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Kim H, Jung J, Singh N, Greenberg A, Doyle JJ, Tyagi W, Chung JW, Kimball J, Hamilton RS, McCouch SR. Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice. RICE (NEW YORK, N.Y.) 2016; 9:56. [PMID: 27730519 PMCID: PMC5059230 DOI: 10.1186/s12284-016-0119-0] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 09/08/2016] [Indexed: 05/17/2023]
Abstract
BACKGROUND Understanding population structure of the wild progenitor of Asian cultivated rice (O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing (113,739 SNPs) and for chloroplast variation using Sanger sequencing (25 polymorphic sites). RESULTS Six wild subpopulations were identified, with 25 % of accessions classified as admixed. Three of the wild groups were genetically and geographically closely related to the O. sativa subpopulations, indica, aus and japonica, and carried O. sativa introgressions; the other three wild groups were genetically divergent, had unique chloroplast haplotypes, and were located at the geographical extremes of the species range. The genetic subpopulations were significantly correlated (r 2 = 0.562) with traditional species designations, O. rufipogon (perennial) and O. nivara (annual), differentiated based on morphology and life history. A wild diversity panel of 95 purified (inbred) accessions was developed for future genetic studies. CONCLUSIONS Our results suggest that the cultivated aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wild relative, and indica to an admixed population of diverse annual and perennial wild ancestors. Gene flow between ORSC and O. sativa is common in regions where rice is cultivated, threatening the identity and diversity of wild ORSC populations. The three geographically isolated ORSC populations harbor variation rarely seen in cultivated rice and provide a unique window into the genetic composition of ancient rice subpopulations.
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Affiliation(s)
- HyunJung Kim
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
- Present Address: Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Janelle Jung
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
| | - Namrata Singh
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
| | - Anthony Greenberg
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
| | - Jeff J Doyle
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
| | - Wricha Tyagi
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
- Present Address: School of Crop Improvement, College of PG Studies, Central Agricultural University, Umroi Road, Umiam, Meghalaya, India
| | - Jong-Wook Chung
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
- Present Address: Department of Industrial Plant Science and Technology, Chungbuk National University, Cheongju, Chungubk, 28644, Republic of Korea
| | - Jennifer Kimball
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA
- Present Address: Department of Crop Science, North Carolina State University, Raleigh, NC, 27695-762, USA
| | - Ruaraidh Sackville Hamilton
- TT Chang Genetics Resource Center and International Rice Genebank, International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Susan R McCouch
- Section of Plant Breeding and Genetics, School of Integrative Plant Science, Cornell University, 162 Emerson Hall, Ithaca, NY, 14853, USA.
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Jackson SA. Rice: The First Crop Genome. RICE (NEW YORK, N.Y.) 2016; 9:14. [PMID: 27003180 PMCID: PMC4803718 DOI: 10.1186/s12284-016-0087-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 03/16/2016] [Indexed: 05/24/2023]
Abstract
Rice was the first sequenced crop genome, paving the way for the sequencing of additional and more complicated crop genomes. The impact that the genome sequence made on rice genetics and breeding research was immediate, as evidence by citations and DNA marker use. The impact on other crop genomes was evident too, particularly for those within the grass family. As we celebrate 10 years since the completion of the rice genome sequence, we look forward to new empowering tool sets that will further revolutionize research in rice genetics and breeding and result in varieties that will continue to feed a growing population.
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Affiliation(s)
- Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, 30621, USA.
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Clark LV, Dzyubenko E, Dzyubenko N, Bagmet L, Sabitov A, Chebukin P, Johnson DA, Kjeldsen JB, Petersen KK, Jørgensen U, Yoo JH, Heo K, Yu CY, Zhao H, Jin X, Peng J, Yamada T, Sacks EJ. Ecological characteristics and in situ genetic associations for yield-component traits of wild Miscanthus from eastern Russia. ANNALS OF BOTANY 2016; 118:941-955. [PMID: 27451985 PMCID: PMC5055818 DOI: 10.1093/aob/mcw137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 05/24/2016] [Indexed: 05/08/2023]
Abstract
Background and aims Miscanthus is a genus of perennial C4 grasses native to East Asia. It includes the emerging ligno-cellulosic biomass crop M. ×giganteus, a hybrid between M. sinensis and M. sacchariflorus. Biomass yield and cold tolerance are of particular interest in Miscanthus, given that this crop is more temperate adapted than its C4 relatives maize, sorghum and sugarcane. Methods A plant exploration was conducted in eastern Russia, at the northern extreme of the native range for Miscanthus, with collections including 174 clonal germplasm accessions (160 M. sacchariflorus and 14 M. sinensis) from 47 sites. Accessions were genotyped by restriction site-associated DNA sequencing (RAD-seq) and plastid microsatellites. Key Results Miscanthus sinensis was found in maritime climates near Vladivostok (43·6°N) and on southern Sakhalin Island (46·6°N). Miscanthus sacchariflorus was found inland at latitudes as high as 49·3°N, where M. sinensis was absent. Most M. sacchariflorus accessions were diploid, but approx. 2 % were tetraploids. Molecular markers revealed little population structure (Jost's D < 0·007 among diploid groups) but high genetic diversity (expected heterozygosity = 0·14) within the collection of Russian M. sacchariflorus. Genome-wide association (GWA) analysis for traits measured at the collection sites revealed three M. sacchariflorus single nucleotide polymorphisms (SNPs) significantly associated with the number of stems per unit area, one with height and one with basal stem diameter; three were near or within previously described sorghum quantitative trait loci for related traits. Conclusions This new Miscanthus germplasm collection from eastern Russia will be useful for breeding Miscanthus and sugarcane cultivars with improved adaptation to cold. Moreover, a strategy is proposed to facilitate the rapid utilization of new germplasm collections: by implementing low-cost SNP genotyping to conduct GWA studies of phenotypic data obtained at collection sites, plant breeders can be provided with actionable information on which accessions have desirable traits and alleles.
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Affiliation(s)
- Lindsay V. Clark
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802, USA
| | - Elena Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Nikolay Dzyubenko
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Larisa Bagmet
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Andrey Sabitov
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Pavel Chebukin
- Vavilov All-Russian Institute of Plant Genetic Resources, 42–44 Bolshaya Morskaya Street, 190000 St. Petersburg, Russia
| | - Douglas A. Johnson
- USDA-ARS Forage and Range Research Lab, Utah State University, Logan, UT 84322-6300, USA
| | | | - Karen Koefoed Petersen
- Department of Food Science, Aarhus University, Kirstinebjergvej 10, DK-5792 Årslev, Denmark
| | - Uffe Jørgensen
- Department of Agroecology, Aarhus University, Blichers Allé 20, DK-8830 Tjele, Denmark
| | - Ji Hye Yoo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Kweon Heo
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Chang Yeon Yu
- Kangwon National University, Chuncheon, Gangwon 200-701, South Korea
| | - Hua Zhao
- College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Xiaoli Jin
- Agronomy Department, Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou 310058, China
| | - Junhua Peng
- Science and Technology Center, China Seed Group Co. Ltd, Wuhan, Hubei 430040, China
| | - Toshihiko Yamada
- Field Science Center for Northern Biosphere, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Erik J. Sacks
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Drive, Urbana, IL 61802, USA
- *For correspondence. E-mail
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Jarquin D, Specht J, Lorenz A. Prospects of Genomic Prediction in the USDA Soybean Germplasm Collection: Historical Data Creates Robust Models for Enhancing Selection of Accessions. G3 (BETHESDA, MD.) 2016; 6:2329-41. [PMID: 27247288 PMCID: PMC4978888 DOI: 10.1534/g3.116.031443] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 05/23/2016] [Indexed: 02/05/2023]
Abstract
The identification and mobilization of useful genetic variation from germplasm banks for use in breeding programs is critical for future genetic gain and protection against crop pests. Plummeting costs of next-generation sequencing and genotyping is revolutionizing the way in which researchers and breeders interface with plant germplasm collections. An example of this is the high density genotyping of the entire USDA Soybean Germplasm Collection. We assessed the usefulness of 50K single nucleotide polymorphism data collected on 18,480 domesticated soybean (Glycine max) accessions and vast historical phenotypic data for developing genomic prediction models for protein, oil, and yield. Resulting genomic prediction models explained an appreciable amount of the variation in accession performance in independent validation trials, with correlations between predicted and observed reaching up to 0.92 for oil and protein and 0.79 for yield. The optimization of training set design was explored using a series of cross-validation schemes. It was found that the target population and environment need to be well represented in the training set. Second, genomic prediction training sets appear to be robust to the presence of data from diverse geographical locations and genetic clusters. This finding, however, depends on the influence of shattering and lodging, and may be specific to soybean with its presence of maturity groups. The distribution of 7608 nonphenotyped accessions was examined through the application of genomic prediction models. The distribution of predictions of phenotyped accessions was representative of the distribution of predictions for nonphenotyped accessions, with no nonphenotyped accessions being predicted to fall far outside the range of predictions of phenotyped accessions.
