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Pandey MK, Gangurde SS, Shasidhar Y, Sharma V, Kale SM, Khan AW, Shah P, Joshi P, Bhat RS, Janila P, Bera SK, Varshney RK. Correction: High-throughput diagnostic markers for foliar fungal disease resistance and high oleic acid content in groundnut. BMC Plant Biol 2024; 24:336. [PMID: 38664611 PMCID: PMC11044379 DOI: 10.1186/s12870-024-05039-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/29/2024]
Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Priya Shah
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pushpesh Joshi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip K Bera
- ICAR-Directorate of Groundnut Research, Junagadh, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Australia.
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Pandey MK, Gangurde SS, Shasidhar Y, Sharma V, Kale SM, Khan AW, Shah P, Joshi P, Bhat RS, Janila P, Bera SK, Varshney RK. High-throughput diagnostic markers for foliar fungal disease resistance and high oleic acid content in groundnut. BMC Plant Biol 2024; 24:262. [PMID: 38594614 PMCID: PMC11005153 DOI: 10.1186/s12870-024-04987-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Accepted: 04/03/2024] [Indexed: 04/11/2024]
Abstract
BACKGROUND Foliar diseases namely late leaf spot (LLS) and leaf rust (LR) reduce yield and deteriorate fodder quality in groundnut. Also the high oleic acid content has emerged as one of the most important traits for industries and consumers due to its increased shelf life and health benefits. RESULTS Genetic mapping combined with pooled sequencing approaches identified candidate resistance genes (LLSR1 and LLSR2 for LLS and LR1 for LR) for both foliar fungal diseases. The LLS-A02 locus housed LLSR1 gene for LLS resistance, while, LLS-A03 housed LLSR2 and LR1 genes for LLS and LR resistance, respectively. A total of 49 KASPs markers were developed from the genomic regions of important disease resistance genes, such as NBS-LRR, purple acid phosphatase, pentatricopeptide repeat-containing protein, and serine/threonine-protein phosphatase. Among the 49 KASP markers, 41 KASPs were validated successfully on a validation panel of contrasting germplasm and breeding lines. Of the 41 validated KASPs, 39 KASPs were designed for rust and LLS resistance, while two KASPs were developed using fatty acid desaturase (FAD) genes to control high oleic acid levels. These validated KASP markers have been extensively used by various groundnut breeding programs across the world which led to development of thousands of advanced breeding lines and few of them also released for commercial cultivation. CONCLUSION In this study, high-throughput and cost-effective KASP assays were developed, validated and successfully deployed to improve the resistance against foliar fungal diseases and oleic acid in groundnut. So far deployment of allele-specific and KASP diagnostic markers facilitated development and release of two rust- and LLS-resistant varieties and five high-oleic acid groundnut varieties in India. These validated markers provide opportunities for routine deployment in groundnut breeding programs.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | - Sunil S Gangurde
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinay Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip M Kale
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Aamir W Khan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Priya Shah
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pushpesh Joshi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sandip K Bera
- ICAR-Directorate of Groundnut Research, Junagadh, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- Centre for Crop and Food Innovation, WA State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Australia.
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Parmar S, Janila P, Gangurde SS, Variath MT, Sharma V, Bomireddy D, Manohar SS, Varshney RK, Singam P, Pandey MK. Genetic mapping identified major main-effect and three co-localized quantitative trait loci controlling high iron and zinc content in groundnut. Plant Genome 2023; 16:e20361. [PMID: 37408143 DOI: 10.1002/tpg2.20361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 07/07/2023]
Abstract
Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine deployment of genomic-assisted breeding. This study aimed to identify genomic regions and candidate genes for high iron (Fe) and zinc (Zn) content, utilizing a biparental mapping population (ICGV 00440 × ICGV 06040;). Genetic mapping and quantitative trait locus (QTL) analysis (474 mapped single-nucleotide polymorphism loci; 1536.33 cM) using 2 seasons of phenotypic data together with genotypic data identified 5 major main-effect QTLs for Fe content. These QTLs exhibited log-of-odds (LOD) scores ranging from 6.5 to 7.4, explaining phenotypic variation (PVE) ranging from 22% (qFe-Ah01) to 30.0% (qFe-Ah14). Likewise, four major main effect QTLs were identified for Zn content, with LOD score ranging from 4.4 to 6.8 and PVE ranging from 21.8% (qZn-Ah01) to 32.8% (qZn-Ah08). Interestingly, three co-localized major and main effect QTLs (qFe-Ah01, qZn-Ah03, and qFe-Ah11) were identified for both Fe and Zn contents. These genomic regions harbored key candidate genes, including zinc/iron permease transporter, bZIP transcription factor, and vacuolar iron transporter which likely play pivotal roles in the accumulation of Fe and Zn contents in seeds. The findings of this study hold potential for fine mapping and diagnostic marker development for high Fe and Zn contents in groundnut.
