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Mahto RK, Chandana BS, Singh RK, Talukdar A, Swarnalakshmi K, Suman A, Vaishali, Dey D, Kumar R. Uncovering potentials of an association panel subset for nitrogen fixation and sustainable chickpea productivity. BMC PLANT BIOLOGY 2025; 25:693. [PMID: 40413423 DOI: 10.1186/s12870-025-06244-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 02/11/2025] [Indexed: 05/27/2025]
Abstract
BACKGROUND Chickpea (Cicer arietinum L.) is a nutritious legume that fixes atmospheric nitrogen through Rhizobium symbiosis, enhancing growth and yield. Sustainable agriculture is essential to address food security, climate change, and environmental sustainability. Plant Growth-Promoting Rhizobacteria (PGPR) improve crop productivity, reduce chemical fertilizer use, and support eco-friendly farming. This study highlights PGPR's role in enhancing chickpea yield, resilience, and resource efficiency while minimizing environmental impacts. PGPR reduces chemical dependency, preserves ecosystems, and supports global sustainability goals. Findings demonstrate PGPR's potential to improve food security and promote equitable distribution. This research offers innovative strategies for advancing sustainable agriculture. RESULTS The study revealed significant variability in nodulation, nitrogen fixation, and yield among 20 chickpea genotypes under different treatments, including Rhizobium, vesicular-arbuscular mycorrhiza (VAM), and chemical fertilizers (NPK), applied alone and in combinations. Genotype ICC9085 consistently outperformed others, exhibiting the highest nodules per plant (22.67), nitrogen content (3.65%), and protein content (22.85%), while ICC1083 and ICC6579 showed minimal nodulation (< 5 nodules). Rhizobium treatment proved the most effective, achieving the highest nitrogenase activity (mean: 35.806; max: 189.2) and yielding superior growth-promoting results compared to VAM and control treatments. Molecular genotyping identified 20 out of 128 SSR markers as polymorphic, with an average polymorphic information content (PIC) of 0.35 and two alleles per marker, revealing moderate polymorphism and significant genetic diversity. Cluster analysis grouped the genotypes into four primary clusters, reflecting geographical and genetic diversity in nodulation traits. Environmental factors such as soil nutrients, temperature, and water stress, alongside genetic traits like root architecture and nitrogen-fixing efficiency, contributed to variations in growth and productivity. This interplay of genotype and environment underscores the adaptability and superior performance of certain varieties like ICC9085 under specific conditions. CONCLUSION These observations suggest that the identified superior genotypes can be used to introduce desirable traits into allied chickpea cultivars through marker-assisted selection and crop improvement programs.The research of the chickpea, a crop with significant agricultural and industrial value, will eventually help develop efficient methods for the production of climate-smart food crops to meet the food and feed needs of future generations for a sustainable environment.
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Affiliation(s)
- Rohit Kumar Mahto
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India
- School of Biotechnology, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, 221005, India
| | - B S Chandana
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India
| | - Rajesh Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India
| | - Akshay Talukdar
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India
| | - K Swarnalakshmi
- Division of Microbiology, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012, India
| | - Archana Suman
- Division of Microbiology, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, 110012, India
| | - Vaishali
- Sardar Vallabhbhai Patel University of Agriculture and Technology, Modipuram, Meerut, Uttar Pradesh, 250110, India
| | - Debashish Dey
- School of Biotechnology, Institute of Science, Banaras Hindu University (BHU), Varanasi, Uttar Pradesh, 221005, India
| | - Rajendra Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), New Delhi, Delhi, 110012, India.
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Altaf MT, Liaqat W, Ali A, Jamil A, Fahad M, Rahman MAU, Baloch FS, Mohamed HI. Advancing Chickpea Breeding: Omics Insights for Targeted Abiotic Stress Mitigation and Genetic Enhancement. Biochem Genet 2025; 63:1063-1115. [PMID: 39532827 DOI: 10.1007/s10528-024-10954-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 10/26/2024] [Indexed: 11/16/2024]
Abstract
Chickpea is a major source of proteins and is considered the most economically vital food legume. Chickpea production is threatened by several abiotic and biotic factors worldwide. The main constraints limiting worldwide chickpea production are abiotic conditions such as drought, heat, salinity, and cold. It is clear that chickpea is treasured for its nutritive value, in particular its high protein content, and hence study of problems like drought, cold and salinity stresses are very important concerning chickpeas. In this regard, several physiological, biochemical, and molecular mechanisms are reviewed to confer tolerance to abiotic stress. The most crippling economic losses in agriculture occur due to these abiotic stressors, which affect plants in many ways. All these abiotic stresses affect the water relations of the plant, both at the cellular level as well as the whole-plant level, causing both specific and non-specific reactions, damage and adaptation reactions. These stresses share common features. Breeding programs use a huge collection of over 100,000 chickpea accessions as their foundation. Significant advancements in conventional breeding, including mutagenesis, gene/allele introgression, and germplasm introduction, have been made through this method. Abiotic tolerance and yield component selection are made easier by creating unique DNA markers for the genus Cicer, which has been made possible by developments in high-throughput sequencing and molecular biology. Transcriptomics, proteomics, and metabolomics have also made it possible to identify particular genes, proteins, and metabolites linked to chickpea tolerance to abiotic stress. Chickpea abiotic stress tolerance has been directly and potentially improved by biotechnological applications, which are covered by all 'Omics' approaches. It requires information on the abiotic stress response at the different molecular levels, which comprises gene expression analysis for metabolites or proteins and its impact on phenotype. Studies on chickpea genome-wide expression profiling have been conducted to determine important candidate genes and their regulatory networks for abiotic stress response. This study aimed to offer a detailed overview of the diverse 'Omics' approaches for resilience's to abiotic stresses on chickpea plants.
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Affiliation(s)
- Muhammad Tanveer Altaf
- Department of Field Crops, Faculty of Agriculture, Recep Tayyip Erdoğan University, Rize/Pazar, Türkiye.
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Institute of Natural and Applied Sciences, Çukurova University, 01330, Adana, Türkiye
| | - Amjad Ali
- Department of Plant Protection, Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, 58140, Sivas, Türkiye
| | - Amna Jamil
- Department of Horticulture, MNS University of Agriculture, Multan, Pakistan
| | - Muhammad Fahad
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Muhammad Aneeq Ur Rahman
- Biotechnology Research Institute, Graduate School of Chinese Academy of Agricultural Sciences, Beijing, 10081, China
| | - Faheem Shehzad Baloch
- Department of biotechnology, faculty of science, Mersin University, Mersin, Türkiye
- Department of Plant Resources and Environment, Jeju National University, Jeju, 63243, Korea
| | - Heba I Mohamed
- Department of Biological and Geological Sciences, Faculty of Education, Ain Shams University, Cairo, 11341, Egypt.
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Naveed M, Aslam M, Ahmed SR, Tan DKY, De Mastro F, Tariq MS, Sakhawat A, Asad MA, Liu Y. An overview of heat stress in Chickpea ( Cicer arietinum L.): effects, mechanisms and diverse molecular breeding approaches for enhancing resilience and productivity. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2025; 45:18. [PMID: 39850651 PMCID: PMC11751345 DOI: 10.1007/s11032-025-01538-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 01/07/2025] [Indexed: 01/25/2025]
Abstract
Chickpea (Cicer arietinum. L) holds the esteemed position of being the second most cultivated and consumed legume crop globally. Nevertheless, both biotic and abiotic constraints limit chickpea production. This legume is sensitive to heat stress at its reproductive stage leading to reduced flowering, flower abortion, and lack of pod formation, therefore emerging as a major limiting factor for yield. Chickpea, predominantly cultivated in semi-arid regions, is frequently subjected to high-temperature stress, which adversely affects its growth and yield. Given the escalating impacts of climate change, the development of heat-tolerant chickpea genotypes is imperative and can be achieved through the integration of advanced biotechnological approaches. The appropriate solution devised by some researchers is the modification of genetic architecture by targeting specific genes associated with tolerance to heat stress and harnessing them in the development of more robust chickpea varieties. Besides this, multi-omics strategies (Genomics, Transcriptomics, Proteomics, and Metabolomics) have made it easier to reveal the distinct genes / quantitative trait loci (QTLs) / markers, proteins, and metabolites correlated with heat tolerance. This review compiles noteworthy revelations and different tactics to boost chickpea tolerance under heat temperatures. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-025-01538-4.
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Affiliation(s)
- Mahak Naveed
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Mariyah Aslam
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Plant Breeding and Genetics Division, Chickpea Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Syed Riaz Ahmed
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Horticulture Research Institute (HRI), Pakistan Agricultural Research Council, Islamabad, Pakistan
| | - Daniel K. Y. Tan
- School of Life and Environmental Sciences, Plant Breeding Institute, Faculty of Science, Sydney Institute of Agriculture, The University of Sydney, Sydney, NSW 2006 Australia
| | - Francesco De Mastro
- Department of Soil, Plant, and Food Sciences, University of Bari “Aldo Moro”, 70126 Bari, Italy
| | - Muhammad Sayyam Tariq
- Plant Breeding and Genetics Division, Chickpea Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Ammara Sakhawat
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Azeem Asad
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Plant Breeding and Genetics Division, Chickpea Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Yongming Liu
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, 572024 China
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Sari D. Identification of Insertion and Deletion (InDel) Markers for Chickpea ( Cicer arietinum L.) Based on Double-Digest Restriction Site-Associated DNA Sequencing. PLANTS (BASEL, SWITZERLAND) 2024; 13:2530. [PMID: 39274014 PMCID: PMC11397535 DOI: 10.3390/plants13172530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2024] [Revised: 09/03/2024] [Accepted: 09/04/2024] [Indexed: 09/16/2024]
Abstract
Enhancing the marker repository and the development of breeder-friendly markers in chickpeas is important in relation to chickpea genomics-assisted breeding applications. Insertion-deletion (InDel) markers are widely distributed across genomes and easily observed with specifically designed primers, leading to less time, cost, and labor requirements. In light of this, the present study focused on the identification and development of InDel markers through the use of double-digest restriction site-associated DNA sequencing (ddRADSeq) data from 20 chickpea accessions. Bioinformatic analysis identified 20,700 InDel sites, including 15,031 (72.61%) deletions and 5669 (27.39%) insertions, among the chickpea accessions. The InDel markers ranged from 1 to 25 bp in length, while single-nucleotide-length InDel markers were found to represent the majority of the InDel sites and account for 79% of the total InDel markers. However, we focused on InDel markers wherein the length was greater than a single nucleotide to avoid any read or alignment errors. Among all of the InDel markers, 96.1% were less than 10 bp, 3.6% were between 10 and 20 bp, and 0.3% were more than 20 bp in length. We examined the InDel markers that were 10 bp and longer for the development of InDel markers based on a consideration of the genomic distribution and low-cost genotyping with agarose gels. A total of 29 InDel regions were selected, and primers were successfully designed to evaluate their efficiency. Annotation analysis of the InDel markers revealed them to be found with the highest frequency in the intergenic regions (82.76%), followed by the introns (6.90%), coding sequences (6.90%), and exons (3.45%). Genetic diversity analysis demonstrated that the polymorphic information content of the markers varied from 0.09 to 0.37, with an average of 0.20. Taken together, these results showed the efficiency of InDel marker development for chickpea genetic and genomic studies using the ddRADSeq method. The identified markers might prove valuable for chickpea breeders.
