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Sharma V, Gangurde SS, Nayak SN, Gowda AS, Sukanth B, Mahadevaiah SS, Manohar SS, Choudhary RS, Anitha T, Malavalli SS, Srikanth S, Bajaj P, Sharma S, Varshney RK, Latha P, Janila P, Bhat RS, Pandey MK. Genetic mapping identified three hotspot genomic regions and candidate genes controlling heat tolerance-related traits in groundnut. FRONTIERS IN PLANT SCIENCE 2023; 14:1182867. [PMID: 37287715 PMCID: PMC10243373 DOI: 10.3389/fpls.2023.1182867] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/12/2023] [Indexed: 06/09/2023]
Abstract
Groundnut productivity and quality have been impeded by rising temperatures in semi-arid environments. Hence, understanding the effects and molecular mechanisms of heat stress tolerance will aid in tackling yield losses. In this context, a recombinant inbred line (RIL) population was developed and phenotyped for eight seasons at three locations for agronomic, phenological, and physiological traits under heat stress. A genetic map was constructed using genotyping-by-sequencing with 478 single-nucleotide polymorphism (SNP) loci spanning a map distance of 1,961.39 cM. Quantitative trait locus (QTL) analysis using phenotypic and genotypic data identified 45 major main-effect QTLs for 21 traits. Intriguingly, three QTL clusters (Cluster-1-Ah03, Cluster-2-Ah12, and Cluster-3-Ah20) harbor more than half of the major QTLs (30/45, 66.6%) for various heat tolerant traits, explaining 10.4%-38.6%, 10.6%-44.6%, and 10.1%-49.5% of phenotypic variance, respectively. Furthermore, important candidate genes encoding DHHC-type zinc finger family protein (arahy.J0Y6Y5), peptide transporter 1 (arahy.8ZMT0C), pentatricopeptide repeat-containing protein (arahy.4A4JE9), Ulp1 protease family (arahy.X568GS), Kelch repeat F-box protein (arahy.I7X4PC), FRIGIDA-like protein (arahy.0C3V8Z), and post-illumination chlorophyll fluorescence increase (arahy.92ZGJC) were the underlying three QTL clusters. The putative functions of these genes suggested their involvement in seed development, regulating plant architecture, yield, genesis and growth of plants, flowering time regulation, and photosynthesis. Our results could provide a platform for further fine mapping, gene discovery, and developing markers for genomics-assisted breeding to develop heat-tolerant groundnut varieties.
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Affiliation(s)
- Vinay Sharma
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, India
| | - Sunil S. Gangurde
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Spurthi N. Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Anjan S. Gowda
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B.S. Sukanth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | | | - Surendra S. Manohar
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | | | - T. Anitha
- Regional Agricultural Research Station, Acharya N G Ranga Agricultural University (ANGRAU), Tirupati, India
| | - Sachin S. Malavalli
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - S.N. Srikanth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Putta Latha
- Regional Agricultural Research Station, Acharya N G Ranga Agricultural University (ANGRAU), Tirupati, India
| | - Pasupuleti Janila
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Ramesh S. Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
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Desmae H, Janila P, Okori P, Pandey MK, Motagi BN, Monyo E, Mponda O, Okello D, Sako D, Echeckwu C, Oteng‐Frimpong R, Miningou A, Ojiewo C, Varshney RK. Genetics, genomics and breeding of groundnut ( Arachis hypogaea L.). PLANT BREEDING = ZEITSCHRIFT FUR PFLANZENZUCHTUNG 2019; 138:425-444. [PMID: 31598026 PMCID: PMC6774334 DOI: 10.1111/pbr.12645] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 04/10/2018] [Accepted: 07/13/2018] [Indexed: 05/04/2023]
Abstract
Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker-assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.
