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Wimalarathna NA, Wickramasuriya AM, Metschina D, Cauz-Santos LA, Bandupriya D, Ariyawansa KGSU, Gopallawa B, Chase MW, Samuel R, Silva TD. Genetic diversity and population structure of Piper nigrum (black pepper) accessions based on next-generation SNP markers. PLoS One 2024; 19:e0305990. [PMID: 38924027 PMCID: PMC11207170 DOI: 10.1371/journal.pone.0305990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
Despite the economic importance of Piper nigrum (black pepper), a highly valued crop worldwide, development and utilization of genomic resources have remained limited, with diversity assessments often relying on only a few samples or DNA markers. Here we employed restriction-site associated DNA sequencing to analyze 175 P. nigrum accessions from eight main black pepper growing regions in Sri Lanka. The sequencing effort resulted in 1,976 million raw reads, averaging 11.3 million reads per accession, revealing 150,356 high-quality single nucleotide polymorphisms (SNPs) distributed across 26 chromosomes. Population structure analysis revealed two subpopulations (K = 2): a dominant group consisting of 152 accessions sourced from both home gardens and large-scale cultivations, and a smaller group comprising 23 accessions exclusively from native collections in home gardens. This clustering was further supported by principal component analysis, with the first two principal components explaining 35.2 and 12.1% of the total variation. Genetic diversity analysis indicated substantial gene flow (Nm = 342.21) and a low fixation index (FST = 0.00073) between the two subpopulations, with no clear genetic differentiation among accessions from different agro-climatic regions. These findings demonstrate that most current black pepper genotypes grown in Sri Lanka share a common genetic background, emphasizing the necessity to broaden the genetic base to enhance resilience to biotic and abiotic stresses. This study represents the first attempt at analyzing black pepper genetic diversity using high-resolution SNP markers, laying the foundation for future genome-wide association studies for SNP-based gene discovery and breeding.
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Affiliation(s)
- Nilni A. Wimalarathna
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | | | - Dominik Metschina
- Department of Botany and Biodiversity of Research, University of Vienna, Vienna, Austria
| | - Luiz A. Cauz-Santos
- Department of Botany and Biodiversity of Research, University of Vienna, Vienna, Austria
| | - Dharshani Bandupriya
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | | | - Bhathiya Gopallawa
- Department of Botany, Faculty of Science, University of Peradeniya, Peradeniya, Sri Lanka
| | - Mark W. Chase
- Department of Botany and Biodiversity of Research, University of Vienna, Vienna, Austria
- Royal Botanic Gardens, Kew, United Kingdom
- Department of Environment and Agriculture, Curtin University, Perth, Western Australia, Australia
| | - Rosabelle Samuel
- Department of Botany and Biodiversity of Research, University of Vienna, Vienna, Austria
| | - Tara D. Silva
- Department of Plant Sciences, Faculty of Science, University of Colombo, Colombo, Sri Lanka
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Agre PA, Clark LV, Garcia-Oliveira AL, Bohar R, Adebola P, Asiedu R, Terauchi R, Asfaw A. Identification of diagnostic KASP-SNP markers for routine breeding activities in yam (Dioscorea spp.). THE PLANT GENOME 2024; 17:e20419. [PMID: 38093501 DOI: 10.1002/tpg2.20419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 09/16/2023] [Accepted: 11/02/2023] [Indexed: 07/02/2024]
Abstract
Maintaining genetic purity and true-to-type clone identification are important action steps in breeding programs. This study aimed to develop a universal set of kompetitive allele-specific polymerase chain reaction (KASP)-based single nucleotide polymorphism (SNP) markers for routine breeding activities. Ultra-low-density SNP markers were created using an initial set of 173,675 SNPs that were obtained from whole-genome resequencing of 333 diverse white Guinea yam (Dioscorea rotundata Poir) genotypes. From whole-genome resequencing data, 99 putative SNP markers were found and successfully converted to high-throughput KASP genotyping assays. The markers set was validated on 374 genotypes representing six yam species. Out of the 99 markers, 50 were highly polymorphic across the species and could distinguish different yam species and pedigree origins. The selected SNP markers classified the validation population based on the different yam species and identified potential duplicates within yam species. Through penalized analysis, the male parent of progenies involved in polycrosses was successfully predicted and validated. Our research was a trailblazer in validating KASP-based SNP assays for species identification, parental fingerprinting, and quality control (QC) and quality assurance (QA) in yam breeding programs.
