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Diouf M, Zoclanclounon YAB, Mboup PA, Diouf D, Malédon E, Rivallan R, Chair H, Dossa K. Genome-wide development of intra- and inter-specific transferable SSR markers and construction of a dynamic web resource for yam molecular breeding: Y2MD. THE PLANT GENOME 2024; 17:e20428. [PMID: 38234122 DOI: 10.1002/tpg2.20428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 12/04/2023] [Accepted: 12/23/2023] [Indexed: 01/19/2024]
Abstract
Microsatellite markers are widely used in population genetics and breeding. Despite the economic significance of yams in developing countries, there is a paucity of microsatellite markers, and as of now, no comprehensive microsatellite marker database exists. In this study, we conducted genome-wide microsatellite marker development across four yam species, identified cross-species transferable markers, and designed an easy-to-use web portal for the yam researchers. The screening of Dioscorea alata, Dioscorea rotundata, Dioscorea dumetorum, and Dioscorea zingiberensis genomes resulted in 318,713, 322,501, 307,040, and 253,856 microsatellites, respectively. Mono-, di-, and tri-nucleotides were the most important types of repeats in the different species, and a total of 864,128 primer pairs were designed. Furthermore, we identified 1170 cross-species transferable microsatellite markers. Among them, 17 out of 18 randomly selected were experimentally validated with good discriminatory power, regardless of the species and ploidy levels. Ultimately, we created and deployed a dynamic Yam Microsatellite Markers Database (Y2MD) available at https://y2md.ucad.sn/. Y2MD is embedded with various useful tools such as JBrowse, Blast, insilicoPCR, and SSR Finder to facilitate the exploitation of microsatellite markers in yams. This study represents the first comprehensive microsatellite marker mining across several yam species and will contribute to advancing yam genetic research and marker-assisted breeding. The released user-friendly database constitutes a valuable platform for yam researchers.
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Affiliation(s)
- Moussa Diouf
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | | | - Pape Adama Mboup
- Département de Mathématiques et Informatique, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Diaga Diouf
- Laboratoire Campus de Biotechnologies Végétales, Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop, Dakar, Senegal
| | - Erick Malédon
- UMR AGAP Institut, CIRAD, Petit Bourg, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Ronan Rivallan
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Hâna Chair
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
| | - Komivi Dossa
- UMR AGAP Institut, CIRAD, Petit Bourg, France
- UMR AGAP Institut, University of Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, France
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Kaul T, Thangaraj A, Jain R, Bharti J, Kaul R, Verma R, Sony SK, Abdel Motelb KF, Yadav P, Agrawal PK. CRISPR/Cas9-mediated homology donor repair base editing system to confer herbicide resistance in maize (Zea mays L.). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108374. [PMID: 38310724 DOI: 10.1016/j.plaphy.2024.108374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 12/20/2023] [Accepted: 01/12/2024] [Indexed: 02/06/2024]
Abstract
Weed infestation is a significant concern to crop yield loss, globally. The potent broad-spectrum glyphosate (N-phosphomethyl-glycine) has a widely utilized herbicide, acting on the shikimic acid pathway within chloroplast by inhibiting 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). This crucial enzyme plays a vital role in aromatic amino acid synthesis. Repurposing of CRISPR/Cas9-mediated gene-editing was the inflection point for generating novel crop germplasm with diverse genetic variations in essential agronomic traits, achieved through the introduction of nucleotide substitutions at target sites within the native genes, and subsequent induction of indels through error-prone non-homologous end-joining DNA repair mechanisms. Here, we describe the development of efficient herbicide-resistant maize lines by using CRISPR/Cas9 mediated site-specific native ZmEPSPS gene fragment replacement via knock-out of conserved region followed by knock-in of desired homologous donor repair (HDR-GATIPS-mZmEPSPS) with triple amino acid substitution. The novel triple substitution conferred high herbicide tolerance in edited maize plants. Transgene-free progeny harbouring the triple amino acid substitutions revealed agronomic performances similar to that of wild-type plants, suggesting that the GATIPS-mZmEPSPS allele substitutions are crucial for developing elite maize varieties with significantly enhanced glyphosate resistance. Furthermore, the aromatic amino acid contents in edited maize lines were significantly higher than in wild-type plants. The present study describing the introduction of site-specific CRISPR/Cas9- GATIPS mutations in the ZmEPSPS gene via genome editing has immense potential for higher tolerance to glyphosate with no yield penalty in maize.
