crop diseases, namely stem rust (Puccinia graminis Pers.) in wheat (Triticum aestivum L. and Triticum turgidum L.) and net blotch (Pyrenophora teres Drechs.) in barley (Hordeum vulgare L.). The results indicate that the climate layers from freely available eco‐geographic databases are well suited to model and predict the reaction in these crops to biotic stress traits. This result has the potential to improve the efficiency of field screening trials to find novel sources of economically valuable crop traits.

Collecting crop genetic resources in Italian towns of Albanian origin across the Molise, Calabria and Sicily regions

A project on collecting and safeguarding crop genetic resources in Italian linguistic islands by the Institute of Plant Genetics (IGV) of the National Research Council (CNR) of Bari (Italy) and the Institute of Crop Science of Kassel University (Germany) started in 1996 with a first mission in Italian towns (Basilicata region) of Albanian origin. In 2008 three other regions (Calabria, Molise and Sicily) were visited with the same aim. Ninety-six accessions belonging to 38 taxa were collected from 23 collecting sites. The Albanian linguistic islands still preserve valuable crop genetic resources that are severely threatened by genetic erosion. To halt this phenomenon a good example comes from Molise where the municipal government and scientific sector are starting to co-operate in the preservation of genetic diversity.

The GCP molecular marker toolkit, an instrument for use in breeding food security crops

Crop genetic resources carry variation useful for overcoming the challenges of modern agriculture. Molecular markers can facilitate the selection of agronomically important traits. The pervasiveness of genomics research has led to an overwhelming number of publications and databases, which are, nevertheless, scattered and hence often difficult for plant breeders to access, particularly those in developing countries. This situation separates them from developed countries, which have better endowed programs for developing varieties. To close this growing knowledge gap, we conducted an intensive literature review and consulted with more than 150 crop experts on the use of molecular markers in the breeding program of 19 food security crops. The result was a list of effectively used and highly reproducible sequence tagged site (STS), simple sequence repeat (SSR), single nucleotide polymorphism (SNP), and sequence characterized amplified region (SCAR) markers. However, only 12 food crops had molecular markers suitable for improvement. That is, marker-assisted selection is not yet used for Musa spp., coconut, lentils, millets, pigeonpea, sweet potato, and yam. For the other 12 crops, 214 molecular markers were found to be effectively used in association with 74 different traits. Results were compiled as the GCP Molecular Marker Toolkit, a free online tool that aims to promote the adoption of molecular approaches in breeding activities.

Variability, Correlation, and Path Analysis Studies in Lettuce

Lettuce (Lactuca sativa L.) is an important crop due to its potential to return profit, nutritional value, and production potential. Twenty-seven genotypes of lettuce procured from the Crop Genetic Resources, Wageningen, The Netherlands, check cultivars Great Lakes and Alamo-1, were planted at the experimental farm of the Dept. of Vegetable Science UHF, Nauni, Solan, India, in Sept. 2008 and evaluated in Apr. 2009 for variability, association between characters, direct and indirect effects of component traits on yield and quality characters, and to identify desirable genotypes. Genotype CGN-10944 had the best yield compared to checks. Genotype CGN-19088 had better β-carotene and iron content but lower yield than checks. There were wide ranges for different horticultural traits, seed vigor index II, and bacterial soft rot disease severity. Moderate to high phenotypic coefficient of variation and genotypic coefficient of variation for gross head weight, net head weight, nonwrapper leaves, iron content, β-carotene, and disease severity exist. The magnitude of heritability for characters was low for 1000 seed weight and high for heading percentage. Genetic advance as percentage of mean (genetic gain) was low for 1000 seed weight and high for β-carotene. Correlation indicated that net head weight was significantly and positively correlated with gross head weight, heading percentage, equatorial diameter, seed vigor index I, and disease severity and significantly and negatively with days to marketable maturity, nonwrapper leaves, and head shape index. Among quality characters β-carotene had a significant positive association with seed germination and negative association with disease severity. Iron content had a positive and significant association with seed vigor index II. Path coefficient analysis indicated that of all characters' positive direct effects for net head weight was contributed by gross head weight, equatorial diameter, disease severity, heading percentage, seed vigor index I, and nonwrapper leaves. Maximum positive indirect effects were observed for equatorial diameter, seed vigor index I, and disease severity via gross head weight. For quality characters genotype CGN-19088 had higher β-carotene and iron contents. Genotypes CGN-04778, CGN-04925, and CGN-20721 had minimum disease severity and were resistant to bacterial soft rot.

Evolutionary response of landraces to climate change in centers of crop diversity.