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Affiliation(s)
- Duygu Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07070 Antalya, Turkey
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Hu L, Wang J, Wang X, Zhang D, Sun Y, Lu T, Shi W. Development of SSR Markers and Evaluation of Genetic Diversity of Endangered Plant Saussurea involucrata. Biomolecules 2024; 14:1010. [PMID: 39199397 PMCID: PMC11353235 DOI: 10.3390/biom14081010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/12/2024] [Accepted: 08/13/2024] [Indexed: 09/01/2024] Open
Abstract
The conservation biology field underscores the importance of understanding genetic diversity and gene flow within plant populations and the factors that influence them. This study employs Simple Sequence Repeat (SSR) molecular markers to investigate the genetic diversity of the endangered plant species Saussurea involucrata, offering a theoretical foundation for its conservation efforts. Utilizing sequencing results to screen SSR loci, we designed and scrutinized 18 polymorphic microsatellite primers across 112 samples from 11 populations in the Bayinbuluke region. Our findings reveal high genetic diversity (I = 0.837, He = 0.470) and substantial gene flow (Nm = 1.390) among S. involucrata populations (China, Xinjiang), potentially attributed to efficient pollen and seed dispersal mechanisms. Principal Coordinate Analysis (PCoA) indicates a lack of distinct genetic structuring within the Bayinbuluke populations. The cluster analysis using STRUCTURE reflected the genetic structure of S. involucrata to a certain extent compared with PCoA. The results showed that all samples were divided into four groups. To safeguard this species, we advocate for the in situ conservation of all S. involucrata populations in the area. The SSR markers developed in this study provide a valuable resource for future genetic research on S. involucrata.
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Affiliation(s)
- Lin Hu
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830011, China;
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (J.W.); (X.W.); (D.Z.)
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Jiancheng Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (J.W.); (X.W.); (D.Z.)
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Xiyong Wang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (J.W.); (X.W.); (D.Z.)
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Daoyuan Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (J.W.); (X.W.); (D.Z.)
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
| | - Yanxia Sun
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan 430074, China;
| | - Ting Lu
- College of Forestry and Landscape Architecture, Xinjiang Agricultural University, Urumqi 830011, China;
| | - Wei Shi
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; (J.W.); (X.W.); (D.Z.)
- Xinjiang Key Lab of Conservation and Utilization of Plant Gene Resources, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
- Turpan Eremophytes Botanical Garden, Chinese Academy of Sciences, Turpan 838008, China
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Thakro V, Varshney N, Malik N, Daware A, Srivastava R, Mohanty JK, Basu U, Narnoliya L, Jha UC, Tripathi S, Tyagi AK, Parida SK. Functional allele of a MATE gene selected during domestication modulates seed color in chickpea. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 117:53-71. [PMID: 37738381 DOI: 10.1111/tpj.16469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/14/2023] [Accepted: 08/29/2023] [Indexed: 09/24/2023]
Abstract
Seed color is one of the key target traits of domestication and artificial selection in chickpeas due to its implications on consumer preference and market value. The complex seed color trait has been well dissected in several crop species; however, the genetic mechanism underlying seed color variation in chickpea remains poorly understood. Here, we employed an integrated genomics strategy involving QTL mapping, high-density mapping, map-based cloning, association analysis, and molecular haplotyping in an inter-specific RIL mapping population, association panel, wild accessions, and introgression lines (ILs) of Cicer gene pool. This delineated a MATE gene, CaMATE23, encoding a Transparent Testa (TT) and its natural allele (8-bp insertion) and haplotype underlying a major QTL governing seed color on chickpea chromosome 4. Signatures of selective sweep and a strong purifying selection reflected that CaMATE23, especially its 8-bp insertion natural allelic variant, underwent selection during chickpea domestication. Functional investigations revealed that the 8-bp insertion containing the third cis-regulatory RY-motif element in the CaMATE23 promoter is critical for enhanced binding of CaFUSCA3 transcription factor, a key regulator of seed development and flavonoid biosynthesis, thereby affecting CaMATE23 expression and proanthocyanidin (PA) accumulation in the seed coat to impart varied seed color in chickpea. Consequently, overexpression of CaMATE23 in Arabidopsis tt12 mutant partially restored the seed color phenotype to brown pigmentation, ascertaining its functional role in PA accumulation in the seed coat. These findings shed new light on the seed color regulation and evolutionary history, and highlight the transcriptional regulation of CaMATE23 by CaFUSCA3 in modulating seed color in chickpea. The functionally relevant InDel variation, natural allele, and haplotype from CaMATE23 are vital for translational genomic research, including marker-assisted breeding, for developing chickpea cultivars with desirable seed color that appeal to consumers and meet global market demand.
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Affiliation(s)
- Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Nidhi Varshney
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, 303002, India
| | - Anurag Daware
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Rishi Srivastava
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Jitendra K Mohanty
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Udita Basu
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Laxmi Narnoliya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
| | - Shailesh Tripathi
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
- Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi, 110021, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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Mittal N, Bhardwaj J, Verma S, Singh RK, Yadav R, Kaur D, Talukdar A, Yadav N, Kumar R. Disentangling potential genotypes for macro and micro nutrients and polymorphic markers in Chickpea. Sci Rep 2023; 13:10731. [PMID: 37400481 DOI: 10.1038/s41598-023-37602-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 06/23/2023] [Indexed: 07/05/2023] Open
Abstract
The present investigation was conducted to assess the nutritional diverseness and identify novel genetic resources to be utilized in chickpea breeding for macro and micro nutrients. The plants were grown in randomized block design. Nutritional and phytochemical properties of nine chickpea genotypes were estimated. The EST sequences from NCBI database were downloaded in FASTA format, clustered into contigs using CAP3, mined for novel SSRs using TROLL analysis and primer pairs were designed using Primer 3 software. Jaccard's similarity coefficients were used to compare the nutritional and molecular indexes followed by dendrograms construction employing UPGMA approach. The genotypes PUSA-1103, K-850, PUSA-1108, PUSA-1053 and the EST-SSR markers including the 5 newly designed namely ICCeM0012, ICCeM0049, ICCeM0067, ICCeM0070, ICCeM0078, SVP55, SVP95, SVP96, SVP146, and SVP217 were found as potential donor/marker resources for the macro-micro nutrients. The genotypes differed (p < 0.05) for nutritional properties. Amongst newly designed primers, 6 were found polymorphic with median PIC (0.46). The alleles per primer ranged 1 to 8. Cluster analysis based on nutritional and molecular diversities partially matched to each other in principle. The identified novel genetic resources may be used to widen the germplasm base, prepare maintainable catalogue and identify systematic blueprints for future chickpea breeding strategies targeting macro-micro nutrients.
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Affiliation(s)
- Neha Mittal
- Department of Biotechnology, Meerut Institute of Engineering & Technology, Meerut, 250005, India
| | - Juhi Bhardwaj
- Department of Biotechnology, Meerut Institute of Engineering & Technology, Meerut, 250005, India
| | - Shruti Verma
- NCoE-SAM, Department of Pediatrics, KSCH, Lady Hardinge Medical College, New Delhi, 110001, India
| | - Rajesh Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Renu Yadav
- AIOA, Amity University, Noida, UP, 201313, India
| | - D Kaur
- Centre for Food Technology, University of Allahabad, Prayagraj, UP, 211002, India
| | - Akshay Talukdar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Neelam Yadav
- Centre for Food Technology, University of Allahabad, Prayagraj, UP, 211002, India
| | - Rajendra Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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Nagpal S, Sirari A, Sharma P, Singh S, Mandahal KS, Singh H, Singh S. Marker trait association for biological nitrogen fixation traits in an interspecific cross of chickpea ( Cicer arietinum × Cicer reticulatum). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1005-1018. [PMID: 37649881 PMCID: PMC10462594 DOI: 10.1007/s12298-023-01335-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 09/01/2023]
Abstract
A set of 165 Recombinant inbred lines (RILs) derived from an interspecific cross of chickpea was used to identify QTLs for key biological nitrogen fixation (BNF) traits. The phenotyping of BNF and related traits was done at two different agroclimatic zones viz., Central plain zone (Ludhiana) and Sub-Mountainous undulating zone (Gurdaspur) for 2 consecutive rabi seasons (2018-2020). Wild parent C. reticulatum ILWC292 showed significantly high performance in terms of biological nitrogen fixation (BNF) traits over the cultivated C. arietinum GPF-2. The triple interaction of genotypes × locations × years was significant (p 0.05) for all BNF traits in parental lines. Highly significant positive correlation was obtained between grain yield and key growth and symbiotic parameters at both the sites. Phenotypic analysis revealed nodule dry weight and leghaemoglobin content as key traits for BNF efficiency and contrasting DNA bulks were constituted on the basis of these traits. Out of 535 SSR markers, 139 exhibited polymorphism between the parental lines on polyacrylamide gel electrophoresis. A total of 30 SSR markers showed polymorphism between the higher and lower bulks for nodule dry weight and leghaemoglobin content. Out of these, 20 SSRs did not show any segregation distortion in RIL population as determined by chi square analysis (p < 0.05) and were used for quantitative trait loci (QTL) analysis. Using QTL cartographer, markers- CAGM02697, CAGM09835, CAGM09777, CAGM09227, CAGM09021, CAGM08679 were found linked with QTLs for BNF. These markers can be validated further for identification of genes for BNF traits and marker assisted selection in chickpea. To the best of our knowledge this is the first report on identification of genomic regions associated with key BNF traits in chickpea across different agro-climatic zones. Supplementary information The online version contains supplementary material available at 10.1007/s12298-023-01335-3.