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Affiliation(s)
- Diego Jarquin
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Nebraska 68583-0915
| | - James Specht
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Nebraska 68583-0915
| | - Aaron Lorenz
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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55
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Roa C, Hamilton RS, Wenzl P, Powell W. Plant Genetic Resources: Needs, Rights, and Opportunities. TRENDS IN PLANT SCIENCE 2016; 21:633-636. [PMID: 27422334 DOI: 10.1016/j.tplants.2016.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 06/10/2016] [Accepted: 06/13/2016] [Indexed: 06/06/2023]
Abstract
Technological advances allow us to tap into genetic resources to address food and nutritional security in the face of population growth, urbanization, climate change, and environmental degradation. It is vital, particularly for developing countries, to ensure that the policy framework regulating access and use of genetic resources keeps pace with technological developments.
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Affiliation(s)
| | | | - Peter Wenzl
- International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira, Apartado Aéreo 6713, Cali, Colombia
| | - Wayne Powell
- CGIAR Consortium Office, 34394 Montpellier Cedex 5, France; SRUC, Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG, UK.
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Migicovsky Z, Gardner KM, Money D, Sawler J, Bloom JS, Moffett P, Chao CT, Schwaninger H, Fazio G, Zhong GY, Myles S. Genome to Phenome Mapping in Apple Using Historical Data. THE PLANT GENOME 2016; 9. [PMID: 27898813 DOI: 10.3835/plantgenome2015.11.0113] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Apple ( X Borkh.) is one of the world's most valuable fruit crops. Its large size and long juvenile phase make it a particularly promising candidate for marker-assisted selection (MAS). However, advances in MAS in apple have been limited by a lack of phenotype and genotype data from sufficiently large samples. To establish genotype-phenotype relationships and advance MAS in apple, we extracted over 24,000 phenotype scores from the USDA-Germplasm Resources Information Network (GRIN) database and linked them with over 8000 single nucleotide polymorphisms (SNPs) from 689 apple accessions from the USDA apple germplasm collection clonally preserved in Geneva, NY. We find significant genetic differentiation between Old World and New World cultivars and demonstrate that the genetic structure of the domesticated apple also reflects the time required for ripening. A genome-wide association study (GWAS) of 36 phenotypes confirms the association between fruit color and the MYB1 locus, and we also report a novel association between the transcription factor, NAC18.1, and harvest date and fruit firmness. We demonstrate that harvest time and fruit size can be predicted with relatively high accuracies ( > 0.46) using genomic prediction. Rapid decay of linkage disequilibrium (LD) in apples means millions of SNPs may be required for well-powered GWAS. However, rapid LD decay also promises to enable extremely high resolution mapping of causal variants, which holds great potential for advancing MAS.
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Vasudevan K, Vera Cruz CM, Gruissem W, Bhullar NK. Geographically Distinct and Domain-Specific Sequence Variations in the Alleles of Rice Blast Resistance Gene Pib. FRONTIERS IN PLANT SCIENCE 2016; 7:915. [PMID: 27446145 PMCID: PMC4917536 DOI: 10.3389/fpls.2016.00915] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 06/09/2016] [Indexed: 06/06/2023]
Abstract
Rice blast is caused by Magnaporthe oryzae, which is the most destructive fungal pathogen affecting rice growing regions worldwide. The rice blast resistance gene Pib confers broad-spectrum resistance against Southeast Asian M. oryzae races. We investigated the allelic diversity of Pib in rice germplasm originating from 12 major rice growing countries. Twenty-five new Pib alleles were identified that have unique single nucleotide polymorphisms (SNPs), insertions and/or deletions, in addition to the polymorphic nucleotides that are shared between the different alleles. These partially or completely shared polymorphic nucleotides indicate frequent sequence exchange events between the Pib alleles. In some of the new Pib alleles, nucleotide diversity is high in the LRR domain, whereas, in others it is distributed among the NB-ARC and LRR domains. Most of the polymorphic amino acids in LRR and NB-ARC2 domains are predicted as solvent-exposed. Several of the alleles and the unique SNPs are country specific, suggesting a diversifying selection of alleles in various geographical locations in response to the locally prevalent M. oryzae population. Together, the new Pib alleles are an important genetic resource for rice blast resistance breeding programs and provide new information on rice-M. oryzae interactions at the molecular level.
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Affiliation(s)
- Kumar Vasudevan
- Plant Biotechnology, Department of Biology ETH Zurich, Switzerland
| | | | - Wilhelm Gruissem
- Plant Biotechnology, Department of Biology ETH Zurich, Switzerland
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Urrestarazu J, Denancé C, Ravon E, Guyader A, Guisnel R, Feugey L, Poncet C, Lateur M, Houben P, Ordidge M, Fernandez-Fernandez F, Evans KM, Paprstein F, Sedlak J, Nybom H, Garkava-Gustavsson L, Miranda C, Gassmann J, Kellerhals M, Suprun I, Pikunova AV, Krasova NG, Torutaeva E, Dondini L, Tartarini S, Laurens F, Durel CE. Analysis of the genetic diversity and structure across a wide range of germplasm reveals prominent gene flow in apple at the European level. BMC PLANT BIOLOGY 2016; 16:130. [PMID: 27277533 PMCID: PMC4898379 DOI: 10.1186/s12870-016-0818-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/23/2016] [Indexed: 05/18/2023]
Abstract
BACKGROUND The amount and structure of genetic diversity in dessert apple germplasm conserved at a European level is mostly unknown, since all diversity studies conducted in Europe until now have been performed on regional or national collections. Here, we applied a common set of 16 SSR markers to genotype more than 2,400 accessions across 14 collections representing three broad European geographic regions (North + East, West and South) with the aim to analyze the extent, distribution and structure of variation in the apple genetic resources in Europe. RESULTS A Bayesian model-based clustering approach showed that diversity was organized in three groups, although these were only moderately differentiated (FST = 0.031). A nested Bayesian clustering approach allowed identification of subgroups which revealed internal patterns of substructure within the groups, allowing a finer delineation of the variation into eight subgroups (FST = 0.044). The first level of stratification revealed an asymmetric division of the germplasm among the three groups, and a clear association was found with the geographical regions of origin of the cultivars. The substructure revealed clear partitioning of genetic groups among countries, but also interesting associations between subgroups and breeding purposes of recent cultivars or particular usage such as cider production. Additional parentage analyses allowed us to identify both putative parents of more than 40 old and/or local cultivars giving interesting insights in the pedigree of some emblematic cultivars. CONCLUSIONS The variation found at group and subgroup levels may reflect a combination of historical processes of migration/selection and adaptive factors to diverse agricultural environments that, together with genetic drift, have resulted in extensive genetic variation but limited population structure. The European dessert apple germplasm represents an important source of genetic diversity with a strong historical and patrimonial value. The present work thus constitutes a decisive step in the field of conservation genetics. Moreover, the obtained data can be used for defining a European apple core collection useful for further identification of genomic regions associated with commercially important horticultural traits in apple through genome-wide association studies.
