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Mascher M, Marone MP, Schreiber M, Stein N. Are cereal grasses a single genetic system? NATURE PLANTS 2024; 10:719-731. [PMID: 38605239 DOI: 10.1038/s41477-024-01674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 03/17/2024] [Indexed: 04/13/2024]
Abstract
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.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Marina Püpke Marone
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mona Schreiber
- University of Marburg, Department of Biology, Marburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
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Mahendran A, Yadav MC, Tiwari S, Bairwa RK, Krishnan SG, Rana MK, Singh R, Mondal TK. Population structure and genetic differentiation analyses reveal high level of diversity and allelic richness in crop wild relatives of AA genome species of rice (Oryza sativa L.) in India. J Appl Genet 2023; 64:645-666. [PMID: 37743422 DOI: 10.1007/s13353-023-00787-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/27/2023] [Accepted: 09/04/2023] [Indexed: 09/26/2023]
Abstract
Crop wild relatives (CWRs) are vital sources of variation for genetic improvement, but their populations are few in genebanks, eroded in natural habitats and inadequately characterized. With a view to explore genetic diversity in CWRs of AA genome rice (Oryza sativa L.) species in India, we analyzed 96 accessions of 10 Oryza species by using 17 quantitative traits and 45 microsatellite markers. The morpho-quantitative traits revealed a high extent of phenotypic variation in the germplasm. Diversity index (H') revealed a high level of within-species variability in O. nivara (H' = 1.09) and O. rufipogon (H' = 1.12). Principal component (PC) analysis explained 79.22% variance with five PCs. Among the traits related to phenology, morphology, and yield, days to heading showed strong positive association with days to 50% flowering (r = 0.99). However, filled grains per panicle revealed positive association with spikelet fertility (0.71) but negative with awn length (- 0.58) and panicle bearing tillers (- 0.39). Cluster analysis grouped all the accessions into three major clusters. Microsatellite analysis revealed 676 alleles with 15.02 alleles per locus. High polymorphism information content (PIC = 0.83) and Shannon's information index (I = 2.31) indicated a high level of genetic variation in the CWRs. Structure analysis revealed four subpopulations; first and second subpopulations comprised only of O. nivara accessions, while the third subpopulation included both O. nivara and O. rufipogon accessions. Population statistics revealed a moderate level of genetic differentiation (FST = 0.14), high gene diversity (HE = 0.87), and high gene flow (Nm = 1.53) among the subpopulations. We found a high level of molecular variance among the genotypes (70%) and low among populations (11%) and within genotypes (19%). The high level of molecular and morphological variability detected in the germplasm of CWRs could be utilized for the improvement of cultivated rice.
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Affiliation(s)
- Aswin Mahendran
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India
- The Graduate School, ICAR - Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Mahesh C Yadav
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India.
| | - Shailesh Tiwari
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Rakesh Kumar Bairwa
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - S Gopala Krishnan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Mukesh Kumar Rana
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Rakesh Singh
- Division of Genomic Resources, Indian Council of Agricultural Research (ICAR) - National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Tapan Kumar Mondal
- ICAR-National Institute of Plant Biotechnology, New Delhi, 110012, India
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Yadav IS, Singh N, Wu S, Raupp J, Wilson DL, Rawat N, Gill BS, Poland J, Tiwari VK. Exploring genetic diversity of wild and related tetraploid wheat species Triticum turgidum and Triticum timopheevii. J Adv Res 2023; 48:47-60. [PMID: 36084813 PMCID: PMC10248793 DOI: 10.1016/j.jare.2022.08.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/25/2022] [Accepted: 08/31/2022] [Indexed: 11/27/2022] Open
Abstract
INTRODUCTION The domestication bottleneck has reduced genetic diversity inwheat, necessitating the use of wild relatives in breeding programs. Wild tetraploid wheat are widely used in the breeding programs but with morphological characters, it is difficult to distinguish these, resulting in misclassification/mislabeling or duplication of accessions in the Gene bank. OBJECTIVES The study aims to exploreGenotyping by sequencing (GBS) to characterize wild and domesticated tetraploid wheat accessions to generate a core set of accessions to be used in the breeding program. METHODS TASSEL-GBS pipeline was used for SNP discovery, fastStructure was used to determine the population structure and PowerCore was used to generate a core sets. Nucleotide diversity matrices of Nie's and F-statistics (FST) index were used to determine the center of genetic diversity. RESULTS We found 65 % and 47 % duplicated accessions in Triticum timopheevii and T. turgidum respectively. Genome-wide nucleotide diversity and FST scan uncovered a lower intra and higher inter-species differentiation. Distinct FST regions were identified in genomic regions belonging to domestication genes: non-brittle rachis (Btr1) and vernalization (VRN-1).Our results suggest that Israel, Jordan, Syria, and Lebanonas the hub of genetic diversity of wild emmer;Turkey, and Georgia for T. durum; and Iraq, Azerbaijan, and Armenia for theT. timopheevii. Identified core set accessions preserved more than 93 % of the available genetic diversity. Genome wide association study (GWAS) indicated the potential chromosomal segment for resistance to leaf rust in T. timopheevii. CONCLUSION The present study explored the potential of GBS technology in data reduction while maintaining the significant genetic diversity of the species. Wild germplasm showed more differentiation than domesticated accessions, indicating the availability of sufficient diversity for crop improvement. With reduced complexity, the core set preserves the genetic diversity of the gene bank collections and will aid in a more robust characterization of wild germplasm.
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Affiliation(s)
- Inderjit S. Yadav
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | | | - Shuangye Wu
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jon Raupp
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Duane L. Wilson
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Nidhi Rawat
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
| | - Bikram S. Gill
- Department of Plant Pathology and Wheat Genetics Resource Center, Kansas State University, 1712 Claflin Road, Manhattan, KS 66506, USA
| | - Jesse Poland
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Vijay K. Tiwari
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD 20742, USA
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Arca M, Gouesnard B, Mary-Huard T, Le Paslier MC, Bauland C, Combes V, Madur D, Charcosset A, Nicolas SD. Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next-generation varieties. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:1123-1139. [PMID: 36740649 DOI: 10.1111/pbi.14022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 01/18/2023] [Indexed: 05/27/2023]
Abstract
Landraces, that is, traditional varieties, have a large diversity that is underexploited in modern breeding. A novel DNA pooling strategy was implemented to identify promising landraces and genomic regions to enlarge the genetic diversity of modern varieties. As proof of concept, DNA pools from 156 American and European maize landraces representing 2340 individuals were genotyped with an SNP array to assess their genome-wide diversity. They were compared to elite cultivars produced across the 20th century, represented by 327 inbred lines. Detection of selective footprints between landraces of different geographic origin identified genes involved in environmental adaptation (flowering times, growth) and tolerance to abiotic and biotic stress (drought, cold, salinity). Promising landraces were identified by developing two novel indicators that estimate their contribution to the genome of inbred lines: (i) a modified Roger's distance standardized by gene diversity and (ii) the assignation of lines to landraces using supervised analysis. It showed that most landraces do not have closely related lines and that only 10 landraces, including famous landraces as Reid's Yellow Dent, Lancaster Surecrop and Lacaune, cumulated half of the total contribution to inbred lines. Comparison of ancestral lines directly derived from landraces with lines from more advanced breeding cycles showed a decrease in the number of landraces with a large contribution. New inbred lines derived from landraces with limited contributions enriched more the haplotype diversity of reference inbred lines than those with a high contribution. Our approach opens an avenue for the identification of promising landraces for pre-breeding.
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Affiliation(s)
- Mariangela Arca
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Brigitte Gouesnard
- UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Tristan Mary-Huard
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | | | - Cyril Bauland
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Valérie Combes
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Delphine Madur
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alain Charcosset
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Stéphane D Nicolas
- INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Université Paris-Saclay, Gif-sur-Yvette, France
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Sahu TK, Singh AK, Mittal S, Jha SK, Kumar S, Jacob SR, Singh K. G-DIRT: a web server for identification and removal of duplicate germplasms based on identity-by-state analysis using single nucleotide polymorphism genotyping data. Brief Bioinform 2022; 23:6678959. [PMID: 36040109 DOI: 10.1093/bib/bbac348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 07/11/2022] [Accepted: 07/26/2022] [Indexed: 01/26/2023] Open
Abstract
Maintaining duplicate germplasms in genebanks hampers effective conservation and utilization of genebank resources. The redundant germplasm adds to the cost of germplasm conservation by requiring a large proportion of the genebank financial resources towards conservation rather than enriching the diversity. Besides, genome-wide-association analysis using an association panel with over-represented germplasms can be biased resulting in spurious marker-trait associations. The conventional methods of germplasm duplicate removal using passport information suffer from incomplete or missing passport information and data handling errors at various stages of germplasm enrichment. This limitation is less likely in the case of genotypic data. Therefore, we developed a web-based tool, Germplasm Duplicate Identification and Removal Tool (G-DIRT), which allows germplasm duplicate identification based on identity-by-state analysis using single-nucleotide polymorphism genotyping information along with pre-processing of genotypic data. A homozygous genotypic difference threshold of 0.1% for germplasm duplicates has been determined using tetraploid wheat genotypic data with 94.97% of accuracy. Based on the genotypic difference, the tool also builds a dendrogram that can visually depict the relationship between genotypes. To overcome the constraint of high-dimensional genotypic data, an offline version of G-DIRT in the interface of R has also been developed. The G-DIRT is expected to help genebank curators, breeders and other researchers across the world in identifying germplasm duplicates from the global genebank collections by only using the easily sharable genotypic data instead of physically exchanging the seeds or propagating materials. The web server will complement the existing methods of germplasm duplicate identification based on passport or phenotypic information being freely accessible at http://webtools.nbpgr.ernet.in/gdirt/.
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Affiliation(s)
- Tanmaya Kumar Sahu
- ICAR-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, India
| | - Shikha Mittal
- ICAR-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, India
| | | | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, India
| | - Sherry Rachel Jacob
- ICAR-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources (ICAR-NBPGR), New Delhi, India.,ICAR- Indian Agricultural Research Institute (ICAR-IARI), New Delhi, India.,International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Reeves PA, Richards CM. A pan-genome data structure induced by pooled sequencing facilitates variant mining in heterogeneous germplasm. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:36. [PMID: 37313509 PMCID: PMC10248589 DOI: 10.1007/s11032-022-01308-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/08/2022] [Indexed: 06/15/2023]
Abstract
Valuable genetic variation lies unused in gene banks due to the difficulty of exploiting heterogeneous germplasm accessions. Advances in molecular breeding, including transgenics and genome editing, present the opportunity to exploit hidden sequence variation directly. Here we describe the pan-genome data structure induced by whole-genome sequencing of pooled individuals from wild populations of Patellifolia spp., a source of disease resistance genes for the related crop species sugar beet (Beta vulgaris). We represent the pan-genome as a map of reads from pooled sequencing of a heterogeneous population sample to a reference genome, plus a BLAST data base of the mapped reads. We show that this basic data structure can be queried by reference genome position or homology to identify sequence variants present in the wild relative, at genes of agronomic interest in the crop, a process known as allele or variant mining. Further we demonstrate the possibility of cataloging variants in all Patellifolia genomic regions that have corresponding single copy orthologous regions in sugar beet. The data structure, termed a "pooled read archive," can be produced, altered, and queried using standard tools to facilitate discovery of agronomically-important sequence variation. Supplementary information The online version contains supplementary material available at 10.1007/s11032-022-01308-6.
