2
|
McCouch S, Navabi ZK, Abberton M, Anglin NL, Barbieri RL, Baum M, Bett K, Booker H, Brown GL, Bryan GJ, Cattivelli L, Charest D, Eversole K, Freitas M, Ghamkhar K, Grattapaglia D, Henry R, Valadares Inglis MC, Islam T, Kehel Z, Kersey PJ, King GJ, Kresovich S, Marden E, Mayes S, Ndjiondjop MN, Nguyen HT, Paiva SR, Papa R, Phillips PWB, Rasheed A, Richards C, Rouard M, Amstalden Sampaio MJ, Scholz U, Shaw PD, Sherman B, Staton SE, Stein N, Svensson J, Tester M, Montenegro Valls JF, Varshney R, Visscher S, von Wettberg E, Waugh R, Wenzl P, Rieseberg LH. Mobilizing Crop Biodiversity. Mol Plant 2020; 13:1341-1344. [PMID: 32835887 DOI: 10.1016/j.molp.2020.08.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 05/10/2023]
Affiliation(s)
- Susan McCouch
- Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Zahra Katy Navabi
- DivSeek, Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada; Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Michael Abberton
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, Nigeria
| | - Noelle L Anglin
- International Potato Center (CIP) 1895 Avenida La Molina, Lima Peru 12, Lima 15023, Peru
| | - Rosa Lia Barbieri
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas (ICARDA), Station Exp. INRA-Quich. Rue Hafiane Cherkaoui. Agdal. Rabat - Instituts, 10111, Rabat, Morocco
| | - Kirstin Bett
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK S7N 5A8, Canada
| | - Helen Booker
- Department of Plant Agriculture, University of Guelph, Rm 316, Crop Science Bldg, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
| | - Gerald L Brown
- Genome Prairie, 111 Research Drive, Suite 101, Saskatoon, SK, S7N 3R2, Canada
| | - Glenn J Bryan
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Luigi Cattivelli
- CREA, Research Centre for Genomics and Bioinformatics, via San Protaso 302, Fiorenzuola d'Arda, 29017, Italy
| | - David Charest
- Genome British Columbia, 400-575 West 8th Avenue, Vancouver, BC, V5Z 0C4, Canada
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium, 2841 NE Marywood Ct, Lee's Summit, MO, 64086, USA
| | - Marcelo Freitas
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Kioumars Ghamkhar
- Forage Science, Grasslands Research Centre, AgResearch, Palmerston North, 4410, New Zealand
| | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Maria Cleria Valadares Inglis
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), Station Exp. INRA-Quich. Rue Hafiane Cherkaoui. Agdal. Rabat - Instituts, 10111, Rabat, Morocco
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Graham J King
- Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
| | - Stephen Kresovich
- Feed the Future Innovation Lab for Crop Improvement, 431 Weill Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Emily Marden
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada
| | - Sean Mayes
- Crops For the Future (UK) CIC 76-80 Baddow Road, Chelmsford, Essex, CM2 7PJ, UK
| | - Marie Noelle Ndjiondjop
- Africa Rice Center (AfricaRice), Mbe Research Station, Bouaké, 01 BP 2511 Bouaké, Côte d'Ivoire
| | - Henry T Nguyen
- University of Missouri, Division of Plant Sciences, 25 Agriculture Lab Bldg, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Samuel Rezende Paiva
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Roberto Papa
- Università Politecnica delle Marche, D3A-Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Via Brecce Bianche, 60131, Ancona, Italy
| | - Peter W B Phillips
- Johnson Shoyama Graduate School of Public Policy, University of Saskatchewan, 101 Diefenbaker Place, Saskatoon, S7N 5B8, Canada
| | - Awais Rasheed
- CIMMYT-China office, Beijing 100081, Beijing, P.R. China
| | - Christopher Richards
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 South Mason St, Fort Collins, CO, 80521, USA
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Maria Jose Amstalden Sampaio
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany
| | - Paul D Shaw
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Brad Sherman
- Law School, University of Queensland, St Lucia, QLD, 4072, Australia
| | - S Evan Staton
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; CiBreed - Center for Integrated Breeding Research, Department of Crop Sciences, Georg-August University Göttingen, Von Siebold Straße 8, D-37075 Göttingen, Germany
| | | | - Mark Tester
- King Abdullah University of Science & Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jose Francisco Montenegro Valls
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Rajeev Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru - 502 324, Telangana State, India
| | - Stephen Visscher
- Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Eric von Wettberg
- University of Vermont, 63 Carrigan Drive, Jeffords Hall, Burlington, VT, 05405, USA
| | - Robbie Waugh
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK; School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Peter Wenzl
- Centro Internacional de Agricultura Tropical (CIAT), Km 17 Recta Cali-Palmira, 763537 Cali, Colombia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada.
| |
Collapse
|
3
|
Ndjiondjop MN, Alachiotis N, Pavlidis P, Goungoulou A, Kpeki SB, Zhao D, Semagn K. Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice. Theor Appl Genet 2019; 132:1145-1158. [PMID: 30578434 PMCID: PMC6449321 DOI: 10.1007/s00122-018-3268-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/11/2018] [Indexed: 05/20/2023]
Abstract
The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1-32.1 and 16.3-37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10-4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10-2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.