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Affiliation(s)
- Jorge Urrestarazu
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
- Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy
- Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Spain
| | - Caroline Denancé
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Elisa Ravon
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Arnaud Guyader
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Rémi Guisnel
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Laurence Feugey
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Charles Poncet
- Plateforme Gentyane, INRA UMR1095 Genetics, Diversity and Ecophysiology of Cereals, 63100, Clermont-Ferrand, France
| | - Marc Lateur
- CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium
| | - Patrick Houben
- CRA-W, Centre Wallon de Recherches Agronomiques, Plant Breeding & Biodiversity, Bâtiment Emile Marchal, Rue de Liroux, 4 - 5030, Gembloux, Belgium
| | - Matthew Ordidge
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, Reading, RG6 6AR, UK
| | | | - Kate M Evans
- Washington State University Tree Fruit Research and Extension Center, 1100 N Western Ave, Wenatchee, WA, 98801, USA
| | - Frantisek Paprstein
- RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic
| | - Jiri Sedlak
- RBIPH, Research and Breeding Institute of Pomology Holovousy Ltd., 508 01, Horice, Czech Republic
| | - Hilde Nybom
- Department of Plant Breeding, Balsgård, Fjälkestadsvägen 459, Swedish University of Agricultural Sciences, 291 94, Kristianstad, Sweden
| | - Larisa Garkava-Gustavsson
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, 230 53, Alnarp, Sweden
| | - Carlos Miranda
- Public University of Navarre (UPNA), Campus Arrosadia, 31006, Pamplona, Spain
| | - Jennifer Gassmann
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland
| | - Markus Kellerhals
- Agroscope, Institute for Plant Production Sciences IPS, Schloss 1, P.O. Box, 8820, Wädenswil, Switzerland
| | - Ivan Suprun
- NCRRIH&V, North Caucasian Regional Research Institute of Horticulture and Viticulture, 39, 40-letiya Pobedy street, Krasnodar, 350901, Russian Federation
| | - Anna V Pikunova
- VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation
| | - Nina G Krasova
- VNIISPK, The All Russian Research Institute of Fruit Crop Breeding, 302530, p/o Zhilina, Orel district, Russian Federation
| | - Elnura Torutaeva
- Kyrgyz National Agrarian University, 68 Mederova Street, 720005, Bishkek, Kyrgyzstan
| | - Luca Dondini
- Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy
| | - Stefano Tartarini
- Department of Agricultural Sciences, University of Bologna, Viale Giuseppe Fanin 44, 40127, Bologna, Italy
| | - François Laurens
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France
| | - Charles-Eric Durel
- IRHS, INRA, AGROCAMPUS-Ouest, Université d'Angers, SFR 4207 QUASAV, 42 rue Georges Morel, 49071, Beaucouzé cedex, France.
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Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era. BMC Genomics 2016; 17:408. [PMID: 27229151 PMCID: PMC4882841 DOI: 10.1186/s12864-016-2734-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 05/12/2016] [Indexed: 11/10/2022] Open
Abstract
Background Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization. Results Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes. Conclusion This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2734-y) contains supplementary material, which is available to authorized users.
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Spindel JE, Begum H, Akdemir D, Collard B, Redoña E, Jannink JL, McCouch S. Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement. Heredity (Edinb) 2016; 116:395-408. [PMID: 26860200 PMCID: PMC4806696 DOI: 10.1038/hdy.2015.113] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 11/17/2015] [Accepted: 11/25/2015] [Indexed: 12/23/2022] Open
Abstract
To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity and environmental sustainability. Current breeding practices, however, are unable to keep pace with demand. Genomic selection (GS) is a new technique that helps accelerate the rate of genetic gain in breeding by using whole-genome data to predict the breeding value of offspring. Here, we describe a new GS model that combines RR-BLUP with markers fit as fixed effects selected from the results of a genome-wide-association study (GWAS) on the RR-BLUP training data. We term this model GS + de novo GWAS. In a breeding population of tropical rice, GS + de novo GWAS outperformed six other models for a variety of traits and in multiple environments. On the basis of these results, we propose an extended, two-part breeding design that can be used to efficiently integrate novel variation into elite breeding populations, thus expanding genetic diversity and enhancing the potential for sustainable productivity gains.
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Affiliation(s)
- J E Spindel
- Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY, USA
| | - H Begum
- Department of Plant Breeding, Genetics and Biotechnology, International Rice Research Institute, Los Baños, Philippines
| | - D Akdemir
- Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY, USA
| | - B Collard
- Department of Plant Breeding, Genetics and Biotechnology, International Rice Research Institute, Los Baños, Philippines
| | - E Redoña
- Department of Plant Breeding, Genetics and Biotechnology, International Rice Research Institute, Los Baños, Philippines
| | - J-L Jannink
- Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY, USA
- USDA-ARS, North Atlantic Ares, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA
| | - S McCouch
- Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY, USA
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Castañeda-Álvarez NP, Khoury CK, Achicanoy HA, Bernau V, Dempewolf H, Eastwood RJ, Guarino L, Harker RH, Jarvis A, Maxted N, Müller JV, Ramirez-Villegas J, Sosa CC, Struik PC, Vincent H, Toll J. Global conservation priorities for crop wild relatives. NATURE PLANTS 2016; 2:16022. [PMID: 27249561 DOI: 10.1038/nplants.2016.22] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/05/2016] [Indexed: 05/04/2023]
Abstract
The wild relatives of domesticated crops possess genetic diversity useful for developing more productive, nutritious and resilient crop varieties. However, their conservation status and availability for utilization are a concern, and have not been quantified globally. Here, we model the global distribution of 1,076 taxa related to 81 crops, using occurrence information collected from biodiversity, herbarium and gene bank databases. We compare the potential geographic and ecological diversity encompassed in these distributions with that currently accessible in gene banks, as a means to estimate the comprehensiveness of the conservation of genetic diversity. Our results indicate that the diversity of crop wild relatives is poorly represented in gene banks. For 313 (29.1% of total) taxa associated with 63 crops, no germplasm accessions exist, and a further 257 (23.9%) are represented by fewer than ten accessions. Over 70% of taxa are identified as high priority for further collecting in order to improve their representation in gene banks, and over 95% are insufficiently represented in regard to the full range of geographic and ecological variation in their native distributions. The most critical collecting gaps occur in the Mediterranean and the Near East, western and southern Europe, Southeast and East Asia, and South America. We conclude that a systematic effort is needed to improve the conservation and availability of crop wild relatives for use in plant breeding.
