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Ruperao P, Bajaj P, Yadav R, Angamuthu M, Subramani R, Rai V, Tiwari K, Rathore A, Singh K, Singh GP, Angadi UB, Mayes S, Rangan P. Double-digest restriction-associated DNA sequencing-based genotyping and its applications in sesame germplasm management. THE PLANT GENOME 2024; 17:e20447. [PMID: 38628142 DOI: 10.1002/tpg2.20447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 02/29/2024] [Accepted: 03/03/2024] [Indexed: 07/02/2024]
Abstract
Sesame (Sesamum indicum L.) is an ancient oilseed crop belonging to the family Pedaliaceae and a globally cultivated crop for its use as oil and food. In this study, 2496 sesame accessions, being conserved at the National Genebank of ICAR-National Bureau of Plant Genetic Resources (NBPGR), were genotyped using genomics-assisted double-digest restriction-associated DNA sequencing (ddRAD-seq) approach. A total of 64,910 filtered single-nucleotide polymorphisms (SNPs) were utilized to assess the genome-scale diversity. Applications of this genome-scale information (reduced representation using restriction enzymes) are demonstrated through the development of a molecular core collection (CC) representing maximal SNP diversity. This information is also applied in developing a mid-density panel (MDP) comprising 2515 hyper-variable SNPs, representing almost equally the genic and non-genic regions. The sesame CC comprising 384 accessions, a representative set of accessions with maximal diversity, was identified using multiple criteria such as k-mer (subsequence of length "k" in a sequence read) diversity, observed heterozygosity, CoreHunter3, GenoCore, and genetic differentiation. The coreset constituted around 15% of the total accessions studied, and this small subset had captured >60% SNP diversity of the entire population. In the coreset, the admixture analysis shows reduced genetic complexity, increased nucleotide diversity (π), and is geographically distributed without any repetitiveness in the CC germplasm. Within the CC, India-originated accessions exhibit higher diversity (as expected based on the center of diversity concept), than those accessions that were procured from various other countries. The identified CC set and the MDP will be a valuable resource for genomics-assisted accelerated sesame improvement program.
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Affiliation(s)
- Pradeep Ruperao
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rashmi Yadav
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, India
| | | | - Rajkumar Subramani
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, India
| | - Vandana Rai
- ICAR-National Institute of Plant Biotechnology, PUSA Campus, New Delhi, India
| | - Kapil Tiwari
- Sardarkrushinagar Dantiwada Agricultural University, Sardarkrushinagar, India
| | | | - Kuldeep Singh
- Genebank, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Ulavappa B Angadi
- ICAR-Indian Agricultural Statistical Research Institute, New Delhi, India
| | - Sean Mayes
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Parimalan Rangan
- ICAR-National Bureau of Plant Genetic Resources, PUSA Campus, New Delhi, India
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, Queensland, Australia
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Fofana B, Soto-Cerda B, Zaidi M, Main D, Fillmore S. Genome-wide genetic architecture for plant maturity and drought tolerance in diploid potatoes. Front Genet 2024; 14:1306519. [PMID: 38357658 PMCID: PMC10864671 DOI: 10.3389/fgene.2023.1306519] [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: 10/03/2023] [Accepted: 12/18/2023] [Indexed: 02/16/2024] Open
Abstract
Cultivated potato (Solanum tuberosum) is known to be highly susceptible to drought. With climate change and its frequent episodes of drought, potato growers will face increased challenges to achieving their yield goals. Currently, a high proportion of untapped potato germplasm remains within the diploid potato relatives, and the genetic architecture of the drought tolerance and maturity traits of diploid potatoes is still unknown. As such, a panel of 384 ethyl methanesulfonate-mutagenized diploid potato clones were evaluated for drought tolerance and plant maturity under field conditions. Genome-wide association studies (GWAS) were conducted to dissect the genetic architecture of the traits. The results obtained from the genetic structure analysis of the panel showed five main groups and seven subgroups. Using the Genome Association and Prediction Integrated Tool-mixed linear model GWAS statistical model, 34 and 17 significant quantitative trait nucleotides (QTNs) were found associated with maturity and drought traits, respectively. Chromosome 5 carried most of the QTNs, some of which were also detected by using the restricted two-stage multi-locus multi-allele-GWAS haploblock-based model, and two QTNs were found to be pleiotropic for both maturity and drought traits. Using the non-parametric U-test, one and three QTNs, with 5.13%-7.4% phenotypic variations explained, showed favorable allelic effects that increase the maturity and drought trait values. The quantitaive trait loci (QTLs)/QTNs associated with maturity and drought trait were found co-located in narrow (0.5-1 kb) genomic regions with 56 candidate genes playing roles in plant development and senescence and in abiotic stress responses. A total of 127 potato clones were found to be late maturing and tolerant to drought, while nine were early to moderate-late maturing and tolerant to drought. Taken together, the data show that the studied germplasm panel and the identified candidate genes are prime genetic resources for breeders and biologists in conventional breeding and targeted gene editing as climate adaptation tools.
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Affiliation(s)
- Bourlaye Fofana
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - Braulio Soto-Cerda
- Departamento de Ciencias Agropecuarias y Acuícolas, Universidad Católica de Temuco, Temuco, Chile
- Núcleo de Investigación en Producción Alimentaria, Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
| | - Moshin Zaidi
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - David Main
- Charlottetown Research and Development Centre, Agriculture and Agri-Food Canada, Charlottetown, PE, Canada
| | - Sherry Fillmore
- Kentville Research and Development Centre, Agriculture and Agri-Food Canada, Kentville, NS, Canada
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