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Affiliation(s)
- Haile Desmae
- International Crop Research Institute for the Semi‐Arid Tropics (ICRISAT)BamakoMali
| | | | | | | | | | | | - Omari Mponda
- Division of Research and Development (DRD)Tanzania Agricultural Research Institute (TARI) ‐ NaliendeleMtwaraTanzania
| | - David Okello
- National Agricultural Research Organization (NARO)EntebbeUganda
| | | | | | | | - Amos Miningou
- Institut National d'Environnement et de Recherches Agricoles (INERA)OuagadougouBurkina Faso
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Jeyaramraja P, Meenakshi SN, Woldesenbet F. Relationship between drought and preharvest aflatoxin contamination in groundnut (Arachis hypogaea L.). WORLD MYCOTOXIN J 2018. [DOI: 10.3920/wmj2017.2248] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Groundnut is a commercial oilseed crop that is prone to infection by Aspergillus flavus or Aspergillus parasiticus. Drought impairs the defence mechanism of the plant and favours the production of aflatoxin by the fungus. Aflatoxin is a carcinogen and its presence in food and feed causes significant economic loss. The answer to the question, ‘how drought tolerance and aflatoxin resistance are related?’ is not clear. In this review paper, the relationship of drought and preharvest aflatoxin contamination (AC), the relationship of drought tolerance traits and AC, and the approaches to enhance resistance to AC are discussed using up-to-date literature. Factors leading to AC are drought, high geocarposphere temperature, kernel/pod damage, and reduced phytoalexin synthesis by the plant. If the fungus colonises a kernel with reduced water activity, the plant cannot synthesise phytoalexin and then, the fungus synthesises aflatoxin. Breeding for resistance to AC is complicated because aflatoxin concentration is costly to measure, highly variable, and influenced by the environment. Since drought tolerant cultivars have resistance to AC, traits of drought tolerance have been used as indirect selection tools for reduced AC. The genetics of aflatoxin resistance mechanisms have not been made clear as the environment influences the host-pathogen relationship. Host-pathogen interactions under the influence of environment should be studied at molecular level to identify plant resistant factors using the tools of genomics, proteomics, and metabolomics in order to develop cultivars with durable resistance. Many candidate genes involved in host-pathogen interactions have been identified due to improvements in fungal expressed sequence tags, microarrays, and genome sequencing techniques. Moreover, research projects are underway on identifying genes coding for antifungal compounds, resistance associated proteins and quantitative trait loci associated with aflatoxin resistance. This review is expected to help those who wish to work on reducing AC in groundnuts.
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Affiliation(s)
- P.R. Jeyaramraja
- Department of Biology, College of Natural Sciences, Arba Minch University, P.O. Box 21, Arba Minch, Gamo Gofa Zone, Ethiopia
| | - S. Nithya Meenakshi
- Department of Botany, PSGR Krishnammal College for Women, Peelamedu, Coimbatore 641 004, Tamilnadu, India
| | - F. Woldesenbet
- Department of Biology, College of Natural Sciences, Arba Minch University, P.O. Box 21, Arba Minch, Gamo Gofa Zone, Ethiopia
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Zongo A, Khera P, Sawadogo M, Shasidhar Y, Sriswathi M, Vishwakarma MK, Sankara P, Ntare BR, Varshney RK, Pandey MK, Desmae H. SSR markers associated to early leaf spot disease resistance through selective genotyping and single marker analysis in groundnut ( Arachis hypogaea L.). BIOTECHNOLOGY REPORTS (AMSTERDAM, NETHERLANDS) 2017; 15:132-137. [PMID: 28856109 PMCID: PMC5565779 DOI: 10.1016/j.btre.2017.07.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 07/27/2017] [Accepted: 07/28/2017] [Indexed: 11/28/2022]
Abstract
Groundnut (Arachis hypogaea L.) is an important oilseed and food crop of the world. Breeding for disease resistance is one of major objectives in groundnut breeding. Early leaf spot (ELS) is one of the major destructive diseases worldwide and in West Africa, particularly in Burkina Faso causing significant yield losses. Conventional breeding approaches have been employed to develop improved varieties resistant to ELS. Molecular dissection of resistance traits using QTL analysis can improve the efficiency of resistance breeding. In the present study, an ELS susceptible genotype QH243C and an ELS resistant genotype NAMA were crossed and the F2 population genotypic and F3 progenies phenotypic data were used for marker-trait association analysis. Parents were surveyed with 179 simple sequence repeat (SSR) markers out of which 103 SSR markers were found to be polymorphic between the parents. These polymorphic markers were utilized to genotype the F2 population followed by marker-trait analysis through single marker analysis (SMA) and selective genotyping of the population using 23 resistant and 23 susceptible genotypes. The SMA revealed 13 markers while the selective genotyping method identified 8 markers associated with ELS resistance. Four markers (GM1911, GM1883, GM1000 and Seq13E09) were found common between the two trait mapping methods. These four markers could be employed in genomics-assisted breeding for selection of ELS resistant genotypes in groundnut breeding.
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Affiliation(s)
- Adama Zongo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), BP 320 Bamako, Mali
- University Ouaga 1Joseph Ki Zerbo, BP 7021 Ouagadougou, Burkina Faso
| | - Pawan Khera
- International Crops Research Institute for the Semi-AridTropics (ICRISAT), Hyderabad 502 324, India
| | | | - Yaduru Shasidhar
- International Crops Research Institute for the Semi-AridTropics (ICRISAT), Hyderabad 502 324, India
| | - Manda Sriswathi
- International Crops Research Institute for the Semi-AridTropics (ICRISAT), Hyderabad 502 324, India
| | - Manish K. Vishwakarma
- International Crops Research Institute for the Semi-AridTropics (ICRISAT), Hyderabad 502 324, India
| | - Philippe Sankara
- University Ouaga 1Joseph Ki Zerbo, BP 7021 Ouagadougou, Burkina Faso
| | - Bonny R. Ntare
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), BP 320 Bamako, Mali
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-AridTropics (ICRISAT), Hyderabad 502 324, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-AridTropics (ICRISAT), Hyderabad 502 324, India
| | - Haile Desmae
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), BP 320 Bamako, Mali
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