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Affiliation(s)
- Nora P Castañeda-Álvarez
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Colin K Khoury
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
- Centre for Crop Systems Analysis, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Harold A Achicanoy
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
| | - Vivian Bernau
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
| | - Hannes Dempewolf
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53115 Bonn, Germany
| | - Ruth J Eastwood
- Royal Botanic Gardens, Kew, Conservation Science, Millennium Seed Bank, Wakehurst Place, Ardingly RH17 6TN, UK
| | - Luigi Guarino
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53115 Bonn, Germany
| | - Ruth H Harker
- Royal Botanic Gardens, Kew, Conservation Science, Millennium Seed Bank, Wakehurst Place, Ardingly RH17 6TN, UK
| | - Andy Jarvis
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
| | - Nigel Maxted
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jonas V Müller
- Royal Botanic Gardens, Kew, Conservation Science, Millennium Seed Bank, Wakehurst Place, Ardingly RH17 6TN, UK
| | - Julian Ramirez-Villegas
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
- Institute for Climate and Atmospheric Science, School of Earth and Environment, University of Leeds, LS2 9JT, UK
| | - Chrystian C Sosa
- International Center for Tropical Agriculture (CIAT), Km 17, Recta Cali-Palmira, Cali 763537, Colombia
| | - Paul C Struik
- Centre for Crop Systems Analysis, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Holly Vincent
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK
| | - Jane Toll
- Global Crop Diversity Trust, Platz der Vereinten Nationen 7, 53115 Bonn, Germany
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Blackmore T, Thorogood D, Skøt L, McMahon R, Powell W, Hegarty M. Germplasm dynamics: the role of ecotypic diversity in shaping the patterns of genetic variation in Lolium perenne. Sci Rep 2016; 6:22603. [PMID: 26935901 PMCID: PMC4776279 DOI: 10.1038/srep22603] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/05/2016] [Indexed: 11/09/2022] Open
Abstract
Perennial ryegrass (Lolium perenne) is the most widely grown temperate grass species globally. Intensive plant breeding in ryegrass compared to many other crops species is a relatively recent exercise (last 100 years) and provides an interesting experimental system to trace the extent, impact and trajectory of undomesticated ecotypic variation represented in modern ryegrass cultivars. To explore germplasm dynamics in Lolium perenne, 2199 SNPs were genotyped in 716 ecotypes sampled from 90 European locations together with 249 cultivars representing 33 forage/amenity accessions. In addition three pseudo-cross mapping populations (450 individual recombinants) were genotyped to create a consensus genetic linkage map. Multivariate analyses revealed strong differentiation between cultivars with a small proportion of the ecotypic variation captured in improved cultivars. Ryegrass cultivars generated as part of a recurrent selection programme (RSP) are strongly associated with a small number of geographically localised Italian ecotypes which were among the founders of the RSP. Changes in haplotype frequency revealed signatures of selection in genes putatively involved in water-soluble carbohydrate (WSC) accumulation (a trait selected in the RSP). Retrospective analysis of germplasm in breeding programmes (germplasm dynamics) provides an experimental framework for the identification of candidate genes for novel traits such as WSC accumulation in ryegrass.
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Affiliation(s)
- T. Blackmore
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales. SY23 3EE
| | - D. Thorogood
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales. SY23 3EE
| | - L. Skøt
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales. SY23 3EE
| | - R. McMahon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales. SY23 3EE
| | - W. Powell
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales. SY23 3EE
| | - M. Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, Wales. SY23 3EE
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Borrayo E, Machida-Hirano R, Takeya M, Kawase M, Watanabe K. Principal components analysis--K-means transposon element based foxtail millet core collection selection method. BMC Genet 2016; 17:42. [PMID: 26880119 PMCID: PMC4754896 DOI: 10.1186/s12863-016-0343-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 02/01/2016] [Indexed: 11/21/2022] Open
Abstract
Background Core collections are important tools in genetic resources research and administration. At present, most core collection selection criteria are based on one of the following item characteristics: passport data, genetic markers, or morphological traits, which may lead to inadequate representations of variability in the complete collection. The development of a comprehensive methodology that includes as much element data as possible has been explored poorly. Using a collection of (Setaria italica sbsp. italica (L.) P. Beauv.) as a model, we developed a method for core collection construction based on genotype data and numerical representations of agromorphological traits, thereby improving the selection process. Results Principal component analysis allows the selection of the most informative discriminators among the various elements evaluated, regardless of whether they are genetic or morphological, thereby providing an adequate criterion for further K-mean clustering. Overall, the core collections of S. italica constructed using only genotype data demonstrated overall better validation scores than other core collections that we generated. However, core collection based on both genotype and agromorphological characteristics represented the overall diversity adequately. Conclusions The inclusion of both genotype and agromorphological characteristics as a comprehensive dataset in this methodology ensures that agricultural traits are considered in the core collection construction. This approach will be beneficial for genetic resources management and research activities for S. italica as well as other genetic resources. Electronic supplementary material The online version of this article (doi:10.1186/s12863-016-0343-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ernesto Borrayo
- Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba City, 305-8571, Ibaraki, Japan. .,Genetc Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannodai, Tsukuba City, 305-8602, Ibaraki, Japan.
| | - Ryoko Machida-Hirano
- Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba City, 305-8571, Ibaraki, Japan.
| | - Masaru Takeya
- Genetc Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Kannodai, Tsukuba City, 305-8602, Ibaraki, Japan.
| | - Makoto Kawase
- Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba City, 305-8571, Ibaraki, Japan.
| | - Kazuo Watanabe
- Gene Research Center, University of Tsukuba, 1-1-1 Tennodai, Tsukuba City, 305-8571, Ibaraki, Japan.
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Bandillo N, Jarquin D, Song Q, Nelson R, Cregan P, Specht J, Lorenz A. A Population Structure and Genome-Wide Association Analysis on the USDA Soybean Germplasm Collection. THE PLANT GENOME 2015; 8:eplantgenome2015.04.0024. [PMID: 33228276 DOI: 10.3835/plantgenome2015.04.0024] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Accepted: 06/23/2015] [Indexed: 05/13/2023]
Abstract
Population structure analyses and genome-wide association studies (GWAS) conducted on crop germplasm collections provide valuable information on the frequency and distribution of alleles governing economically important traits. The value of these analyses is substantially enhanced when the accession numbers can be increased from ∼1,000 to ∼10,000 or more. In this research, we conducted the first comprehensive analysis of population structure on the collection of 14,000 soybean accessions [Glycine max (L.) Merr. and G. soja Siebold & Zucc.] using a 50K-SNP chip. Accessions originating from Japan were relatively homogenous and distinct from the Korean accessions. As a whole, both Japanese and Korean accessions diverged from the Chinese accessions. The ancestry of founders of the American accessions derived mostly from two Chinese subpopulations, which reflects the composition of the American accessions as a whole. A 12,000 accession GWAS conducted on seed protein and oil is the largest reported to date in plants and identified single nucleotide polymorphisms (SNPs) with strong signals on chromosomes 20 and 15. A chromosome 20 region previously reported to be important for protein and oil content was further narrowed and now contains only three plausible candidate genes. The haplotype effects show a strong negative relationship between oil and protein at this locus, indicating negative pleiotropic effects or multiple closely linked loci in repulsion phase linkage. The vast majority of accessions carry the haplotype allele conferring lower protein and higher oil. Our results provide a fuller understanding of the distribution of genetic variation contained within the USDA soybean collection and how it relates to phenotypic variation for economically important traits.
