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Abstract

Only a small fraction of the naturally occurring genetic diversity available in the world's germplasm repositories has been explored to date, but this is expected to change with the advent of affordable, high-throughput genotyping and sequencing technology. It is now possible to examine genome-wide patterns of natural variation and link sequence polymorphisms with downstream phenotypic consequences. In this paper, we discuss how dramatic changes in the cost and efficiency of sequencing and genotyping are revolutionizing the way gene bank scientists approach the responsibilities of their job. Sequencing technology provides a set of tools that can be used to enhance the quality, efficiency, and cost-effectiveness of gene bank operations, the depth of scientific knowledge of gene bank holdings, and the level of public interest in natural variation. As a result, gene banks have the chance to take on new life. Previously seen as "warehouses" where seeds were diligently maintained, but evolutionarily frozen in time, gene banks could transform into vibrant research centers that actively investigate the genetic potential of their holdings. In this paper, we will discuss how genotyping and sequencing can be integrated into the activities of a modern gene bank to revolutionize the way scientists document the genetic identity of their accessions; track seed lots, varieties, and alleles; identify duplicates; and rationalize active collections, and how the availability of genomics data are likely to motivate innovative collaborations with the larger research and breeding communities to engage in systematic and rigorous phenotyping and multilocation evaluation of the genetic resources in gene banks around the world. The objective is to understand and eventually predict how variation at the DNA level helps determine the phenotypic potential of an individual or population. Leadership and vision are needed to coordinate the characterization of collections and to integrate genotypic and phenotypic information in ways that will illuminate the value of these resources. Genotyping of collections represents a powerful starting point that will enable gene banks to become more effective as stewards of crop biodiversity.
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... Whole genome sequence or genotyping data combined with phenotyping can be used for discovery of alleles that are unique to accessions as well as identify genetically similar or distinct accessions. Genomic and phenotypic tools have been used to assess representativeness of crop genepools for major crops, including rice (McCouch et al., 2012), wheat (Kabbaj et al., 2017), Aegilops tauschii, a wild progenitor of wheat (Singh et al., 2019), maize (Franco-Duran et al., 2019) and banana (Van den Houwe et al., 2020; Rouard et al., 2022). These studies concluded that many genebanks contain genetically similar accessions, due to both recollection of germplasm over time by different collection missions and exchange of germplasm among genebanks (Singh et al., 2019). ...
... It is undoubtedly challenging for any genebank manager to consider throwing accessions away. There is ample evidence of useful traits and diversity being discovered in unexpected places (McCouch et al., 2012;Mascher et al., 2019). Similarly, apparently genetically identical materials have exhibited phenotypic diversity and vice versa (Castillo et al., 2018). ...
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Efficient conservation and sustainable use of crop diversity is critical to support global food and nutritional security with ex situ collections stored in over 800 genebanks in 115 countries. The challenge is to manage those collections for long-term conservation of crop diversity and sustainable use to respond to global challenges of food security and climate change. The Genebank Standards for Plant Genetic Resources for Food and Agricutlure (Genebank Standards) form the overall framework for curation of ex situ crop collections, allowing considerable flexibility to develop customized approaches to conserving different crops. Stratified curation involves strategically tailoring curation to specific genebank goals, crops, priorities and resources for each accession based on all available information to prioritize accessions for long-term conservation. It implies using scarce resources where they are most needed and recognizes that accessions can be (a) fully curated to international standards; (b) partially curated for storage for a limited time; (c) archived and stored but no longer curated and available from the genebank; or (d) historical and removed entirely from the genebank. The stratified approach is consistent with the Genebank Standards and the policy framework of the International Treaty on Plant Genetic Resources for Food and Agriculture. Stratified curation encourages curators to make difficult decisions on accession management to better respond to challenges of curating large collections of crop diversity.
... Kalinowski (2004). The private alleles may be associated with adaptation (McCouch et al. 2012;Reyes-Valdés et al. 2018) and have been implicated in occurrence of specific haplotypes and genes (Lu et al. 2022). ...