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Affiliation(s)
- Patrick A. Reeves
- Agricultural Research Service, United States Department of Agriculture, National Laboratory for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, CO 80521 USA
| | - Christopher M. Richards
- Agricultural Research Service, United States Department of Agriculture, National Laboratory for Genetic Resources Preservation, 1111 South Mason Street, Fort Collins, CO 80521 USA
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Pariasca-Tanaka J, Rakotondramanana MF, Tojo Mangaharisoa S, Ranaivo HN, Tanaka R, Wissuwa M. Phenotyping of a rice (Oryza sativa L.) association panel identifies loci associated with tolerance to low soil fertility on smallholder farm conditions in Madagascar. PLoS One 2022; 17:e0262707. [PMID: 35584097 PMCID: PMC9116655 DOI: 10.1371/journal.pone.0262707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 01/02/2022] [Indexed: 11/18/2022] Open
Abstract
Rice (Oryza sativa L.) is a staple food of Madagascar, where per capita rice consumption is among the highest worldwide. Rice in Madagascar is mainly grown on smallholder farms on soils with low fertility and in the absence of external inputs such as mineral fertilizers. Consequently, rice productivity remains low and the gap between rice production and consumption is widening at the national level. This study evaluates genetic resources imported from the IRRI rice gene bank to identify potential donors and loci associated with low soil fertility tolerance (LFT) that could be utilized in improving rice yield under local cultivation conditions. Accessions were grown on-farm without fertilizer inputs in the central highlands of Madagascar. A Genome-wide association study (GWAS) identified quantitative trait loci (QTL) for total panicle weight per plant, straw weight, total plant biomass, heading date and plant height. We detected loci at locations of known major genes for heading date (hd1) and plant height (sd1), confirming the validity of GWAS procedures. Two QTLs for total panicle weight were detected on chromosomes 5 (qLFT5) and 11 (qLFT11) and superior panicle weight was conferred by minor alleles. Further phenotyping under P and N deficiency suggested qLFT11 to be related to preferential resource allocation to root growth under nutrient deficiency. A donor (IRIS 313–11949) carrying both minor advantageous alleles was identified and crossed to a local variety (X265) lacking these alleles to initiate variety development through a combination of marker-assisted selection with selection on-farm in the target environment rather than on-station as typically practiced.
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Affiliation(s)
- Juan Pariasca-Tanaka
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | | | - Sarah Tojo Mangaharisoa
- Rice Research Department, The National Center for Applied Research on Rural Development (FOFIFA), Antananarivo, Madagascar
| | - Harisoa Nicole Ranaivo
- Rice Research Department, The National Center for Applied Research on Rural Development (FOFIFA), Antananarivo, Madagascar
| | - Ryokei Tanaka
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Matthias Wissuwa
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
- * E-mail:
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Wang C, Han B. Twenty years of rice genomics research: From sequencing and functional genomics to quantitative genomics. MOLECULAR PLANT 2022; 15:593-619. [PMID: 35331914 DOI: 10.1016/j.molp.2022.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Since the completion of the rice genome sequencing project in 2005, we have entered the era of rice genomics, which is still in its ascendancy. Rice genomics studies can be classified into three stages: structural genomics, functional genomics, and quantitative genomics. Structural genomics refers primarily to genome sequencing for the construction of a complete map of rice genome sequence. This is fundamental for rice genetics and molecular biology research. Functional genomics aims to decode the functions of rice genes. Quantitative genomics is large-scale sequence- and statistics-based research to define the quantitative traits and genetic features of rice populations. Rice genomics has been a transformative influence on rice biological research and contributes significantly to rice breeding, making rice a good model plant for studying crop sciences.
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Affiliation(s)
- Changsheng Wang
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
| | - Bin Han
- National Center for Gene Research, State Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200233, China.
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Muktar MS, Habte E, Teshome A, Assefa Y, Negawo AT, Lee KW, Zhang J, Jones CS. Insights Into the Genetic Architecture of Complex Traits in Napier Grass ( Cenchrus purpureus) and QTL Regions Governing Forage Biomass Yield, Water Use Efficiency and Feed Quality Traits. FRONTIERS IN PLANT SCIENCE 2022; 12:678862. [PMID: 35069609 PMCID: PMC8776657 DOI: 10.3389/fpls.2021.678862] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 12/06/2021] [Indexed: 05/14/2023]
Abstract
Napier grass is the most important perennial tropical grass native to Sub-Saharan Africa and widely grown in tropical and subtropical regions around the world, primarily as a forage crop for animal feed, but with potential as an energy crop and in a wide range of other areas. Genomic resources have recently been developed for Napier grass that need to be deployed for genetic improvement and molecular dissection of important agro-morphological and feed quality traits. From a diverse set of Napier grass genotypes assembled from two independent collections, a subset of 84 genotypes (although a small population size, the genotypes were selected to best represent the genetic diversity of the collections) were selected and evaluated for 2 years in dry (DS) and wet (WS) seasons under three soil moisture conditions: moderate water stress in DS (DS-MWS); severe water stress in DS (DS-SWS) and, under rainfed (RF) conditions in WS (WS-RF). Data for agro-morphological and feed quality traits, adjusted for the spatial heterogeneity in the experimental blocks, were collected over a 2-year period from 2018 to 2020. A total of 135,706 molecular markers were filtered, after removing markers with missing values >10% and a minor allele frequency (MAF) <5%, from the high-density genome-wide markers generated previously using the genotyping by sequencing (GBS) method of the DArTseq platform. A genome-wide association study (GWAS), using two different mixed linear model algorithms implemented in the GAPIT R package, identified more than 35 QTL regions and markers associated with agronomic, morphological, and water-use efficiency traits. QTL regions governing purple pigmentation and feed quality traits were also identified. The identified markers will be useful in the genetic improvement of Napier grass through the application of marker-assisted selection and for further characterization and map-based cloning of the QTLs.
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Affiliation(s)
- Meki S. Muktar
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Ermias Habte
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Abel Teshome
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Yilikal Assefa
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Alemayehu T. Negawo
- Feed and Forage Development, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Ki-Won Lee
- Grassland and Forages Division, National Institute of Animal Science, Rural Development Administration, Cheonan, South Korea
| | - Jiyu Zhang
- State Key Laboratory of Grassland Agro-Ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Chris S. Jones
- Feed and Forage Development, International Livestock Research Institute, Nairobi, Kenya
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Dzievit MJ, Guo T, Li X, Yu J. Comprehensive analytical and empirical evaluation of genomic prediction across diverse accessions in maize. THE PLANT GENOME 2021; 14:e20160. [PMID: 34661990 DOI: 10.1002/tpg2.20160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
Efficiently exploiting natural genetic diversity captured by accessions stored in genebanks is crucial to genetic improvement of major crops. Selecting accessions of interest from genebanks has traditionally required information from extensive and expensive evaluation; however, low-cost genotyping combined with genomic prediction have enabled us to generate predicted genetic merits for the entire set with targeted phenotypic evaluation of representative subsets. To explore this general approach, analytical assessment and empirical validation of the maize (Zea mays L.) association population (MAP) as a training population were conducted in the present study. Cross-validation within the MAP revealed mostly modest to strong predictive ability for 36 traits, generally in parallel with the square root of heritability. The MAP was then used to train the prediction models to generate genomic estimated breeding values (GEBVs) for the Ames Diversity Panel. Empirical validation conducted for nine traits across two validation populations confirmed the accuracy level indicated by the cross-validation of the training population. An upper bound for reliability (U value) was calculated for the accessions in the prediction population using genotypic data. The group of accessions with high U values generally had high predictive ability, even though the range of observed trait values was similar to the group of accessions with low U values. Our comprehensive analysis validated the general approach of turbocharging genebanks with genomics and genomic prediction. In addition, breeders and researchers can consider both GEBVs and U values to balance the needs of improving specific traits and broadening genetic diversity when selecting accessions from genebanks.
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Affiliation(s)
| | - Tingting Guo
- Dep. of Agronomy, Iowa State Univ., Ames, IA, 50011, USA
| | - Xianran Li
- Dep. of Agronomy, Iowa State Univ., Ames, IA, 50011, USA
| | - Jianming Yu
- Dep. of Agronomy, Iowa State Univ., Ames, IA, 50011, USA
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Anglin NL, Robles R, Rossel G, Alagon R, Panta A, Jarret RL, Manrique N, Ellis D. Genetic Identity, Diversity, and Population Structure of CIP's Sweetpotato ( I. batatas) Germplasm Collection. FRONTIERS IN PLANT SCIENCE 2021; 12:660012. [PMID: 34777403 PMCID: PMC8589021 DOI: 10.3389/fpls.2021.660012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Accepted: 08/06/2021] [Indexed: 05/27/2023]
Abstract
The in trust sweetpotato collection housed by the International Center of Potato (CIP) is one of the largest assemblages of plant material representing the genetic resources of this important staple crop. The collection currently contains almost 6,000 accessions of Ipomoea batatas (cultivated sweetpotato) and over 1,000 accessions of sweetpotato crop wild relatives (CWRs). In this study, the entire cultivated collection (5,979 accessions) was genotyped with a panel of 20 simple sequence repeat (SSR) markers to assess genetic identity, diversity, and population structure. Genotyping and phenotyping of in vitro plantlets and mother plants were conducted simultaneously on 2,711 accessions (45% of the total collection) to identify and correct possible genetic identity errors which could have occurred at any time over the thirty plus years of maintenance in the in vitro collection. Within this group, 533 accessions (19.6%) had errors in identity. Field evaluations of morphological descriptors were carried out to confirm the marker data. A phylogenetic tree was constructed to reveal the intraspecific relationships in the population which uncovered high levels of redundancy in material from Peru and Latin America. These genotypic data were supported by morphological data. Population structure analysis demonstrated support for four ancestral populations with many of the accessions having lower levels of gene flow from the other populations. This was especially true of germplasm derived from Peru, Ecuador, and Africa. The set of 20 SSR markers was subsequently utilized to examine a subset of 189 accessions from the USDA sweetpotato germplasm collection and to identify and reconcile potential errors in the identification of clones shared between these collections. Marker analysis demonstrated that the USDA subset of material had 65 unique accessions that were not found in the larger CIP collection. As far as the authors are aware, this is the first report of genotyping an entire sweetpotato germplasm collection in its entirety.
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Affiliation(s)
| | | | | | | | - Ana Panta
- International Potato Center (CIP), Lima, Peru
| | - Robert L. Jarret
- Plant Genetic Resources Conservation Unit, United States Department of Agriculture, Agricultural Research Service, Griffin, GA, United States
| | | | - David Ellis
- International Potato Center (CIP), Lima, Peru
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12
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Tanaka R, Lui-King J, Mandaharisoa ST, Rakotondramanana M, Ranaivo HN, Pariasca-Tanaka J, Kanegae HK, Iwata H, Wissuwa M. From gene banks to farmer's fields: using genomic selection to identify donors for a breeding program in rice to close the yield gap on smallholder farms. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3397-3410. [PMID: 34264372 PMCID: PMC8440315 DOI: 10.1007/s00122-021-03909-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Despite phenotyping the training set under unfavorable conditions on smallholder farms in Madagascar, we were able to successfully apply genomic prediction to select donors among gene bank accessions. Poor soil fertility and low fertilizer application rates are main reasons for the large yield gap observed for rice produced in sub-Saharan Africa. Traditional varieties that are preserved in gene banks were shown to possess traits and alleles that would improve the performance of modern variety under such low-input conditions. How to accelerate the utilization of gene bank resources in crop improvement is an unresolved question and here our objective was to test whether genomic prediction could aid in the selection of promising donors. A subset of the 3,024 sequenced accessions from the IRRI rice gene bank was phenotyped for yield and agronomic traits for two years in unfertilized farmers' fields in Madagascar, and based on these data, a genomic prediction model was developed. This model was applied to predict the performance of the entire set of 3024 accessions, and the top predicted performers were sent to Madagascar for confirmatory trials. The prediction accuracies ranged from 0.10 to 0.30 for grain yield, from 0.25 to 0.63 for straw biomass, to 0.71 for heading date. Two accessions have subsequently been utilized as donors in rice breeding programs in Madagascar. Despite having conducted phenotypic evaluations under challenging conditions on smallholder farms, our results are encouraging as the prediction accuracy realized in on-farm experiments was in the range of accuracies achieved in on-station studies. Thus, we could provide clear empirical evidence on the value of genomic selection in identifying suitable genetic resources for crop improvement, if genotypic data are available.
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Affiliation(s)
- Ryokei Tanaka
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - James Lui-King
- International Program in Agricultural Development Studies, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Sarah Tojo Mandaharisoa
- Rice Research Department, The National Center for Applied Research On Rural Development (FOFIFA), Antananarivo, 101, Madagascar
| | - Mbolatantely Rakotondramanana
- Rice Research Department, The National Center for Applied Research On Rural Development (FOFIFA), Antananarivo, 101, Madagascar
| | - Harisoa Nicole Ranaivo
- Rice Research Department, The National Center for Applied Research On Rural Development (FOFIFA), Antananarivo, 101, Madagascar
| | - Juan Pariasca-Tanaka
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan
| | - Hiromi Kajiya Kanegae
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Hiroyoshi Iwata
- Department of Agricultural and Environmental Biology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo, 113-8657, Japan
| | - Matthias Wissuwa
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki, 305-8686, Japan.