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Affiliation(s)
- Paterne A Agre
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Lindsay V Clark
- HPCBio, Roy J. Carver Biotechnology Center, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Ana Luisa Garcia-Oliveira
- Excellence in Breeding (EiB), CIMMYT-ICRAF, UN Av, Nairobi, Kenya
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Basic Sciences and Humanities, CCS Haryana Agricultural University, Hisar, Haryana, India
| | - Rajaguru Bohar
- Excellence in Breeding (EiB), CIMMYT-ICRISAT, Hyderabad, Telangana, India
| | - Patrick Adebola
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Robert Asiedu
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ryohei Terauchi
- Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Iwate Biotechnology Research Center, Kitakami, Japan
| | - Asrat Asfaw
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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Sedah P, Djedatin LG, Loko LYE, Ewedje EEBK, Orobiyi A, Gbemavo CDSJ, Toffa J, Tchakpa C, Cubry P, Sabot F. Impact of Seed Origin and Genetic Drift of Improved Rice Variety IR841 in Benin. RICE (NEW YORK, N.Y.) 2023; 16:48. [PMID: 37878087 PMCID: PMC10600083 DOI: 10.1186/s12284-023-00657-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 08/26/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Rice production is important for food security in Benin, with a national production largely dominated by the cultivation of the aromatic ecotype IR841, by far the most appreciated by Beninese consumers. However, to maintain agronomical qualities of a given cultivar, the origin and quality of seeds are mandatory and at the heart of the maintenance of yield and of market requests. Following this idea, the objective of the current study was thus to investigate the genetic purity of IR841 varieties collected from rice producers across 22 villages in Benin in relation to their agronomical performances. RESULTS For this, agromorphological evaluation of 72 accessions based on 13 quantitative descriptors followed by genotyping with the Illumina Infinium rice 7 K SNP array of 9 accessions was carried out in the presence of 2 controls. Agromorphologic as well as genetic and phylogenetic analyses revealed two groups, the first one Okouta97, Koum47, Nana30, Man118, Ang1 and control sample IR841-2) was characterized by seed accessions provided by the formal seed system, while the second (Koum53, Tchaka41 and Koud46) comprising seeds from local markets or from previous harvests and showing a depression in agronomic performances. CONCLUSION We showed that IR841 seed purity is mandatory for the completion of agronomical performance, and that the farmers' choice of seeds must be guided and informed to ensure sustainability and food security.
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Affiliation(s)
- Paulin Sedah
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Lambert Gustave Djedatin
- Ecole Normale Supérieure de l'Enseignement Technique (ENSET), Lokossa, Bénin.
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin.
| | - Laura Yêyinou Estelle Loko
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Eben-Ezer Baba Kayodé Ewedje
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Azize Orobiyi
- Centre de Recherche Agricole Plantes Pérennes (CRA-PP- INRAB), Pobè, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Chalemagne Dossou Seblodo Judes Gbemavo
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Joelle Toffa
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Cyrille Tchakpa
- Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
| | - Philippe Cubry
- DIADE unit, UM, CIRAD IRD, Centre IRD de Montpellier, 911 Agropolis BP 604501, Montpellier Cedex 5, F- 34 394, France
| | - Francois Sabot
- DIADE unit, UM, CIRAD IRD, Centre IRD de Montpellier, 911 Agropolis BP 604501, Montpellier Cedex 5, F- 34 394, France
- JEAI-GRAB, Ecole Nationale Supérieure des Biosciences et Biotechnologies Appliquées (ENSBBA), Dassa-Zoumé, Bénin
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Yongbin Q, Summat P, Panyawut N, Sikaewtung K, Ditthab K, Tongmark K, Chakhonkaen S, Sangarwut N, Wasinanon T, Kaewmungkun K, Muangprom A. Identification of Rice Accessions Having Cold Tolerance at the Seedling Stage and Development of Novel Genotypic Assays for Predicting Cold Tolerance. PLANTS (BASEL, SWITZERLAND) 2023; 12:215. [PMID: 36616346 PMCID: PMC9823403 DOI: 10.3390/plants12010215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/08/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Rice is susceptible to cold stress at the seedling stage, which can delay growth and decrease yield. We evaluated 187 rice accessions for cold tolerance at the seedling stage and developed genotypic assays for three markers. All japonica (20/20) and 20/140 indica accessions were highly cold tolerant. Two SNP markers specific for COLD1 and LOC_Os10g34840 were practical to use by normal agarose gel. The SNP marker specific for COLD1 was highly specific for predicting cold tolerance. However, the sensitivity of this marker was low as several cold-tolerant indica accessions lacked the cold-tolerant allele. The LOC_Os10g34840 marker was slightly more sensitive than the COLD1 marker for predicting highly cold-tolerant accessions. An insertion/deletion variant in the NAC6 gene was identified as a novel cold tolerance marker. The NAC6 marker predicted more highly cold-tolerant accessions compared with the other two markers. The SNP marker specific for LOC_Os10g34840 and the NAC6 marker were present in several tested subgroups, suggesting their wide effects and distribution. The three markers combined predicted the most highly cold-tolerant accessions, indicating that the marker combination is superior for applications such as marker-assisted breeding. The cold-tolerant accessions and the genotypic marker assays will be useful for future rice breeding.