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Affiliation(s)
- Sejal Parmar
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Pasupuleti Janila
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sunil S Gangurde
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Murali T Variath
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinay Sharma
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Deekshitha Bomireddy
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Surendra S Manohar
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad, India
| | - Manish K Pandey
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Gangurde SS, Khan AW, Janila P, Variath MT, Manohar SS, Singam P, Chitikineni A, Varshney RK, Pandey MK. Whole-genome sequencing based discovery of candidate genes and diagnostic markers for seed weight in groundnut. Plant Genome 2023; 16:e20265. [PMID: 36478184 DOI: 10.1002/tpg2.20265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 08/16/2022] [Indexed: 06/17/2023]
Abstract
Seed weight in groundnut (Arachis hypogaea L.) has direct impact on yield as well as market price because of preference for bold seeds by consumers and industry, thereby making seed-size improvement as one of the most important objectives of groundnut breeding programs globally. Marker-based early generation selection can accelerate the process of breeding for developing large-seeded varieties. In this context, we deployed the quantitative trait locus-sequencing (QTL-seq) approach on a biparental mapping population (Chico × ICGV 02251) to identify candidate genes and develop markers for seed weight in groundnut. A total of 289.4-389.4 million reads sequencing data were generated from three libraries (ICGV 02251 and two extreme bulks) achieving 93.9-95.1% genome coverage and 8.34-9.29× average read depth. The analysis of sequencing data using QTL-seq pipeline identified five genomic regions (three on chromosome B06 and one each on chromosomes B08 and B09) for seed weight. Detailed analysis of above associated genomic regions detected 182 single-nucleotide polymorphisms (SNPs) in genic and intergenic regions, and 11 of these SNPs were nonsynonymous in the genomic regions of 10 candidate genes including Ulp proteases and BIG SEED locus genes. Kompetitive allele specific polymerase chain reaction (KASP) markers for 14 SNPs were developed, and four of these markers (snpAH0031, snpAH0033, snpAH0037, and snpAH0038) were successfully validated for deployment in breeding for large-seeded groundnut varieties.
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Affiliation(s)
- Sunil S Gangurde
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
- Dep. of Genetics, Osmania Univ., Hyderabad, 500007, India
| | - Aamir W Khan
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Pasupuleti Janila
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Murali T Variath
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Surendra S Manohar
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | | | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Rajeev K Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
- State Agricultural Biotechnology Centre, Crop Research Innovation Centre, Food Futures Institute, Murdoch Univ., Murdoch, Western Australia, 6150, Australia
| | - Manish K Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
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Yu B, Liu N, Huang L, Luo H, Zhou X, Lei Y, Yan L, Wang X, Chen W, Kang Y, Ding Y, Jin G, Pandey MK, Janila P, Kishan Sudini H, Varshney RK, Jiang H, Liu S, Liao B. Identification and application of a candidate gene AhAftr1 for aflatoxin production resistance in peanut seed (Arachis hypogaea L.). J Adv Res 2023:S2090-1232(23)00263-1. [PMID: 37739123 DOI: 10.1016/j.jare.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Revised: 09/15/2023] [Accepted: 09/17/2023] [Indexed: 09/24/2023] Open
Abstract
INTRODUCTION Peanut is susceptible to infection of Aspergillus fungi and conducive to aflatoxin contamination, hence developing aflatoxin-resistant variety is highly meaningful. Identifying functional genes or loci conferring aflatoxin resistance and molecular diagnostic marker are crucial for peanut breeding. OBJECTIVES This work aims to (1) identify candidate gene for aflatoxin production resistance, (2) reveal the related resistance mechanism, and (3) develop diagnostic marker for resistance breeding program. METHODS Resistance to aflatoxin production in a recombined inbred line (RIL) population derived from a high-yielding variety Xuhua13 crossed with an aflatoxin-resistant genotype Zhonghua 6 was evaluated under artificial inoculation for three consecutive years. Both genetic linkage analysis and QTL-seq were conducted for QTL mapping. The candidate gene was further fine-mapped using a secondary segregation mapping population and validated by transgenic experiments. RNA-Seq analysis among resistant and susceptible RILs was used to reveal the resistance pathway for the candidate genes. RESULTS The major effect QTL qAFTRA07.1 for aflatoxin production resistance was mapped to a 1.98 Mbp interval. A gene, AhAftr1 (Arachis hypogaea Aflatoxin resistance 1), was detected structure variation (SV) in leucine rich repeat (LRR) domain of its production, and involved in disease resistance response through the effector-triggered immunity (ETI) pathway. Transgenic plants with overexpression of AhAftr1(ZH6) exhibited 57.3% aflatoxin reduction compared to that of AhAftr1(XH13). A molecular diagnostic marker AFTR.Del.A07 was developed based on the SV. Thirty-six lines, with aflatoxin content decrease by over 77.67% compared to the susceptible control Zhonghua12 (ZH12), were identified from a panel of peanut germplasm accessions and breeding lines through using AFTR.Del.A07. CONCLUSION Our findings would provide insights of aflatoxin production resistance mechanisms and laid meaningful foundation for further breeding programs.
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Affiliation(s)
- Bolun Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Nian Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Li Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Huaiyong Luo
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xiaojing Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yong Lei
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Liying Yan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Xin Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Weigang Chen
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yanping Kang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Yingbin Ding
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Gaorui Jin
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Aird Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Aird Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Hari Kishan Sudini
- International Crops Research Institute for the Semi-Aird Tropics (ICRISAT), Hyderabad, Telangana, India
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Food Futures Institute, Murdoch University, Murdoch, Australia
| | - Huifang Jiang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | - Boshou Liao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture Oil Crops Research Institute (OCRI), Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China.