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Affiliation(s)
- Nonoy Bandillo
- Dep. of Agronomy & Horticulture, Keim Hall, Univ. of Nebraska-Lincoln, Lincoln, NE, 68583-0915
| | - Diego Jarquin
- Dep. of Agronomy & Horticulture, Keim Hall, Univ. of Nebraska-Lincoln, Lincoln, NE, 68583-0915
| | - Qijian Song
- Soybean Genomics and Improvement Lab., Beltsville Agricultural Research Center, Beltsville, MD, 20705
| | - Randall Nelson
- USDA-ARS, Soybean/Maize Germplasm, Pathology, and Genetics Research Unit, 1101 W. Peabody Dr., Urbana, IL, 61801-0000
| | - Perry Cregan
- Soybean Genomics and Improvement Lab., Beltsville Agricultural Research Center, Beltsville, MD, 20705
| | - Jim Specht
- Dep. of Agronomy & Horticulture, Keim Hall, Univ. of Nebraska-Lincoln, Lincoln, NE, 68583-0915
| | - Aaron Lorenz
- Dep. of Agronomy & Horticulture, Keim Hall, Univ. of Nebraska-Lincoln, Lincoln, NE, 68583-0915
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Blackmore T, Thomas I, McMahon R, Powell W, Hegarty M. Genetic-geographic correlation revealed across a broad European ecotypic sample of perennial ryegrass (Lolium perenne) using array-based SNP genotyping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1917-1932. [PMID: 26093611 PMCID: PMC4572065 DOI: 10.1007/s00122-015-2556-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 06/05/2015] [Indexed: 05/29/2023]
Abstract
Publically available SNP array increases the marker density for genotyping of forage crop, Lolium perenne. Applied to 90 European ecotypes composed of 716 individuals identifies a significant genetic-geographic correlation. Grassland ecosystems are ubiquitous across temperate and tropical regions, totalling 37% of the terrestrial land cover of the planet, and thus represent a global resource for understanding local adaptations to environment. However, genomic resources for grass species (outside cereals) are relatively poor. The advent of next-generation DNA sequencing and high-density SNP genotyping platforms enables the development of dense marker assays for population genetics analyses and genome-wide association studies. A high-density SNP marker resource (Illumina Infinium assay) for perennial ryegrass (Lolium perenne) was created and validated in a broad ecotype collection of 716 individuals sampled from 90 sites across Europe. Genetic diversity within and between populations was assessed. A strong correlation of geographic origin to genetic structure was found using principal component analysis, with significant correlation to longitude and latitude (P < 0.001). The potential of this array as a resource for studies of germplasm diversity and identifying traits underpinning adaptive variation is highlighted.
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Affiliation(s)
- T Blackmore
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, Wales, UK.
| | - I Thomas
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, Wales, UK
| | - R McMahon
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, Wales, UK
| | - W Powell
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, Wales, UK
| | - M Hegarty
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Gogerddan, Aberystwyth, Ceredigion, SY23 3EE, Wales, UK.
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Suzuki Y, Miura K, Shigemune A, Sasahara H, Ohta H, Uehara Y, Ishikawa T, Hamada S, Shirasawa K. Marker-assisted breeding of a LOX-3-null rice line with improved storability and resistance to preharvest sprouting. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:1421-1430. [PMID: 25917598 DOI: 10.1007/s00122-015-2516-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 04/11/2015] [Indexed: 06/04/2023]
Abstract
Breakage of the tight linkage between rice seed lipoxygenase - 3 and easy preharvest sprouting trait led to breeding of lines with few stale flavors after long storage and desirable preharvest sprouting resistance. Lipoxygenase-3 (LOX-3) is involved in the production of volatile constituents in stored rice, and the development of stale flavor is delayed in LOX-3 null rice. In the process of breeding new LOX-3-null lines with long storability, we found a close association between LOX-3 and preharvest sprouting resistance. To determine whether this relationship was due to the tight linkage of two genes or the pleiotropic effect of LOX-3, we performed marker-assisted selection using a BC3F3 population derived from crosses between LOX-3-present/preharvest sprouting-resistant lines and LOX-3-null/preharvest susceptible lines. In one individual, a recombination event occurred 13 kb downstream of LOX-3 (RM15750) and a significant quantitative trait locus, namely qPHS3, for easy preharvest sprouting trait (LOD = 10.4) was detected in an 842-kb region between RM15711 and RM15768. Using BC3F4 and BC3F5 populations, we succeeded in selecting LOX-3-absent and preharvest sprouting-resistant lines with only a 393-kb introgressed chromosome segment from the donor line for LOX-3-null at the LOX-3 locus on chromosome 3. This result indicated that the LOX-3 gene and the locus affecting preharvest sprouting are distinct. The selected line was named 'Hokuriku 244'. Sensory testing of rice grains with and without LOX-3 confirmed that stale flavor production in LOX-3-null rice during storage was lower than in normal LOX-3 rice. These results indicated that rice varieties with little stale flavor after long storage and preharvest sprouting resistance had been selected.
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Affiliation(s)
- Yasuhiro Suzuki
- NARO, Institute of Crop Science, 2-1-18 Kannondai, Tsukuba, Ibaraki, 305-8518, Japan,
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Longin CFH, Reif JC. Redesigning the exploitation of wheat genetic resources. TRENDS IN PLANT SCIENCE 2014; 19:631-6. [PMID: 25052155 DOI: 10.1016/j.tplants.2014.06.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Revised: 06/20/2014] [Accepted: 06/29/2014] [Indexed: 05/19/2023]
Abstract
More than half a million wheat genetic resources are resting in gene banks worldwide. Unlocking their hidden favorable genetic diversity for breeding is pivotal for enhancing grain yield potential, and averting future food shortages. Here, we propose exploiting recent advances in hybrid wheat technology to uncover the masked breeding values of wheat genetic resources. The gathered phenotypic information will enable a targeted choice of accessions with high value for pre-breeding among this plethora of genetic resources. We intend to provoke a paradigm shift in pre-breeding strategies for grain yield, moving away from allele mining toward genome-wide selection to bridge the yield gap between genetic resources and elite breeding pools.
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Affiliation(s)
- C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, 70599 Stuttgart, Germany
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), 06466 Gatersleben, Germany.
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68
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Huang YF, Poland JA, Wight CP, Jackson EW, Tinker NA. Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat. PLoS One 2014; 9:e102448. [PMID: 25047601 PMCID: PMC4105502 DOI: 10.1371/journal.pone.0102448] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 06/19/2014] [Indexed: 01/23/2023] Open
Abstract
Advances in next-generation sequencing offer high-throughput and cost-effective genotyping alternatives, including genotyping-by-sequencing (GBS). Results have shown that this methodology is efficient for genotyping a variety of species, including those with complex genomes. To assess the utility of GBS in cultivated hexaploid oat (Avena sativa L.), seven bi-parental mapping populations and diverse inbred lines from breeding programs around the world were studied. We examined technical factors that influence GBS SNP calls, established a workflow that combines two bioinformatics pipelines for GBS SNP calling, and provided a nomenclature for oat GBS loci. The high-throughput GBS system enabled us to place 45,117 loci on an oat consensus map, thus establishing a positional reference for further genomic studies. Using the diversity lines, we estimated that a minimum density of one marker per 2 to 2.8 cM would be required for genome-wide association studies (GWAS), and GBS markers met this density requirement in most chromosome regions. We also demonstrated the utility of GBS in additional diagnostic applications related to oat breeding. We conclude that GBS is a powerful and useful approach, which will have many additional applications in oat breeding and genomic studies.