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Affiliation(s)
- Sharon Nagpal
- Department of Microbiology, Punjab Agricultural University, Ludhiana, 141004 India
| | - Asmita Sirari
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Poonam Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | - Satinder Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
| | | | - Harpreet Singh
- Regional Research Station, Punjab Agricultural University, Gurdaspur, 143521 India
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004 India
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Sari D, Sari H, Ikten C, Toker C. Genome-wide discovery of di-nucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz. Sci Rep 2023; 13:10351. [PMID: 37365279 DOI: 10.1038/s41598-023-37268-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 06/19/2023] [Indexed: 06/28/2023] Open
Abstract
Simple sequence repeats (SSRs) are valuable genetic markers due to their co-dominant inheritance, multi-allelic and reproducible nature. They have been largely used for exploiting genetic architecture of plant germplasms, phylogenetic analysis, and mapping studies. Among the SSRs, di-nucleotide repeats are the most frequent of the simple repeats distributed throughout the plant genomes. In present study, we aimed to discover and develop di-nucleotide SSR markers by using the whole genome re-sequencing (WGRS) data from Cicer arietinum L. and C. reticulatum Ladiz. A total of 35,329 InDels were obtained in C. arietinum, whereas 44,331 InDels in C. reticulatum. 3387 InDels with 2 bp length were detected in C. arietinum, there were 4704 in C. reticulatum. Among 8091 InDels, 58 di-nucleotide regions that were polymorphic between two species were selected and used for validation. We tested primers for evaluation of genetic diversity in 30 chickpea genotypes including C. arietinum, C. reticulatum, C. echinospermum P.H. Davis, C. anatolicum Alef., C. canariense A. Santos & G.P. Lewis, C. microphyllum Benth., C. multijugum Maesen, C. oxyodon Boiss. & Hohen. and C. songaricum Steph ex DC. A total of 244 alleles were obtained for 58 SSR markers giving an average of 2.36 alleles per locus. The observed heterozygosity was 0.08 while the expected heterozygosity was 0.345. Polymorphism information content was found to be 0.73 across all loci. Phylogenetic tree and principal coordinate analysis clearly divided the accessions into four groups. The SSR markers were also evaluated in 30 genotypes of a RIL population obtained from an interspecific cross between C. arietinum and C. reticulatum. Chi-square (χ2) test revealed an expected 1:1 segregation ratio in the population. These results demonstrated the success of SSR identification and marker development for chickpea with the use of WGRS data. The newly developed 58 SSR markers are expected to be useful for chickpea breeders.
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Affiliation(s)
- Duygu Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07070, Antalya, Turkey.
| | - Hatice Sari
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07070, Antalya, Turkey
| | - Cengiz Ikten
- Department of Plant Protection, Faculty of Agriculture, Akdeniz University, 07070, Antalya, Turkey
| | - Cengiz Toker
- Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07070, Antalya, Turkey
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10
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Yadav RK, Tripathi MK, Tiwari S, Tripathi N, Asati R, Patel V, Sikarwar RS, Payasi DK. Breeding and Genomic Approaches towards Development of Fusarium Wilt Resistance in Chickpea. Life (Basel) 2023; 13:988. [PMID: 37109518 PMCID: PMC10144025 DOI: 10.3390/life13040988] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/29/2023] Open
Abstract
Chickpea is an important leguminous crop with potential to provide dietary proteins to both humans and animals. It also ameliorates soil nitrogen through biological nitrogen fixation. The crop is affected by an array of biotic and abiotic factors. Among different biotic stresses, a major fungal disease called Fusarium wilt, caused by Fusarium oxysporum f. sp. ciceris (FOC), is responsible for low productivity in chickpea. To date, eight pathogenic races of FOC (race 0, 1A, and 1B/C, 2-6) have been reported worldwide. The development of resistant cultivars using different conventional breeding methods is very time consuming and depends upon the environment. Modern technologies can improve conventional methods to solve these major constraints. Understanding the molecular response of chickpea to Fusarium wilt can help to provide effective management strategies. The identification of molecular markers closely linked to genes/QTLs has provided great potential for chickpea improvement programs. Moreover, omics approaches, including transcriptomics, metabolomics, and proteomics give scientists a vast viewpoint of functional genomics. In this review, we will discuss the integration of all available strategies and provide comprehensive knowledge about chickpea plant defense against Fusarium wilt.
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Affiliation(s)
- Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Manoj Kumar Tripathi
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Sushma Tiwari
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
- Department of Plant Molecular Biology & Biotechnology, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Krishi Vishwa Vidyalaya, Jabalpur 482004, India
| | - Ruchi Asati
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Vinod Patel
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - R. S. Sikarwar
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
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11
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Mir AH, Bhat MA, Fayaz H, Wani AA, Dar SA, Maqbool S, Yasin M, Mir JI, Khan MA, Sofi PA, El-Sappah AH, Thudi M, Varshney RK, Mir RR. SSR markers in revealing extent of genetic diversity and phylogenetic relationships among chickpea core collection accessions for Western Himalayas. Mol Biol Rep 2022; 49:11469-11479. [PMID: 36006503 DOI: 10.1007/s11033-022-07858-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 08/11/2022] [Indexed: 10/15/2022]
Abstract
BACKGROUND The exploration of genetic diversity is the key source of germplasm conservation and potential to broaden its genetic base. The globally growing demand for chickpea suggests superior/climate-resilient varieties, which in turn necessitates the germplasm characterization to unravel underlying genetic variation. METHODOLOGY AND RESULTS A chickpea core collection comprising of diverse 192 accessions which include cultivated Cicer arietinum, and wild C. reticulatum, C. echinospermum, and C. microphyllum species were investigated to analyze their genetic diversity and relationship, by assaying 33 unlinked simple sequence repeat (SSR) markers. The results amplified a total of 323 alleles (Na), ranging from 2 to 8 with an average of 4.25 alleles per locus. Expected heterozygosity (He) differed from 0.46 to 0.86 with an average of 0.68. Polymorphic information content (PIC) ranged from 0.73 to 0.98 with an average of 0.89. Analysis of molecular variance (AMOVA) showed that most of the variation was among individuals (87%). Cluster analysis resulted in the formation of four distinct clusters. Cluster I represented all cultivated and clusters II, III, and IV comprised a heterogeneous group of cultivated and wild chickpea accessions. CONCLUSION We report considerable diversity and greater resolving power of SSR markers for assessing variability and interrelationship among the chickpea accessions. The chickpea core is expected to be an efficient resource for breeders for broadening the chickpea genetic base and could be useful for selective breeding of desirable traits and in the identification of target genes for genomics-assisted breeding.
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Affiliation(s)
- Asma Hamid Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, India
| | - Mohd Ashraf Bhat
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, India
| | - Humara Fayaz
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, India.,Department of Botany, Cytogenetics and Reproductive Biology Laboratory, University of Kashmir, Srinagar, Kashmir, India
| | - Aijaz A Wani
- Department of Botany, Cytogenetics and Reproductive Biology Laboratory, University of Kashmir, Srinagar, Kashmir, India
| | - Sher A Dar
- Dryland Agriculture Research Station (DARS), SKUAST-Kashmir, Budgam, Kashmir, India
| | - Showkat Maqbool
- Division of Animal Genetics and Breeding, SKUAST-Kashmir, FVSc & AH, Shuhama, Srinagar, Kashmir, India
| | - Mohammad Yasin
- Rafi Amhad Kidwai (RAK) College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya (RVSKV), Sehore, Madhya Pradesh, India
| | - Javid Iqbal Mir
- ICAR-Central Institute of Temperate Horticulture (CITH), Srinagar, Kashmir, India
| | - Mohd Anwar Khan
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, India
| | - Parvaze A Sofi
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, India
| | - Ahmed H El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Mahendar Thudi
- Center of Excellence in Genomics & Systems Biology (CEGSB), Iinternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India.,Department of Agricultural Biotechnology and Biotechnology, Rajendra Prasad Central Agricultural University, Pusa, Samasthipur, Bihar, India
| | - Rajeev Kumar Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), Iinternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, India.,State Agricultural Biotechnology Centre, Crop & Food Innovation Centre, Food Futures Institute, Murdoch University, Murdoch, WA, Australia
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST-Kashmir, Wadura Campus, Sopore, Kashmir, India.
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12
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Yadav G, Jayaswal D, Jayaswall K, Bhandawat A, Singh A, Tilgam J, Rai AK, Chaturvedi R, Kumar A, Kumar S, Jeevan Kumar SP. Identification and characterization of chickpea genotypes for early flowering and higher seed germination through molecular markers. Mol Biol Rep 2022; 49:6181-6188. [PMID: 35526245 DOI: 10.1007/s11033-022-07410-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 03/18/2022] [Accepted: 03/22/2022] [Indexed: 10/18/2022]
Abstract
BACKGROUND Chickpea is the fourth most important legume crop contributing 15.42% to the total legume production and a rich source of proteins, minerals, and vitamins. Determination of genetic diversity of wild and elite cultivars coupled with early flowering and higher seed germination lines are quintessential for variety improvement. METHODS AND RESULTS In the present study, we have analyzed the genetic diversity, population structure, cross-species transferability, and allelic richness in 50 chickpea collections using 23 Inter simple sequence repeats (ISSR) markers. The observed parameters such as allele number varied from 3 to 16, range of allele size varied from 150 to 1600 bp and polymorphic information content (PIC) range lies in between 0.15 and 0.49. Dendrogram was constructed with ISSR marker genotypic data and classified 50 chickpea germplasms into groups I and II, where the accession P 74 - 1 is in group I and the rest are in group II. Dendrogram, Principal component analysis (PCA), dissimilarity matrix, and Bayesian model-based genetic clustering of 50 chickpea germplasms revealed that P 74 - 1 and P 1883 are very diverse chickpea accessions. CONCLUSION Based on genetic diversity analysis, 15 chickpea germplasm having been screened for early flowering and higher seed germination and found that the P 1857-1 and P 3971 have early flowering and higher seed germination percentage in comparison to P 1883 and other germplasm. These agronomic traits are essential for crop improvement and imply the potential of ISSR markers in crop improvement.