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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. Front Plant Sci 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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abady S, Shimelis H, Janila P, Yaduru S, Shayanowako AIT, Deshmukh D, Chaudhari S, Manohar SS. Assessment of the genetic diversity and population structure of groundnut germplasm collections using phenotypic traits and SNP markers: Implications for drought tolerance breeding. PLoS One 2021; 16:e0259883. [PMID: 34788339 PMCID: PMC8598071 DOI: 10.1371/journal.pone.0259883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Accepted: 10/28/2021] [Indexed: 01/15/2023] Open
Abstract
Profiling the genetic composition and relationships among groundnut germplasm collections is essential for the breeding of new cultivars. The objectives of this study were to assess the genetic diversity and population structure among 100 improved groundnut genotypes using agronomic traits and high-density single nucleotide polymorphism (SNP) markers. The genotypes were evaluated for agronomic traits and drought tolerance at the International Crop Research Institute for the Semi-Arid Tropics (ICRISAT)/India across two seasons. Ninety-nine of the test genotypes were profiled with 16363 SNP markers. Pod yield per plant (PY), seed yield per plant (SY), and harvest index (HI) were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes ICGV 07222, ICGV 06040, ICGV 01260, ICGV 15083, ICGV 10143, ICGV 03042, ICGV 06039, ICGV 14001, ICGV 11380, and ICGV 13200 ranked top in terms of pod yield under both drought-stressed and optimum conditions. PY exhibited a significant (p ≤ 0.05) correlation with SY, HI, and total biomass (TBM) under both test conditions. Based on the principal component (PC) analysis, PY, SY, HSW, shelling percentage (SHP), and HI were allocated in PC 1 and contributed to the maximum variability for yield under the two water regimes. Hence, selecting these traits could be successful for screening groundnut genotypes under drought-stressed and optimum conditions. The model-based population structure analysis grouped the studied genotypes into three sub-populations. Dendrogram for phenotypic and genotypic also grouped the studied 99 genotypes into three heterogeneous clusters. Analysis of molecular variance revealed that 98% of the total genetic variation was attributed to individuals, while only 2% of the total variance was due to variation among the subspecies. The genetic distance between the Spanish bunch and Virginia bunch types ranged from 0.11 to 0.52. The genotypes ICGV 13189, ICGV 95111, ICGV 14421, and ICGV 171007 were selected for further breeding based on their wide genetic divergence. Data presented in this study will guide groundnut cultivar development emphasizing economic traits and adaptation to water-limited agro-ecologies, including in Ethiopia.
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Affiliation(s)
- Seltene Abady
- African Centre for Crop Improvement (ACCI), School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, South Africa
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
- * E-mail:
| | - Hussein Shimelis
- African Centre for Crop Improvement (ACCI), School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, South Africa
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Telangana, India
| | - Shasidhar Yaduru
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Telangana, India
| | - Admire I. T. Shayanowako
- African Centre for Crop Improvement (ACCI), School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, South Africa
| | - Dnyaneshwar Deshmukh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Telangana, India
| | - Sunil Chaudhari
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Telangana, India
| | - Surendra S. Manohar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Telangana, India
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Pandey MK, Chaudhari S, Jarquin D, Janila P, Crossa J, Patil SC, Sundravadana S, Khare D, Bhat RS, Radhakrishnan T, Hickey JM, Varshney RK. Genome-based trait prediction in multi- environment breeding trials in groundnut. Theor Appl Genet 2020; 133:3101-3117. [PMID: 32809035 PMCID: PMC7547976 DOI: 10.1007/s00122-020-03658-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/03/2020] [Indexed: 05/13/2023]
Abstract
KEY MESSAGE Comparative assessment identified naïve interaction model, and naïve and informed interaction GS models suitable for achieving higher prediction accuracy in groundnut keeping in mind the high genotype × environment interaction for complex traits. Genomic selection (GS) can be an efficient and cost-effective breeding approach which captures both small- and large-effect genetic factors and therefore promises to achieve higher genetic gains for complex traits such as yield and oil content in groundnut. A training population was constituted with 340 elite lines followed by genotyping with 58 K 'Axiom_Arachis' SNP array and phenotyping for key agronomic traits at three locations in India. Four GS models were tested using three different random cross-validation schemes (CV0, CV1 and CV2). These models are: (1) model 1 (M1 = E + L) which includes the main effects of environment (E) and line (L); (2) model 2 (M2 = E + L + G) which includes the main effects of markers (G) in addition to E and L; (3) model 3 (M3 = E + L + G + GE), a naïve interaction model; and (4) model 4 (E + L + G + LE + GE), a naïve and informed interaction model. Prediction accuracy estimated for four models indicated clear advantage of the inclusion of marker information which was reflected in better prediction accuracy achieved with models M2, M3 and M4 as compared to M1 model. High prediction accuracies (> 0.600) were observed for days to 50% flowering, days to maturity, hundred seed weight, oleic acid, rust@90 days, rust@105 days and late leaf spot@90 days, while medium prediction accuracies (0.400-0.600) were obtained for pods/plant, shelling %, and total yield/plant. Assessment of comparative prediction accuracy for different GS models to perform selection for untested genotypes, and unobserved and unevaluated environments provided greater insights on potential application of GS breeding in groundnut.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