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Affiliation(s)
- Qi Yongbin
- Institute of Crop Science and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Patcharaporn Summat
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Centre, Khlong Luang, Pathum Thani 12120, Thailand
| | - Natjaree Panyawut
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
- Nadi District Agricultural Extension Office, Chamanan Road, Nadi Subdistrict, Nadi District, Prachinburi 25220, Thailand
| | - Kannika Sikaewtung
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Khanittha Ditthab
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Keasinee Tongmark
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Sriprapai Chakhonkaen
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Numphet Sangarwut
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Thiwawan Wasinanon
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Kanokwan Kaewmungkun
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
| | - Amorntip Muangprom
- National Center for Genetic Engineering and Biotechnology, Thailand Science Park, Khlong Luang, Pathum Thani 12120, Thailand
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Hasan N, Rafii MY, Harun AR, Alı NS, Mazlan N, Abdullah S. Genetic analysis of yield and yield contributing traits in rice ( Oryza sativa L.) BC 2F 3 population derived from MR264 × PS2. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2060760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Nor’Aishah Hasan
- School of Biology, Faculty of Applied Sciences, Universiti Teknologi MARA, Cawangan Negeri Sembilan, Negeri Sembilan, Malaysia
- Biotechnology, Microbiology and Environmental Collaboration Sciences, Universiti Teknologi MARA, Negeri Sembilan, Malaysia
| | - Mohd Yusop Rafii
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Abdul Rahim Harun
- Crop Improvement Unit, Agrotechnology and Bioscience Division, Malaysian Nuclear Agency, Kajang, Selangor, Malaysia
| | - Nusaibah Syed Alı
- Department of Agriculture Technology, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Norida Mazlan
- Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Shamsiah Abdullah
- Agricultural Biotechnology Research Group, Faculty of Plantation and Agrotechnology, Universiti Teknologi MARA Cawangan Melaka, Merlimau, Melaka, Malaysia
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6
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Kirk GJD, Manwaring HR, Ueda Y, Semwal VK, Wissuwa M. Below-ground plant-soil interactions affecting adaptations of rice to iron toxicity. PLANT, CELL & ENVIRONMENT 2022; 45:705-718. [PMID: 34628670 DOI: 10.1111/pce.14199] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 08/11/2021] [Accepted: 08/13/2021] [Indexed: 06/13/2023]
Abstract
Iron toxicity is a major constraint to rice production, particularly in highly weathered soils of inland valleys in sub-Saharan Africa where the rice growing area is rapidly expanding. There is a wide variation in tolerance of iron toxicity in the rice germplasm. However, the introgression of tolerance traits into high-yielding germplasm has been slow owing to the complexity of the tolerance mechanisms and large genotype-by-environment effects. We review current understanding of tolerance mechanisms, particularly those involving below-ground plant-soil interactions. Until now these have been less studied than above-ground mechanisms. We cover processes in the rhizosphere linked to exclusion of toxic ferrous iron by oxidation, and resulting effects on the mobility of nutrient ions. We also cover the molecular physiology of below-ground processes controlling iron retention in roots and root-shoot transport, and also plant iron sensing. We conclude that future breeding programmes should be based on well-characterized molecular markers for iron toxicity tolerance traits. To successfully identify such markers, the complex tolerance response should be broken down into its components based on understanding of tolerance mechanisms, and tailored screening methods should be developed for individual mechanisms.