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13
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Development and validation of diagnostic SNP markers for quality control genotyping in a collection of four rice (Oryza) species. Sci Rep 2021; 11:18617. [PMID: 34545105 PMCID: PMC8452751 DOI: 10.1038/s41598-021-97689-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 08/30/2021] [Indexed: 02/08/2023] Open
Abstract
Morphological identification of closely related rice species, particularly those in the Oryza AA genome group, presents major challenges and often results in cases of misidentification. Recent work by this group identified diagnostic single nucleotide polymorphic (SNP) markers specific for several rice species and subspecies based on DArTseq next-generation sequencing technology ("DArTseq"). These SNPs can be used for quality control (QC) analysis in rice breeding and germplasm maintenance programs. Here, we present the DArTseq-based diagnostic SNPs converted into Kompetitive allele-specific PCR (KASPar or KASP) assays and validation data for a subset of them; these can be used for low-cost routine genotyping quality control (QC) analysis. Of the 224 species/subspecies' diagnostic SNPs tested, 158 of them produced working KASP assays, a conversion success rate of 70%. Two validation experiments were run with 87 of the 158 SNP markers to ensure that the assays amplified, were polymorphic, and distinguished the five species/subspecies tested. Based on these validation test results, we recommend a panel of 36 SNP markers that clearly delineate O. barthii, O. glaberrima, O. longistaminata, O. sativa spp. indica and japonica. The KASP assays provide a flexible, rapid turnaround and cost-effective tool to facilitate germplasm curation and management of these four Oryza AA genome species across multiple genebanks.
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14
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Engels JMM, Ebert AW. A Critical Review of the Current Global Ex Situ Conservation System for Plant Agrobiodiversity. II. Strengths and Weaknesses of the Current System and Recommendations for Its Improvement. PLANTS (BASEL, SWITZERLAND) 2021; 10:1904. [PMID: 34579439 PMCID: PMC8472064 DOI: 10.3390/plants10091904] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 09/05/2021] [Accepted: 09/09/2021] [Indexed: 02/08/2023]
Abstract
In this paper, we review gene bank operations that have an influence on the global conservation system, with the intention to identify critical aspects that should be improved for optimum performance. We describe the role of active and base collections and the importance of linking germplasm conservation and use, also in view of new developments in genomics and phenomics that facilitate more effective and efficient conservation and use of plant agrobiodiversity. Strengths, limitations, and opportunities of the existing global ex situ conservation system are discussed, and measures are proposed to achieve a rational, more effective, and efficient global system for germplasm conservation and sustainable use. The proposed measures include filling genetic and geographic gaps in current ex situ collections; determining unique accessions at the global level for long-term conservation in virtual base collections; intensifying existing international collaborations among gene banks and forging collaborations with the botanic gardens community; increasing investment in conservation research and user-oriented supportive research; improved accession-level description of the genetic diversity of crop collections; improvements of the legal and policy framework; and oversight of the proposed network of global base collections.
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15
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Fu YB, Cober ER, Morrison MJ, Marsolais F, Peterson GW, Horbach C. Patterns of Genetic Variation in a Soybean Germplasm Collection as Characterized with Genotyping-by-Sequencing. PLANTS 2021; 10:plants10081611. [PMID: 34451656 PMCID: PMC8399144 DOI: 10.3390/plants10081611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 11/21/2022]
Abstract
Genomic characterization is playing an increasing role in plant germplasm conservation and utilization, as it can provide higher resolution with genome-wide SNP markers than before to identify and analyze genetic variation. A genotyping-by-sequencing technique was applied to genotype 541 soybean accessions conserved at Plant Gene Resources of Canada and 30 soybean cultivars and breeding lines developed by the Ottawa soybean breeding program of Agriculture and Agri-Food Canada. The sequencing generated an average of 952,074 raw sequence reads per sample. SNP calling identified 43,891 SNPs across 20 soybean chromosomes and 69 scaffolds with variable levels of missing values. Based on 19,898 SNPs with up to 50% missing values, three distinct genetic groups were found in the assayed samples. These groups were a mixture of the samples that originated from different countries and the samples of known maturity groups. The samples that originated from Canada were clustered into all three distinct groups, but 30 Ottawa breeding lines fell into two groups only. Based on the average pairwise dissimilarity estimates, 40 samples with the most genetic distinctness were identified from three genetic groups with diverse sample origin and known maturity. Additionally, 40 samples with the highest genetic redundancy were detected and they consisted of different sample origins and maturity groups, largely from one genetic group. Moreover, some genetically duplicated samples were identified, but the overall level of genetic duplication was relatively low in the collection. These findings are useful for soybean germplasm management and utilization.
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Affiliation(s)
- Yong-Bi Fu
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada; (G.W.P.); (C.H.)
- Correspondence:
| | - Elroy R. Cober
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (E.R.C.); (M.J.M.)
| | - Malcolm J. Morrison
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON K1A 0C6, Canada; (E.R.C.); (M.J.M.)
| | - Frédéric Marsolais
- Genomics and Biotechnology, London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N5V 4T3, Canada;
| | - Gregory W. Peterson
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada; (G.W.P.); (C.H.)
| | - Carolee Horbach
- Plant Gene Resources of Canada, Saskatoon Research and Development Centre, Agriculture and Agri-Food Canada, 107 Science Place, Saskatoon, SK S7N 0X2, Canada; (G.W.P.); (C.H.)
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16
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Massa AN, Bressano M, Soave JH, Buteler MI, Seijo G, Sobolev VS, Orner VA, Oddino C, Soave SJ, Faustinelli PC, de Blas FJ, Lamb MC, Arias RS. Genotyping tools and resources to assess peanut germplasm: smut-resistant landraces as a case study. PeerJ 2021; 9:e10581. [PMID: 33575123 PMCID: PMC7849506 DOI: 10.7717/peerj.10581] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Accepted: 11/24/2020] [Indexed: 11/20/2022] Open
Abstract
Peanut smut caused by Thecaphora frezii is a severe fungal disease currently endemic to Argentina and Brazil. The identification of smut resistant germplasm is crucial in view of the potential risk of a global spread. In a recent study, we reported new sources of smut resistance and demonstrated its introgression into elite peanut cultivars. Here, we revisited one of these sources (line I0322) to verify its presence in the U.S. peanut germplasm collection and to identify single nucleotide polymorphisms (SNPs) potentially associated with resistance. Five accessions of Arachis hypogaea subsp. fastigiata from the U.S. peanut collection, along with the resistant source and derived inbred lines were genotyped with a 48K SNP peanut array. A recently developed SNP genotyping platform called RNase H2 enzyme-based amplification (rhAmp) was further applied to validate selected SNPs in a larger number of individuals per accession. More than 14,000 SNPs and nine rhAmp assays confirmed the presence of a germplasm in the U.S. peanut collection that is 98.6% identical (P < 0.01, bootstrap t-test) to the resistant line I0322. We report this germplasm with accompanying genetic information, genotyping data, and diagnostic SNP markers.
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Affiliation(s)
- Alicia N Massa
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
| | - Marina Bressano
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Juan H Soave
- Criadero El Carmen, General Cabrera, Córdoba, Argentina
| | | | - Guillermo Seijo
- Instituto de Botánica del Nordeste (IBONE, CONICET-UNNE) and Facultad de Ciencias Exactas y Naturales y Agrimensura, Universidad Nacional del Nordeste, Corrientes, Argentina
| | | | - Valerie A Orner
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
| | | | - Sara J Soave
- Criadero El Carmen, General Cabrera, Córdoba, Argentina
| | | | - Francisco J de Blas
- Instituto Multidisciplinario de Biología Vegetal-(IMBIV-CONICET-UNC), Córdoba, Argentina
| | - Marshall C Lamb
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
| | - Renee S Arias
- National Peanut Research Laboratory, USDA-ARS, Dawson, GA, USA
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17
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Arca M, Mary-Huard T, Gouesnard B, Bérard A, Bauland C, Combes V, Madur D, Charcosset A, Nicolas SD. Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array. FRONTIERS IN PLANT SCIENCE 2021; 11:568699. [PMID: 33488638 PMCID: PMC7817617 DOI: 10.3389/fpls.2020.568699] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 11/12/2020] [Indexed: 05/13/2023]
Abstract
Genebanks harbor original landraces carrying many original favorable alleles for mitigating biotic and abiotic stresses. Their genetic diversity remains, however, poorly characterized due to their large within genetic diversity. We developed a high-throughput, cheap and labor saving DNA bulk approach based on single-nucleotide polymorphism (SNP) Illumina Infinium HD array to genotype landraces. Samples were gathered for each landrace by mixing equal weights from young leaves, from which DNA was extracted. We then estimated allelic frequencies in each DNA bulk based on fluorescent intensity ratio (FIR) between two alleles at each SNP using a two step-approach. We first tested either whether the DNA bulk was monomorphic or polymorphic according to the two FIR distributions of individuals homozygous for allele A or B, respectively. If the DNA bulk was polymorphic, we estimated its allelic frequency by using a predictive equation calibrated on FIR from DNA bulks with known allelic frequencies. Our approach: (i) gives accurate allelic frequency estimations that are highly reproducible across laboratories, (ii) protects against false detection of allele fixation within landraces. We estimated allelic frequencies of 23,412 SNPs in 156 landraces representing American and European maize diversity. Modified Roger's genetic Distance between 156 landraces estimated from 23,412 SNPs and 17 simple sequence repeats using the same DNA bulks were highly correlated, suggesting that the ascertainment bias is low. Our approach is affordable, easy to implement and does not require specific bioinformatics support and laboratory equipment, and therefore should be highly relevant for large-scale characterization of genebanks for a wide range of species.
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Affiliation(s)
- Mariangela Arca
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Brigitte Gouesnard
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Aurélie Bérard
- Université Paris-Saclay, INRAE, Etude du Polymorphisme des Génomes Végétaux, Evry-Courcouronnes, France
| | - Cyril Bauland
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Valérie Combes
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Delphine Madur
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
| | - Stéphane D. Nicolas
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE – Le Moulon, Gif-sur-Yvette, France
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18
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Ebert AW, Engels JMM. Plant Biodiversity and Genetic Resources Matter! PLANTS (BASEL, SWITZERLAND) 2020; 9:E1706. [PMID: 33291549 PMCID: PMC7761872 DOI: 10.3390/plants9121706] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 12/03/2020] [Indexed: 12/24/2022]
Abstract
Plant biodiversity is the foundation of our present-day food supply (including functional food and medicine) and offers humankind multiple other benefits in terms of ecosystem functions and resilience to climate change, as well as other perturbations. This Special Issue on 'Plant Biodiversity and Genetic Resources' comprises 32 papers covering a wide array of aspects from the definition and identification of hotspots of wild and domesticated plant biodiversity to the specifics of conservation of genetic resources of crop genepools, including breeding and research materials, landraces and crop wild relatives which collectively are the pillars of modern plant breeding, as well as of localized breeding efforts by farmers and farming communities. The integration of genomics and phenomics into germplasm and genebank management enhances the value of crop germplasm conserved ex situ, and is likely to increase its utilization in plant breeding, but presents major challenges for data management and the sharing of this information with potential users. Furthermore, also a better integration of in situ and ex situ conservation efforts will contribute to a more effective conservation and certainly to a more sustainable and efficient utilization. Other aspects such as policy, access and benefit-sharing that directly impact the use of plant biodiversity and genetic resources, as well as balanced nutrition and enhanced resilience of production systems that depend on their increased use, are also being treated. The editorial concludes with six key messages on plant biodiversity, genetic erosion, genetic resources and plant breeding, agricultural diversification, conservation of agrobiodiversity, and the evolving role and importance of genebanks.
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Affiliation(s)
- Andreas W. Ebert
- World Vegetable Center, 60 Yi-Min Liao, Shanhua, Tainan 74151, Taiwan
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19
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‘Warehouse’ or research centre? Analyzing public preferences for conservation, pre-breeding and characterization activities at the Czech genebank. Food Secur 2020. [DOI: 10.1007/s12571-020-01040-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Vasumathy SK, Peringottillam M, Sundaram KT, Kumar SHK, Alagu M. Genome- wide structural and functional variant discovery of rice landraces using genotyping by sequencing. Mol Biol Rep 2020; 47:7391-7402. [PMID: 32886328 DOI: 10.1007/s11033-020-05794-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022]
Abstract
Rice landraces are vital genetic resources for agronomic and quality traits but the undeniable collection of Kerala landraces remains poorly delineated. To effectively conserve, manage, and use these resources, understanding the genomic structure of germplasm is essential. Genotyping by sequencing (GBS) enables identification of an immense number of single nucleotide polymorphism (SNP) and insertion deletion (InDel) from 96 rice germplasm. In the present study, a total of 16.9 × 107 reads were generated, and among that 16.3 × 107 reads were mapped to the indica reference genome. Exploring GBS data unfolded a wide genomic variations including 82,59,639 SNPs and 1,07,140 Indels. Both neighbor-joining tree and principal coordinate analysis with InDel markers revealed the selected germplasm in this study as highly diverse in structure. We assembled unmapped reads which were further employed for gene ontology analysis. These unmapped sequences that are generally expelled from subsequent studies of GBS data analysis may exist as an unexplored resort for several novel significant biological findings. The discovery of SNPs from the haplotyping results of GS3 and GIF1 genes provided insight into marker- assisted selection based on grain size and yield and can be utilized for rice yield improvement. To our knowledge, this is the first report on structural variation analysis using the GBS platform in rice landraces collected from Kerala. Genomic information from this study endows with valuable resources for perceptive rice landrace structure and can also facilitate sequencing-based molecular breeding.