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Affiliation(s)
- Garima Yadav
- ICAR- Indian Institute of Seed Science, 275103, Mau, Uttar Pradesh, India
| | - Deepanshu Jayaswal
- ICAR- Indian Institute of Seed Science, 275103, Mau, Uttar Pradesh, India.
| | - Kuldip Jayaswall
- ICAR- Indian Institute of Seed Science, 275103, Mau, Uttar Pradesh, India
- Department of Botany, Banaras Hindu University, 221005, Varanasi, Uttar Pradesh, India
| | - Abhishek Bhandawat
- Agri-Biotechnology Department, National Agri-Food Biotechnology Institute, 140507, Mohali, Punjab, India
| | - ArvindNath Singh
- ICAR- Indian Institute of Seed Science, 275103, Mau, Uttar Pradesh, India
| | - Jyotsana Tilgam
- ICAR- National Bureau of Agriculturally Important Microorganisms, 275103, Mau, Uttar Pradesh, India
- Amity Institute of Biotechnology, Amity University, 226028, Lucknow, Uttar Pradesh, India
| | - Abhishek Kumar Rai
- ICAR- Indian Institute of Seed Science, 275103, Mau, Uttar Pradesh, India
| | - Rachna Chaturvedi
- ICAR- National Bureau of Agriculturally Important Microorganisms, 275103, Mau, Uttar Pradesh, India
- Amity Institute of Biotechnology, Amity University, 226028, Lucknow, Uttar Pradesh, India
| | - Ashutosh Kumar
- ICAR- Indian Institute of Seed Science, 275103, Mau, Uttar Pradesh, India
| | - Sanjay Kumar
- ICAR- Indian Institute of Seed Science, 275103, Mau, Uttar Pradesh, India
| | - S P Jeevan Kumar
- ICAR- Directorate of Floricultural Research, 411005, Pune, Maharashtra, India.
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13
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Arriagada O, Cacciuttolo F, Cabeza RA, Carrasco B, Schwember AR. A Comprehensive Review on Chickpea ( Cicer arietinum L.) Breeding for Abiotic Stress Tolerance and Climate Change Resilience. Int J Mol Sci 2022; 23:ijms23126794. [PMID: 35743237 PMCID: PMC9223724 DOI: 10.3390/ijms23126794] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 02/05/2023] Open
Abstract
Chickpea is one of the most important pulse crops worldwide, being an excellent source of protein. It is grown under rain-fed conditions averaging yields of 1 t/ha, far from its potential of 6 t/ha under optimum conditions. The combined effects of heat, cold, drought, and salinity affect species productivity. In this regard, several physiological, biochemical, and molecular mechanisms are reviewed to confer tolerance to abiotic stress. A large collection of nearly 100,000 chickpea accessions is the basis of breeding programs, and important advances have been achieved through conventional breeding, such as germplasm introduction, gene/allele introgression, and mutagenesis. In parallel, advances in molecular biology and high-throughput sequencing have allowed the development of specific molecular markers for the genus Cicer, facilitating marker-assisted selection for yield components and abiotic tolerance. Further, transcriptomics, proteomics, and metabolomics have permitted the identification of specific genes, proteins, and metabolites associated with tolerance to abiotic stress of chickpea. Furthermore, some promising results have been obtained in studies with transgenic plants and with the use of gene editing to obtain drought-tolerant chickpea. Finally, we propose some future lines of research that may be useful to obtain chickpea genotypes tolerant to abiotic stress in a scenario of climate change.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
| | - Felipe Cacciuttolo
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
| | - Ricardo A. Cabeza
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile;
| | - Basilio Carrasco
- Centro de Estudios en Alimentos Procesados (CEAP), Av. Lircay s/n, Talca 3480094, Chile;
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile; (O.A.); (F.C.)
- Correspondence:
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14
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Parmar R, Seth R, Sharma RK. Genome-wide identification and characterization of functionally relevant microsatellite markers from transcription factor genes of Tea (Camellia sinensis (L.) O. Kuntze). Sci Rep 2022; 12:201. [PMID: 34996959 PMCID: PMC8742041 DOI: 10.1038/s41598-021-03848-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 12/08/2021] [Indexed: 11/25/2022] Open
Abstract
Tea, being one of the most popular beverages requires large set of molecular markers for genetic improvement of quality, yield and stress tolerance. Identification of functionally relevant microsatellite or simple sequence repeat (SSR) marker resources from regulatory “Transcription factor (TF) genes” can be potential targets to expedite molecular breeding efforts. In current study, 2776 transcripts encoding TFs harbouring 3687 SSR loci yielding 1843 flanking markers were identified from traits specific transcriptome resource of 20 popular tea cultivars. Of these, 689 functionally relevant SSR markers were successfully validated and assigned to 15 chromosomes (Chr) of CSS genome. Interestingly, 589 polymorphic markers including 403 core-set of TF-SSR markers amplified 2864 alleles in key TF families (bHLH, WRKY, MYB-related, C2H2, ERF, C3H, NAC, FAR1, MYB and G2-like). Their significant network interactions with key genes corresponding to aroma, quality and stress tolerance suggests their potential implications in traits dissection. Furthermore, single amino acid repeat reiteration in CDS revealed presence of favoured and hydrophobic amino acids. Successful deployment of markers for genetic diversity characterization of 135 popular tea cultivars and segregation in bi-parental population suggests their wider utility in high-throughput genotyping studies in tea.
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Affiliation(s)
- Rajni Parmar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.,Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Romit Seth
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India
| | - Ram Kumar Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India. .,Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India.
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15
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Validation of the markers linked with drought tolerance related traits for use in MAS programme in chickpea. J Genet 2021. [DOI: 10.1007/s12041-021-01324-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Discerning molecular diversity and association mapping for phenological, physiological and yield traits under high temperature stress in chickpea (Cicer arietinum L.). J Genet 2021. [DOI: 10.1007/s12041-020-01254-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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17
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Genetic diversity and population structure of the endangered fish Pseudobagrus brevicorpus (Bagridae) using a newly developed 12-microsatellite marker. Genes Genomics 2020; 42:1291-1298. [PMID: 32955716 DOI: 10.1007/s13258-020-00992-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 08/28/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Pseudobagrus brevicorpus is an endangered species in Korea. The development of genetic markers and genetic information regarding the populations of this species are needed to establish conservation strategies. OBJECTIVE As part of the conservation of P. brevicorpus, a 12-microsatellite marker was developed using next-generation sequencing (NGS) to provide current genetic population information. METHODS Microsatellites from P. brevicorpus were identified by NGS analysis. Genetic diversity and genetic structure analysis of six populations (Seojeong Stream [SJ], Gokgang Stream [GK], Jaho Stream [JH], Daega Stream [DG], Nam River [NG], and Deokcheon River [DC]) of P. brevicorpus were conducted using the newly developed microsatellite marker. RESULTS NGS generated 10,347,578 reads and identified 659,507 simple sequence repeats. Twelve microsatellites were successfully amplified and verified in 30 individuals of P. brevicorpus. The genetic diversity of the six P. brevicorpus populations in terms of the number of alleles ranged from 3.667 to 7.111. All populations except DG deviated significantly from Hardy-Weinberg equilibrium (HWE) at one or more loci. The genetic distances of the six populations showed the closest relationship between the SJ and GK populations (independent Stream populations), and there was a close relationship with the JH population among the Nakdong River. Structure analysis showed that P. brevicorpus is largely divided into two groups. CONCLUSIONS The developed microsatellite marker will be used to provide basic genetic data of P. brevicorpus. Genetic diversity and structure analysis of the population will provide useful information for conservation management of P. brevicorpus.
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Pavan Kumar P, Janakiram T, Bhat KV. Microsatellite based DNA fingerprinting and assessment of genetic diversity in bougainvillea cultivars. Gene 2020; 753:144794. [PMID: 32464245 DOI: 10.1016/j.gene.2020.144794] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 05/16/2020] [Accepted: 05/18/2020] [Indexed: 11/16/2022]
Abstract
Novel microsatellite markers were developed to investigate the genetic diversity and DNA fingerprinting of bougainvillea cultivars. Total of 175 SSRs were designed from over 50,000 SSRs identified in the whole genome sequence data, 33 highly polymorphic markers were identified. These selected SSRs produced a total of 165 alleles with 2 (BOUG-3 and BOUG-50) to 9 (BOUG-69) alleles per loci with an average of 5 alleles per locus. The overall size of the amplified products ranged from 90 bp (BOUG-51 and BOUG-81) to 320 bp (BOUG-162). The gene diversity per locus ranged from 0.13 to 0.91 with a mean of 0.71. Primer BOUG-73 and BOUG-124 exhibited highest gene diversity with greater number of alleles. The mean Nei's genetic diversity index was 0.678 with range of 0.134 (BOUG-77) to 0.958 (BOUG-69). The UPGMA based dendrogram divided the cultivars into seven major clusters. Clustering pattern was more distinct for bract types and variegated cultivars which were also confirmed by PCA scatter plot diagram. The pair-wise genetic distance estimates ranged from 0.089 to 0.86 with an average of 0.56. Each of the 125 cultivar profiled had unique marker profile indicating that the SSR markers identified are useful for identification and differentiation of bougainvillea cultivars. These informative markers identified from the study will be of great utility to assess the genetic diversity, understanding the population structure and in marker assisted breeding for improvement of bougainvillea.