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Affiliation(s)
- Tanushri Kaul
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India.
| | - Arulprakash Thangaraj
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Rashmi Jain
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Jyotsna Bharti
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Rashmi Kaul
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Rachana Verma
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Sonia Khan Sony
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Khaled Fathy Abdel Motelb
- Nutritional Improvement of Crops Group, Plant Molecular Biology Division, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, 110067, India
| | - Pranjal Yadav
- Indian Council of Agricultural Research- Indian Institute of Maize Research, Pusa Campus, New Delhi, 110012, India
| | - Pawan Kumar Agrawal
- Indian Council of Agricultural Research, New Delhi, 110012, India; ICAR-National Institute of Biotic Stress Management, Raipur, 493225, Chhattisgarh, India
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Divya K, Thangaraj M, Krishna Radhika N. CRISPR/Cas9: an advanced platform for root and tuber crops improvement. Front Genome Ed 2024; 5:1242510. [PMID: 38312197 PMCID: PMC10836405 DOI: 10.3389/fgeed.2023.1242510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 12/26/2023] [Indexed: 02/06/2024] Open
Abstract
Root and tuber crops (RTCs), which include cassava, potato, sweet potato, and yams, principally function as staple crops for a considerable fraction of the world population, in addition to their diverse applications in nutrition, industry, and bioenergy sectors. Even then, RTCs are an underutilized group considering their potential as industrial raw material. Complexities in conventional RTC improvement programs curb the extensive exploitation of the potentials of this group of crop species for food, energy production, value addition, and sustainable development. Now, with the advent of whole-genome sequencing, sufficient sequence data are available for cassava, sweet potato, and potato. These genomic resources provide enormous scope for the improvement of tuber crops, to make them better suited for agronomic and industrial applications. There has been remarkable progress in RTC improvement through the deployment of new strategies like gene editing over the last decade. This review brings out the major areas where CRISPR/Cas technology has improved tuber crops. Strategies for genetic transformation of RTCs with CRISPR/Cas9 constructs and regeneration of edited lines and the bottlenecks encountered in their establishment are also discussed. Certain attributes of tuber crops requiring focus in future research along with putative editing targets are also indicated. Altogether, this review provides a comprehensive account of developments achieved, future lines of research, bottlenecks, and major experimental concerns regarding the establishment of CRISPR/Cas9-based gene editing in RTCs.
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Affiliation(s)
- K Divya
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
| | | | - N Krishna Radhika
- ICAR-Central Tuber Crops Research Institute, Thiruvananthapuram, India
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Automatic identification and annotation of MYB gene family members in plants. BMC Genomics 2022; 23:220. [PMID: 35305581 PMCID: PMC8933966 DOI: 10.1186/s12864-022-08452-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 03/07/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND MYBs are among the largest transcription factor families in plants. Consequently, members of this family are involved in a plethora of processes including development and specialized metabolism. The MYB families of many plant species were investigated in the last two decades since the first investigation looked at Arabidopsis thaliana. This body of knowledge and characterized sequences provide the basis for the identification, classification, and functional annotation of candidate sequences in new genome and transcriptome assemblies. RESULTS A pipeline for the automatic identification and functional annotation of MYBs in a given sequence data set was implemented in Python. MYB candidates are identified, screened for the presence of a MYB domain and other motifs, and finally placed in a phylogenetic context with well characterized sequences. In addition to technical benchmarking based on existing annotation, the transcriptome assembly of Croton tiglium and the annotated genome sequence of Castanea crenata were screened for MYBs. Results of both analyses are presented in this study to illustrate the potential of this application. The analysis of one species takes only a few minutes depending on the number of predicted sequences and the size of the MYB gene family. This pipeline, the required bait sequences, and reference sequences for a classification are freely available on github: https://github.com/bpucker/MYB_annotator . CONCLUSIONS This automatic annotation of the MYB gene family in novel assemblies makes genome-wide investigations consistent and paves the way for comparative studies in the future. Candidate genes for in-depth analyses are presented based on their orthology to previously characterized sequences which allows the functional annotation of the newly identified MYBs with high confidence. The identification of orthologs can also be harnessed to detect duplication and deletion events.
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Syombua ED, Tripathi JN, Obiero GO, Nguu EK, Yang B, Wang K, Tripathi L. Potential applications of the CRISPR/Cas technology for genetic improvement of yam (
Dioscorea
spp.). Food Energy Secur 2021. [DOI: 10.1002/fes3.330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Easter D. Syombua
- International Institute of Tropical Agriculture (IITA) Nairobi Kenya
- Centre for Biotechnology and Bioinformatics (CEBIB) University of Nairobi Nairobi Kenya
| | | | - George O. Obiero
- Centre for Biotechnology and Bioinformatics (CEBIB) University of Nairobi Nairobi Kenya
| | - Edward K. Nguu
- Department of Biochemistry University of Nairobi Nairobi Kenya
| | - Bing Yang
- Division of Plant Sciences Bond Life Sciences Center University of Missouri Columbia MO USA
- Donald Danforth Plant Science Center St. Louis MO USA
| | - Kan Wang
- Department of Agronomy Iowa State University Ames IA USA
| | - Leena Tripathi
- International Institute of Tropical Agriculture (IITA) Nairobi Kenya
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