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Affiliation(s)
| | - Maya Peringottillam
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Krishna T Sundaram
- South Asia hub, ICRISAT Campus, International Rice Research Institute, Secundarabad, Telangana, India
| | - S Hari Krishna Kumar
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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22
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Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing. Sci Rep 2020; 10:13995. [PMID: 32814806 PMCID: PMC7438528 DOI: 10.1038/s41598-020-70842-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022] Open
Abstract
To minimize the cost of sample preparation and genotyping, most genebank genomics studies in self-pollinating species are conducted on a single individual to represent an accession, which may be heterogeneous with larger than expected intra-accession genetic variation. Here, we compared various population genetics parameters among six DNA (leaf) sampling methods on 90 accessions representing a wild species (O. barthii), cultivated and landraces (O. glaberrima, O. sativa), and improved varieties derived through interspecific hybridizations. A total of 1,527 DNA samples were genotyped with 46,818 polymorphic single nucleotide polymorphisms (SNPs) using DArTseq. Various statistical analyses were performed on eleven datasets corresponding to 5 plants per accession individually and in a bulk (two sets), 10 plants individually and in a bulk (two sets), all 15 plants individually (one set), and a randomly sampled individual repeated six times (six sets). Overall, we arrived at broadly similar conclusions across 11 datasets in terms of SNP polymorphism, heterozygosity/heterogeneity, diversity indices, concordance among genetic dissimilarity matrices, population structure, and genetic differentiation; there were, however, a few discrepancies between some pairs of datasets. Detailed results of each sampling method, the concordance in their outputs, and the technical and cost implications of each method were discussed.
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Palmé AE, Hagenblad J, Solberg SØ, Aloisi K, Artemyeva A. SNP Markers and Evaluation of Duplicate Holdings of Brassica oleracea in Two European Genebanks. PLANTS 2020; 9:plants9080925. [PMID: 32707792 PMCID: PMC7465924 DOI: 10.3390/plants9080925] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/19/2020] [Accepted: 07/20/2020] [Indexed: 11/26/2022]
Abstract
Around the world, there are more than 1500 genebanks storing plant genetic resources to be used in breeding and research. Such resources are essential for future food security, but many genebanks experience backlogs in their conservation work, often combined with limited budgets. Therefore, avoiding duplicate holdings is on the agenda. A process of coordination has started, aiming at sharing the responsibility of maintaining the unique accessions while allowing access according to the international treaty for plant genetic resources. Identifying duplicate holdings based on passport data has been one component of this. In the past, and especially in vegetables, different selections within the same varieties were common and the naming practices of cultivars/selections were flexible. Here, we examined 10 accession pairs/groups of cabbage (Brassica oleracea var. capitata) with similar names maintained in the Russian and Nordic genebanks. The accessions were analyzed for 11 morphological traits and with a SNP (Single Nucleotide Polymorphism) array developed for B. napus. Both proved to be useful tools for understanding the genetic structure among the accessions and for identifying duplicates, and a subset of 500 SNP markers are suggested for future Brassica oleracea genetic characterization. Within five out of 10 pairs/groups, we detected clear genetic differences among the accessions, and three of these were confirmed by significant differences in one or several morphological traits. In one case, a white cabbage and a red cabbage had similar accession names. The study highlights the necessity to be careful when identifying duplicate accessions based solely on the name, especially in older cross-pollinated species such as cabbage.
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Affiliation(s)
- Anna E. Palmé
- Nordic Genetic Resource Centre, Smedjevägen 3, SE-230 53 Alnarp, Sweden; (A.E.P.); (K.A.)
| | - Jenny Hagenblad
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden;
| | - Svein Øivind Solberg
- Faculty of Applied Ecology, Agricultural Sciences and Biotechnology, Inland Norway University of Applied Sciences, NO-2418 Elverum, Norway
- Correspondence: ; Tel.: +46-735-401-516
| | - Karolina Aloisi
- Nordic Genetic Resource Centre, Smedjevägen 3, SE-230 53 Alnarp, Sweden; (A.E.P.); (K.A.)
| | - Anna Artemyeva
- N. I. Vavilov Institute of Plant Genetic Resources (VIR), 42-44, B. Morskaya Street, 190000 St. Petersburg, Russia;
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Nguyen GN, Norton SL. Genebank Phenomics: A Strategic Approach to Enhance Value and Utilization of Crop Germplasm. PLANTS (BASEL, SWITZERLAND) 2020; 9:E817. [PMID: 32610615 PMCID: PMC7411623 DOI: 10.3390/plants9070817] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/25/2020] [Accepted: 06/26/2020] [Indexed: 02/07/2023]
Abstract
Genetically diverse plant germplasm stored in ex-situ genebanks are excellent resources for breeding new high yielding and sustainable crop varieties to ensure future food security. Novel alleles have been discovered through routine genebank activities such as seed regeneration and characterization, with subsequent utilization providing significant genetic gains and improvements for the selection of favorable traits, including yield, biotic, and abiotic resistance. Although some genebanks have implemented cost-effective genotyping technologies through advances in DNA technology, the adoption of modern phenotyping is lagging. The introduction of advanced phenotyping technologies in recent decades has provided genebank scientists with time and cost-effective screening tools to obtain valuable phenotypic data for more traits on large germplasm collections during routine activities. The utilization of these phenotyping tools, coupled with high-throughput genotyping, will accelerate the use of genetic resources and fast-track the development of more resilient food crops for the future. In this review, we highlight current digital phenotyping methods that can capture traits during annual seed regeneration to enrich genebank phenotypic datasets. Next, we describe strategies for the collection and use of phenotypic data of specific traits for downstream research using high-throughput phenotyping technology. Finally, we examine the challenges and future perspectives of genebank phenomics.
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Affiliation(s)
- Giao N. Nguyen
- Australian Grains Genebank, Agriculture Victoria, 110 Natimuk Road, Horsham 3400, Australia;
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Falk KG, Jubery TZ, O'Rourke JA, Singh A, Sarkar S, Ganapathysubramanian B, Singh AK. Soybean Root System Architecture Trait Study through Genotypic, Phenotypic, and Shape-Based Clusters. PLANT PHENOMICS (WASHINGTON, D.C.) 2020; 2020:1925495. [PMID: 33313543 PMCID: PMC7706349 DOI: 10.34133/2020/1925495] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 04/16/2020] [Indexed: 05/24/2023]
Abstract
We report a root system architecture (RSA) traits examination of a larger scale soybean accession set to study trait genetic diversity. Suffering from the limitation of scale, scope, and susceptibility to measurement variation, RSA traits are tedious to phenotype. Combining 35,448 SNPs with an imaging phenotyping platform, 292 accessions (replications = 14) were studied for RSA traits to decipher the genetic diversity. Based on literature search for root shape and morphology parameters, we used an ideotype-based approach to develop informative root (iRoot) categories using root traits. The RSA traits displayed genetic variability for root shape, length, number, mass, and angle. Soybean accessions clustered into eight genotype- and phenotype-based clusters and displayed similarity. Genotype-based clusters correlated with geographical origins. SNP profiles indicated that much of US origin genotypes lack genetic diversity for RSA traits, while diverse accession could infuse useful genetic variation for these traits. Shape-based clusters were created by integrating convolution neural net and Fourier transformation methods, enabling trait cataloging for breeding and research applications. The combination of genetic and phenotypic analyses in conjunction with machine learning and mathematical models provides opportunities for targeted root trait breeding efforts to maximize the beneficial genetic diversity for future genetic gains.
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Affiliation(s)
- Kevin G. Falk
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | | | - Jamie A. O'Rourke
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
- USDA-Agricultural Research Service, Corn Insects and Crop Genetics Research Unit, Ames, Iowa, USA
| | - Arti Singh
- Department of Agronomy, Iowa State University, Ames, Iowa, USA
| | - Soumik Sarkar
- Department of Mechanical Engineering, Iowa State University, Ames, Iowa, USA
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Abstract
AbstractNew challenges have arrived for the conservation of plant genetic resources for food and agriculture. Increased pressure on the environment, including the added threat of climate change, has had adverse effects on biodiversity and agricultural systems. Emerging science and new technologies have at the same time altered the scope of possibilities for collection, conservation, and utilization of genetic resources for agriculture. Taken together, these changes imply a need for a refocusing of global strategies for the management of genetic resources for agriculture. This paper argues that simple theoretical models provide relatively little guidance for key questions about genebank management. The fundamental uncertainty of scientific possibility and global futures makes it challenging – and perhaps futile – to attempt economic valuation of gene banks. A more useful application of economic tools will be in the prioritization of collection and conservation. Economic analysis may also offer useful insights into the efficient management of genetic resources.
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Abstract
AbstractThe UN Sustainable Development Goal (SDG) Target 2.5 explicitly calls for the maintenance of genetic diversity of seeds through soundly managed and diversified seed and plant banks at national, regional, and international levels as an essential undertaking to end global hunger (SDG Goal 2). This special issue results from a renewed call to demonstrate the value-in-use of conserving and supplying plant genetic resources conserved in genebanks to researchers, plant breeders, and farmers. We present these studies as a collective contribution to a relatively small body of literature that highlights not only the importance of crop plant diversity managed by genebanks but also the diversity of genebank functions and uses. In this overview, we begin by restating foundation concepts that economists have applied to study the value of crop genetic resources conserved as genebank accessions. We then provide a synthesis of previous research on genebank values from the late 1990s until the present. We summarize the main messages of the studies included in this special issue of Food Security and explain how they contribute to a better understanding of the role, function, and value of genebanks, particularly as we address food security challenges in a changing agricultural context. Finally, we draw implications for further applied research and policy.
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Assessment of Genetic Heritability in Rice Breeding Lines Based on Morphological Traits and Caryopsis Ultrastructure. Sci Rep 2020; 10:7830. [PMID: 32385288 PMCID: PMC7210993 DOI: 10.1038/s41598-020-63976-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 04/03/2020] [Indexed: 11/22/2022] Open
Abstract
Rice (Oryza sativa L) is a most important staple food crop of the world because more than half of the World’s population is dependent on it for their livelihood. Global rice production must be doubled by 2050 to cope up with the situation of population growth. Narrow genetic base in the released varieties has made the improvement in plateaus. Widening the genetic base is necessary to overcome the yield barrier. Hybridization and pre-breeding has been carried out to broaden the genetic base. Heritability and genetic advances were measured in the F5 lines (Tulaipanji × IR64), F3 lines (Tulaipanji × IR64 × PB1460), and F3 lines (Badshabhog × Swarna sub1). Some of the breeding lines were showing promising field performance with high yield potentiality. Wide crosses were performed to widen the genetic base between (Ranjit × O. rufipogon) and (Badshabhog × O. rufipogon) and the heritability pattern of the morphological characteristics in the progeny lines was evaluated. Nutritional quality of the rice grain is totally dependent on the morphology and histological characteristics of the caryopsis which are genetically determined. Caryopses ultrastructural analyses were carried out in seventeen different rice breeding lines through SEM. SEM analysis showed distinguishing ultrastructure in respect to pericarp, testa, aleurone layer, protein bodies and starchy endosperm in the breeding lines with distinctive inheritance pattern. This study provides information about the cross compatibility of the wide hybridization and heritability measures of the morphological traits which may supplement the breeding program to break the yield plateaus.
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Advances in Molecular Genetics and Genomics of African Rice ( Oryza glaberrima Steud). PLANTS 2019; 8:plants8100376. [PMID: 31561516 PMCID: PMC6843444 DOI: 10.3390/plants8100376] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 09/23/2019] [Accepted: 09/25/2019] [Indexed: 02/07/2023]
Abstract
African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. Challenges in deploying African rice genetic resources in rice improvement and the genomics efforts made in addressing them are highlighted.