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To access genetic diversity and strategize germplasm conservation for posterity, a total of 478 oil palm (Elaeis guineensis) accessions from 11 origins in Africa were analysed via genotype-by-sequencing (GBS). The GBS revealed 7048 high-quality single nucleotide polymorphism (SNP) markers distributed across the 16 oil palm chromosomes. Polymorphic information content (PIC) and the genetic diversity parameters estimated using the SNPs revealed higher diversity for palms from the Nigerian collection, compared to other origins. Furthermore, only the Nigerian population possess private allele with the frequency of 0.016. Analysis of molecular variance (AMOVA) showed major variation occurred within the populations (74%). We also found a high geneflow and low Fst between Angola and Zaire populations. Population structure analysis revealed that the germplasm palms were stratified into six subpopulations with admixture in palms from Nigeria, Cameroon, Ghana, Sierra Leone and Guinea Conakry. Rapid linkage disequilibrium decay was observed, at 1.69 kb for r² = 0.1. A core collection could be established by conserving 96 palms, which together preserved all the alleles present in the germplasm collection.
... It has been recommended that genebanks create, maintain, and provide such pure lines, or single seed descent lines, because the repeatability of observations made by users on such material is enhanced (Cross and Wallace 1994). The arrival of molecular tools detecting all genetic differences that may exist among single lines in a self-pollinator such as flax has even increased such demand (McCouch et al. 2012;Engels and Ebert 2021). ...
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Four field trials were conducted in western Canada in 2020 and 2021 to assess cadmium (Cd) concentration in seed from 166 pure lines of flax originating from 26 countries that were derived by single seed descent from a genetically diverse flax core collection preserved by Plant Gene Resources of Canada. Associations of Cd concentration with morphological and phenological traits, as well as the country of origin were considered. The mean Cd concentration in the seed ranged from 0.31 to 1.50 mg/kg with an overall mean value of 0.93 ± 0.22 mg/kg. The Cd in the soil from the field sites ranged from 0.35 to 2.80 mg/kg and was positively correlated with the Cd concentration in the seed harvested from the respective sites. The consistency of the Cd concentration in the seed of pure lines across the four site-years was low, with correlation coefficients ranging from 0.35 to 0.53. Pure lines with consistently low Cd concentration in the seed were identified and may be useful for breeding linseed cultivars for human consumption while pure lines with consistently high Cd concentration might be used for phytoremediation of Cd-contaminated soils. Cd concentration in the seed was not significantly correlated with thousand seed weight, plant height, petal colour, seed colour, or country of origin. As a tendency, the longer the vegetative period and the later the accessions matured, the more Cd they accumulated in the seed. For linseed production in western Canada, choosing locations with a low Cd content in the soil is very important when growing flax for human consumption or feed use.
... In addition, understanding of heterozygosity is important as it helps inform conservation management decisions. Assessing patterns of heterozygosity can, for example, help in determining the suitability and effectiveness of a regeneration method in maintaining genetic diversity and integrity (McCouch et al., 2012). Rice is a self-pollinated crop with an outcrossing rate of between 2% and 5% (Semon et al., 2005). ...
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Utilizing the full potential of rice collections mainly depends on an in‐depth exploration and understanding of the vast diversity in its germplasm. The AfricaRice genebank holds the largest collection of rice germplasm originating from the African continent. In the present study, we comprehensively characterized a collection of 9013 accessions, including Oryza barthii A. Chev., Oryza glaberrima Steud., Oryza longistaminata A. Chev. & Roehr., Oryza sativa L. ssp. indica, and Oryza sativa L. ssp. japonica, for genetic diversity and population structure using genotyping‐by‐sequencing through DArTseq analysis. We identified 27,718 high‐quality single nucleotide polymorphism markers after the genotypic data were filtered. Based on the analyses, the collection has extensive genetic diversity, and the average genetic distance of the entire set was 0.267 (range 0.001–0.469), with 45.1% of pairs of accessions being highly distant and 40.1% moderately distant from each other. Neighbor‐joining tree, principal component, and Bayesian population structure analyses clustered the 9013 accessions into six groups, based roughly on their taxonomic and biological status. The first, second, and third groups consisted of accessions belonging to O. glaberrima, O. barthii, and O. longistaminata, respectively. The fourth, fifth, and sixth groups were improved‐indica, japonica, and traditional‐indica accessions, respectively. The highest value of genetic variance proportion (PhiPT) was found in the species group followed by groups based on cluster analysis and on Bayesian population structure at K = 6. These results allow us to better understand the genetic diversity present in 9013 rice accessions maintained in the AfricaRice genebank and offer a valuable tool for pre breeding, breeding, and further genetic applications.
... Convinced that such optimism is not misplaced, we and others have argued for using genome sequencing to better understand and utilize genetic diversity in crops 55,56 . These tasks entail the processing of tens of thousands of DNA samples. ...
Article
In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.