| | - Sunil Chaudhari
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Diego Jarquin
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Jose Crossa
- International Maize and Wheat Improvement Center (CIMMYT), Mexico City, Mexico
| | - Sudam C Patil
- Mahatma Phule Krishi Vidyapeeth (MPKV), Jalgaon, India
| | | | - Dhirendra Khare
- Jawaharlal Nehru Krishi Vishwa Vidyalaya (JNKVV), Jabalpur, India
| | - Ramesh S Bhat
- University of Agricultural Sciences (UAS)-Dharwad, Dharwad, India
| | | | - John M Hickey
- The Roslin Institute, The University of Edinburgh, Edinburgh, Scotland, UK
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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Kumar R, Janila P, Vishwakarma MK, Khan AW, Manohar SS, Gangurde SS, Variath MT, Shasidhar Y, Pandey MK, Varshney RK. Whole-genome resequencing-based QTL-seq identified candidate genes and molecular markers for fresh seed dormancy in groundnut. Plant Biotechnol J 2020; 18:992-1003. [PMID: 31553830 PMCID: PMC7061874 DOI: 10.1111/pbi.13266] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 07/28/2019] [Accepted: 09/22/2019] [Indexed: 05/11/2023]
Abstract
The subspecies fastigiata of cultivated groundnut lost fresh seed dormancy (FSD) during domestication and human-made selection. Groundnut varieties lacking FSD experience precocious seed germination during harvest imposing severe losses. Development of easy-to-use genetic markers enables early-generation selection in different molecular breeding approaches. In this context, one recombinant inbred lines (RIL) population (ICGV 00350 × ICGV 97045) segregating for FSD was used for deploying QTL-seq approach for identification of key genomic regions and candidate genes. Whole-genome sequencing (WGS) data (87.93 Gbp) were generated and analysed for the dormant parent (ICGV 97045) and two DNA pools (dormant and nondormant). After analysis of resequenced data from the pooled samples with dormant parent (reference genome), we calculated delta-SNP index and identified a total of 10,759 genomewide high-confidence SNPs. Two candidate genomic regions spanning 2.4 Mb and 0.74 Mb on the B05 and A09 pseudomolecules, respectively, were identified controlling FSD. Two candidate genes-RING-H2 finger protein and zeaxanthin epoxidase-were identified in these two regions, which significantly express during seed development and control abscisic acid (ABA) accumulation. QTL-seq study presented here laid out development of a marker, GMFSD1, which was validated on a diverse panel and could be used in molecular breeding to improve dormancy in groundnut.
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Affiliation(s)
- Rakesh Kumar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | | | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Surendra S. Manohar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Sunil S. Gangurde
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Murali T. Variath
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Manish K. Pandey
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
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10
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Ojiewo CO, Janila P, Bhatnagar-Mathur P, Pandey MK, Desmae H, Okori P, Mwololo J, Ajeigbe H, Njuguna-Mungai E, Muricho G, Akpo E, Gichohi-Wainaina WN, Variath MT, Radhakrishnan T, Dobariya KL, Bera SK, Rathnakumar AL, Manivannan N, Vasanthi RP, Kumar MVN, Varshney RK. Advances in Crop Improvement and Delivery Research for Nutritional Quality and Health Benefits of Groundnut ( Arachis hypogaea L.). Front Plant Sci 2020; 11:29. [PMID: 32153601 PMCID: PMC7046547 DOI: 10.3389/fpls.2020.00029] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 01/13/2020] [Indexed: 05/28/2023]
Abstract
Groundnut is an important global food and oil crop that underpins agriculture-dependent livelihood strategies meeting food, nutrition, and income security. Aflatoxins, pose a major challenge to increased competitiveness of groundnut limiting access to lucrative markets and affecting populations that consume it. Other drivers of low competitiveness include allergens and limited shelf life occasioned by low oleic acid profile in the oil. Thus grain off-takers such as consumers, domestic, and export markets as well as processors need solutions to increase profitability of the grain. There are some technological solutions to these challenges and this review paper highlights advances in crop improvement to enhance groundnut grain quality and nutrient profile for food, nutrition, and economic benefits. Significant advances have been made in setting the stage for marker-assisted allele pyramiding for different aflatoxin resistance mechanisms-in vitro seed colonization, pre-harvest aflatoxin contamination, and aflatoxin production-which, together with pre- and post-harvest management practices, will go a long way in mitigating the aflatoxin menace. A breakthrough in aflatoxin control is in sight with overexpression of antifungal plant defensins, and through host-induced gene silencing in the aflatoxin biosynthetic pathway. Similarly, genomic and biochemical approaches to allergen control are in good progress, with the identification of homologs of the allergen encoding genes and development of monoclonal antibody based ELISA protocol to screen for and quantify major allergens. Double mutation of the allotetraploid homeologous genes, FAD2A and FAD2B, has shown potential for achieving >75% oleic acid as demonstrated among introgression lines. Significant advances have been made in seed systems research to bridge the gap between trait discovery, deployment, and delivery through innovative partnerships and action learning.