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Wambugu PW, Ndjiondjop MN, Henry RJ. Role of genomics in promoting the utilization of plant genetic resources in genebanks. Brief Funct Genomics 2019; 17:198-206. [PMID: 29688255 PMCID: PMC5967547 DOI: 10.1093/bfgp/ely014] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Global efforts have seen the world's plant genetic resources (PGRs) conserved in about 1625 germ plasm repositories. Utility of these resources is important in increasing the resilience and productivity of agricultural production systems. However, despite their importance, utility of these resources has been poor. This article reviews the real and potential application of the current advances in genomic technologies in improving the utilization of these resources. The actual and potential application of these genomic approaches in plant identification, phylogenetic analysis, analysing the genetic value of germ plasm, facilitating germ plasm selection in genebanks as well as instilling confidence in international germ plasm exchange system is discussed. We note that if genebanks are to benefit from this genomic revolution, there is need for fundamental changes in the way genebanks are managed, perceived, organized and funded. Increased collaboration between genebank managers and the user community is also recommended.
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Affiliation(s)
- Peterson W Wambugu
- Corresponding author: Robert Henry, Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia. Tel.: ±61733460551; Fax: ±61733460555; E-mail:
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31
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Jeong SC, Moon JK, Park SK, Kim MS, Lee K, Lee SR, Jeong N, Choi MS, Kim N, Kang ST, Park E. Genetic diversity patterns and domestication origin of soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1179-1193. [PMID: 30588539 PMCID: PMC6449312 DOI: 10.1007/s00122-018-3271-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 12/19/2018] [Indexed: 05/20/2023]
Abstract
KEY MESSAGE Genotyping data of a comprehensive Korean soybean collection obtained using a large SNP array were used to clarify global distribution patterns of soybean and address the evolutionary history of soybean. Understanding diversity and evolution of a crop is an essential step to implement a strategy to expand its germplasm base for crop improvement research. Accessions intensively collected from Korea, which is a small but central region in the distribution geography of soybean, were genotyped to provide sufficient data to underpin population genetic questions. After removing natural hybrids and duplicated or redundant accessions, we obtained a non-redundant set comprising 1957 domesticated and 1079 wild accessions to perform population structure analyses. Our analysis demonstrates that while wild soybean germplasm will require additional sampling from diverse indigenous areas to expand the germplasm base, the current domesticated soybean germplasm is saturated in terms of genetic diversity. We then showed that our genome-wide polymorphism map enabled us to detect genetic loci underlying flower color, seed-coat color, and domestication syndrome. A representative soybean set consisting of 194 accessions was divided into one domesticated subpopulation and four wild subpopulations that could be traced back to their geographic collection areas. Population genomics analyses suggested that the monophyletic group of domesticated soybeans was likely originated at a Japanese region. The results were further substantiated by a phylogenetic tree constructed from domestication-associated single nucleotide polymorphisms identified in this study.
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Affiliation(s)
- Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea.
| | - Jung-Kyung Moon
- Agricultural Genome Center, National Academy of Agricultural Sciences, Rural Development Administration, Jeonju, Jeonbuk, 55365, Korea.
| | - Soo-Kwon Park
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Myung-Shin Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
| | - Kwanghee Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
| | - Soo Rang Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk, 28116, Korea
| | - Namhee Jeong
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Man Soo Choi
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk, 55365, Korea
| | - Namshin Kim
- Epigenomics Research Center, Genome Institute, Institute of Bioscience and Biotechnology, Korea Research, Taejon, 34141, Korea
| | - Sung-Taeg Kang
- Department of Crop Science and Biotechnology, Dankook University, Cheonan, Chungnam, 31116, Korea
| | - Euiho Park
- School of Biotechnology, Yeungnam University, Gyeongsan, Gyeongbuk, 38541, Korea
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32
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Singh N, Wu S, Raupp WJ, Sehgal S, Arora S, Tiwari V, Vikram P, Singh S, Chhuneja P, Gill BS, Poland J. Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions. Sci Rep 2019; 9:650. [PMID: 30679756 PMCID: PMC6346010 DOI: 10.1038/s41598-018-37269-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 11/30/2018] [Indexed: 01/03/2023] Open
Abstract
Genebanks are valuable resources for crop improvement through the acquisition, ex-situ conservation and sharing of unique germplasm among plant breeders and geneticists. With over seven million existing accessions and increasing storage demands and costs, genebanks need efficient characterization and curation to make them more accessible and usable and to reduce operating costs, so that the crop improvement community can most effectively leverage this vast resource of untapped novel genetic diversity. However, the sharing and inconsistent documentation of germplasm often results in unintentionally duplicated collections with poor characterization and many identical accessions that can be hard or impossible to identify without passport information and unmatched accession identifiers. Here we demonstrate the use of genotypic information from these accessions using a cost-effective next generation sequencing platform to find and remove duplications. We identify and characterize over 50% duplicated accessions both within and across genebank collections of Aegilops tauschii, an important wild relative of wheat and source of genetic diversity for wheat improvement. We present a pipeline to identify and remove identical accessions within and among genebanks and curate globally unique accessions. We also show how this approach can also be applied to future collection efforts to avoid the accumulation of identical material. When coordinated across global genebanks, this approach will ultimately allow for cost effective and efficient management of germplasm and better stewarding of these valuable resources.
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Affiliation(s)
- Narinder Singh
- Interdepartmental Genetics Program, Kansas State University, Manhattan, KS, 66506, USA.,Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Shuangye Wu
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - W John Raupp
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Sunish Sehgal
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Sanu Arora
- Crop Genetics, John Innes Center, Norwich, NR4 7UH, United Kingdom
| | - Vijay Tiwari
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.,Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Prashant Vikram
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45 Carretera México-Veracruz, Colonia El Batán, Texcoco, Edo, De México, CP, 56130, Mexico
| | - Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45 Carretera México-Veracruz, Colonia El Batán, Texcoco, Edo, De México, CP, 56130, Mexico
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
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Singh N, Wu S, Raupp WJ, Sehgal S, Arora S, Tiwari V, Vikram P, Singh S, Chhuneja P, Gill BS, Poland J. Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions. Sci Rep 2019; 9:650. [PMID: 30679756 DOI: 10.1101/410779] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 11/30/2018] [Indexed: 05/25/2023] Open
Abstract
Genebanks are valuable resources for crop improvement through the acquisition, ex-situ conservation and sharing of unique germplasm among plant breeders and geneticists. With over seven million existing accessions and increasing storage demands and costs, genebanks need efficient characterization and curation to make them more accessible and usable and to reduce operating costs, so that the crop improvement community can most effectively leverage this vast resource of untapped novel genetic diversity. However, the sharing and inconsistent documentation of germplasm often results in unintentionally duplicated collections with poor characterization and many identical accessions that can be hard or impossible to identify without passport information and unmatched accession identifiers. Here we demonstrate the use of genotypic information from these accessions using a cost-effective next generation sequencing platform to find and remove duplications. We identify and characterize over 50% duplicated accessions both within and across genebank collections of Aegilops tauschii, an important wild relative of wheat and source of genetic diversity for wheat improvement. We present a pipeline to identify and remove identical accessions within and among genebanks and curate globally unique accessions. We also show how this approach can also be applied to future collection efforts to avoid the accumulation of identical material. When coordinated across global genebanks, this approach will ultimately allow for cost effective and efficient management of germplasm and better stewarding of these valuable resources.
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Affiliation(s)
- Narinder Singh
- Interdepartmental Genetics Program, Kansas State University, Manhattan, KS, 66506, USA
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Shuangye Wu
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - W John Raupp
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Sunish Sehgal
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Sanu Arora
- Crop Genetics, John Innes Center, Norwich, NR4 7UH, United Kingdom
| | - Vijay Tiwari
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
- Department of Plant Sciences and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA
| | - Prashant Vikram
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45 Carretera México-Veracruz, Colonia El Batán, Texcoco, Edo, De México, CP, 56130, Mexico
| | - Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45 Carretera México-Veracruz, Colonia El Batán, Texcoco, Edo, De México, CP, 56130, Mexico
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Bikram S Gill
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA
| | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, Manhattan, KS, 66506, USA.
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Yadav MK, Aravindan S, Ngangkham U, Raghu S, Prabhukarthikeyan SR, Keerthana U, Marndi BC, Adak T, Munda S, Deshmukh R, Pramesh D, Samantaray S, Rath PC. Blast resistance in Indian rice landraces: Genetic dissection by gene specific markers. PLoS One 2019; 14:e0211061. [PMID: 30673751 PMCID: PMC6343911 DOI: 10.1371/journal.pone.0211061] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Accepted: 01/07/2019] [Indexed: 11/18/2022] Open
Abstract
Understanding of genetic diversity is important to explore existing gene in any crop breeding program. Most of the diversity preserved in the landraces which are well–known reservoirs of important traits for biotic and abiotic stresses. In the present study, the genetic diversity at twenty-four most significant blast resistance gene loci using twenty-eight gene specific markers were investigated in landraces originated from nine diverse rice ecologies of India. Based on phenotypic evaluation, landraces were classified into three distinct groups: highly resistant (21), moderately resistant (70) and susceptible (70). The landraces harbour a range of five to nineteen genes representing blast resistance allele with the frequency varied from 4.96% to 100%. The cluster analysis grouped entire 161 landraces into two major groups. Population structure along with other parameters was also analyzed to understand the evolution of blast resistance gene in rice. The population structure analysis and principal coordinate analysis classified the landraces into two sub–populations. Analysis of molecular variance showed maximum (93%) diversity within the population and least (7%) between populations. Five markers viz; K3957, Pikh, Pi2–i, RM212and RM302 were strongly associated with blast disease with the phenotypic variance of 1.4% to 7.6%. These resistant landraces will serve as a valuable genetic resource for future genomic studies, host–pathogen interaction, identification of novel R genes and rice improvement strategies.
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Affiliation(s)
| | - S. Aravindan
- ICAR-National Rice Research Institute, Odisha, India
| | | | - S. Raghu
- ICAR-National Rice Research Institute, Odisha, India
| | | | - U. Keerthana
- ICAR-National Rice Research Institute, Odisha, India
| | - B. C. Marndi
- ICAR-National Rice Research Institute, Odisha, India
| | - Totan Adak
- ICAR-National Rice Research Institute, Odisha, India
| | - Susmita Munda
- ICAR-National Rice Research Institute, Odisha, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali Punjab, India
| | - D. Pramesh
- Rice Pathology Laboratory, AICRIP, Gangavathi, University of Agricultural Sciences, Raichur, India
| | | | - P. C. Rath
- ICAR-National Rice Research Institute, Odisha, India
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35
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Halewood M, Lopez Noriega I, Ellis D, Roa C, Rouard M, Sackville Hamilton R. Using Genomic Sequence Information to Increase Conservation and Sustainable Use of Crop Diversity and Benefit-Sharing. Biopreserv Biobank 2018; 16:368-376. [PMID: 30325667 PMCID: PMC6204560 DOI: 10.1089/bio.2018.0043] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
This article describes how CGIAR centers and partners are using genomic sequence information to promote the conservation and sustainable use of crop genetic diversity, and to generate and share benefits derived from those uses. The article highlights combined institutional, and benefit-sharing-related challenges that need to be addressed to support expanded use of digital sequence information in agricultural research and development.
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Affiliation(s)
| | | | - Dave Ellis
- 2 International Potato Center , Lima, Peru
| | - Carolina Roa
- 3 Centro Internacional de Agricultura Tropical , Cali, Colombia
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Díez MJ, De la Rosa L, Martín I, Guasch L, Cartea ME, Mallor C, Casals J, Simó J, Rivera A, Anastasio G, Prohens J, Soler S, Blanca J, Valcárcel JV, Casañas F. Plant Genebanks: Present Situation and Proposals for Their Improvement. the Case of the Spanish Network. FRONTIERS IN PLANT SCIENCE 2018; 9:1794. [PMID: 30564263 PMCID: PMC6288731 DOI: 10.3389/fpls.2018.01794] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 11/19/2018] [Indexed: 05/20/2023]
Abstract
Genebanks were created by the middle of the twentieth century to preserve cultivated biodiversity when landraces began to be substituted by modern varieties. This move was generally accepted as a necessary step to safeguard the future. After about 75 years of collecting and maintaining genetic resources, the increasing ability of biotechnology to create new variability brings the roles of genebanks in the present and near future into question. As a continuation of several workshops that started in 2014, staff of some representative genebanks have met to discuss how the Spanish Plant Genetic Resources Network can be improved, identifying the following major shortcomings: lack of efficient coordination in the distribution of species among genebanks; too many genebanks; existence of detected and undetected duplicates; insufficient rate of regeneration; insufficient phenotyping, genotyping, and epiphenotyping; unsatisfactory rate of use by end users; and, insufficient funding. As a considerable increase in public funding is unlikely, we propose some strategies to increase the efficiency of the system. The most urgent tasks are to strengthen the rationalization of the network by establishing a clear hierarchy and functions, to improve the information in the base collection by deep characterization including not only phenotypes but also uses and utilities, to progressively replace the active collections with focused core collections constructed to meet users' needs, to optimize regeneration protocols, to limit new collecting expeditions of Spanish crop wild relatives to those growing in threatened habitats, and to develop user-friendly platforms to access germplasm documentation, including a unified system of descriptors and classification categories. Current advances in biotechnology, and especially those in gene editing will have without doubt an impact on the role of genebanks. However, the high number of genes and gene combinations created by evolution they hold cannot be produced by these techniques at present. So, these reservoirs of variability will continue to be indispensable for the near-medium future while the function of all the genes is unveiled. In turn, biotechnologies and gene editing will allow us to take advantage of the information held in genebanks in a more efficient and fast way, contributing to a better rationalization and functioning.
