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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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Loko YLE, Gbemavo CDSJ, Agre PA, Dassou AG, Yelome OI, Idossou R, Etchiha Afoha SA, Dadonougbo E, Fakorede J, Dansi AA. White Guinea yam (Dioscorea rotundata Poir.) landraces trait profiling and setting benchmark for breeding programs in the Republic of Benin. PLoS One 2022; 17:e0273043. [PMID: 35976964 PMCID: PMC9384998 DOI: 10.1371/journal.pone.0273043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 08/01/2022] [Indexed: 11/28/2022] Open
Abstract
To meet the high demand for white Guinea yam, there is a need to develop and release improved varieties to farmers. Unfortunately, low rate of adoption of most of the improved yam varieties by both producers and consumers was observed. Information regarding agronomic characteristics and food qualities of popular white Guinea yam landraces with high market value are not available to establish minimum standards to be considered by breeding programs. To fill this gap, surveys using rural appraisal tools were carried out in 20 villages and 16 markets throughout Benin. Data on the agronomic performance suggested that for an improved variety to be adopted by Beninese farmers it should have a minimum yield of 4.16 ± 0.15 kg per mound, and average number of marketable tubers of 1.23 ± 0.05, a mean tuber length of 36.41 ± 1.22 cm, and a minimum diameter of 25.44 ± 1.16 cm. The sensorial attributes for boiled and pounded tubers of this improved variety should have minimum score of 3.16 for texture, 0.75 for softness, 3.75 for elasticity, and 1.34 for colour during the sensory evaluation. The improved variety must also have a minimum average severity score of 1.1 for yam mosaic virus disease, 1.33 for anthracnose and 1 for nematodes. Landraces Amoula, Laboko, and Djilaadja should be considered as the standard for yield, sensory attributes, and tolerance to pest and diseases while landraces Danwari, Kodjewe, Mondji, and Gnidou should be characterized as possessing good flowering and fruit setting capacities for breeding programs.
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Affiliation(s)
- Yêyinou Laura Estelle Loko
- Laboratory of Biotechnology, Genetic Resources and Plant and Animal Breeding (BIORAVE), National High School of Applied Biosciences and Biotechnologies (ENSBBA/UNSTIM), Dassa-Zoumé, Benin
- Laboratory of Applied Entomology (LEnA), National High School of Applied Biosciences and Biotechnologies (ENSBBA), National University of Sciences, Technologies, Engineering and Mathematics, Dassa, Benin
- * E-mail:
| | - Charlemagne D. S. J. Gbemavo
- Laboratory of Biotechnology, Genetic Resources and Plant and Animal Breeding (BIORAVE), National High School of Applied Biosciences and Biotechnologies (ENSBBA/UNSTIM), Dassa-Zoumé, Benin
| | - Paterne A. Agre
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Anicet G. Dassou
- Laboratory of Biotechnology, Genetic Resources and Plant and Animal Breeding (BIORAVE), National High School of Applied Biosciences and Biotechnologies (ENSBBA/UNSTIM), Dassa-Zoumé, Benin
| | - Octaviano Igor Yelome
- Laboratory of Biotechnology, Genetic Resources and Plant and Animal Breeding (BIORAVE), National High School of Applied Biosciences and Biotechnologies (ENSBBA/UNSTIM), Dassa-Zoumé, Benin
| | - Roger Idossou
- Laboratory of Biotechnology, Genetic Resources and Plant and Animal Breeding (BIORAVE), National High School of Applied Biosciences and Biotechnologies (ENSBBA/UNSTIM), Dassa-Zoumé, Benin
| | - S. Alban Etchiha Afoha
- Laboratory of Biotechnology, Genetic Resources and Plant and Animal Breeding (BIORAVE), National High School of Applied Biosciences and Biotechnologies (ENSBBA/UNSTIM), Dassa-Zoumé, Benin
| | - Eric Dadonougbo
- Laboratory of Biotechnology, Genetic Resources and Plant and Animal Breeding (BIORAVE), National High School of Applied Biosciences and Biotechnologies (ENSBBA/UNSTIM), Dassa-Zoumé, Benin
| | - Jeannette Fakorede
- Laboratory of Biotechnology, Genetic Resources and Plant and Animal Breeding (BIORAVE), National High School of Applied Biosciences and Biotechnologies (ENSBBA/UNSTIM), Dassa-Zoumé, Benin
| | - Alexandre A. Dansi
- Laboratory of Biotechnology, Genetic Resources and Plant and Animal Breeding (BIORAVE), National High School of Applied Biosciences and Biotechnologies (ENSBBA/UNSTIM), Dassa-Zoumé, Benin
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