Landraces cultivated in centers of crop diversity result from past and contemporary patterns of natural and farmer-mediated evolutionary forces. Successful in situ conservation of crop genetic resources depends on continuity of these evolutionary processes. Climate change is projected to affect agricultural production, yet analyses of impacts on in situ conservation of crop genetic diversity and farmers who conserve it have been absent. How will crop landraces respond to alterations in climate? We review the roles that phenotypic plasticity, evolution, and gene flow might play in sustaining production, although we might expect erosion of genetic diversity if landrace populations or entire races lose productivity. For example, highland maize landraces in southern Mexico do not express the plasticity necessary to sustain productivity under climate change, but may evolve in response to altered conditions. The outcome for any given crop in a given region will depend on the distribution of genetic variation that affects fitness and patterns of climate change. Understanding patterns of neutral and adaptive diversity from the population to the landscape scale is essential to clarify how landraces conserved in situ will continue to evolve and how to minimize genetic erosion of this essential natural resource.

THE GENETIC RESOURCES OF TEMPERATE FRUIT TREES IN THE TROPICAL AND SUBTROPICAL ZONES OF ASIA, THEIR CONSERVATION AND UTILIZATION FOR BREEDING

ISHS VIII International Symposium on Temperate Zone Fruits in the Tropics and Subtropics THE GENETIC RESOURCES OF TEMPERATE FRUIT TREES IN THE TROPICAL AND SUBTROPICAL ZONES OF ASIA, THEIR CONSERVATION AND UTILIZATION FOR BREEDING

Gene flow between crops and their wild relatives

Gene flow between crops and their wild relatives

A Select List of Articles on Africa Appearing in Non-Africanist Periodicals: July-September 2009

Ademola, O. T., Bankole, A. S. and Adewuyi, A. O. China–Africa trade relations: insights from AERC scoping studies. European Journal of Development Research21, 4 (2009), pp. 485–505. Ajakaiye, O. and Kaplinsky, R. China in Africa: a relationship in transition. European Journal of Development Research21, 4 (2009), pp. 479–84. Brown, W. Reconsidering the aid relationship: international relations and social development. The Round Table98, 402 (2009), pp. 285–99. Brown, W. and others. Editorial: New directions in international relations and Africa. The Round Table98, 402 (2009), pp. 263–7. Burke, M. B., Lobell, D. B. and Guarino, L. Shifts in African crop climates by 2050 and the implications for crop improvement and genetic resources conservation. Global Environmental Change19, 3 (2009), pp. 317–25. Carey, G. The growth and future of African Christianity: a personal view. Anvil26, 2 (2009), pp. 147–59. Cheesman, D. Butskell and the Empire: the House of Commons prepares for the Scramble from Africa, Commonwealth and Comparative Politics47, 3 (2009), pp. 248–66.

Genetic diversity in a crop metapopulation

The need to protect crop genetic resources has sparked a growing interest in the genetic diversity maintained in traditional farming systems worldwide. Although traditional seed management has been proposed as an important determinant of genetic diversity and structure in crops, no models exist that can adequately describe the genetic effects of seed management. We present a metapopulation model that accounts for several features unique to managed crop populations. Using traditional maize agriculture as an example, we develop a coalescence-based model of a crop metapopulation undergoing pollen and seed flow as well as seed replacement. In contrast to metapopulation work on natural systems, we model seed migration as episodic and originating from a single source per population rather than as a constant immigration from the entire metapopulation. We find that the correlated origin of migrants leads to surprising results, including a loss of invariance of within-deme diversity and a parabolic relationship between F(ST) and migration quantity. In contrast, the effects of migration frequency on diversity and structure are more similar to classical predictions, suggesting that seed migration in managed crop populations cannot be described by a single parameter. In addition to migration, we investigate the effects of deme size and extinction rates on genetic structure, and show that high levels of pollen migration may mask the effects of seed management on structure. Our results highlight the importance of analytically evaluating the effects of deviations from classical metapopulation models, especially in systems for which data are available to estimate specific model parameters.

Shifts in African crop climates by 2050, and the implications for crop improvement and genetic resources conservation

Increased understanding of the substantial threat climate change poses to agriculture has not been met with a similarly improved understanding of how best to respond. Here we examine likely shifts in crop climates in Sub-Saharan Africa under climate change to 2050, and explore the implications for agricultural adaptation, with particular focus on identifying priorities in crop breeding and the conservation of crop genetic resources. We find that for three of Africa's primary cereal crops – maize, millet, and sorghum – expected changes in growing season temperature are considerable and dwarf changes projected for precipitation, with the warmest recent temperatures on average cooler than almost 9 out of 10 expected observations by 2050. For the “novel” crop climates currently unrepresented in each country but likely extant there in 2050, we identify current analogs across the continent. The majority of African countries will have novel climates over at least half of their current crop area by 2050. Of these countries, 75% will have novel climates with analogs in the current climate of at least five other countries, suggesting that international movement of germplasm will be necessary for adaptation. A more troubling set of countries – largely the hotter Sahelian countries – will have climates with few analogs for any crop. Finally, we identify countries, such as Sudan, Cameroon, and Nigeria, whose current crop areas are analogs to many future climates but that are poorly represented in major genebanks – promising locations in which to focus future genetic resource conservation efforts.