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Affiliation(s)
- María José Díez
- Mixed Unity for the Valorization and Breeding of Horticultural Landraces, Institute for the Conservation and Improvement of Valencian Agrodiversity, Universitat Politècnica de València, Valencia, Spain
| | - Lucía De la Rosa
- Spanish Plant Genetic Resources National Center, National Institute for Agricultural and Food Research and Technology, Alcalá de Henares, Spain
| | - Isaura Martín
- Spanish Plant Genetic Resources National Center, National Institute for Agricultural and Food Research and Technology, Alcalá de Henares, Spain
| | - Luís Guasch
- Spanish Plant Genetic Resources National Center, National Institute for Agricultural and Food Research and Technology, Alcalá de Henares, Spain
| | - María Elena Cartea
- Group of Genetics, Breeding and Biochemistry of Brassicas, Misión Biológica de Galicia, Spanish Council for Scientific Research, Pontevedra, Spain
| | - Cristina Mallor
- Agrifood Research and Technology Centre of Aragón, Agrifood Institute of Aragón, University of Zaragoza, Zaragoza, Spain
| | - Joan Casals
- Mixed Unity for the Valorization and Breeding of Horticultural Landraces, Miquel Agustí Foundation. Department of Agrifood Engineering and Biotechnology, BarcelonaTech, Castelldefels, Spain
| | - Joan Simó
- Mixed Unity for the Valorization and Breeding of Horticultural Landraces, Miquel Agustí Foundation. Department of Agrifood Engineering and Biotechnology, BarcelonaTech, Castelldefels, Spain
| | - Ana Rivera
- Mixed Unity for the Valorization and Breeding of Horticultural Landraces, Miquel Agustí Foundation. Department of Agrifood Engineering and Biotechnology, BarcelonaTech, Castelldefels, Spain
| | | | - Jaime Prohens
- Mixed Unity for the Valorization and Breeding of Horticultural Landraces, Institute for the Conservation and Improvement of Valencian Agrodiversity, Universitat Politècnica de València, Valencia, Spain
| | - Salvador Soler
- Mixed Unity for the Valorization and Breeding of Horticultural Landraces, Institute for the Conservation and Improvement of Valencian Agrodiversity, Universitat Politècnica de València, Valencia, Spain
| | - José Blanca
- Institute for the Conservation and Improvement of Valencian Agrodiversity, Universitat Politècnica de València, Valencia, Spain
| | - José Vicente Valcárcel
- Institute for the Conservation and Improvement of Valencian Agrodiversity, Universitat Politècnica de València, Valencia, Spain
| | - Francesc Casañas
- Mixed Unity for the Valorization and Breeding of Horticultural Landraces, Miquel Agustí Foundation. Department of Agrifood Engineering and Biotechnology, BarcelonaTech, Castelldefels, Spain
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Halewood M, Chiurugwi T, Sackville Hamilton R, Kurtz B, Marden E, Welch E, Michiels F, Mozafari J, Sabran M, Patron N, Kersey P, Bastow R, Dorius S, Dias S, McCouch S, Powell W. Plant genetic resources for food and agriculture: opportunities and challenges emerging from the science and information technology revolution. THE NEW PHYTOLOGIST 2018; 217:1407-1419. [PMID: 29359808 DOI: 10.1111/nph.14993] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/21/2017] [Indexed: 05/21/2023]
Abstract
Contents Summary 1407 I. Introduction 1408 II. Technological advances and their utility for gene banks and breeding, and longer-term contributions to SDGs 1408 III. The challenges that must be overcome to realise emerging R&D opportunities 1410 IV. Renewed governance structures for PGR (and related big data) 1413 V. Access and benefit sharing and big data 1416 VI. Conclusion 1417 Acknowledgements 1417 ORCID 1417 References 1417 SUMMARY: Over the last decade, there has been an ongoing revolution in the exploration, manipulation and synthesis of biological systems, through the development of new technologies that generate, analyse and exploit big data. Users of Plant Genetic Resources (PGR) can potentially leverage these capacities to significantly increase the efficiency and effectiveness of their efforts to conserve, discover and utilise novel qualities in PGR, and help achieve the Sustainable Development Goals (SDGs). This review advances the discussion on these emerging opportunities and discusses how taking advantage of them will require data integration and synthesis across disciplinary, organisational and international boundaries, and the formation of multi-disciplinary, international partnerships. We explore some of the institutional and policy challenges that these efforts will face, particularly how these new technologies may influence the structure and role of research for sustainable development, ownership of resources, and access and benefit sharing. We discuss potential responses to political and institutional challenges, ranging from options for enhanced structure and governance of research discovery platforms to internationally brokered benefit-sharing agreements, and identify a set of broad principles that could guide the global community as it seeks or considers solutions.
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Affiliation(s)
- Michael Halewood
- Bioversity International, Via dei Tre Denari, 472/a, 00054, Maccarese, Rome, Italy
| | | | - Ruaraidh Sackville Hamilton
- T. T. Chang Genetic Resources Center, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Brad Kurtz
- Independent Crop Biodiversity and Intellectual Property Expert, 25057 River Ridge Road, Adel, IA, 50003, USA
| | - Emily Marden
- University of British Columbia, Peter A. Allard School of Law, 1822 East Mall, Vancouver, BC, V6T 1Z1, Canada
| | - Eric Welch
- School of Public Affairs, College of Public Programs, Arizona State University, 411 North Central Avenue, Suite 463, Phoenix, AZ, 85004-0687, USA
| | - Frank Michiels
- Independent Crop Biodiversity and Intellectual Property Expert, Technologiepark 38, 9052, Gent, Belgium
| | - Javad Mozafari
- Agricultural Research, Education and Extension Organization, Yemen St., Chamran Freeway, Tehran, Iran
| | - Muhamad Sabran
- Indonesian Centre for Biotechnology and Genetic Resources, JL Tentara Pelajar No. 3A, Kampus Penelitian Pertanian Cimanggu, Bogor, 16111, Indonesia
| | - Nicola Patron
- Earlham Institute, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Paul Kersey
- EMBL -The European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | - Ruth Bastow
- Global Plant Council, Bow House, 1a Bow Lane, London, EC4M 9EE, UK
| | - Shawn Dorius
- Department of Sociology, Iowa State University, 308 East Hall, Ames, IA, 50010, USA
| | - Sonia Dias
- Secretariat of International Treaty on Plant Genetic Resources for Food and Agriculture, Viale delle Terme di Caracalla, 00153, Rome, Italy
| | - Susan McCouch
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, 240 Emerson Hall, Ithaca, NY, 14853, USA
| | - Wayne Powell
- SRUC (Scotland's Rural College), Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG, UK
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Reyes-Valdés MH, Burgueño J, Singh S, Martínez O, Sansaloni CP. An informational view of accession rarity and allele specificity in germplasm banks for management and conservation. PLoS One 2018; 13:e0193346. [PMID: 29489873 PMCID: PMC5831390 DOI: 10.1371/journal.pone.0193346] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 02/08/2018] [Indexed: 11/19/2022] Open
Abstract
Germplasm banks are growing in their importance, number of accessions and amount of characterization data, with a large emphasis on molecular genetic markers. In this work, we offer an integrated view of accessions and marker data in an information theory framework. The basis of this development is the mutual information between accessions and allele frequencies for molecular marker loci, which can be decomposed in allele specificities, as well as in rarity and divergence of accessions. In this way, formulas are provided to calculate the specificity of the different marker alleles with reference to their distribution across accessions, accession rarity, defined as the weighted average of the specificity of its alleles, and divergence, defined by the Kullback-Leibler formula. Albeit being different measures, it is demonstrated that average rarity and divergence are equal for any collection. These parameters can contribute to the knowledge of the structure of a germplasm collection and to make decisions about the preservation of rare variants. The concepts herein developed served as the basis for a strategy for core subset selection called HCore, implemented in a publicly available R script. As a proof of concept, the mathematical view and tools developed in this research were applied to a large collection of Mexican wheat accessions, widely characterized by SNP markers. The most specific alleles were found to be private of a single accession, and the distribution of this parameter had its highest frequencies at low levels of specificity. Accession rarity and divergence had largely symmetrical distributions, and had a positive, albeit non-strictly linear relationship. Comparison of the HCore approach for core subset selection, with three state-of-the-art methods, showed it to be superior for average divergence and rarity, mean genetic distance and diversity. The proposed approach can be used for knowledge extraction and decision making in germplasm collections of diploid, inbred or outbred species.
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Affiliation(s)
- M. Humberto Reyes-Valdés
- Department of Plant Breeding/Universidad Autónoma Agraria Antonio Narro, Saltillo, Coahuila, Mexico
| | - Juan Burgueño
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Octavio Martínez
- Centro de Investigación y Estudios Avanzados/Instituto Politécnico Nacional, Irapuato, Guanajuato, Mexico
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Müller T, Schierscher-Viret B, Fossati D, Brabant C, Schori A, Keller B, Krattinger SG. Unlocking the diversity of genebanks: whole-genome marker analysis of Swiss bread wheat and spelt. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:407-416. [PMID: 29103142 DOI: 10.1007/s00122-017-3010-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 10/26/2017] [Indexed: 05/22/2023]
Abstract
High-throughput genotyping of Swiss bread wheat and spelt accessions revealed differences in their gene pools and identified bread wheat landraces that were not used in breeding. Genebanks play a pivotal role in preserving the genetic diversity present among old landraces and wild progenitors of modern crops and they represent sources of agriculturally important genes that were lost during domestication and in modern breeding. However, undesirable genes that negatively affect crop performance are often co-introduced when landraces and wild crop progenitors are crossed with elite cultivars, which often limit the use of genebank material in modern breeding programs. A detailed genetic characterization is an important prerequisite to solve this problem and to make genebank material more accessible to breeding. Here, we genotyped 502 bread wheat and 293 spelt accessions held in the Swiss National Genebank using a 15K wheat SNP array. The material included both spring and winter wheats and consisted of old landraces and modern cultivars. Genome- and sub-genome-wide analyses revealed that spelt and bread wheat form two distinct gene pools. In addition, we identified bread wheat landraces that were genetically distinct from modern cultivars. Such accessions were possibly missed in the early Swiss wheat breeding program and are promising targets for the identification of novel genes. The genetic information obtained in this study is appropriate to perform genome-wide association studies, which will facilitate the identification and transfer of agriculturally important genes from the genebank into modern cultivars through marker-assisted selection.
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Affiliation(s)
- Thomas Müller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
| | | | - Dario Fossati
- Department of Plant Production Sciences, Agroscope, Changins, Nyon, Switzerland
| | - Cécile Brabant
- Department of Plant Production Sciences, Agroscope, Changins, Nyon, Switzerland
| | - Arnold Schori
- Department of Plant Production Sciences, Agroscope, Changins, Nyon, Switzerland
| | - Beat Keller
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
| | - Simon G Krattinger
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland.
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia.