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Affiliation(s)
- P Pavan Kumar
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - T Janakiram
- Division of Floriculture and Landscaping, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - K V Bhat
- Division of Genomic Resources, ICAR-National Bureau of Plant Genomic Resources, New Delhi, India.
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19
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Jha UC, Jha R, Bohra A, Parida SK, Kole PC, Thakro V, Singh D, Singh NP. Population structure and association analysis of heat stress relevant traits in chickpea ( Cicer arietinum L.). 3 Biotech 2018; 8:43. [PMID: 29354354 PMCID: PMC5750240 DOI: 10.1007/s13205-017-1057-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 12/19/2017] [Indexed: 12/27/2022] Open
Abstract
Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.
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Affiliation(s)
- Uday Chand Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Rintu Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Paresh Chandra Kole
- Department of Genetics & Plant Breeding and Crop Physiology, Institute of Agriculture, Visva Bharati University, Sriniketan, Bolpur, West Bengal 731236 India
| | - Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Deepak Singh
- Indian Agricultural Statistical Research Institute (IASRI), New Delhi, India
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20
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Jha UC, Jha R, Bohra A, Parida SK, Kole PC, Thakro V, Singh D, Singh NP. Population structure and association analysis of heat stress relevant traits in chickpea ( Cicer arietinum L.). 3 Biotech 2018. [PMID: 29354354 DOI: 10.1007/s1320] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023] Open
Abstract
Understanding genetic diversity and population structure is prerequisite to broaden the cultivated base of any crop. In the current investigation, we report discovery of a total of 319 alleles by assaying 81 SSRs on 71 chickpea genotypes. The cluster analysis based on Jaccard coefficient and unweighted neighbor joining algorithm categorized all genotypes into two major clusters. Cultivars grown within the same agro-climatic zones were clustered together, whereas the remaining genotypes particularly advanced breeding lines and accessions assigned to another cluster. Population structure analysis separated the entire collection into two subpopulations (K = 2) and the clustering pattern remained in close agreement with those of distance-based methods. Importantly, we also discovered marker trait association for membrane stability index (MSI) and leaf chlorophyll content measured as SPAD chlorophyll meter reading (SCMR), the two important physiological parameters indicative of heat stress (HS) tolerance in chickpea. Association analysis using both general linear and mixed linear models of the mean phenotypic data of traits recorded in 2016 and 2017 uncovered significant association of NCPGR206 and H2L102 with the MSI trait. Likewise, SSR markers GA9, TR31 and TA113 exhibited significant association with SCMR trait. The genomic regions putatively linked with two traits may be investigated in greater detail to further improve knowledge about the genetic architecture of HS tolerance in chickpea.
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Affiliation(s)
- Uday Chand Jha
- 1Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Rintu Jha
- 1Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Abhishek Bohra
- 1Indian Institute of Pulses Research (IIPR), Kanpur, UP 208 024 India
| | - Swarup Kumar Parida
- 2National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Paresh Chandra Kole
- 3Department of Genetics & Plant Breeding and Crop Physiology, Institute of Agriculture, Visva Bharati University, Sriniketan, Bolpur, West Bengal 731236 India
| | - Virevol Thakro
- 2National Institute of Plant Genome Research (NIPGR), New Delhi, 110067 India
| | - Deepak Singh
- Indian Agricultural Statistical Research Institute (IASRI), New Delhi, India
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21
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De Giovanni C, Pavan S, Taranto F, Di Rienzo V, Miazzi MM, Marcotrigiano AR, Mangini G, Montemurro C, Ricciardi L, Lotti C. Genetic variation of a global germplasm collection of chickpea ( Cicer arietinum L.) including Italian accessions at risk of genetic erosion. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:197-205. [PMID: 28250595 PMCID: PMC5313401 DOI: 10.1007/s12298-016-0397-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/18/2016] [Accepted: 11/18/2016] [Indexed: 05/17/2023]
Abstract
Chickpea (Cicer arietinum L.) is one of the most important legumes worldwide. We addressed this study to the genetic characterization of a germplasm collection from main chickpea growing countries. Several Italian traditional landraces at risk of genetic erosion were included in the analysis. Twenty-two simple sequence repeat (SSR) markers, widely used to explore genetic variation in plants, were selected and yielded 218 different alleles. Structure analysis and hierarchical clustering indicated that a model with three distinct subpopulations best fits the data. The composition of two subpopulations, named K1 and K2, broadly reflects the commercial classification of chickpea in the two types desi and kabuli, respectively. The third subpopulation (K3) is composed by both desi and kabuli genotypes. Italian accessions group both in K2 and K3. Interestingly, this study highlights genetic distance between desi genotypes cultivated in Asia and Ethiopia, which respectively represent the chickpea primary and the secondary centres of diversity. Moreover, European desi are closer to the Ethiopian gene pool. Overall, this study will be of importance for chickpea conservation genetics and breeding, which is limited by the poor characterization of germplasm collection.
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Affiliation(s)
- C. De Giovanni
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - S. Pavan
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - F. Taranto
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - V. Di Rienzo
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - M. M. Miazzi
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - A. R. Marcotrigiano
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - G. Mangini
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - C. Montemurro
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - L. Ricciardi
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Via Amendola 165/A, 70126 Bari, Italy
| | - C. Lotti
- Department of Agriculture, Food and Environmental Science, University of Foggia, Via Napoli 25, 71100 Foggia, Italy
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Mallikarjuna BP, Samineni S, Thudi M, Sajja SB, Khan AW, Patil A, Viswanatha KP, Varshney RK, Gaur PM. Molecular Mapping of Flowering Time Major Genes and QTLs in Chickpea ( Cicer arietinum L.). FRONTIERS IN PLANT SCIENCE 2017; 8:1140. [PMID: 28729871 PMCID: PMC5498527 DOI: 10.3389/fpls.2017.01140] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 06/14/2017] [Indexed: 05/20/2023]
Abstract
Flowering time is an important trait for adaptation and productivity of chickpea in the arid and the semi-arid environments. This study was conducted for molecular mapping of genes/quantitative trait loci (QTLs) controlling flowering time in chickpea using F2 populations derived from four crosses (ICCV 96029 × CDC Frontier, ICC 5810 × CDC Frontier, BGD 132 × CDC Frontier and ICC 16641 × CDC Frontier). Genetic studies revealed monogenic control of flowering time in the crosses ICCV 96029 × CDC Frontier, BGD 132 × CDC Frontier and ICC 16641 × CDC Frontier, while digenic control with complementary gene action in ICC 5810 × CDC Frontier. The intraspecific genetic maps developed from these crosses consisted 75, 75, 68 and 67 markers spanning 248.8 cM, 331.4 cM, 311.1 cM and 385.1 cM, respectively. A consensus map spanning 363.8 cM with 109 loci was constructed by integrating four genetic maps. Major QTLs corresponding to flowering time genes efl-1 from ICCV 96029, efl-3 from BGD 132 and efl-4 from ICC 16641 were mapped on CaLG04, CaLG08 and CaLG06, respectively. The QTLs and linked markers identified in this study can be used in marker-assisted breeding for developing early maturing chickpea.
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Affiliation(s)
- Bingi P. Mallikarjuna
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- Department of Genetics and Plant Breeding, University of Agricultural SciencesRaichur, India
| | - Srinivasan Samineni
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Sobhan B. Sajja
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Aamir W. Khan
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Ayyanagowda Patil
- Department of Genetics and Plant Breeding, University of Agricultural SciencesRaichur, India
| | - Kannalli P. Viswanatha
- Department of Genetics and Plant Breeding, University of Agricultural SciencesRaichur, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
| | - Pooran M. Gaur
- International Crops Research Institute for the Semi-Arid TropicsPatancheru, India
- The UWA Institute of Agriculture, University of Western AustraliaPerth, WA, Australia
- *Correspondence: Pooran M. Gaur
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23
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Gupta S, Kumar T, Verma S, Bharadwaj C, Bhatia S. Development of gene-based markers for use in construction of the chickpea (Cicer arietinum L.) genetic linkage map and identification of QTLs associated with seed weight and plant height. Mol Biol Rep 2015; 42:1571-80. [PMID: 26446030 DOI: 10.1007/s11033-015-3925-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 10/03/2015] [Indexed: 11/28/2022]
Abstract
Seed weight and plant height are important agronomic traits and contribute to seed yield. The objective of this study was to identify QTLs underlying these traits using an intra-specific mapping population of chickpea. A F11 population of 177 recombinant inbred lines derived from a cross between SBD377 (100-seed weight--48 g and plant height--53 cm) and BGD112 (100-seed weight--15 g and plant height--65 cm) was used. A total of 367 novel EST-derived functional markers were developed which included 187 EST-SSRs, 130 potential intron polymorphisms (PIPs) and 50 expressed sequence tag polymorphisms (ESTPs). Along with these, 590 previously published markers including 385 EST-based markers and 205 genomic SSRs were utilized. Of the 957 markers tested for analysis of parental polymorphism between the two parents of the mapping population, 135 (14.64%) were found to be polymorphic. Of these, 131 polymorphic markers could be mapped to the 8 linkage groups. The linkage map had a total length of 1140.54 cM with an average marker density of 8.7 cM. The map was further used for QTL identification using composite interval mapping method (CIM). Two QTLs each for seed weight, qSW-1 and qSW-2 (explaining 11.54 and 19.24% of phenotypic variance, respectively) and plant height, qPH-1 and qPH-2 (explaining 13.98 and 12.17% of phenotypic variance, respectively) were detected. The novel set of genic markers, the intra-specific linkage map and the QTLs identified in the present study will serve as valuable genomic resources in improving the chickpea seed yield using marker-assisted selection (MAS) strategies.
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Affiliation(s)
- Shefali Gupta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | - Tapan Kumar
- Indian Agricultural Research Institute, Pusa, New Delhi, 110012, India
| | - Subodh Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India
| | | | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi, 110067, India.