... However, the preservation of PGRs in gene banks is lagging behind when it comes to employing advanced methods (e.g., NGS, intelligent image processing, and high-throughput phenotyping) in comparison with other plant biology areas (Wambugu et al. 2018). As suggested by McCouch et al. (2012), current dormant gene banks can be transformed into active research centers by the use of advanced biological and computational methods. ...
Chapter
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Chapter
Celery (Apium graveolens L.) is a low-calorie vegetable and herbaceous plant species from the Apiaceae family. It is a biennial plant, popular worldwide due to its nutritional and medicinal values. The oleoresin and oil content present in celery seeds are valuable for food flavoring, perfumery, and pharmaceutical applications. Celery is high in fiber and mineral content, including calcium, potassium, phosphorus, iron, and magnesium. It also contains vitamins B1, B2, B3, A, and C, as well as flavonoids, which aid to regulate blood flow and strengthen the uterine muscles. The crop improvement generally involves two main approaches: conventional breeding and advanced breeding. The conventional breeding approaches such as intergeneric crossings have been used to improve celery. The disease-resistant hybrids have been developed to combat issues like late blight, Fusarium yellows, and celery mosaic virus, as well as pests like Spodoptera exigua and Liriomyza trifolii. Additionally, genomic resources for celery, including EST-SSRs (Expressed Sequence Tag-Simple Sequence Repeats), micro-RNAs, and transcriptome and genome data, are available. However, there is a scarcity of improved celery varieties using advanced biotechnological tools. The existing genomic resources could be valuable for future crop improvement programs, particularly with advanced biotechnological tools like CRISPR/Cas9-based genome editing.
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Crop translational genomics applies breeding techniques based on genomic datasets to improve crops. Technological breakthroughs in the past ten years have made it possible to sequence the genomes of increasing numbers of crop varieties and have assisted in the genetic dissection of crop performance. However, translating research findings to breeding applications remains challenging. Here we review recent progress and future prospects for crop translational genomics in bringing results from the laboratory to the field. Genetic mapping, genomic selection and sequence-assisted characterization and deployment of plant genetic resources utilize rapid genotyping of large populations. These approaches have all had an impact on breeding for qualitative traits, where single genes with large phenotypic effects exert their influence. Characterization of the complex genetic architectures that underlie quantitative traits such as yield and flowering time, especially in newly domesticated crops, will require further basic research, including research into regulation and interactions of genes and the integration of genomic approaches and high-throughput phenotyping, before targeted interventions can be designed. Future priorities for translation include supporting genomics-assisted breeding in low-income countries and adaptation of crops to changing environments.
Thesis
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Food security is one of the major global challenges of the twenty-first century. Crop yield is estimated to decline by 5 to 30% from 2050 onwards compared to 1990. Climate change has a major impact on crop production. Drought stress is a significant environmental factor affecting crop growth and productivity. Understanding its impact on capsicum production is crucial for development of drought-tolerant varieties. So, this experiment is carried out to identify the tolerant varieties. The study was conducted in two factorial completely randomized designs with three replications, subjecting the seeds of four different varieties to three different polyethylene glycol (PEG) concentrations. The observation revealed that Boxer and California wonder showed statistically similarity in most of the growth parameters where Ganga showed significantly reduced performances in few parameters at seedling stage with increase in PEG concentration. Unlike these, Red Variety showed drastic reduction in all parameters. Results showed Boxer and California wonder were more tolerant even up to higher drought conditions (-0.36 MPa), but red variety was susceptible even to lower drought conditions (-0.18 MPa). The four capsicum varieties were grouped into two clusters, with Red variety in one and Boxer, California Wonder, and Ganga under another. The screened drought tolerant varieties can be utilized in breeding programs aimed at developing drought tolerant capsicum varieties or can be recommended in areas with lower irrigation facilities. Furthermore, breeding programs should be initiated to develop new capsicum varieties with enhanced drought tolerance, incorporating the identified drought-tolerant genetic traits and genes.
Chapter
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Asian rice, Oryza sativa is a cultivated, inbreeding species that feeds over half of the world's population. Understanding the genetic basis of diverse physiological, developmental, and morphological traits provides the basis for improving yield, quality and sustainability of rice. Here we show the results of a genome-wide association study based on genotyping 44,100 SNP variants across 413 diverse accessions of O. sativa collected from 82 countries that were systematically phenotyped for 34 traits. Using cross-population-based mapping strategies, we identified dozens of common variants influencing numerous complex traits. Significant heterogeneity was observed in the genetic architecture associated with subpopulation structure and response to environment. This work establishes an open-source translational research platform for genome-wide association studies in rice that directly links molecular variation in genes and metabolic pathways with the germplasm resources needed to accelerate varietal development and crop improvement.