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Ruas M, Guignon V, Sempere G, Sardos J, Hueber Y, Duvergey H, Andrieu A, Chase R, Jenny C, Hazekamp T, Irish B, Jelali K, Adeka J, Ayala-Silva T, Chao CP, Daniells J, Dowiya B, Effa Effa B, Gueco L, Herradura L, Ibobondji L, Kempenaers E, Kilangi J, Muhangi S, Ngo Xuan P, Paofa J, Pavis C, Thiemele D, Tossou C, Sandoval J, Sutanto A, Vangu Paka G, Yi G, Van den Houwe I, Roux N, Rouard M. MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2017:3866796. [PMID: 29220435 PMCID: PMC5502358 DOI: 10.1093/database/bax046] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 05/12/2017] [Indexed: 12/22/2022]
Abstract
Unraveling the genetic diversity held in genebanks on a large scale is underway, due to advances in Next-generation sequence (NGS) based technologies that produce high-density genetic markers for a large number of samples at low cost. Genebank users should be in a position to identify and select germplasm from the global genepool based on a combination of passport, genotypic and phenotypic data. To facilitate this, a new generation of information systems is being designed to efficiently handle data and link it with other external resources such as genome or breeding databases. The Musa Germplasm Information System (MGIS), the database for global ex situ-held banana genetic resources, has been developed to address those needs in a user-friendly way. In developing MGIS, we selected a generic database schema (Chado), the robust content management system Drupal for the user interface, and Tripal, a set of Drupal modules which links the Chado schema to Drupal. MGIS allows germplasm collection examination, accession browsing, advanced search functions, and germplasm orders. Additionally, we developed unique graphical interfaces to compare accessions and to explore them based on their taxonomic information. Accession-based data has been enriched with publications, genotyping studies and associated genotyping datasets reporting on germplasm use. Finally, an interoperability layer has been implemented to facilitate the link with complementary databases like the Banana Genome Hub and the MusaBase breeding database. Database URL:https://www.crop-diversity.org/mgis/
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Affiliation(s)
- Max Ruas
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - V Guignon
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
| | - G Sempere
- South Green Bioinformatics Platform, Montpellier, France.,CIRAD, UMR AGAP 34398 Montpellier Cedex 5, France
| | - J Sardos
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - Y Hueber
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
| | - H Duvergey
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - A Andrieu
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - R Chase
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - C Jenny
- CIRAD, UMR AGAP 34398 Montpellier Cedex 5, France
| | - T Hazekamp
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - B Irish
- USDA-ARS-Tropical Agriculture Research Station, Mayaguez, Puerto Rico
| | - K Jelali
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France
| | - J Adeka
- University of Kisangani, Kisangani (UNIKIS), Democratic Republic of Congo
| | - T Ayala-Silva
- USDA-ARS-Tropical Agriculture Research Station, Mayaguez, Puerto Rico
| | - C P Chao
- Taiwan Banana Research Institute (TBRI), Chiuju, Pingtung, Taiwan, Republic of China
| | - J Daniells
- Department of Agriculture, Fisheries and Forestry, Queensland Government (DAFF South Johnstone), Brisbane, Australia
| | - B Dowiya
- Institut National pour l'Etude et la Recherche Agronomiques (INERA), Democratic Republic of Congo
| | - B Effa Effa
- Centre National de la Recherche Scientifique et Technologique (CENAREST), Libreville, Gabon
| | - L Gueco
- Institute of Plant Breeding (IPB), University of the Philippines (UPLB), Los Baños, Philippines
| | - L Herradura
- Bureau of Plant Industry (BPI) - Davao National Crop Research and Development Center, Davao City, Philippines
| | - L Ibobondji
- Centre Africain de Recherche sur Bananes et Plantains (CARBAP), Njombe, Cameroon
| | - E Kempenaers
- Bioversity International, International Musa Germplasm Transit Center (ITC), KULeuven, Leuven, Belgium
| | - J Kilangi
- Agricultural Research Institute (ARI) Maruku, Bukoba, Tanzania
| | - S Muhangi
- National Agricultural Research Organization (NARO), Mbarara, Uganda
| | - P Ngo Xuan
- Fruit and Vegetable Research Institute (FAVRI), Hanoi, Vietnam
| | - J Paofa
- National Agricultural Research Institute (NARI), Laloki Papua, New Guinea
| | - C Pavis
- CRB Plantes Tropicales, CIRAD INRA - Neufchâteau, Guadeloupe, France
| | - D Thiemele
- Centre National de Recherches Agronomiques (CNRA), Abidjan, Cote d'Ivoire
| | - C Tossou
- Institut National de Recherche Agronomique du Bénin (INRAB), Cotonou, Bénin
| | - J Sandoval
- Corporación Bananera Nacional S.A (CORBANA), San José, Costa Rica
| | - A Sutanto
- Indonesian Centre for Horticultural Research and Development (ICHORD), Bogor, Indonesia
| | - G Vangu Paka
- Institut National pour l'Etude et la Recherche Agronomiques (INERA), Democratic Republic of Congo
| | - G Yi
- Institute of Fruit Tree Research (IFTR), Guangdong Academy of Agricultural Sciences (GDAAS), Guangdong, China
| | - I Van den Houwe
- Bioversity International, International Musa Germplasm Transit Center (ITC), KULeuven, Leuven, Belgium
| | - N Roux
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,Bioversity International, International Musa Germplasm Transit Center (ITC), KULeuven, Leuven, Belgium
| | - M Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397 Montpellier Cedex 5, France.,South Green Bioinformatics Platform, Montpellier, France
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41
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Feng K, Hou XL, Li MY, Jiang Q, Xu ZS, Liu JX, Xiong AS. CeleryDB: a genomic database for celery. Database (Oxford) 2018; 2018:5051103. [PMID: 29992323 PMCID: PMC6041746 DOI: 10.1093/database/bay070] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/03/2018] [Accepted: 06/12/2018] [Indexed: 01/14/2023]
Abstract
Celery (Apium graveolens L.) is a plant belonging to the Apiaceae family, and a popular vegetable worldwide because of its abundant nutrients and various medical functions. Although extensive genetic and molecular biological studies have been conducted on celery, its genomic data remain unclear. Given the significance of celery and the growing demand for its genomic data, the whole genome of 'Q2-JN11' celery (a highly inbred line obtained by artificial selfing of 'Jinnan Shiqin') was sequenced using HiSeq 2000 sequencing technology. For the convenience of researchers to study celery, an online database of the whole-genome sequences of celery, CeleryDB, was constructed. The sequences of the whole genome, nucleotide sequences of the predicted genes and amino acid sequences of the predicted proteins are available online on CeleryDB. Home, BLAST, Genome Browser, Transcription Factor and Download interfaces composed of the organizational structure of CeleryDB. Users can search the celery genomic data by using two user-friendly query tools: basic local alignment search tool and Genome Browser. In the future, CeleryDB will be constantly updated to satisfy the needs of celery researchers worldwide.Database URL: http://apiaceae.njau.edu.cn/celerydb.
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Affiliation(s)
- Kai Feng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xi-Lin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Meng-Yao Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Qian Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zhi-Sheng Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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Ndjiondjop MN, Semagn K, Zhang J, Gouda AC, Kpeki SB, Goungoulou A, Wambugu P, Dramé KN, Bimpong IK, Zhao D. Development of species diagnostic SNP markers for quality control genotyping in four rice ( Oryza L.) species. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:131. [PMID: 30416368 PMCID: PMC6208651 DOI: 10.1007/s11032-018-0885-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/17/2018] [Indexed: 05/04/2023]
Abstract
Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.
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Affiliation(s)
- Marie Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Kassa Semagn
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta T6G 2P5 Canada
| | - Jianwei Zhang
- Arizona Genomics Institute and The School of Plant Sciences, University of Arizona, Thomas W. Keating Bioresearch Bldg., 1657 E. Helen Street, Tucson, AZ 85721 USA
| | - Arnaud Comlan Gouda
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Sèdjro Bienvenu Kpeki
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Alphonse Goungoulou
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Peterson Wambugu
- Kenya Agricultural and Livestock Research Organization (KALRO), Genetic Resources Research Institute, Nairobi, Kenya
| | | | - Isaac Kofi Bimpong
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Dule Zhao
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
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Swamy BPM, Shamsudin NAA, Rahman SNA, Mauleon R, Ratnam W, Sta. Cruz MT, Kumar A. Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2017; 10:21. [PMID: 28523639 PMCID: PMC5436998 DOI: 10.1186/s12284-017-0161-6] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/09/2017] [Indexed: 05/05/2023]
Abstract
BACKGROUND The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. CONCLUSION The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
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Affiliation(s)
- B. P. Mallikarjuna Swamy
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Site Noorzuraini Abd Rahman
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
- MARDI, Seberang Perai, P.O. Box No. 203, 13200 Kepala Batas, Pulau Pinang Malaysia
| | - Ramil Mauleon
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
| | - Ma. Teressa Sta. Cruz
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777 Metro Manila, Philippines
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44
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Swamy BPM, Shamsudin NAA, Rahman SNA, Mauleon R, Ratnam W, Sta Cruz MT, Kumar A. Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.). RICE (NEW YORK, N.Y.) 2017. [PMID: 28523639 DOI: 10.1186/s12284-017-0161-6©] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
BACKGROUND The identification and introgression of major-effect QTLs for grain yield under drought are some of the best and well-proven approaches for improving the drought tolerance of rice varieties. In the present study, we characterized Malaysian rice germplasm for yield and yield-related traits and identified significant trait marker associations by structured association mapping. RESULTS The drought screening was successful in screening germplasm with a yield reduction of up to 60% and heritability for grain yield under drought was up to 78%. There was a wider phenotypic and molecular diversity within the panel, indicating the suitability of the population for quantitative trait loci (QTL) mapping. Structure analyses clearly grouped the accessions into three subgroups with admixtures. Linkage disequilibrium (LD) analysis revealed that LD decreased with an increase in distance between marker pairs and the LD decay varied from 5-20 cM. The Mixed Linear model-based structured association mapping identified 80 marker trait associations (MTA) for grain yield (GY), plant height (PH) and days to flowering (DTF). Seven MTA were identified for GY under drought stress, four of these MTA were consistently identified in at least two of the three analyses. Most of these MTA identified were on chromosomes 2, 5, 10, 11 and 12, and their phenotypic variance (PV) varied from 5% to 19%. The in silico analysis of drought QTL regions revealed the association of several drought-responsive genes conferring drought tolerance. The major-effect QTLs are useful in marker-assisted QTL pyramiding to improve drought tolerance. CONCLUSION The results have clearly shown that structured association mapping is one of the feasible options to identify major-effect QTLs for drought tolerance-related traits in rice.
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Affiliation(s)
- B P Mallikarjuna Swamy
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Site Noorzuraini Abd Rahman
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- MARDI, Seberang Perai, P.O. Box No. 203, 13200, Kepala Batas, Pulau Pinang, Malaysia
| | - Ramil Mauleon
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ma Teressa Sta Cruz
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding Division, International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines.
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Crossa J, Pérez-Rodríguez P, Cuevas J, Montesinos-López O, Jarquín D, de Los Campos G, Burgueño J, González-Camacho JM, Pérez-Elizalde S, Beyene Y, Dreisigacker S, Singh R, Zhang X, Gowda M, Roorkiwal M, Rutkoski J, Varshney RK. Genomic Selection in Plant Breeding: Methods, Models, and Perspectives. TRENDS IN PLANT SCIENCE 2017; 22:961-975. [PMID: 28965742 DOI: 10.1016/j.tplants.2017.08.011] [Citation(s) in RCA: 573] [Impact Index Per Article: 81.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 08/05/2017] [Accepted: 08/28/2017] [Indexed: 05/17/2023]
Abstract
Genomic selection (GS) facilitates the rapid selection of superior genotypes and accelerates the breeding cycle. In this review, we discuss the history, principles, and basis of GS and genomic-enabled prediction (GP) as well as the genetics and statistical complexities of GP models, including genomic genotype×environment (G×E) interactions. We also examine the accuracy of GP models and methods for two cereal crops and two legume crops based on random cross-validation. GS applied to maize breeding has shown tangible genetic gains. Based on GP results, we speculate how GS in germplasm enhancement (i.e., prebreeding) programs could accelerate the flow of genes from gene bank accessions to elite lines. Recent advances in hyperspectral image technology could be combined with GS and pedigree-assisted breeding.
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Affiliation(s)
- José Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, Mexico.
| | | | - Jaime Cuevas
- Universidad de Quintana Roo, Quintana Roo, 77019, Mexico
| | | | - Diego Jarquín
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, 321 Keim Hall, Lincoln, NE 68503-0915, USA
| | - Gustavo de Los Campos
- Department of Epidemiology & Biostatistics, Michigan State University, 909 Fee Road, Room B601, East Lansing, MI 48824, USA
| | - Juan Burgueño
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, Mexico
| | | | | | - Yoseph Beyene
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, Mexico
| | - Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, Mexico
| | - Ravi Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, Mexico
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, Mexico
| | - Manje Gowda
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, 06600, Mexico City, Mexico
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India
| | - Jessica Rutkoski
- International Rice Research Institute, Los Baños, 4030, Philippines
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502 324, Telangana, India.