Collapse
Affiliation(s)
- Marie Noelle Ndjiondjop
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Alphonse Goungoulou
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Sèdjro Bienvenu Kpeki
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Dule Zhao
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Kassa Semagn
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
| |
Collapse
|
4
|
Ndjiondjop MN, Semagn K, Zhang J, Gouda AC, Kpeki SB, Goungoulou A, Wambugu P, Dramé KN, Bimpong IK, Zhao D. Development of species diagnostic SNP markers for quality control genotyping in four rice ( Oryza L.) species. Mol Breed 2018; 38:131. [PMID: 30416368 PMCID: PMC6208651 DOI: 10.1007/s11032-018-0885-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/17/2018] [Indexed: 05/04/2023]
Abstract
Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.
Collapse
Affiliation(s)
- Marie Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Kassa Semagn
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta T6G 2P5 Canada
| | - Jianwei Zhang
- Arizona Genomics Institute and The School of Plant Sciences, University of Arizona, Thomas W. Keating Bioresearch Bldg., 1657 E. Helen Street, Tucson, AZ 85721 USA
| | - Arnaud Comlan Gouda
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Sèdjro Bienvenu Kpeki
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Alphonse Goungoulou
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Peterson Wambugu
- Kenya Agricultural and Livestock Research Organization (KALRO), Genetic Resources Research Institute, Nairobi, Kenya
| | | | - Isaac Kofi Bimpong
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Dule Zhao
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| |
Collapse
|
5
|
Ndjiondjop MN, Semagn K, Sow M, Manneh B, Gouda AC, Kpeki SB, Pegalepo E, Wambugu P, Sié M, Warburton ML. Assessment of Genetic Variation and Population Structure of Diverse Rice Genotypes Adapted to Lowland and Upland Ecologies in Africa Using SNPs. Front Plant Sci 2018; 9:446. [PMID: 29686690 PMCID: PMC5900792 DOI: 10.3389/fpls.2018.00446] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 03/22/2018] [Indexed: 05/04/2023]
Abstract
Using interspecific crosses involving Oryza glaberrima Steud. as donor and O. sativa L. as recurrent parents, rice breeders at the Africa Rice Center developed several 'New Rice for Africa (NERICA)' improved varieties. A smaller number of interspecific and intraspecific varieties have also been released as 'Advanced Rice for Africa (ARICA)'. The objective of the present study was to investigate the genetic variation, relatedness, and population structure of 330 widely used rice genotypes in Africa using DArTseq-based single nucleotide polymorphisms (SNPs). A sample of 11 ARICAs, 85 NERICAs, 62 O. sativa spp. japonica, and 172 O. sativa spp. indica genotypes were genotyped with 27,560 SNPs using diversity array technology (DArT)-based sequencing (DArTseq) platform. Nearly 66% of the SNPs were polymorphic, of which 15,020 SNPs were mapped to the 12 rice chromosomes. Genetic distance between pairs of genotypes that belong to indica, japonica, ARICA, and NERICA varied from 0.016 to 0.623, from 0.020 to 0.692, from 0.075 to 0.763, and from 0.014 to 0.644, respectively. The proportion of pairs of genotypes with genetic distance > 0.400 was the largest within NERICAs (35.1% of the pairs) followed by ARICAs (18.2%), japonica (17.4%), and indica (5.6%). We found one pair of japonica, 11 pairs of indica, and 35 pairs of NERICA genotypes differing by <2% of the total scored alleles, which was due to 26 pairs of genotypes with identical pedigrees. Cluster analysis, principal component analysis, and the model-based population structure analysis all revealed two distinct groups corresponding to the lowland (primarily indica and lowland NERICAs) and upland (japonica and upland NERICAs) growing ecologies. Most of the interspecific lowland NERICAs formed a sub-group, likely caused by differences in the O. glaberrima genome as compared with the indica genotypes. Analysis of molecular variance revealed very great genetic differentiation (FST = 0.688) between the lowland and upland ecologies, and 31.2% of variation attributable to differences within cluster groups. About 8% (1,197 of 15,020) of the 15,020 SNPs were significantly (P < 0.05) different between the lowland and upland ecologies and formed contrasting haplotypes that could clearly discriminate lowland from upland genotypes. This is the first study using high density markers that characterized NERICA and ARICA varieties in comparison with indica and japonica varieties widely used in Africa, which could aid rice breeders on parent selection for developing new improved rice germplasm.
Collapse
Affiliation(s)
- Marie Noelle Ndjiondjop
- Africa Rice Center (AfricaRice), Bouaké, Côte d’Ivoire
- *Correspondence: Marie Noelle Ndjiondjop, Kassa Semagn,
| | - Kassa Semagn
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Marie Noelle Ndjiondjop, Kassa Semagn,
| | | | | | | | | | | | - Peterson Wambugu
- Genetic Resources Research Institute, Kenya Agricultural & Livestock Research Organization, Nairobi, Kenya
| | | | - Marilyn L. Warburton
- Corn Host Plant Resistance Research Unit, United States Department of Agriculture-Agricultural Research Service, Starkville, MS, United States
| |
Collapse
|