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CNMS: The preferred genic markers for comparative genomic, molecular phylogenetic, functional genetic diversity and differential gene regulatory expression analyses in chickpea. J Biosci 2015; 40:579-92. [PMID: 26333404 DOI: 10.1007/s12038-015-9545-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The intra/inter-genomic comparative mapping-based phylogenetic footprinting identified 5 paralogous and 656 orthologous genome-wide CNMS markers in the upstream sequences of chickpea genes. These CNMS markers revealed a high-degree of gene-based syntenic relationship between chickpea and Medicago genomes while minimum between chickpea and Vitis genomes. The time of divergence and duplication estimated using CNMS markers highlight the expected phylogenetic relationships between chickpea and six dicot (legume) species as well as occurrence of ancient genome (approximately 53 Mya) with small-scale recent segmental (approximately 10 Mya) duplication events in chickpea. A wider level of functional molecular diversity (14 to 88 percent) and admixed population genetic structure was detected among desi, kabuli and wild genotypes by genic CNMS markers at a genome-wide scale suggesting their utility in large-scale genetic analysis in chickpea. The subfunctionalization at the cis-regulatory element region and TFBS (transcription factor binding site) motif levels in the upstream sequences of CNMS marker-associated orthologous genes than the paralogues was predominant. Functional constraint might have considerable effect on these CNMScontaining regulatory elements controlling consistent orthologous gene expression in dicots. A rapid subfunctionalization based on diverge differential expression of paralogous CNMS marker-associated genes particularly those that underwent recent small-scale segmental duplication events in chickpea was apparent. The differential regulation of expression and subfunctionalization potential of Ultra CNMS marker-associated genes suggest their utility in deciphering the complex gene regulatory function as well as identification and targeted mapping of potential genes/QTLs governing vital agronomic traits in chickpea. The gene-based CNMS markers with desirable inherent genetic attributes like higher degree of comparative genome mapping, functional genetic diversity and differential gene regulatory expression potential can significantly propel the genomics-assisted chickpea crop improvement.
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25
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Gaur R, Jeena G, Shah N, Gupta S, Pradhan S, Tyagi AK, Jain M, Chattopadhyay D, Bhatia S. High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea. Sci Rep 2015; 5:13387. [PMID: 26303721 PMCID: PMC4548218 DOI: 10.1038/srep13387] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 07/29/2015] [Indexed: 01/07/2023] Open
Abstract
This study presents genome-wide discovery of SNPs through next generation sequencing of the genome of Cicer reticulatum. Mapping of the C. reticulatum sequenced reads onto the draft genome assembly of C. arietinum (desi chickpea) resulted in identification of 842,104 genomic SNPs which were utilized along with an additional 36,446 genic SNPs identified from transcriptome sequences of the aforementioned varieties. Two new chickpea Oligo Pool All (OPAs) each having 3,072 SNPs were designed and utilized for SNP genotyping of 129 Recombinant Inbred Lines (RILs). Using Illumina GoldenGate Technology genotyping data of 5,041 SNPs were generated and combined with the 1,673 marker data from previously published studies, to generate a high resolution linkage map. The map comprised of 6698 markers distributed on eight linkage groups spanning 1083.93 cM with an average inter-marker distance of 0.16 cM. Utility of the present map was demonstrated for improving the anchoring of the earlier reported draft genome sequence of desi chickpea by ~30% and that of kabuli chickpea by 18%. The genetic map reported in this study represents the most dense linkage map of chickpea , with the potential to facilitate efficient anchoring of the draft genome sequences of desi as well as kabuli chickpea varieties.
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Affiliation(s)
- Rashmi Gaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Ganga Jeena
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Niraj Shah
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Shefali Gupta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Seema Pradhan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Mukesh Jain
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi 110067, India
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26
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Parida SK, Verma M, Yadav SK, Ambawat S, Das S, Garg R, Jain M. Development of genome-wide informative simple sequence repeat markers for large-scale genotyping applications in chickpea and development of web resource. FRONTIERS IN PLANT SCIENCE 2015; 6:645. [PMID: 26347762 PMCID: PMC4543896 DOI: 10.3389/fpls.2015.00645] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Accepted: 08/03/2015] [Indexed: 05/18/2023]
Abstract
Development of informative polymorphic simple sequence repeat (SSR) markers at a genome-wide scale is essential for efficient large-scale genotyping applications. We identified genome-wide 1835 SSRs showing polymorphism between desi and kabuli chickpea. A total of 1470 polymorphic SSR markers from diverse coding and non-coding regions of the chickpea genome were developed. These physically mapped SSR markers exhibited robust amplification efficiency (73.9%) and high intra- and inter-specific polymorphic potential (63.5%), thereby suggesting their immense use in various genomics-assisted breeding applications. The SSR markers particularly derived from intergenic and intronic sequences revealed high polymorphic potential. Using the mapped SSR markers, a wider functional molecular diversity (16-94%, mean: 68%), and parentage- and cultivar-specific admixed domestication pattern and phylogenetic relationships in a structured population of desi and kabuli chickpea genotypes was evident. The intra-specific polymorphism (47.6%) and functional molecular diversity (65%) potential of polymorphic SSR markers developed in our study is much higher than that of previous documentations. Finally, we have developed a user-friendly web resource, Chickpea Microsatellite Database (CMsDB; http://www.nipgr.res.in/CMsDB.html), which provides public access to the data and results reported in this study. The developed informative SSR markers can serve as a resource for various genotyping applications, including genetic enhancement studies in chickpea.
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Affiliation(s)
| | | | | | | | | | | | - Mukesh Jain
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome ResearchNew Delhi, India
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27
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Parween S, Nawaz K, Roy R, Pole AK, Venkata Suresh B, Misra G, Jain M, Yadav G, Parida SK, Tyagi AK, Bhatia S, Chattopadhyay D. An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.). Sci Rep 2015; 5:12806. [PMID: 26259924 PMCID: PMC4531285 DOI: 10.1038/srep12806] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Accepted: 07/06/2015] [Indexed: 11/09/2022] Open
Abstract
Chickpea (Cicer arietinum L.) is an important pulse legume crop. We previously reported a draft genome assembly of the desi chickpea cultivar ICC 4958. Here we report an advanced version of the ICC 4958 genome assembly (version 2.0) generated using additional sequence data and an improved genetic map. This resulted in 2.7-fold increase in the length of the pseudomolecules and substantial reduction of sequence gaps. The genome assembly covered more than 94% of the estimated gene space and predicted the presence of 30,257 protein-coding genes including 2230 and 133 genes encoding potential transcription factors (TF) and resistance gene homologs, respectively. Gene expression analysis identified several TF and chickpea-specific genes with tissue-specific expression and displayed functional diversification of the paralogous genes. Pairwise comparison of pseudomolecules in the desi (ICC 4958) and the earlier reported kabuli (CDC Frontier) chickpea assemblies showed an extensive local collinearity with incongruity in the placement of large sequence blocks along the linkage groups, apparently due to use of different genetic maps. Single nucleotide polymorphism (SNP)-based mining of intra-specific polymorphism identified more than four thousand SNPs differentiating a desi group and a kabuli group of chickpea genotypes.
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Affiliation(s)
- Sabiha Parween
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Kashif Nawaz
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Riti Roy
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Anil K. Pole
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - B. Venkata Suresh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Gopal Misra
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Mukesh Jain
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Gitanjali Yadav
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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28
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Yuan CY, Wang P, Chen PP, Xiao WJ, Zhang C, Hu S, Zhou P, Chang HP, He Z, Hu R, Lu XT, Ye JZ, Guo XH. Genetic diversity revealed by morphological traits and ISSR markers in 48 Okras (Abelmoschus escullentus L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2015; 21:359-364. [PMID: 26261400 PMCID: PMC4524858 DOI: 10.1007/s12298-015-0303-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 06/08/2015] [Accepted: 06/08/2015] [Indexed: 06/04/2023]
Abstract
Okra is a widely distributed crop in the tropics, subtropics, and warmer areas of the temperate zones. Its major potential uses as a vegetable, oil and protein source, and source of paper pulp and fuel, or biomass are compatible. It is expected to have high value of exploitation and application. Due to the limited number of molecular studies focused on okras, the methods of morphological and ISSR markers were used to analysis the genetic diversity of 48 okras in the present study. The 22 primers were picked for ISSR-PCR, and a total of 154 fragments were amplified with an overall average polymorphism of 54.55 %. We used the 154 markers to construct the dendrogram based on the unweighted pair group method with arithmetic means (UPGMA). A high level of genetic diversity was found among 48 individuals. The 48 Okras was divided into four clusters at Dice's coefficient of 0.19 with clustering analysis. Based on these data of the genetic diversity, it will be possible to exploit the available resources of okra in more valuable ways.
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Affiliation(s)
- Cong-Ying Yuan
- />College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Ping Wang
- />College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Pang-Pang Chen
- />Jiangxi Wugongshan Agriculture Development Limited Company, Luxi, 337200 Jiangxi People’s Republic of China
| | - Wen-Jun Xiao
- />College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Cheng Zhang
- />College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Shuai Hu
- />College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Ping Zhou
- />College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Hong-Ping Chang
- />College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Zhuang He
- />College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Rong Hu
- />College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Xiu-Tao Lu
- />College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
| | - Jia-Zhuo Ye
- />College of Electrical and Information Engineering, Hunan University, Changsha, 410082 People’s Republic of China
| | - Xin-Hong Guo
- />College of Biology, Hunan University, Changsha, 410082 People’s Republic of China
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Khajuria YP, Saxena MS, Gaur R, Chattopadhyay D, Jain M, Parida SK, Bhatia S. Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea. PLoS One 2015; 10:e0125583. [PMID: 25974327 PMCID: PMC4431833 DOI: 10.1371/journal.pone.0125583] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 03/24/2015] [Indexed: 11/18/2022] Open
Abstract
The identification of informative in silico polymorphic genomic and genic microsatellite markers by comparing the genome and transcriptome sequences of crop genotypes is a rapid, cost-effective and non-laborious approach for large-scale marker validation and genotyping applications, including construction of high-density genetic maps. We designed 1494 markers, including 1016 genomic and 478 transcript-derived microsatellite markers showing in-silico fragment length polymorphism between two parental genotypes (Cicer arietinum ICC4958 and C. reticulatum PI489777) of an inter-specific reference mapping population. High amplification efficiency (87%), experimental validation success rate (81%) and polymorphic potential (55%) of these microsatellite markers suggest their effective use in various applications of chickpea genetics and breeding. Intra-specific polymorphic potential (48%) detected by microsatellite markers in 22 desi and kabuli chickpea genotypes was lower than inter-specific polymorphic potential (59%). An advanced, high-density, integrated and inter-specific chickpea genetic map (ICC4958 x PI489777) having 1697 map positions spanning 1061.16 cM with an average inter-marker distance of 0.625 cM was constructed by assigning 634 novel informative transcript-derived and genomic microsatellite markers on eight linkage groups (LGs) of our prior documented, 1063 marker-based genetic map. The constructed genome map identified 88, including four major (7–23 cM) longest high-resolution genomic regions on LGs 3, 5 and 8, where the maximum number of novel genomic and genic microsatellite markers were specifically clustered within 1 cM genetic distance. It was for the first time in chickpea that in silico FLP analysis at genome-wide level was carried out and such a large number of microsatellite markers were identified, experimentally validated and further used in genetic mapping. To best of our knowledge, in the presently constructed genetic map, we mapped highest number of new sequence-based robust microsatellite markers (634) which is an advancement over the previously documented (~300 markers) inter-specific genetic maps. This advanced high-density map will serve as a foundation for large-scale marker validation and genotyping applications, including identification and targeted mapping of trait-specific genes/QTLs (quantitative trait loci) with sub-optimal use of resources and labour in chickpea.