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Affiliation(s)
- Guy J D Kirk
- School of Water, Energy and Environment, Cranfield University, Cranfield, UK
| | - Hanna R Manwaring
- School of Water, Energy and Environment, Cranfield University, Cranfield, UK
| | - Yoshiaki Ueda
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
| | | | - Matthias Wissuwa
- Crop, Livestock and Environment Division, Japan International Research Center for Agricultural Sciences, Tsukuba, Japan
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7
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Maung TZ, Yoo JM, Chu SH, Kim KW, Chung IM, Park YJ. Haplotype Variations and Evolutionary Analysis of the Granule-Bound Starch Synthase I Gene in the Korean World Rice Collection. FRONTIERS IN PLANT SCIENCE 2021; 12:707237. [PMID: 34504507 PMCID: PMC8421862 DOI: 10.3389/fpls.2021.707237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 07/21/2021] [Indexed: 06/13/2023]
Abstract
Granule-bound starch synthase I (GBSSI) is responsible for Waxy gene encoding the, which is involved in the amylose synthesis step of starch biosynthesis. We investigated the genotypic and haplotypic variations of GBSSI (Os06g0133000) gene, including its evolutionary relatedness in the nucleotide sequence level using single-nucleotide polymorphisms (SNPs), indels, and structural variations (SVs) from 475 Korean World Rice Collection (KRICE_CORE), which comprised 54 wild rice and 421 cultivated represented by 6 ecotypes (temperate japonica, indica, tropical japonica, aus, aromatic, and admixture) or in another way by 3 varietal types (landrace, weedy, and bred). The results revealed that 27 of 59 haplotypes indicated a total of 12 functional SNPs (fSNPs), identifying 9 novel fSNPs. According to the identified novel fSNPs, we classified the entire rice collection into three groups: cultivated, wild, and mixed (cultivated and wild) rice. Five novel fSNPs were localized in wild rice: four G/A fSNPs in exons 2, 9, and 12 and one T/C fSNP in exon 13. We also identified the three previously reported fSNPs, namely, a G/A fSNP (exon 4), an A/C fSNP (exon 6), and a C/T fSNP (exon 10), which were observed only in cultivated rice, whereas an A/G fSNP (exon 4) was observed exclusively in wild rice. All-against-all comparison of four varietal types or six ecotypes of cultivated rice with wild rice showed that the GBSSI diversity was higher only in wild rice (π = 0.0056). The diversity reduction in cultivated rice can be useful to encompass the origin of this gene GBSSI during its evolution. Significant deviations of positive (wild and indica under balancing selection) and negative (temperate and tropical japonica under purifying selection) Tajima's D values from a neutral model can be informative about the selective sweeps of GBSSI genome insights. Despite the estimation of the differences in population structure and principal component analysis (PCA) between wild and subdivided cultivated subgroups, an inbreeding effect was quantified by F ST statistic, signifying the genetic relatedness of GBSSI. Our findings of a novel wild fSNPS can be applicable for future breeding of waxy rice varieties. Furthermore, the signatures of selective sweep can also be of informative into further deeper insights during domestication.