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Affiliation(s)
- Yung-Fen Huang
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Jesse A. Poland
- Department of Plant Pathology, Kansas State University, Manhattan, Kansas, United States of America
| | - Charlene P. Wight
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
| | - Eric W. Jackson
- General Mills Crop Biosciences, Manhattan, Kansas, United States of America
| | - Nicholas A. Tinker
- Eastern Cereal and Oilseed Research Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
- * E-mail:
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Abstract
Background Rice, Oryza sativa L., is the staple food for half the world’s population. By 2030, the production of rice must increase by at least 25% in order to keep up with global population growth and demand. Accelerated genetic gains in rice improvement are needed to mitigate the effects of climate change and loss of arable land, as well as to ensure a stable global food supply. Findings We resequenced a core collection of 3,000 rice accessions from 89 countries. All 3,000 genomes had an average sequencing depth of 14×, with average genome coverages and mapping rates of 94.0% and 92.5%, respectively. From our sequencing efforts, approximately 18.9 million single nucleotide polymorphisms (SNPs) in rice were discovered when aligned to the reference genome of the temperate japonica variety, Nipponbare. Phylogenetic analyses based on SNP data confirmed differentiation of the O. sativa gene pool into 5 varietal groups – indica, aus/boro, basmati/sadri, tropical japonica and temperate japonica. Conclusions Here, we report an international resequencing effort of 3,000 rice genomes. This data serves as a foundation for large-scale discovery of novel alleles for important rice phenotypes using various bioinformatics and/or genetic approaches. It also serves to understand the genomic diversity within O. sativa at a higher level of detail. With the release of the sequencing data, the project calls for the global rice community to take advantage of this data as a foundation for establishing a global, public rice genetic/genomic database and information platform for advancing rice breeding technology for future rice improvement.
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70
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Li JY, Wang J, Zeigler RS. The 3,000 rice genomes project: new opportunities and challenges for future rice research. Gigascience 2014; 3:8. [PMID: 24872878 PMCID: PMC4035671 DOI: 10.1186/2047-217x-3-8] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 05/12/2014] [Indexed: 12/19/2023] Open
Abstract
Rice is the world's most important staple grown by millions of small-holder farmers. Sustaining rice production relies on the intelligent use of rice diversity. The 3,000 Rice Genomes Project is a giga-dataset of publically available genome sequences (averaging 14× depth of coverage) derived from 3,000 accessions of rice with global representation of genetic and functional diversity. The seed of these accessions is available from the International Rice Genebank Collection. Together, they are an unprecedented resource for advancing rice science and breeding technology. Our immediate challenge now is to comprehensively and systematically mine this dataset to link genotypic variation to functional variation with the ultimate goal of creating new and sustainable rice varieties that can support a future world population that will approach 9.6 billion by 2050.
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Affiliation(s)
- Jia-Yang Li
- Chinese Academy of Agricultural Sciences, 12 S. Zhong-Guan-Cun St, Beijing 100081, China
| | - Jun Wang
- BGI, Bei Shan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Robert S Zeigler
- International Rice Research Institute, DAPO 7777, Metro Manila 1301, Philippines
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Muñoz-Amatriaín M, Cuesta-Marcos A, Endelman JB, Comadran J, Bonman JM, Bockelman HE, Chao S, Russell J, Waugh R, Hayes PM, Muehlbauer GJ. The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One 2014; 9:e94688. [PMID: 24732668 PMCID: PMC3986206 DOI: 10.1371/journal.pone.0094688] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/18/2014] [Indexed: 11/18/2022] Open
Abstract
New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Alfonso Cuesta-Marcos
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Jeffrey B. Endelman
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jordi Comadran
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - John M. Bonman
- USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, United States of America
| | - Harold E. Bockelman
- USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, United States of America
| | - Shiaoman Chao
- USDA-ARS, Biosciences Research Lab, Fargo, North Dakota, United States of America
| | - Joanne Russell
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Patrick M. Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Gary J. Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
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Increasing homogeneity in global food supplies and the implications for food security. Proc Natl Acad Sci U S A 2014; 111:4001-6. [PMID: 24591623 DOI: 10.1073/pnas.1313490111] [Citation(s) in RCA: 332] [Impact Index Per Article: 33.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The narrowing of diversity in crop species contributing to the world's food supplies has been considered a potential threat to food security. However, changes in this diversity have not been quantified globally. We assess trends over the past 50 y in the richness, abundance, and composition of crop species in national food supplies worldwide. Over this period, national per capita food supplies expanded in total quantities of food calories, protein, fat, and weight, with increased proportions of those quantities sourcing from energy-dense foods. At the same time the number of measured crop commodities contributing to national food supplies increased, the relative contribution of these commodities within these supplies became more even, and the dominance of the most significant commodities decreased. As a consequence, national food supplies worldwide became more similar in composition, correlated particularly with an increased supply of a number of globally important cereal and oil crops, and a decline of other cereal, oil, and starchy root species. The increase in homogeneity worldwide portends the establishment of a global standard food supply, which is relatively species-rich in regard to measured crops at the national level, but species-poor globally. These changes in food supplies heighten interdependence among countries in regard to availability and access to these food sources and the genetic resources supporting their production, and give further urgency to nutrition development priorities aimed at bolstering food security.
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Atwell BJ, Wang H, Scafaro AP. Could abiotic stress tolerance in wild relatives of rice be used to improve Oryza sativa? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2014; 215-216:48-58. [PMID: 24388514 DOI: 10.1016/j.plantsci.2013.10.007] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Revised: 09/28/2013] [Accepted: 10/11/2013] [Indexed: 05/02/2023]
Abstract
Oryza sativa and Oryza glaberrima have been selected to acquire and partition resources efficiently as part of the process of domestication. However, genetic diversity in cultivated rice is limited compared to wild Oryza species, in spite of 120,000 genotypes being held in gene banks. By contrast, there is untapped diversity in the more than 20 wild species of Oryza, some having been collected from just a few coastal locations (e.g. Oryza schlechteri), while others are widely distributed (e.g. Oryza nivara and Oryza rufipogon). The extent of DNA sequence diversity and phenotypic variation is still being established in wild Oryza, with genetic barriers suggesting a vast range of morphologies and function even within species, such as has been demonstrated for Oryza meridionalis. With increasing climate variability and attempts to make more marginal land arable, abiotic and biotic stresses will be managed over the coming decades by tapping into the genetic diversity of wild relatives of O. sativa. To help create a more targeted approach to sourcing wild rice germplasm for abiotic stress tolerance, we have created a climate distribution map by plotting the natural occurrence of all Oryza species against corresponding temperature and moisture data. We then discuss interspecific variation in phenotype and its significance for rice, followed by a discussion of ways to integrate germplasm from wild relatives into domesticated rice.
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Affiliation(s)
- Brian J Atwell
- Department of Biological Sciences, Faculty of Science, Macquarie University, New South Wales 2109, Australia.
| | - Han Wang
- Department of Biological Sciences, Faculty of Science, Macquarie University, New South Wales 2109, Australia
| | - Andrew P Scafaro
- Department of Biological Sciences, Faculty of Science, Macquarie University, New South Wales 2109, Australia
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74
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Wenefrida I, Utomo HS, Linscombe SD. Mutational breeding and genetic engineering in the development of high grain protein content. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:11702-11710. [PMID: 23869957 DOI: 10.1021/jf4016812] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Cereals are the most important crops in the world for both human consumption and animal feed. Improving their nutritional values, such as high protein content, will have significant implications, from establishing healthy lifestyles to helping remediate malnutrition problems worldwide. Besides providing a source of carbohydrate, grain is also a natural source of dietary fiber, vitamins, minerals, specific oils, and other disease-fighting phytocompounds. Even though cereal grains contain relatively little protein compared to legume seeds, they provide protein for the nutrition of humans and livestock that is about 3 times that of legumes. Most cereal seeds lack a few essential amino acids; therefore, they have imbalanced amino acid profiles. Lysine (Lys), threonine (Thr), methionine (Met), and tryptophan (Trp) are among the most critical and are a limiting factor in many grain crops for human nutrition. Tremendous research has been put into the efforts to improve these essential amino acids. Development of high protein content can be outlined in four different approaches through manipulating seed protein bodies, modulating certain biosynthetic pathways to overproduce essential and limiting amino acids, increasing nitrogen relocation to the grain through the introduction of transgenes, and exploiting new genetic variance. Various technologies have been employed to improve protein content including conventional and mutational breeding, genetic engineering, marker-assisted selection, and genomic analysis. Each approach involves a combination of these technologies. Advancements in nutrigenomics and nutrigenetics continue to improve public knowledge at a rapid pace on the importance of specific aspects of food nutrition for optimum fitness and health. An understanding of the molecular basis for human health and genetic predisposition to certain diseases through human genomes enables individuals to personalize their nutritional requirements. It is critically important, therefore, to improve grain protein quality. Highly nutritious grain can be tailored to functional foods to meet the needs for both specific individuals and human populations as a whole.