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Affiliation(s)
- Chris O. Ojiewo
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Pasupuleti Janila
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooja Bhatnagar-Mathur
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K. Pandey
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Haile Desmae
- Research Program – West and Central Africa, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Bamako, Mali
| | - Patrick Okori
- Research Program – Eastern and Southern Africa, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Lilongwe, Malawi
| | - James Mwololo
- Research Program – Eastern and Southern Africa, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Lilongwe, Malawi
| | - Hakeem Ajeigbe
- Research Program – West and Central Africa, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Kano, Nigeria
| | - Esther Njuguna-Mungai
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Geoffrey Muricho
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Essegbemon Akpo
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Wanjiku N. Gichohi-Wainaina
- Research Program – Eastern and Southern Africa, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Lilongwe, Malawi
| | - Murali T. Variath
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Thankappan Radhakrishnan
- Indian Council of Agricultural Research - Directorate of Groundnut Research (ICAR-DGR), Junagadh, India
| | - Kantilal L. Dobariya
- Main Oilseeds Research Station, Junagadh Agricultural University (JAU), Junagadh, India
| | - Sandip Kumar Bera
- Indian Council of Agricultural Research - Directorate of Groundnut Research (ICAR-DGR), Junagadh, India
| | | | - Narayana Manivannan
- National Pulses Research Center, Tamil Nadu Agricultural University (TNAU), Pudukkottai, India
| | - Ragur Pandu Vasanthi
- Regional Agricultural Research Station, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, India
| | - Mallela Venkata Nagesh Kumar
- Department of Genetics and Plant Breeding, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad, India
| | - Rajeev K. Varshney
- Research Program – Genetic Gains, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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11
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Shasidhar Y, Variath MT, Vishwakarma MK, Manohar SS, Gangurde SS, Sriswathi M, Sudini HK, Dobariya KL, Bera SK, Radhakrishnan T, Pandey MK, Janila P, Varshney RK. Improvement of three popular Indian groundnut varieties for foliar disease resistance and high oleic acid using SSR markers and SNP array in marker-assisted backcrossing. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.cj.2019.07.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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12
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Ojiewo C, Monyo E, Desmae H, Boukar O, Mukankusi‐Mugisha C, Thudi M, Pandey MK, Saxena RK, Gaur PM, Chaturvedi SK, Fikre A, Ganga Rao NPVR, SameerKumar CV, Okori P, Janila P, Rubyogo JC, Godfree C, Akpo E, Omoigui L, Nkalubo S, Fenta B, Binagwa P, Kilango M, Williams M, Mponda O, Okello D, Chichaybelu M, Miningou A, Bationo J, Sako D, Diallo S, Echekwu C, Umar ML, Oteng‐Frimpong R, Mohammed H, Varshney RK. Genomics, genetics and breeding of tropical legumes for better livelihoods of smallholder farmers. Plant Breed 2019; 138:487-499. [PMID: 31787790 PMCID: PMC6876654 DOI: 10.1111/pbr.12554] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 11/04/2017] [Indexed: 05/04/2023]
Abstract
Legumes are important components of sustainable agricultural production, food, nutrition and income systems of developing countries. In spite of their importance, legume crop production is challenged by a number of biotic (diseases and pests) and abiotic stresses (heat, frost, drought and salinity), edaphic factors (associated with soil nutrient deficits) and policy issues (where less emphasis is put on legumes compared to priority starchy staples). Significant research and development work have been done in the past decade on important grain legumes through collaborative bilateral and multilateral projects as well as the CGIAR Research Program on Grain Legumes (CRP-GL). Through these initiatives, genomic resources and genomic tools such as draft genome sequence, resequencing data, large-scale genomewide markers, dense genetic maps, quantitative trait loci (QTLs) and diagnostic markers have been developed for further use in multiple genetic and breeding applications. Also, these mega-initiatives facilitated release of a number of new varieties and also dissemination of on-the-shelf varieties to the farmers. More efforts are needed to enhance genetic gains by reducing the time required in cultivar development through integration of genomics-assisted breeding approaches and rapid generation advancement.
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Affiliation(s)
- Chris Ojiewo
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)NairobiKenya
| | - Emmanuel Monyo
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)NairobiKenya
| | | | - Ousmane Boukar
- International Institute of Tropical Agriculture (IITA)KanoNigeria
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Stanley Nkalubo
- National Agricultural Research Organization (NARO)NamulongeUganda
| | - Berhanu Fenta
- Ethiopian Institute of Agricultural Research (EIAR)MelkassaEthiopia
| | - Papias Binagwa
- Selian Agricultural Research Institute (SARI)ArushaTanzania
| | | | | | | | - David Okello
- National Semi Arid Resources Research Institute (NaSARRI)SorotiUganda
| | | | - Amos Miningou
- Environmental Institute for Agricultural Research (INERA)OuagadougouBurkina Faso
| | - Joseph Bationo
- Environmental Institute for Agricultural Research (INERA)OuagadougouBurkina Faso
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13
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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 Breed 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] [What about the content of this article? (0)] [Affiliation(s)] [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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14
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Khera P, Pandey MK, Mallikarjuna N, Sriswathi M, Roorkiwal M, Janila P, Sharma S, Shilpa K, Sudini H, Guo B, Varshney RK. Genetic imprints of domestication for disease resistance, oil quality, and yield component traits in groundnut (Arachis hypogaea L.). Mol Genet Genomics 2018; 294:365-378. [PMID: 30467595 DOI: 10.1007/s00438-018-1511-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2018] [Accepted: 11/08/2018] [Indexed: 11/29/2022]
Abstract
Ploidy difference between wild Arachis species and cultivated genotypes hinder transfer of useful alleles for agronomically important traits. To overcome this genetic barrier, two synthetic tetraploids, viz., ISATGR 1212 (A. duranensis ICG 8123 × A. ipaensis ICG 8206) and ISATGR 265-5A (A. kempff-mercadoi ICG 8164 × A. hoehnei ICG 8190), were used to generate two advanced backcross (AB) populations. The AB-populations, namely, AB-pop1 (ICGV 91114 × ISATGR 1212) and AB-pop2, (ICGV 87846 × ISATGR 265-5A) were genotyped with DArT and SSR markers. Genetic maps were constructed for AB-pop1 and AB-pop2 populations with 258 loci (1415.7 cM map length and map density of 5.5 cM/loci) and 1043 loci (1500.8 cM map length with map density of 1.4 cM/loci), respectively. Genetic analysis identified large number of wild segments in the population and provided a good source of diversity in these populations. Phenotyping of these two populations identified several introgression lines with good agronomic, oil quality, and disease resistance traits. Quantitative trait locus (QTL) analysis showed that the wild genomic segments contributed favourable alleles for foliar disease resistance while cultivated genomic segments mostly contributed favourable alleles for oil quality and yield component traits. These populations, after achieving higher stability, will be useful resource for genetic mapping and QTL discovery for wild species segments in addition to using population progenies in breeding program for diversifying the gene pool of cultivated groundnut.