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Affiliation(s)
- Thant Zin Maung
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Ji-Min Yoo
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
| | - Sang-Ho Chu
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
| | - Kyu-Won Kim
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
| | - Ill-Min Chung
- Department of Applied Life Science, Konkuk University, Seoul, South Korea
| | - Yong-Jin Park
- Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan-gun, South Korea
- Center of Crop Breeding on Omics and Artificial Intelligence, Kongju National University, Yesan-gun, South Korea
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Song JM, Arif M, Zi Y, Sze SH, Zhang M, Zhang HB. Molecular and genetic dissection of the USDA rice mini-core collection using high-density SNP markers. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 308:110910. [PMID: 34034867 DOI: 10.1016/j.plantsci.2021.110910] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Revised: 04/05/2021] [Accepted: 04/10/2021] [Indexed: 06/12/2023]
Abstract
Molecular tools and knowledge of crop germplasm are vital for their effective utilization. In this study, we developed 40,866 high-quality and well distributed SNPs for a rice mini-core collection (RMC) developed by the United States Department of Agriculture (USDA). The high-quality SNPs clustered the USDA-RMC into five subpopulations (Ind, indica; Aus, aus; Afr, African rice; TeJ, temperate japonica; TrJ, tropical japonica) and one admixture (Adm). This classification was further confirmed by phylogenetic and principal component analyses. The rice ARO (aromatic) subpopulation of previous studies was re-assigned with Adm and the WD (wild-type) subpopulation was re-defined to the Afr subpopulation because most of its accessions are African cultivated rice. The Aus and Ind subpopulations had a substantially wider genetic variation than the TrJ and TeJ subpopulations. The genetic diversities were much larger between the Ind or Aus subpopulation and the TrJ or TeJ subpopulation than between the Afr subpopulation and the Ind, Aus, TrJ or TeJ subpopulation. Comparative agronomic trait analysis between the subpopulations also supported the genetic structure and variation of the RMC, and suggested the existence of extensive variation in the genes controlling agronomic traits among them. Furthermore, analysis of ancestral membership of the RMC accessions revealed that reproductive barrier or wide incompatibility existed between the Indica and Japonica groups, while gene flow occurred between them. These results provide high-quality SNPs and knowledge of genetic structure and diversity of the USDA-RMC necessary for enhanced rice research and breeding.
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Affiliation(s)
- Jian-Min Song
- Crop Research Institute/National Engineering Laboratory for Wheat and Maize, Shandong Academy of Agricultural Sciences (SAAS), Jinan, 250100, PR China; Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA.
| | - Muhammad Arif
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA; Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.
| | - Yan Zi
- Crop Research Institute/National Engineering Laboratory for Wheat and Maize, Shandong Academy of Agricultural Sciences (SAAS), Jinan, 250100, PR China
| | - Sing-Hoi Sze
- Department of Computer Science and Engineering and Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843, USA.
| | - Meiping Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA.
| | - Hong-Bin Zhang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX, 77843-2474, USA.
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Allan V, Vetriventhan M, Senthil R, Geetha S, Deshpande S, Rathore A, Kumar V, Singh P, Reddymalla S, Azevedo VCR. Genome-Wide DArTSeq Genotyping and Phenotypic Based Assessment of Within and Among Accessions Diversity and Effective Sample Size in the Diverse Sorghum, Pearl Millet, and Pigeonpea Landraces. FRONTIERS IN PLANT SCIENCE 2020; 11:587426. [PMID: 33381130 PMCID: PMC7768014 DOI: 10.3389/fpls.2020.587426] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 11/05/2020] [Indexed: 05/30/2023]
Abstract
Germplasm should be conserved in such a way that the genetic integrity of a given accession is maintained. In most genebanks, landraces constitute a major portion of collections, wherein the extent of genetic diversity within and among landraces of crops vary depending on the extent of outcrossing and selection intensity infused by farmers. In this study, we assessed the level of diversity within and among 108 diverse landraces and wild accessions using both phenotypic and genotypic characterization. This included 36 accessions in each of sorghum, pearl millet, and pigeonpea, conserved at ICRISAT genebank. We genotyped about 15 to 25 individuals within each accession, totaling 1,980 individuals using the DArTSeq approach. This resulted in 45,249, 19,052, and 8,211 high-quality single nucleotide polymorphisms (SNPs) in pearl millet, sorghum, and pigeonpea, respectively. Sorghum had the lowest average phenotypic (0.090) and genotypic (0.135) within accession distances, while pearl millet had the highest average phenotypic (0.227) and genotypic (0.245) distances. Pigeonpea had an average of 0.203 phenotypic and 0.168 genotypic within accession distances. Analysis of molecular variance also confirms the lowest variability within accessions of sorghum (26.3%) and the highest of 80.2% in pearl millet, while an intermediate in pigeonpea (57.0%). The effective sample size required to capture maximum variability and to retain rare alleles while regeneration ranged from 47 to 101 for sorghum, 155 to 203 for pearl millet, and 77 to 89 for pigeonpea accessions. This study will support genebank curators, in understanding the dynamics of population within and among accessions, in devising appropriate germplasm conservation strategies, and aid in their utilization for crop improvement.