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Wang C, Hu S, Gardner C, Lübberstedt T. Emerging Avenues for Utilization of Exotic Germplasm. TRENDS IN PLANT SCIENCE 2017; 22:624-637. [PMID: 28476651 DOI: 10.1016/j.tplants.2017.04.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/13/2017] [Accepted: 04/04/2017] [Indexed: 05/21/2023]
Abstract
Breeders have been successful in increasing crop performance by exploiting genetic diversity over time. However, the reported annual yield increases are not sufficient in view of rapid human population growth and global environmental changes. Exotic germplasm possesses high levels of genetic diversity for valuable traits. However, only a small fraction of naturally occurring genetic diversity is utilized. Moreover, the yield gap between elite and exotic germplasm widens, which increases the effort needed to use exotic germplasm and to identify beneficial alleles and for their introgression. The advent of high-throughput genotyping and phenotyping technologies together with emerging biotechnologies provide new opportunities to explore exotic genetic variation. This review will summarize potential challenges for utilization of exotic germplasm and provide solutions.
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Affiliation(s)
- Cuiling Wang
- Department of Agronomy, Henan University of Science and Technology, 263 Kaiyuan Avenue, Luoyang, Henan 471023, China; Department of Agronomy, Iowa State University,100 Osborn Drive, Ames, IA 50011, USA; State Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, 95 Wenhua Road, Zhenzhou, Henan 450002, China
| | - Songlin Hu
- Department of Agronomy, Iowa State University,100 Osborn Drive, Ames, IA 50011, USA
| | - Candice Gardner
- Department of Agronomy, Iowa State University,100 Osborn Drive, Ames, IA 50011, USA; US Department of Agrigulture (USDA) Agricultural Research Service (ARS) Plant Introduction Research Unit, 100 Osborn Drive, Iowa State University, Ames, IA 50011, USA
| | - Thomas Lübberstedt
- Department of Agronomy, Iowa State University,100 Osborn Drive, Ames, IA 50011, USA.
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Han Y, Cameron JN, Wang L, Beavis WD. The Predicted Cross Value for Genetic Introgression of Multiple Alleles. Genetics 2017; 205:1409-1423. [PMID: 28122824 PMCID: PMC5378103 DOI: 10.1534/genetics.116.197095] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Accepted: 01/19/2016] [Indexed: 11/18/2022] Open
Abstract
We consider the plant genetic improvement challenge of introgressing multiple alleles from a homozygous donor to a recipient. First, we frame the project as an algorithmic process that can be mathematically formulated. We then introduce a novel metric for selecting breeding parents that we refer to as the predicted cross value (PCV). Unlike estimated breeding values, which represent predictions of general combining ability, the PCV predicts specific combining ability. The PCV takes estimates of recombination frequencies as an input vector and calculates the probability that a pair of parents will produce a gamete with desirable alleles at all specified loci. We compared the PCV approach with existing estimated-breeding-value approaches in two simulation experiments, in which 7 and 20 desirable alleles were to be introgressed from a donor line into a recipient line. Results suggest that the PCV is more efficient and effective for multi-allelic trait introgression. We also discuss how operations research can be used for other crop genetic improvement projects and suggest several future research directions.
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Affiliation(s)
- Ye Han
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa 50011
| | - John N Cameron
- Department of Agronomy, Iowa State University, Ames, Iowa 50011
| | - Lizhi Wang
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, Iowa 50011
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48
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Hinze LL, Hulse-Kemp AM, Wilson IW, Zhu QH, Llewellyn DJ, Taylor JM, Spriggs A, Fang DD, Ulloa M, Burke JJ, Giband M, Lacape JM, Van Deynze A, Udall JA, Scheffler JA, Hague S, Wendel JF, Pepper AE, Frelichowski J, Lawley CT, Jones DC, Percy RG, Stelly DM. Diversity analysis of cotton (Gossypium hirsutum L.) germplasm using the CottonSNP63K Array. BMC PLANT BIOLOGY 2017; 17:37. [PMID: 28158969 PMCID: PMC5291959 DOI: 10.1186/s12870-017-0981-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2016] [Accepted: 01/23/2017] [Indexed: 05/20/2023]
Abstract
BACKGROUND Cotton germplasm resources contain beneficial alleles that can be exploited to develop germplasm adapted to emerging environmental and climate conditions. Accessions and lines have traditionally been characterized based on phenotypes, but phenotypic profiles are limited by the cost, time, and space required to make visual observations and measurements. With advances in molecular genetic methods, genotypic profiles are increasingly able to identify differences among accessions due to the larger number of genetic markers that can be measured. A combination of both methods would greatly enhance our ability to characterize germplasm resources. Recent efforts have culminated in the identification of sufficient SNP markers to establish high-throughput genotyping systems, such as the CottonSNP63K array, which enables a researcher to efficiently analyze large numbers of SNP markers and obtain highly repeatable results. In the current investigation, we have utilized the SNP array for analyzing genetic diversity primarily among cotton cultivars, making comparisons to SSR-based phylogenetic analyses, and identifying loci associated with seed nutritional traits. RESULTS The SNP markers distinctly separated G. hirsutum from other Gossypium species and distinguished the wild from cultivated types of G. hirsutum. The markers also efficiently discerned differences among cultivars, which was the primary goal when designing the CottonSNP63K array. Population structure within the genus compared favorably with previous results obtained using SSR markers, and an association study identified loci linked to factors that affect cottonseed protein content. CONCLUSIONS Our results provide a large genome-wide variation data set for primarily cultivated cotton. Thousands of SNPs in representative cotton genotypes provide an opportunity to finely discriminate among cultivated cotton from around the world. The SNPs will be relevant as dense markers of genome variation for association mapping approaches aimed at correlating molecular polymorphisms with variation in phenotypic traits, as well as for molecular breeding approaches in cotton.
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Affiliation(s)
- Lori L. Hinze
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - Amanda M. Hulse-Kemp
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Iain W. Wilson
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Qian-Hao Zhu
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Danny J. Llewellyn
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Jen M. Taylor
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - Andrew Spriggs
- CSIRO Agriculture & Food, Black Mountain Laboratories, Canberra, ACT 2601 Australia
| | - David D. Fang
- USDA-ARS, Cotton Fiber Bioscience Research Unit, New Orleans, LA 70124 USA
| | - Mauricio Ulloa
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - John J. Burke
- USDA-ARS, Cropping Systems Research Laboratory, Plant Stress and Germplasm Development Research Unit, Lubbock, TX 79415 USA
| | - Marc Giband
- CIRAD, UMR AGAP, Montpellier, F34398 France
- EMBRAPA, Algodão, Nucleo Cerrado, 75.375-000 Santo Antônio de Goias, GO Brazil
| | | | - Allen Van Deynze
- Department of Plant Sciences and Seed Biotechnology Center, University of California-Davis, Davis, CA 95616 USA
| | - Joshua A. Udall
- Plant and Wildlife Science Department, Brigham Young University, Provo, UT 84602 USA
| | - Jodi A. Scheffler
- USDA-ARS, Jamie Whitten Delta States Research Center, Stoneville, MS 38776 USA
| | - Steve Hague
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
| | - Jonathan F. Wendel
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011 USA
| | - Alan E. Pepper
- Department of Biology, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
| | | | - Cindy T. Lawley
- Illumina Inc., 499 Illinois Street, San Francisco, CA 94158 USA
| | - Don C. Jones
- Cotton Incorporated, Agricultural Research, Cary, NC 27513 USA
| | - Richard G. Percy
- USDA-ARS, Crop Germplasm Research Unit, College Station, TX 77845 USA
| | - David M. Stelly
- Department of Soil & Crop Sciences, Texas A&M University, College Station, TX 77843 USA
- Interdisciplinary Department of Genetics, Texas A&M University, College Station, TX 77843 USA
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49
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Sytar O, Brestic M, Zivcak M, Olsovska K, Kovar M, Shao H, He X. Applying hyperspectral imaging to explore natural plant diversity towards improving salt stress tolerance. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 578:90-99. [PMID: 27524726 DOI: 10.1016/j.scitotenv.2016.08.014] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/03/2016] [Accepted: 08/03/2016] [Indexed: 05/26/2023]
Abstract
Salinity represents an abiotic stress constraint affecting growth and productivity of plants in many regions of the world. One of the possible solutions is to improve the level of salt resistance using natural genetic variability within crop species. In the context of recent knowledge on salt stress effects and mechanisms of salt tolerance, this review present useful phenomic approach employing different non-invasive imaging systems for detection of quantitative and qualitative changes caused by salt stress at the plant and canopy level. The focus is put on hyperspectral imaging technique, which provides unique opportunities for fast and reliable estimate of numerous characteristics associated both with various structural, biochemical and physiological traits. The method also provides possibilities to combine plant and canopy analyses with a direct determination of salinity in soil. The future perspectives in salt stress applications as well as some limits of the method are also identified.
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Affiliation(s)
- Oksana Sytar
- Research Centre AgroBioTech, Slovak University of Agriculture in Nitra, A. Hlinku 2, Nitra, Slovak Republic
| | - Marian Brestic
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Institute of Agro-biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Department of Plant Physiology, Slovak University of Agriculture in Nitra, A. Hlinku 2, Nitra, Slovak Republic.
| | - Marek Zivcak
- Department of Plant Physiology, Slovak University of Agriculture in Nitra, A. Hlinku 2, Nitra, Slovak Republic
| | - Katarina Olsovska
- Department of Plant Physiology, Slovak University of Agriculture in Nitra, A. Hlinku 2, Nitra, Slovak Republic
| | - Marek Kovar
- Department of Plant Physiology, Slovak University of Agriculture in Nitra, A. Hlinku 2, Nitra, Slovak Republic
| | - Hongbo Shao
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Institute of Agro-biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China.
| | - Xiaolan He
- Jiangsu Key Laboratory for Bioresources of Saline Soils, Provincial Key Laboratory of Agrobiology, Institute of Agro-biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
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50
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Ndjiondjop MN, Semagn K, Gouda AC, Kpeki SB, Dro Tia D, Sow M, Goungoulou A, Sie M, Perrier X, Ghesquiere A, Warburton ML. Genetic Variation and Population Structure of Oryza glaberrima and Development of a Mini-Core Collection Using DArTseq. FRONTIERS IN PLANT SCIENCE 2017; 8:1748. [PMID: 29093721 PMCID: PMC5651524 DOI: 10.3389/fpls.2017.01748] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/25/2017] [Indexed: 05/20/2023]
Abstract
The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 Oryza glaberrima Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree method, we propose a subset of 1,330 and 350 accessions to represent a core and mini-core collection, respectively. The core and mini-core sets accounted for ~61 and 16%, respectively, of the whole collection, and captured 97-99% of the SNP polymorphism and nearly all allele and genotype frequencies observed in the whole O. glaberrima collection available at the AfricaRice genebank. Cluster, principal component and model-based population structure analyses all divided the 2,179 accessions into five groups, based roughly on country of origin but less so on ecology. The first, third and fourth groups consisted of accessions primarily from Liberia, Nigeria, and Mali, respectively; the second group consisted primarily of accessions from Togo and Nigeria; and the fifth and smallest group was a mixture of accessions from multiple countries. Analysis of molecular variance showed between 10.8 and 28.9% of the variation among groups with the remaining 71.1-89.2% attributable to differences within groups.
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Affiliation(s)
- Marie-Noelle Ndjiondjop
- Africa Rice Center (AfricaRice), Bouake, Cote d'Ivoire
- *Correspondence: Marie-Noelle Ndjiondjop
| | - Kassa Semagn
- Department of Agriculture, Forestry and Nutrition Science, University of Alberta, Edmonton, Canada
| | | | | | | | - Mounirou Sow
- Africa Rice Center (AfricaRice), Ibadan, Nigeria
| | | | - Moussa Sie
- Africa Rice Center (AfricaRice), Centre National de la Recherche Appliquée au Développement Rural (FOFIFA), Antananarivo, Madagascar
| | - Xavier Perrier
- Unité Mixte de Recherche Amélioration Génétique, CIRAD, Montpellier, France
- University of Montpellier, Montpellier, France
| | - Alain Ghesquiere
- Plant Diversity Adaptation and Development Research Unit, Institut de Recherche pour le Développement - Université de Montpellier, Montpellier, France
| | - Marilyn L. Warburton
- Corn Host Plant Resistance Research Unit, United States Department of Agriculture, Agricultural Research Service, Starkville, Mississippi, United States
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