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Affiliation(s)
- Ida Wenefrida
- Rice Research Station, Lousiana State University Agricultural Center , Crowley, Louisiana 70526, United States
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75
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Wambugu PW, Furtado A, Waters DLE, Nyamongo DO, Henry RJ. Conservation and utilization of African Oryza genetic resources. RICE (NEW YORK, N.Y.) 2013; 6:29. [PMID: 24280189 PMCID: PMC4883696 DOI: 10.1186/1939-8433-6-29] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 10/23/2013] [Indexed: 05/20/2023]
Abstract
Africa contains a huge diversity of both cultivated and wild rice species. The region has eight species representing six of the ten known genome types. Genetic resources of these species are conserved in various global germplasm repositories but they remain under collected and hence underrepresented in germplasm collections. Moreover, they are under characterized and therefore grossly underutilized. The lack of in situ conservation programs further exposes them to possible genetic erosion or extinction. In order to obtain maximum benefits from these resources, it is imperative that they are collected, efficiently conserved and optimally utilized. High throughput molecular approaches such as genome sequencing could be employed to more precisely study their genetic diversity and value and thereby enhance their use in rice improvement. Oryza sativa was the first crop plant to have its reference genome sequence released marking a major milestone that opened numerous opportunities for functional characterization of the entire rice genome. Studies have however demonstrated that one reference genome sequence is not enough to fully explore the genetic variation in the Oryza genus, hence the need to have reference sequences for other species in the genus. An overview of the state of conservation and utilization of African Oryza is hereby presented. Progress in the release of reference genome sequences for these species is also highlighted.
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Affiliation(s)
- Peterson W Wambugu
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
- />Kenya Agricultural Research Institute, Nairobi, Kenya
| | - Agnelo Furtado
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
| | - Daniel LE Waters
- />Southern Cross Plant Science, Southern Cross University, Lismore, NSW Australia
| | | | - Robert J Henry
- />Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, St Lucia, Qld Australia
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76
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Mascher M, Wu S, Amand PS, Stein N, Poland J. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One 2013; 8:e76925. [PMID: 24098570 PMCID: PMC3789676 DOI: 10.1371/journal.pone.0076925] [Citation(s) in RCA: 119] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/04/2013] [Indexed: 12/17/2022] Open
Abstract
The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL) population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new sequencing technologies, analysis tools and genomic resources develop.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Shuangye Wu
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
| | - Paul St. Amand
- United States Department of Agriculture, Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, United States of America
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Jesse Poland
- Department of Agronomy, Kansas State University, Manhattan, Kansas, United States of America
- United States Department of Agriculture, Agricultural Research Service, Hard Winter Wheat Genetics Research Unit, Manhattan, Kansas, United States of America
- * E-mail:
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77
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Mascher M, Wu S, Amand PS, Stein N, Poland J. Application of genotyping-by-sequencing on semiconductor sequencing platforms: a comparison of genetic and reference-based marker ordering in barley. PLoS One 2013; 8:e76925. [PMID: 24098570 DOI: 10.1371/journal.pone.076925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 09/04/2013] [Indexed: 05/27/2023] Open
Abstract
The rapid development of next-generation sequencing platforms has enabled the use of sequencing for routine genotyping across a range of genetics studies and breeding applications. Genotyping-by-sequencing (GBS), a low-cost, reduced representation sequencing method, is becoming a common approach for whole-genome marker profiling in many species. With quickly developing sequencing technologies, adapting current GBS methodologies to new platforms will leverage these advancements for future studies. To test new semiconductor sequencing platforms for GBS, we genotyped a barley recombinant inbred line (RIL) population. Based on a previous GBS approach, we designed bar code and adapter sets for the Ion Torrent platforms. Four sets of 24-plex libraries were constructed consisting of 94 RILs and the two parents and sequenced on two Ion platforms. In parallel, a 96-plex library of the same RILs was sequenced on the Illumina HiSeq 2000. We applied two different computational pipelines to analyze sequencing data; the reference-independent TASSEL pipeline and a reference-based pipeline using SAMtools. Sequence contigs positioned on the integrated physical and genetic map were used for read mapping and variant calling. We found high agreement in genotype calls between the different platforms and high concordance between genetic and reference-based marker order. There was, however, paucity in the number of SNP that were jointly discovered by the different pipelines indicating a strong effect of alignment and filtering parameters on SNP discovery. We show the utility of the current barley genome assembly as a framework for developing very low-cost genetic maps, facilitating high resolution genetic mapping and negating the need for developing de novo genetic maps for future studies in barley. Through demonstration of GBS on semiconductor sequencing platforms, we conclude that the GBS approach is amenable to a range of platforms and can easily be modified as new sequencing technologies, analysis tools and genomic resources develop.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
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78
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Breseghello F, Coelho ASG. Traditional and modern plant breeding methods with examples in rice (Oryza sativa L.). JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:8277-86. [PMID: 23551250 DOI: 10.1021/jf305531j] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plant breeding can be broadly defined as alterations caused in plants as a result of their use by humans, ranging from unintentional changes resulting from the advent of agriculture to the application of molecular tools for precision breeding. The vast diversity of breeding methods can be simplified into three categories: (i) plant breeding based on observed variation by selection of plants based on natural variants appearing in nature or within traditional varieties; (ii) plant breeding based on controlled mating by selection of plants presenting recombination of desirable genes from different parents; and (iii) plant breeding based on monitored recombination by selection of specific genes or marker profiles, using molecular tools for tracking within-genome variation. The continuous application of traditional breeding methods in a given species could lead to the narrowing of the gene pool from which cultivars are drawn, rendering crops vulnerable to biotic and abiotic stresses and hampering future progress. Several methods have been devised for introducing exotic variation into elite germplasm without undesirable effects. Cases in rice are given to illustrate the potential and limitations of different breeding approaches.
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Affiliation(s)
- Flavio Breseghello
- Embrapa Arroz e Feijão. Rod. GO-462, km 12, Santo Antônio de Goiás, Goiás, Brazil 75375-000
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79
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Yang Y, Li Y, Wu C. Genomic resources for functional analyses of the rice genome. CURRENT OPINION IN PLANT BIOLOGY 2013; 16:157-63. [PMID: 23571012 DOI: 10.1016/j.pbi.2013.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2012] [Revised: 03/15/2013] [Accepted: 03/15/2013] [Indexed: 05/07/2023]
Abstract
With the availability of the rice genome sequence, rice research communities are entering a new era of plant functional genomics. The last decade has seen rapid worldwide progress on establishing platforms for rice functional genomic research. These platforms offer practical toolkits and genomic resources for high-throughput identification of genes and pathways. In this review, we summarize available genomic resources for functional analyses of the rice genome. These genomic resources include high-quality bacterial artificial chromosome libraries, large-scale expression sequence tags, full-length cDNA collections, large amounts of data on global expression profiles, various mutant libraries and integrated bioinformatics databases. We not only present the current status of genomic resources but also discuss their usage in elucidating gene functions of the rice genome.