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Affiliation(s)
- Victor Allan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Ramachandran Senthil
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - S. Geetha
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinod Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prabhat Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Surender Reddymalla
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vânia C. R. Azevedo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Vasumathy SK, Peringottillam M, Sundaram KT, Kumar SHK, Alagu M. Genome- wide structural and functional variant discovery of rice landraces using genotyping by sequencing. Mol Biol Rep 2020; 47:7391-7402. [PMID: 32886328 DOI: 10.1007/s11033-020-05794-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 08/28/2020] [Indexed: 12/20/2022]
Abstract
Rice landraces are vital genetic resources for agronomic and quality traits but the undeniable collection of Kerala landraces remains poorly delineated. To effectively conserve, manage, and use these resources, understanding the genomic structure of germplasm is essential. Genotyping by sequencing (GBS) enables identification of an immense number of single nucleotide polymorphism (SNP) and insertion deletion (InDel) from 96 rice germplasm. In the present study, a total of 16.9 × 107 reads were generated, and among that 16.3 × 107 reads were mapped to the indica reference genome. Exploring GBS data unfolded a wide genomic variations including 82,59,639 SNPs and 1,07,140 Indels. Both neighbor-joining tree and principal coordinate analysis with InDel markers revealed the selected germplasm in this study as highly diverse in structure. We assembled unmapped reads which were further employed for gene ontology analysis. These unmapped sequences that are generally expelled from subsequent studies of GBS data analysis may exist as an unexplored resort for several novel significant biological findings. The discovery of SNPs from the haplotyping results of GS3 and GIF1 genes provided insight into marker- assisted selection based on grain size and yield and can be utilized for rice yield improvement. To our knowledge, this is the first report on structural variation analysis using the GBS platform in rice landraces collected from Kerala. Genomic information from this study endows with valuable resources for perceptive rice landrace structure and can also facilitate sequencing-based molecular breeding.
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Affiliation(s)
| | - Maya Peringottillam
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Krishna T Sundaram
- South Asia hub, ICRISAT Campus, International Rice Research Institute, Secundarabad, Telangana, India
| | - S Hari Krishna Kumar
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Manickavelu Alagu
- Department of Genomic Science, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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11
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Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing. Sci Rep 2020; 10:13995. [PMID: 32814806 PMCID: PMC7438528 DOI: 10.1038/s41598-020-70842-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022] Open
Abstract
To minimize the cost of sample preparation and genotyping, most genebank genomics studies in self-pollinating species are conducted on a single individual to represent an accession, which may be heterogeneous with larger than expected intra-accession genetic variation. Here, we compared various population genetics parameters among six DNA (leaf) sampling methods on 90 accessions representing a wild species (O. barthii), cultivated and landraces (O. glaberrima, O. sativa), and improved varieties derived through interspecific hybridizations. A total of 1,527 DNA samples were genotyped with 46,818 polymorphic single nucleotide polymorphisms (SNPs) using DArTseq. Various statistical analyses were performed on eleven datasets corresponding to 5 plants per accession individually and in a bulk (two sets), 10 plants individually and in a bulk (two sets), all 15 plants individually (one set), and a randomly sampled individual repeated six times (six sets). Overall, we arrived at broadly similar conclusions across 11 datasets in terms of SNP polymorphism, heterozygosity/heterogeneity, diversity indices, concordance among genetic dissimilarity matrices, population structure, and genetic differentiation; there were, however, a few discrepancies between some pairs of datasets. Detailed results of each sampling method, the concordance in their outputs, and the technical and cost implications of each method were discussed.