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Affiliation(s)
- Pawan Khera
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Nalini Mallikarjuna
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manda Sriswathi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Krishna Shilpa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Harikishan Sudini
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Baozhu Guo
- Crop Protection and Management Research Unit, US Department of Agriculture-Agricultural Research Service, Tifton, USA
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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15
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Pandey MK, Khan AW, Singh VK, Vishwakarma MK, Shasidhar Y, Kumar V, Garg V, Bhat RS, Chitikineni A, Janila P, Guo B, Varshney RK. QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.). Plant Biotechnol J 2017; 15:927-941. [PMID: 28028892 PMCID: PMC5506652 DOI: 10.1111/pbi.12686] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 05/12/2023]
Abstract
Rust and late leaf spot (LLS) are the two major foliar fungal diseases in groundnut, and their co-occurrence leads to significant yield loss in addition to the deterioration of fodder quality. To identify candidate genomic regions controlling resistance to rust and LLS, whole-genome resequencing (WGRS)-based approach referred as 'QTL-seq' was deployed. A total of 231.67 Gb raw and 192.10 Gb of clean sequence data were generated through WGRS of resistant parent and the resistant and susceptible bulks for rust and LLS. Sequence analysis of bulks for rust and LLS with reference-guided resistant parent assembly identified 3136 single-nucleotide polymorphisms (SNPs) for rust and 66 SNPs for LLS with the read depth of ≥7 in the identified genomic region on pseudomolecule A03. Detailed analysis identified 30 nonsynonymous SNPs affecting 25 candidate genes for rust resistance, while 14 intronic and three synonymous SNPs affecting nine candidate genes for LLS resistance. Subsequently, allele-specific diagnostic markers were identified for three SNPs for rust resistance and one SNP for LLS resistance. Genotyping of one RIL population (TAG 24 × GPBD 4) with these four diagnostic markers revealed higher phenotypic variation for these two diseases. These results suggest usefulness of QTL-seq approach in precise and rapid identification of candidate genomic regions and development of diagnostic markers for breeding applications.
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Affiliation(s)
- Manish K. Pandey
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Aamir W. Khan
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Vikas K. Singh
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Manish K. Vishwakarma
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Vinay Kumar
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Vanika Garg
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Ramesh S. Bhat
- Department of BiotechnologyUniversity of Agricultural SciencesDharwadIndia
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Baozhu Guo
- Crop Protection and Management Research UnitUSDA‐Agricultural Research ServiceTiftonGAUSA
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
- School of Plant Biology and Institute of AgricultureThe University of Western AustraliaCrawleyWAAustralia
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16
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Shasidhar Y, Vishwakarma MK, Pandey MK, Janila P, Variath MT, Manohar SS, Nigam SN, Guo B, Varshney RK. Molecular Mapping of Oil Content and Fatty Acids Using Dense Genetic Maps in Groundnut ( Arachis hypogaea L.). Front Plant Sci 2017; 8:794. [PMID: 28588591 PMCID: PMC5438992 DOI: 10.3389/fpls.2017.00794] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 04/27/2017] [Indexed: 05/04/2023]
Abstract
Enhancing seed oil content with desirable fatty acid composition is one of the most important objectives of groundnut breeding programs globally. Genomics-assisted breeding facilitates combining multiple traits faster, however, requires linked markers. In this context, we have developed two different F2 mapping populations, one for oil content (OC-population, ICGV 07368 × ICGV 06420) and another for fatty acid composition (FA-population, ICGV 06420 × SunOleic 95R). These two populations were phenotyped for respective traits and genotyped using Diversity Array Technology (DArT) and DArTseq genotyping platforms. Two genetic maps were developed with 854 (OC-population) and 1,435 (FA-population) marker loci with total map distance of 3,526 and 1,869 cM, respectively. Quantitative trait locus (QTL) analysis using genotyping and phenotyping data identified eight QTLs for oil content including two major QTLs, qOc-A10 and qOc-A02, with 22.11 and 10.37% phenotypic variance explained (PVE), respectively. For seven different fatty acids, a total of 21 QTLs with 7.6-78.6% PVE were identified and 20 of these QTLs were of major effect. Two mutant alleles, ahFAD2B and ahFAD2A, also had 18.44 and 10.78% PVE for palmitic acid, in addition to oleic (33.8 and 17.4% PVE) and linoleic (41.0 and 19.5% PVE) acids. Furthermore, four QTL clusters harboring more than three QTLs for fatty acids were identified on the three LGs. The QTLs identified in this study could be further dissected for candidate gene discovery and development of diagnostic markers for breeding improved groundnut varieties with high oil content and desirable oil quality.