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Affiliation(s)
- Yash Paul Khajuria
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Maneesha S. Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Rashmi Gaur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Mukesh Jain
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
| | - Sabhyata Bhatia
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India
- * E-mail:
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Bajaj D, Upadhyaya HD, Khan Y, Das S, Badoni S, Shree T, Kumar V, Tripathi S, Gowda CLL, Singh S, Sharma S, Tyagi AK, Chattopdhyay D, Parida SK. A combinatorial approach of comprehensive QTL-based comparative genome mapping and transcript profiling identified a seed weight-regulating candidate gene in chickpea. Sci Rep 2015; 5:9264. [PMID: 25786576 PMCID: PMC4365403 DOI: 10.1038/srep09264] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2014] [Accepted: 02/13/2015] [Indexed: 01/02/2023] Open
Abstract
High experimental validation/genotyping success rate (94-96%) and intra-specific polymorphic potential (82-96%) of 1536 SNP and 472 SSR markers showing in silico polymorphism between desi ICC 4958 and kabuli ICC 12968 chickpea was obtained in a 190 mapping population (ICC 4958 × ICC 12968) and 92 diverse desi and kabuli genotypes. A high-density 2001 marker-based intra-specific genetic linkage map comprising of eight LGs constructed is comparatively much saturated (mean map-density: 0.94 cM) in contrast to existing intra-specific genetic maps in chickpea. Fifteen robust QTLs (PVE: 8.8-25.8% with LOD: 7.0-13.8) associated with pod and seed number/plant (PN and SN) and 100 seed weight (SW) were identified and mapped on 10 major genomic regions of eight LGs. One of 126.8 kb major genomic region harbouring a strong SW-associated robust QTL (Caq'SW1.1: 169.1-171.3 cM) has been delineated by integrating high-resolution QTL mapping with comprehensive marker-based comparative genome mapping and differential expression profiling. This identified one potential regulatory SNP (G/A) in the cis-acting element of candidate ERF (ethylene responsive factor) TF (transcription factor) gene governing seed weight in chickpea. The functionally relevant molecular tags identified have potential to be utilized for marker-assisted genetic improvement of chickpea.
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Affiliation(s)
- Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Yusuf Khan
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Tanima Shree
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Vinod Kumar
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi 110012, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - C. L. L. Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Debasis Chattopdhyay
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Bajaj D, Saxena MS, Kujur A, Das S, Badoni S, Tripathi S, Upadhyaya HD, Gowda CLL, Sharma S, Singh S, Tyagi AK, Parida SK. Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1271-90. [PMID: 25504138 PMCID: PMC4339591 DOI: 10.1093/jxb/eru478] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Phylogenetic footprinting identified 666 genome-wide paralogous and orthologous CNMS (conserved non-coding microsatellite) markers from 5'-untranslated and regulatory regions (URRs) of 603 protein-coding chickpea genes. The (CT)n and (GA)n CNMS carrying CTRMCAMV35S and GAGA8BKN3 regulatory elements, respectively, are abundant in the chickpea genome. The mapped genic CNMS markers with robust amplification efficiencies (94.7%) detected higher intraspecific polymorphic potential (37.6%) among genotypes, implying their immense utility in chickpea breeding and genetic analyses. Seventeen differentially expressed CNMS marker-associated genes showing strong preferential and seed tissue/developmental stage-specific expression in contrasting genotypes were selected to narrow down the gene targets underlying seed weight quantitative trait loci (QTLs)/eQTLs (expression QTLs) through integrative genetical genomics. The integration of transcript profiling with seed weight QTL/eQTL mapping, molecular haplotyping, and association analyses identified potential molecular tags (GAGA8BKN3 and RAV1AAT regulatory elements and alleles/haplotypes) in the LOB-domain-containing protein- and KANADI protein-encoding transcription factor genes controlling the cis-regulated expression for seed weight in the chickpea. This emphasizes the potential of CNMS marker-based integrative genetical genomics for the quantitative genetic dissection of complex seed weight in chickpea.
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Affiliation(s)
- Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Maneesha S Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Alice Kujur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shouvik Das
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Saurabh Badoni
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - C L L Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Shivali Sharma
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Telangana, India
| | - Akhilesh K Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Thudi M, Gaur PM, Krishnamurthy L, Mir RR, Kudapa H, Fikre A, Kimurto P, Tripathi S, Soren KR, Mulwa R, Bharadwaj C, Datta S, Chaturvedi SK, Varshney RK. Genomics-assisted breeding for drought tolerance in chickpea. FUNCTIONAL PLANT BIOLOGY : FPB 2014; 41:1178-1190. [PMID: 32481067 DOI: 10.1071/fp13318] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Accepted: 05/23/2014] [Indexed: 06/11/2023]
Abstract
Terminal drought is one of the major constraints in chickpea (Cicer arietinum L.), causing more than 50% production losses. With the objective of accelerating genetic understanding and crop improvement through genomics-assisted breeding, a draft genome sequence has been assembled for the CDC Frontier variety. In this context, 544.73Mb of sequence data were assembled, capturing of 73.8% of the genome in scaffolds. In addition, large-scale genomic resources including several thousand simple sequence repeats and several million single nucleotide polymorphisms, high-density diversity array technology (15360 clones) and Illumina GoldenGate assay genotyping platforms, high-density genetic maps and transcriptome assemblies have been developed. In parallel, by using linkage mapping approach, one genomic region harbouring quantitative trait loci for several drought tolerance traits has been identified and successfully introgressed in three leading chickpea varieties (e.g. JG 11, Chefe, KAK 2) by using a marker-assisted backcrossing approach. A multilocation evaluation of these marker-assisted backcrossing lines provided several lines with 10-24% higher yield than the respective recurrent parents.Modern breeding approaches like marker-assisted recurrent selection and genomic selection are being deployed for enhancing drought tolerance in chickpea. Some novel mapping populations such as multiparent advanced generation intercross and nested association mapping populations are also being developed for trait mapping at higher resolution, as well as for enhancing the genetic base of chickpea. Such advances in genomics and genomics-assisted breeding will accelerate precision and efficiency in breeding for stress tolerance in chickpea.
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Affiliation(s)
- Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - Lakshmanan Krishnamurthy
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - Reyazul R Mir
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - Himabindu Kudapa
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
| | - Asnake Fikre
- Ethiopian Institute of Agricultural Research (EIAR), Debre Zeit, PO Box 2003, Ethiopia
| | | | - Shailesh Tripathi
- Indian Agricultural Research Institute (IARI), New Delhi 110 012, India
| | - Khela R Soren
- Indian Institute of Pulses Research (IIPR), Kanpur 208 024, India
| | | | | | - Subhojit Datta
- Indian Institute of Pulses Research (IIPR), Kanpur 208 024, India
| | | | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad 502 324, India
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Doddamani D, Katta MAVSK, Khan AW, Agarwal G, Shah TM, Varshney RK. CicArMiSatDB: the chickpea microsatellite database. BMC Bioinformatics 2014; 15:212. [PMID: 24952649 PMCID: PMC4230034 DOI: 10.1186/1471-2105-15-212] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 06/17/2014] [Indexed: 01/12/2023] Open
Abstract
Background Chickpea (Cicer arietinum) is a widely grown legume crop in tropical, sub-tropical and temperate regions. Molecular breeding approaches seem to be essential for enhancing crop productivity in chickpea. Until recently, limited numbers of molecular markers were available in the case of chickpea for use in molecular breeding. However, the recent advances in genomics facilitated the development of large scale markers especially SSRs (simple sequence repeats), the markers of choice in any breeding program. Availability of genome sequence very recently opens new avenues for accelerating molecular breeding approaches for chickpea improvement. Description In order to assist genetic studies and breeding applications, we have developed a user friendly relational database named the Chickpea Microsatellite Database (CicArMiSatDB http://cicarmisatdb.icrisat.org). This database provides detailed information on SSRs along with their features in the genome. SSRs have been classified and made accessible through an easy-to-use web interface. Conclusions This database is expected to help chickpea community in particular and legume community in general, to select SSRs of particular type or from a specific region in the genome to advance both basic genomics research as well as applied aspects of crop improvement.
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Affiliation(s)
| | | | | | | | | | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, India.