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In the framework of a large EU funded project, AFLPs and microsatellites were used to characterise the entire lettuce collection of the Centre for Genetic Resources, The Netherlands (CGN). Some highlights of the results of the analysis of the AFLP data are reported. 8020 Plants of 2323 accessions of lettuce and related wild species (Lactuca spp. plus related genera) were characterised using three AFLP primer combinations. It was clear from the beginning that no suitable software for the analysis was available, a spin-off of the project is another EU funded project for the creation of such software. The genetic diversity within accessions was higher than expected, the comparison between the groups however fully complied with the expectations. The number of cases that plants from one L. sativa accession differed exactly one band was one fifth of the cases where the plants were identical, implying some residual variation or possibly methodological 'noise'. It proved difficult to identify 'identical plants' due to this residual variance, but also due to missing values. However an estimated lower bound showed 20% 'redundancy' based only on homogeneous identical accessions implying that the fingerprints used were not able to distinguish all genotypes. The AFLP fingerprints proved very suitable to describe the wild species collections and its individual accessions. Based on the genetic differentiation between accessions, the self-, or cross-pollinating nature of accessions could be revealed, the genetic structure of the species could be analysed, the taxonomic classification and origin data of the accessions could be validated, and redundancies could be identified. The fingerprint also allowed improvement of the balance in the representation of the species and better selection of material for use. Finally, the association amongst markers and between markers and traits was shown to be highly significant, and can be explained by genetic linkages, but also by effects of geographical isolation, founder effects, etc.
Article
Rice (Oryza sativa L.) productivity is affected by several biotic and abiotic stresses. The genetic variability for some of these stresses is limited in the cultivated rice germplasm. Moreover, changes in insect biotypes and disease races are a continuing threat to increased rice production. There is thus an urgent need to broaden the rice gene pool by introgressing genes for such traits from diverse sources. The wild species of Oryza representing AA, BB, CC, BBCC, CCDD, EE, FF, GG and HHJJ genomes are an important reservoir of useful genes. However, low crossability and limited recombination between chromosomes of cultivated and wild species limit the transfer of such genes. AT IRRI, a series of hybrids and monosomic alien addition lines have been produced through embryo rescue following hybridization between rice and several distantly related species. Cytoplasmic male sterility and genes for resistance to grassy stunt virus and bacterial blight have been transferred from A genome wild species into rice. Similarly, genes for resistance to brown planthopper, bacterial blight and blast have also been introgressed across crossability barriers from distanly related species into rice. Some of the introgressed genes have been mapped via linkage to molecular markers. One of the genes Xa-21 introgressed from O. longistaminata has been cloned and physically mapped on chromosome 11 of rice using BAC library and flourescence in-situ hybridization. RFLP analysis revealed introgression from 11 of the 12 chromosomes of C genome species into rice. Introgression has also been obtained from other distant genomes (EE, FF, GG) into rice and in majority of the cases one or two RFLP markers were introgressed. Reciprocal replacement of RFLP alleles of wild species with the alleles of O. sativa indicates alien gene transfer through crossing over. The rapid recovery of recurrent phenotypes in BC2 and BC3 generations from wide crosses is an indication of limited recombination. Further cytogenetic and molecular investigations are required to determine precisely the mechanism of introgression of small chromosome segments from distant genomes in the face of limited homoeologous chromosome pairing. Future research should focus on enhancing recombination between homoeologous chromosomes. Introgression of QTL from wild species should be attempted to increase the yield potential of rice.
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Naturally occurring variation among wild relatives of cultivated crops is an under-exploited resource in plant breeding. Here, I argue that exotic libraries, which consist of marker-defined genomic regions taken from wild species and introgressed onto the background of elite crop lines, provide plant breeders with an important opportunity to improve the agricultural performance of modern crop varieties. These libraries can also act as reagents for the discovery and characterization of genes that underlie traits of agricultural value.