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Affiliation(s)
- Yaduru Shasidhar
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- Department of Genetics, Osmania UniversityHyderabad, India
| | | | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- *Correspondence: Rajeev K. Varshney, Manish K. Pandey, Pasupuleti Janila,
| | - Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- *Correspondence: Rajeev K. Varshney, Manish K. Pandey, Pasupuleti Janila,
| | - Murali T. Variath
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Surendra S. Manohar
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Shyam N. Nigam
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
| | - Baozhu Guo
- Crop Protection and Management Research Unit, Agricultural Research Service (USDA), TiftonGA, USA
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid TropicsHyderabad, India
- School of Agriculture and Environment, University of Western Australia, CrawleyWA, Australia
- *Correspondence: Rajeev K. Varshney, Manish K. Pandey, Pasupuleti Janila,
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17
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Janila P. Technologies for Intensification of Production and Uses of Grain Legumes for Nutrition Security. Proceedings of the Indian National Science Academy 2016. [DOI: 10.16943/ptinsa/2016/48887] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Janila P, Variath MT, Pandey MK, Desmae H, Motagi BN, Okori P, Manohar SS, Rathnakumar AL, Radhakrishnan T, Liao B, Varshney RK. Genomic Tools in Groundnut Breeding Program: Status and Perspectives. Front Plant Sci 2016; 7:289. [PMID: 27014312 PMCID: PMC4794498 DOI: 10.3389/fpls.2016.00289] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 02/23/2016] [Indexed: 05/20/2023]
Abstract
Groundnut, a nutrient-rich food legume, is cultivated world over. It is valued for its good quality cooking oil, energy and protein rich food, and nutrient-rich fodder. Globally, groundnut improvement programs have developed varieties to meet the preferences of farmers, traders, processors, and consumers. Enhanced yield, tolerance to biotic and abiotic stresses and quality parameters have been the target traits. Spurt in genetic information of groundnut was facilitated by development of molecular markers, genetic, and physical maps, generation of expressed sequence tags (EST), discovery of genes, and identification of quantitative trait loci (QTL) for some important biotic and abiotic stresses and quality traits. The first groundnut variety developed using marker assisted breeding (MAB) was registered in 2003. Since then, USA, China, Japan, and India have begun to use genomic tools in routine groundnut improvement programs. Introgression lines that combine foliar fungal disease resistance and early maturity were developed using MAB. Establishment of marker-trait associations (MTA) paved way to integrate genomic tools in groundnut breeding for accelerated genetic gain. Genomic Selection (GS) tools are employed to improve drought tolerance and pod yield, governed by several minor effect QTLs. Draft genome sequence and low cost genotyping tools such as genotyping by sequencing (GBS) are expected to accelerate use of genomic tools to enhance genetic gains for target traits in groundnut.
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Affiliation(s)
- P. Janila
- International Crops Research Institute for Semi-Arid TropicsPatancheru, India
| | - Murali T. Variath
- International Crops Research Institute for Semi-Arid TropicsPatancheru, India
| | - Manish K. Pandey
- International Crops Research Institute for Semi-Arid TropicsPatancheru, India
| | - Haile Desmae
- International Crops Research Institute for Semi-Arid TropicsBamako, Mali
| | - Babu N. Motagi
- International Crops Research Institute for Semi-Arid TropicsKano, Nigeria
| | - Patrick Okori
- International Crops Research Institute for Semi-Arid TropicsLilongwe, Malawi
| | - Surendra S. Manohar
- International Crops Research Institute for Semi-Arid TropicsPatancheru, India
| | | | | | - Boshou Liao
- Oil Crops Research Institute Chinese Academy of Agricultural SciencesWuhan, China
| | - Rajeev K. Varshney
- International Crops Research Institute for Semi-Arid TropicsPatancheru, India
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19
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Janila P, Pandey MK, Shasidhar Y, Variath MT, Sriswathi M, Khera P, Manohar SS, Nagesh P, Vishwakarma MK, Mishra GP, Radhakrishnan T, Manivannan N, Dobariya KL, Vasanthi RP, Varshney RK. Molecular breeding for introgression of fatty acid desaturase mutant alleles (ahFAD2A and ahFAD2B) enhances oil quality in high and low oil containing peanut genotypes. Plant Sci 2016; 242:203-213. [PMID: 26566838 DOI: 10.1016/j.plantsci.2015.08.013] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2015] [Revised: 08/15/2015] [Accepted: 08/22/2015] [Indexed: 05/20/2023]
Abstract
High oleate peanuts have two marketable benefits, health benefits to consumers and extended shelf life of peanut products. Two mutant alleles present on linkage group a09 (ahFAD2A) and b09 (ahFAD2B) control composition of three major fatty acids, oleic, linoleic and palmitic acids which together determine peanut oil quality. In conventional breeding, selection for fatty acid composition is delayed to advanced generations. However by using DNA markers, breeders can reject large number of plants in early generations and therefore can optimize time and resources. Here, two approaches of molecular breeding namely marker-assisted backcrossing (MABC) and marker-assisted selection (MAS) were employed to transfer two FAD2 mutant alleles from SunOleic 95R into the genetic background of ICGV 06110, ICGV 06142 and ICGV 06420. In summary, 82 MABC and 387 MAS derived introgression lines (ILs) were developed using DNA markers with elevated oleic acid varying from 62 to 83%. Oleic acid increased by 0.5-1.1 folds, with concomitant reduction of linoleic acid by 0.4-1.0 folds and palmitic acid by 0.1-0.6 folds among ILs compared to recurrent parents. Finally, high oleate ILs, 27 with high oil (53-58%), and 28 ILs with low oil content (42-50%) were selected that may be released for cultivation upon further evaluation.