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12
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Ramirez‐Villegas J, Khoury CK, Achicanoy HA, Mendez AC, Diaz MV, Sosa CC, Debouck DG, Kehel Z, Guarino L. A gap analysis modelling framework to prioritize collecting for ex situ conservation of crop landraces. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Julian Ramirez‐Villegas
- International Center for Tropical Agriculture (CIAT) Cali Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), c/o CIAT Cali Colombia
| | - Colin K. Khoury
- International Center for Tropical Agriculture (CIAT) Cali Colombia
- United States Department of Agriculture Agricultural Research Service National Laboratory for Genetic Resources Preservation Fort Collins CO USA
- Department of Biology Saint Louis University St. Louis MO USA
| | | | - Andres C. Mendez
- International Center for Tropical Agriculture (CIAT) Cali Colombia
| | | | | | | | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA) Rabat Morocco
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13
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Melandri G, Sikirou M, Arbelaez JD, Shittu A, Semwal VK, Konaté KA, Maji AT, Ngaujah SA, Akintayo I, Govindaraj V, Shi Y, Agosto-Peréz FJ, Greenberg AJ, Atlin G, Ramaiah V, McCouch SR. Multiple Small-Effect Alleles of Indica Origin Enhance High Iron-Associated Stress Tolerance in Rice Under Field Conditions in West Africa. FRONTIERS IN PLANT SCIENCE 2020; 11:604938. [PMID: 33584748 PMCID: PMC7874229 DOI: 10.3389/fpls.2020.604938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/15/2020] [Indexed: 05/03/2023]
Abstract
Understanding the genetics of field-based tolerance to high iron-associated (HIA) stress in rice can accelerate the development of new varieties with enhanced yield performance in West African lowland ecosystems. To date, few field-based studies have been undertaken to rigorously evaluate rice yield performance under HIA stress conditions. In this study, two NERICA × O. sativa bi-parental rice populations and one O.sativa diversity panel consisting of 296 rice accessions were evaluated for grain yield and leaf bronzing symptoms over multiple years in four West African HIA stress and control sites. Mapping of these traits identified a large number of QTLs and single nucleotide polymorphisms (SNPs) associated with stress tolerance in the field. Favorable alleles associated with tolerance to high levels of iron in anaerobic rice soils were rare and almost exclusively derived from the indica subpopulation, including the most favorable alleles identified in NERICA varieties. These findings highlight the complex genetic architecture underlying rice response to HIA stress and suggest that a recurrent selection program focusing on an expanded indica genepool could be productively used in combination with genomic selection to increase the efficiency of selection in breeding programs designed to enhance tolerance to this prevalent abiotic stress in West Africa.
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Affiliation(s)
- Giovanni Melandri
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Mouritala Sikirou
- Africa Rice Center, Ibadan, Nigeria
- School of Horticulture and Green Landscaping, Kétou, Bénin
| | - Juan D. Arbelaez
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | | | | | | | | | | | - Inoussa Akintayo
- Central Agricultural Research Institute, Suakoko, Liberia
- Africa Rice Center, Suakoko, Liberia
| | - Vishnu Govindaraj
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | - Yuxin Shi
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
| | | | | | - Gary Atlin
- Bill & Melinda Gates Foundation, Seattle, WA, United States
| | | | - Susan R. McCouch
- Plant Breeding and Genetics, Cornell University, Ithaca, NY, United States
- Venuprasad Ramaiah,
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14
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Genetic diversity and population structure analysis of Asian and African aromatic rice (Oryza sativa L.) genotypes. J Genet 2019. [DOI: 10.1007/s12041-019-1131-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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15
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Mishra A, Kumar P, Shamim M, Tiwari KK, Fatima P, Srivastava D, Singh R, Yadav P. Genetic diversity and population structure analysis of Asian and African aromatic rice ( Oryza sativa L.) genotypes. J Genet 2019; 98:92. [PMID: 31544788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rice germplasms collected from different regions could be used as valuable resources for the future breeding programme. For the utilization of such collections, knowledge about the level and distribution of genetic diversity among these collections will facilitate the breeder. In this study, we report the phenotypic correlation, biochemical quality parameters and population genetic analysis of 35 rice accessions including 34 aromatic rice from different countries and a nonaromatic, Nagina 22, a well-known drought resistance variety. Further biochemical quality analysis, gel consistency test, molecular diversity analysis with 55 simple sequence repeat markers, population structure analysis and pair wise FST analysis were also conducted to assess the genetic diversity. The collected rice genotypes showed significant variability in different agronomic traits, i.e. spikelet per panicle, branches per panicle etc. Results obtained from the above tests demonstrated the importance of regional genetic studies for understanding the diversification of aromatic rice in Asian and African rice.
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Affiliation(s)
- Anurag Mishra
- Division of Genetics, Indian Agricultural Research Institute, New Delhi 110 012, India.
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16
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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. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 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] [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.
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Affiliation(s)
- Marie Noelle Ndjiondjop
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
| | - 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.