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Affiliation(s)
- Ying Yang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
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80
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Cobb JN, DeClerck G, Greenberg A, Clark R, McCouch S. Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype-phenotype relationships and its relevance to crop improvement. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:867-87. [PMID: 23471459 PMCID: PMC3607725 DOI: 10.1007/s00122-013-2066-0] [Citation(s) in RCA: 238] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 02/08/2013] [Indexed: 05/19/2023]
Abstract
More accurate and precise phenotyping strategies are necessary to empower high-resolution linkage mapping and genome-wide association studies and for training genomic selection models in plant improvement. Within this framework, the objective of modern phenotyping is to increase the accuracy, precision and throughput of phenotypic estimation at all levels of biological organization while reducing costs and minimizing labor through automation, remote sensing, improved data integration and experimental design. Much like the efforts to optimize genotyping during the 1980s and 1990s, designing effective phenotyping initiatives today requires multi-faceted collaborations between biologists, computer scientists, statisticians and engineers. Robust phenotyping systems are needed to characterize the full suite of genetic factors that contribute to quantitative phenotypic variation across cells, organs and tissues, developmental stages, years, environments, species and research programs. Next-generation phenotyping generates significantly more data than previously and requires novel data management, access and storage systems, increased use of ontologies to facilitate data integration, and new statistical tools for enhancing experimental design and extracting biologically meaningful signal from environmental and experimental noise. To ensure relevance, the implementation of efficient and informative phenotyping experiments also requires familiarity with diverse germplasm resources, population structures, and target populations of environments. Today, phenotyping is quickly emerging as the major operational bottleneck limiting the power of genetic analysis and genomic prediction. The challenge for the next generation of quantitative geneticists and plant breeders is not only to understand the genetic basis of complex trait variation, but also to use that knowledge to efficiently synthesize twenty-first century crop varieties.
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Affiliation(s)
- Joshua N. Cobb
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853 USA
| | - Genevieve DeClerck
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA
| | - Anthony Greenberg
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, NY 14853 USA
| | - Randy Clark
- United States Department of Agriculture-Agricultural Research Service, Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853 USA
- Department of Biological and Environmental Engineering, Cornell University, Ithaca, NY 14853 USA
| | - Susan McCouch
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853 USA
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81
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Byrne S, Czaban A, Studer B, Panitz F, Bendixen C, Asp T. Genome wide allele frequency fingerprints (GWAFFs) of populations via genotyping by sequencing. PLoS One 2013; 8:e57438. [PMID: 23469194 PMCID: PMC3587605 DOI: 10.1371/journal.pone.0057438] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 01/22/2013] [Indexed: 11/23/2022] Open
Abstract
Genotyping-by-Sequencing (GBS) is an excellent tool for characterising genetic variation between plant genomes. To date, its use has been reported only for genotyping of single individuals. However, there are many applications where resolving allele frequencies within populations on a genome-wide scale would be very powerful, examples include the breeding of outbreeding species, varietal protection in outbreeding species, monitoring changes in population allele frequencies. This motivated us to test the potential to use GBS to evaluate allele frequencies within populations. Perennial ryegrass is an outbreeding species, and breeding programs are based upon selection on populations. We tested two restriction enzymes for their efficiency in complexity reduction of the perennial ryegrass genome. The resulting profiles have been termed Genome Wide Allele Frequency Fingerprints (GWAFFs), and we have shown how these fingerprints can be used to distinguish between plant populations. Even at current costs and throughput, using sequencing to directly evaluate populations on a genome-wide scale is viable. GWAFFs should find many applications, from varietal development in outbreeding species right through to playing a role in protecting plant breeders’ rights.
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Affiliation(s)
- Stephen Byrne
- Department of Molecular Biology and Genetics, Aarhus University, Research Centre Flakkebjerg, Slagelse, Denmark.
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82
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Westengen OT, Berg PR, Kent MP, Brysting AK. Spatial structure and climatic adaptation in African maize revealed by surveying SNP diversity in relation to global breeding and landrace panels. PLoS One 2012; 7:e47832. [PMID: 23091649 PMCID: PMC3472975 DOI: 10.1371/journal.pone.0047832] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 09/17/2012] [Indexed: 01/11/2023] Open
Abstract
Background Climate change threatens maize productivity in sub-Saharan Africa. To ensure food security, access to locally adapted genetic resources and varieties is an important adaptation measure. Most of the maize grown in Africa is a genetic mix of varieties introduced at different historic times following the birth of the trans-Atlantic economy, and knowledge about geographic structure and local adaptations is limited. Methodology A panel of 48 accessions of maize representing various introduction routes and sources of historic and recent germplasm introductions in Africa was genotyped with the MaizeSNP50 array. Spatial genetic structure and genetic relationships in the African panel were analysed separately and in the context of a panel of 265 inbred lines representing global breeding material (based on 26,900 SNPs) and a panel of 1127 landraces from the Americas (270 SNPs). Environmental association analysis was used to detect SNPs associated with three climatic variables based on the full 43,963 SNP dataset. Conclusions The genetic structure is consistent between subsets of the data and the markers are well suited for resolving relationships and admixture among the accessions. The African accessions are structured in three clusters reflecting historical and current patterns of gene flow from the New World and within Africa. The Sahelian cluster reflects original introductions of Meso-American landraces via Europe and a modern introduction of temperate breeding material. The Western cluster reflects introduction of Coastal Brazilian landraces, as well as a Northeast-West spread of maize through Arabic trade routes across the continent. The Eastern cluster most strongly reflects gene flow from modern introduced tropical varieties. Controlling for population history in a linear model, we identify 79 SNPs associated with maximum temperature during the growing season. The associations located in genes of known importance for abiotic stress tolerance are interesting candidates for local adaptations.
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Affiliation(s)
- Ola T Westengen
- Centre for Development and the Environment, SUM, University of Oslo, Oslo, Norway.
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83
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Egan AN, Schlueter J, Spooner DM. Applications of next-generation sequencing in plant biology. AMERICAN JOURNAL OF BOTANY 2012; 99:175-85. [PMID: 22312116 DOI: 10.3732/ajb.1200020] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The last several years have seen revolutionary advances in DNA sequencing technologies with the advent of next-generation sequencing (NGS) techniques. NGS methods now allow millions of bases to be sequenced in one round, at a fraction of the cost relative to traditional Sanger sequencing. As costs and capabilities of these technologies continue to improve, we are only beginning to see the possibilities of NGS platforms, which are developing in parallel with online availability of a wide range of biological data sets and scientific publications and allowing us to address a variety of questions not possible before. As techniques and data sets continue to improve and grow, we are rapidly moving to the point where every organism, not just select "model organisms", is open to the power of NGS. This volume presents a brief synopsis of NGS technologies and the development of exemplary applications of such methods in the fields of molecular marker development, hybridization and introgression, transcriptome investigations, phylogenetic and ecological studies, polyploid genetics, and applications for large genebank collections.
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Affiliation(s)
- Ashley N Egan
- East Carolina University, Department of Biology, Howell Science Complex N303a, Mailstop 551, Greenville, North Carolina 27858, USA.
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