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Affiliation(s)
- Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Yaduru Shasidhar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Murali T Variath
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manda Sriswathi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pawan Khera
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Surendra S Manohar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Patne Nagesh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K Vishwakarma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Gyan P Mishra
- Directorate of Groundnut Research (DGR) of Indian Council of Agricultural Research (ICAR), Junagadh, India
| | - T Radhakrishnan
- Directorate of Groundnut Research (DGR) of Indian Council of Agricultural Research (ICAR), Junagadh, India
| | - N Manivannan
- Department of Oilseeds, Centre of Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - K L Dobariya
- Main Oilseeds Research Station, Junagadh Agricultural University (JAU), Junagadh, India
| | - R P Vasanthi
- Regional Agricultural Research Station, Acharya NG Ranga Agricultural University (ANGRAU), Tirupati, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
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Varshney RK, Pandey MK, Janila P, Nigam SN, Sudini H, Gowda MVC, Sriswathi M, Radhakrishnan T, Manohar SS, Nagesh P. Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.). Theor Appl Genet 2014; 127:1771-81. [PMID: 24927821 PMCID: PMC4110420 DOI: 10.1007/s00122-014-2338-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 05/22/2014] [Indexed: 05/04/2023]
Abstract
Successful introgression of a major QTL for rust resistance, through marker-assisted backcrossing, in three popular Indian peanut cultivars generated several promising introgression lines with enhanced rust resistance and higher yield. Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut (Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar 'GPBD 4' into three rust susceptible varieties ('ICGV 91114', 'JL 24' and 'TAG 24') through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2-3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56-96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India,
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Janila P, Nigam SN, Pandey MK, Nagesh P, Varshney RK. Groundnut improvement: use of genetic and genomic tools. Front Plant Sci 2013; 4:23. [PMID: 23443056 PMCID: PMC3580887 DOI: 10.3389/fpls.2013.00023] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Accepted: 02/02/2013] [Indexed: 05/04/2023]
Abstract
Groundnut (Arachis hypogaea L.), a self-pollinated legume is an important crop cultivated in 24 million ha world over for extraction of edible oil and food uses. The kernels are rich in oil (48-50%) and protein (25-28%), and are source of several vitamins, minerals, antioxidants, biologically active polyphenols, flavonoids, and isoflavones. Improved varieties of groundnut with high yield potential were developed and released for cultivation world over. The improved varieties belong to different maturity durations and possess resistance to diseases, tolerance to drought, enhanced oil content, and improved quality traits for food uses. Conventional breeding procedures along with the tools for phenotyping were largely used in groundnut improvement programs. Mutations were used to induce variability and wide hybridization was attempted to tap variability from wild species. Low genetic variability has been a bottleneck for groundnut improvement. The vast potential of wild species, reservoir of new alleles remains under-utilized. Development of linkage maps of groundnut during the last decade was followed by identification of markers and quantitative trait loci for the target traits. Consequently, the last decade has witnessed the deployment of molecular breeding approaches to complement the ongoing groundnut improvement programs in USA, China, India, and Japan. The other potential advantages of molecular breeding are the feasibility to target multiple traits for improvement and provide tools to tap new alleles from wild species. The first groundnut variety developed through marker-assisted back-crossing is a root-knot nematode-resistant variety, NemaTAM in USA. The uptake of molecular breeding approaches in groundnut improvement programs by NARS partners in India and many African countries is slow or needs to be initiated in part due to inadequate infrastructure, high genotyping costs, and human capacities. Availability of draft genome sequence for diploid (AA and BB) and tetraploid, AABB genome species of Arachis in coming years is expected to bring low-cost genotyping to the groundnut community that will facilitate use of modern genetics and breeding approaches such as genome-wide association studies for trait mapping and genomic selection for crop improvement.
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Affiliation(s)
- Pasupuleti Janila
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, Andhra Pradesh, India
| | - S. N. Nigam
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, Andhra Pradesh, India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, Andhra Pradesh, India
| | - P. Nagesh
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, Andhra Pradesh, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, Andhra Pradesh, India
- Generation Challenge Programme, c/o Centro Internacional de Mejoramiento de Maíz y TrigoMexico DF, Mexico
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Varshney RK, Mohan SM, Gaur PM, Gangarao NVPR, Pandey MK, Bohra A, Sawargaonkar SL, Chitikineni A, Kimurto PK, Janila P, Saxena KB, Fikre A, Sharma M, Rathore A, Pratap A, Tripathi S, Datta S, Chaturvedi SK, Mallikarjuna N, Anuradha G, Babbar A, Choudhary AK, Mhase MB, Bharadwaj C, Mannur DM, Harer PN, Guo B, Liang X, Nadarajan N, Gowda CLL. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol Adv 2013; 31:1120-34. [PMID: 23313999 DOI: 10.1016/j.biotechadv.2013.01.001] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 12/16/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
Abstract
Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, DF 06600, Mexico; The University of Western Australia, Crawley 6009, Australia; Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou 510640, China.
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Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK. Advances in Arachis genomics for peanut improvement. Biotechnol Adv 2011; 30:639-51. [PMID: 22094114 DOI: 10.1016/j.biotechadv.2011.11.001] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/24/2011] [Accepted: 11/01/2011] [Indexed: 01/01/2023]
Abstract
Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid; cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic diversity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely hampered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
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