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17
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Ansari S, Solouki M, Fakheri B, Fazeli-Nasab B, Mahdinezhad N. Assesment of molecular diversity of internal transcribed spacer region in some lines and landrace of Persian clover (Trifolium resupinatum L.). POTRAVINARSTVO 2018. [DOI: 10.5219/960] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Clover which is an herbaceous, annual, and self-pollinated plant belongs to fabaceae family (legumes) and has become naturalized in Iran, Asia Minor and the Mediterranean eastern suburban countries. The aim of the present study is ITS molecular evaluation of the nuclear ribosomal genes of lines and landraces of Persian Clover. The sequences were aligned using ClustalW method and by MegAlign software and the dendrogram of different phylogenetic and matrix relationships between the sequences were drawn. The results showed little genetic diversity between the lines and the landrace. The conserved sequence of the analyzed gene in the Persian clover is 561 base. Totally, 740 loci (69 and 671 loci, respectively, with and without removal and addition), 9 Singletons, and 5 haplotypes were identified. The highest rate of transfer was observed in pyrimidine (%16.3). The numerical value of the ratio (dN/dS) was 0.86, and since it was less than 1, the pure selection on the studied gene happened. The lines and landraces were not separated based on their geographic locations. In general, the results indicated that the highest rate of the regional diversity belonged to the clover plants in Lorestan region. Moreover, ITS markers did not seem suitable enough for evaluating the intra- species genetic variation, but it was quite well- suited for inter-species or intergeneric evaluation.
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18
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Ndjiondjop MN, Semagn K, Zhang J, Gouda AC, Kpeki SB, Goungoulou A, Wambugu P, Dramé KN, Bimpong IK, Zhao D. Development of species diagnostic SNP markers for quality control genotyping in four rice ( Oryza L.) species. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2018; 38:131. [PMID: 30416368 PMCID: PMC6208651 DOI: 10.1007/s11032-018-0885-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 09/17/2018] [Indexed: 05/04/2023]
Abstract
Species misclassification (misidentification) and handling errors have been frequently reported in various plant species conserved at diverse gene banks, which could restrict use of germplasm for correct purpose. The objectives of the present study were to (i) determine the extent of genotyping error (reproducibility) on DArTseq-based single-nucleotide polymorphisms (SNPs); (ii) determine the proportion of misclassified accessions across 3134 samples representing three African rice species complex (Oryza glaberrima, O. barthii, and O. longistaminata) and an Asian rice (O. sativa), which are conserved at the AfricaRice gene bank; and (iii) develop species- and sub-species (ecotype)-specific diagnostic SNP markers for rapid and low-cost quality control (QC) analysis. Genotyping error estimated from 15 accessions, each replicated from 2 to 16 times, varied from 0.2 to 3.1%, with an overall average of 0.8%. Using a total of 3134 accessions genotyped with 31,739 SNPs, the proportion of misclassified samples was 3.1% (97 of the 3134 accessions). Excluding the 97 misclassified accessions, we identified a total of 332 diagnostic SNPs that clearly discriminated the three indigenous African species complex from Asian rice (156 SNPs), O. longistaminata accessions from both O. barthii and O. glaberrima (131 SNPs), and O. sativa spp. indica from O. sativa spp. japonica (45 SNPs). Using chromosomal position, minor allele frequency, and polymorphic information content as selection criteria, we recommended a subset of 24 to 36 of the 332 diagnostic SNPs for routine QC genotyping, which would be highly useful in determining the genetic identity of each species and correct human errors during routine gene bank operations.
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Affiliation(s)
- Marie Noelle Ndjiondjop
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Kassa Semagn
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta T6G 2P5 Canada
| | - Jianwei Zhang
- Arizona Genomics Institute and The School of Plant Sciences, University of Arizona, Thomas W. Keating Bioresearch Bldg., 1657 E. Helen Street, Tucson, AZ 85721 USA
| | - Arnaud Comlan Gouda
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Sèdjro Bienvenu Kpeki
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Alphonse Goungoulou
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Peterson Wambugu
- Kenya Agricultural and Livestock Research Organization (KALRO), Genetic Resources Research Institute, Nairobi, Kenya
| | | | - Isaac Kofi Bimpong
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
| | - Dule Zhao
- M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké, 01 Côte d’Ivoire
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