Chapter
Rice (Oryza sativa L.) productivity is affected by several biotic and abiotic stresses. The genetic variability for some of these stresses is limited in the cultivated rice germplasm. Moreover, changes in insect biotypes and disease races are a continuing threat to increased rice production. There is thus an urgent need to broaden the rice gene pool by introgressing genes for such traits from diverse sources. The wild species of Oryza representing AA, BB, CC, BBCC, CCDD, EE, FF, GG and HHJJ genomes are an important reservoir of useful genes. However, low crossability and limited recombination between chromosomes of cultivated and wild species limit the transfer of such genes. At IRRI, a series of hybrids and monosomic alien addition lines have been produced through embryo rescue following hybridization between rice and several distantly related species. Cytoplasmic male sterility and genes for resistance to grassy stunt virus and bacterial blight have been transferred from A genome wild species into rice. Similarly, genes for resistance to brown planthopper, bacterial blight and blast have also been introgressed across crossability barriers from distanly related species into rice. Some of the introgressed genes have been mapped via linkage to molecular markers. One of the genes Xa-21 introgressed from O. longistaminata has been cloned and physically mapped on chromosome 11 of rice using BAC library and flourescence in-situ hybridization. RFLP analysis revealed introgression from 11 of the 12 chromosomes of C genome species into rice. Introgression has also been obtained from other distant genomes (EE, FF, GG) into rice and in majority of the cases one or two RFLP markers were introgressed. Reciprocal replacement of RFLP alleles of wild species with the alleles of O. sativa indicates alien gene transfer through crossing over. The rapid recovery of recurrent phenotypes in BC2 and BC3 generations from wide crosses is an indication of limited recombination. Further cytogenetic and molecular investigations are required to determine precisely the mechanism of introgression of small chromosome segments from distant genomes in the face of limited homoeologous chromosome pairing. Future research should focus on enhancing recombination between homoeologous chromosomes. Introgression of QTL from wild species should be attempted to increase the yield potential of rice.
Article
This report reviews some tools that curators of ex situ plant germplasm collections can employ to manage seed regeneration. It examines the various roles of germplasm users as sources of technical expertise and advice about germplasm needs. Analysis of past demand for germplasm and forecasts of future demand trends are valuable guides to plan regeneration. Seed quantity and viability are key planning criteria, but regeneration planning should also weigh such factors as overall genetic diversity within collections, institutional duplication, and the relative quality and completeness of passport and characterization data. The North Central Regional Plant Introduction Station conducts applied research to develop effective techniques for seed multiplication of cross-pollinated crops and their wild relatives. An overview of the Station's experiences with insect pollination in field cages, high-density pot culture, and mating scheme evaluation for maize is presented. Optimal use of all these management tools relies on the development of a corps of crop-specific curators, who can gain the expertise needed to anticipate users' needs and understand the intricate patterns of genetic diversity and reproductive biology within their respective crops.
Article
The Rice Germplasm Collection of Embrapa consists of approximately 10,000 accessions. This study aimed to establish a core collection using the currently available information data for those accessions. The strategy Core Collection (CN) was introduced in the management of plant genetic resources with the main purpose of improving the use of these resources. CN should be selected in order to preserve the genetic variability of the whole collection (CI), with minimum redundancy. The accessions within the rice collection were classified into three strata: a) landraces from Brazil (VT); b) breeding materials from Brazil (LCM); and c) introductions (LCI). The landraces were further classified according to crop system (uplands, lowlands and facultative). These three strata were represented in the Core Collection, but more emphasis was considered in representing the landraces, which are represented by 308 accessions. The accessions were allocated, for each crop system, proportionally to the product of the logarithm of the number of landraces by the Shannon Diversity Index (a measure of genetic diversity) within each crop system. Curators and breeders, supported by a Geographical Information System (GIS) made the selection of the accessions. The final Brazilian rice Core Collection consists of 550 accesses.
Chapter
"Genomic selection," the ability to select for even complex, quantitative traits based on marker data alone, has arisen from the conjunction of new high-throughput marker technologies and new statistical methods needed to analyze the data. This review surveys what is known about these technologies, with sections on population and quantitative genetic background, DNA marker development, statistical methods, reported accuracies of genomic selection (GS) predictions, prediction of nonadditive genetic effects, prediction in the presence of subpopulation structure, and impacts of GS on long-term gain. GS works by estimating the effects of many loci spread across the genome. Marker and observation numbers therefore need to scale with the genetic map length in Morgans and with the effective population size of the population under GS. For typical crops, the requirements range from at least 200 to at most 10,000 markers and observations. With that baseline, GS can greatly accelerate the breeding cycle while also using marker information to maintain genetic diversity and potentially prolong gain beyond what is possible with phenotypic selection. With the costs of marker technologies continuing to decline and the statistical methods becoming more routine, the results reviewed here suggest that GS will play a large role in the plant breeding of the future. Our summary and interpretation should prove useful to breeders as they assess the value of GS in the context of their populations and resources.