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Wang S, Liu Y, Ma L, Liu H, Tang Y, Wu L, Wang Z, Li Y, Wu R, Pang X. Isolation and characterization of microsatellite markers and analysis of genetic diversity in Chinese jujube (Ziziphus jujuba Mill.). PLoS One 2014; 9:e99842. [PMID: 24932973 PMCID: PMC4059666 DOI: 10.1371/journal.pone.0099842] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2014] [Accepted: 05/17/2014] [Indexed: 11/18/2022] Open
Abstract
Chinese jujube (Ziziphus jujuba Mill, 2n = 2× = 24, Rhamnaceae) is an economically important Chinese native species. It has high nutritional value, and its medicinal properties have led to extensive use in traditional oriental medicine. The characterization of genotypes using molecular markers is important for genetic studies and plant breeding. However, few simple sequence repeat (SSR) markers are available for this species. In this study, 1,488 unique SSR clones were isolated from Z. jujuba 'Dongzao' using enriched genomic libraries coupled with a three-primer colony PCR screening strategy, yielding a high enrichment rate of 73.3%. Finally, 1,188 (80.87%) primer pairs were amplified successfully in the size expected for 'Dongzao'. A total of 350 primer pairs were further selected and evaluated for their ability to detect polymorphisms across a panel of six diverse cultivars; among these, 301 primer pairs detected polymorphisms, and the polymorphism information content (PIC) value across all loci ranged from 0.15 to 0.82, with an average of 0.52. An analysis of 76 major cultivars employed in Chinese jujube production using 31 primer pairs revealed comparatively high genetic diversity among these cultivars. Within-population differences among individuals accounted for 98.2% of the observed genetic variation. Neighbor-joining clustering divided the cultivars into three main groups, none of which correspond to major geographic regions, suggesting that the genetics and geographical origin of modern Chinese jujube cultivars might not be linked. The current work firstly reports the large-scale development of Chinese jujube SSR markers. The development of these markers and their polymorphic information represent a significant improvement in the available Chinese jujube genomic resources and will facilitate both genetic and breeding applications, further accelerating the development of new cultivars.
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Affiliation(s)
- Siqi Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Ying Liu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Liying Ma
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Huabo Liu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yan Tang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Liping Wu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Zhe Wang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Yingyue Li
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Xiaoming Pang
- National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, Center for Computational Biology, College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
- * E-mail:
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Expanding the repertoire of microsatellite markers for polymorphism studies in Indian accessions of mung bean (Vigna radiata L. Wilczek). Mol Biol Rep 2014; 41:5669-80. [PMID: 24913033 DOI: 10.1007/s11033-014-3436-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 05/26/2014] [Indexed: 10/25/2022]
Abstract
Limited availability of validated, polymorphic microsatellite markers in mung bean (Vigna radiata), an important food legume of India, has been a major hurdle towards its improvement and higher yield. The present study was undertaken in order to develop a new set of microsatellite markers and utilize them for the analysis of genetic diversity within mung bean accessions from India. A GA/CT enriched library was constructed from V. radiata which resulted in 1,250 putative recombinant clones of which 850 were sequenced. SSR motifs were identified and their flanking sequences were utilized to design 328 SSR primer pairs. Of these, 48 SSR markers were employed for assessing genetic diversity among 76 mung bean accessions from various geographical locations in India. Two hundred and thirty four alleles with an average of 4.85 alleles per locus were detected at 48 loci. The polymorphic information content (PIC) per locus varied from 0.1 to 0.88 (average: 0.49 per locus). The observed and expected heterozygosities ranged from 0.40 to 0.95 and 0.40 to 0.81 respectively. Based on Jaccard's similarity matrix, a dendrogram was constructed using the unweighted pair-group method with arithmetic averages (UPGMA) analysis which revealed that one accession from Bundi, Rajasthan was clustered out separately while remaining accessions were grouped into two major clusters. The markers generated in this study will help in expanding the repertoire of the available SSR markers thereby facilitating analysis of genetic diversity, molecular mapping and ultimately broadening the scope for genetic improvement of this legume.
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Verma P, Sharma TR, Srivastava PS, Abdin MZ, Bhatia S. Exploring genetic variability within lentil (Lens culinaris Medik.) and across related legumes using a newly developed set of microsatellite markers. Mol Biol Rep 2014; 41:5607-25. [PMID: 24893599 DOI: 10.1007/s11033-014-3431-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 05/21/2014] [Indexed: 12/01/2022]
Abstract
Lentil (Lens culinaris Medik.) is an economically important grain legume, yet the genetic and genomic resources remain largely uncharacterized and unexploited in this crop. Microsatellites have become markers of choice for crop improvement applications. Hence, simple sequence repeat (SSR) markers were developed for lentil through the construction of genomic library enriched for GA/CT motifs. As a result 122 functional SSR primer pairs were developed from 151 microsatellite loci and validated in L. culinaris cv. Precoz. Thirty three SSR markers were utilized for the analysis of genetic relationships between cultivated and wild species of Lens and related legumes. A total of 123 alleles were amplified at 33 loci ranging from 2-5 alleles with an average of 3.73 alleles per locus. Polymorphic information content (PIC) for all the loci ranged from 0.13 to 0.99 with an average of 0.66 per locus. Varied levels of cross genera transferability were obtained ranging from 69.70 % across Pisum sativum to 12.12 % across Vigna radiata. The UPGMA based dendrogram was able to establish the uniqueness of each genotype and grouped them into two major clusters clearly resolving the genetic relationships within lentil and related species. The new set of SSR markers reported here were efficient and highly polymorphic and would add to the existing repertoire of lentil SSR markers to be utilized in molecular breeding. Moreover, the improved knowledge about intra- and inter-specific genetic relationships would facilitate germplasm utilization for lentil improvement.
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Affiliation(s)
- Priyanka Verma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India
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Südüpak MA. SSR-Based Genetic Diversity Assessment of Turkish Chickpea Varieties. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.5504/bbeq.2013.0070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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Varshney RK, Thudi M, Nayak SN, Gaur PM, Kashiwagi J, Krishnamurthy L, Jaganathan D, Koppolu J, Bohra A, Tripathi S, Rathore A, Jukanti AK, Jayalakshmi V, Vemula A, Singh SJ, Yasin M, Sheshshayee MS, Viswanatha KP. Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:445-62. [PMID: 24326458 PMCID: PMC3910274 DOI: 10.1007/s00122-013-2230-6] [Citation(s) in RCA: 190] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Accepted: 10/31/2013] [Indexed: 05/19/2023]
Abstract
Analysis of phenotypic data for 20 drought tolerance traits in 1-7 seasons at 1-5 locations together with genetic mapping data for two mapping populations provided 9 QTL clusters of which one present on CaLG04 has a high potential to enhance drought tolerance in chickpea improvement. Chickpea (Cicer arietinum L.) is the second most important grain legume cultivated by resource poor farmers in the arid and semi-arid regions of the world. Drought is one of the major constraints leading up to 50% production losses in chickpea. In order to dissect the complex nature of drought tolerance and to use genomics tools for enhancing yield of chickpea under drought conditions, two mapping populations-ICCRIL03 (ICC 4958 × ICC 1882) and ICCRIL04 (ICC 283 × ICC 8261) segregating for drought tolerance-related root traits were phenotyped for a total of 20 drought component traits in 1-7 seasons at 1-5 locations in India. Individual genetic maps comprising 241 loci and 168 loci for ICCRIL03 and ICCRIL04, respectively, and a consensus genetic map comprising 352 loci were constructed ( http://cmap.icrisat.ac.in/cmap/sm/cp/varshney/). Analysis of extensive genotypic and precise phenotypic data revealed 45 robust main-effect QTLs (M-QTLs) explaining up to 58.20% phenotypic variation and 973 epistatic QTLs (E-QTLs) explaining up to 92.19% phenotypic variation for several target traits. Nine QTL clusters containing QTLs for several drought tolerance traits have been identified that can be targeted for molecular breeding. Among these clusters, one cluster harboring 48% robust M-QTLs for 12 traits and explaining about 58.20% phenotypic variation present on CaLG04 has been referred as "QTL-hotspot". This genomic region contains seven SSR markers (ICCM0249, NCPGR127, TAA170, NCPGR21, TR11, GA24 and STMS11). Introgression of this region into elite cultivars is expected to enhance drought tolerance in chickpea.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India,
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Kujur A, Saxena MS, Bajaj D, Laxmi, Parida SK. Integrated genomics and molecular breeding approaches for dissecting the complex quantitative traits in crop plants. J Biosci 2013; 38:971-87. [DOI: 10.1007/s12038-013-9388-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Kujur A, Bajaj D, Saxena MS, Tripathi S, Upadhyaya HD, Gowda C, Singh S, Jain M, Tyagi AK, Parida SK. Functionally relevant microsatellite markers from chickpea transcription factor genes for efficient genotyping applications and trait association mapping. DNA Res 2013; 20:355-74. [PMID: 23633531 PMCID: PMC3738162 DOI: 10.1093/dnares/dst015] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 04/02/2013] [Indexed: 12/30/2022] Open
Abstract
We developed 1108 transcription factor gene-derived microsatellite (TFGMS) and 161 transcription factor functional domain-associated microsatellite (TFFDMS) markers from 707 TFs of chickpea. The robust amplification efficiency (96.5%) and high intra-specific polymorphic potential (34%) detected by markers suggest their immense utilities in efficient large-scale genotyping applications, including construction of both physical and functional transcript maps and understanding population structure. Candidate gene-based association analysis revealed strong genetic association of TFFDMS markers with three major seed and pod traits. Further, TFGMS markers in the 5' untranslated regions of TF genes showing differential expression during seed development had higher trait association potential. The significance of TFFDMS markers was demonstrated by correlating their allelic variation with amino acid sequence expansion/contraction in the functional domain and alteration of secondary protein structure encoded by genes. The seed weight-associated markers were validated through traditional bi-parental genetic mapping. The determination of gene-specific linkage disequilibrium (LD) patterns in desi and kabuli based on single nucleotide polymorphism-microsatellite marker haplotypes revealed extended LD decay, enhanced LD resolution and trait association potential of genes. The evolutionary history of a strong seed-size/weight-associated TF based on natural variation and haplotype sharing among desi, kabuli and wild unravelled useful information having implication for seed-size trait evolution during chickpea domestication.
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Affiliation(s)
- Alice Kujur
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepak Bajaj
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Maneesha S. Saxena
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi 110012, India
| | - Hari D. Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Andhra Pradesh, India
| | - C.L.L. Gowda
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Andhra Pradesh, India
| | - Sube Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru 502324, Andhra Pradesh, India
| | - Mukesh Jain
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Akhilesh K. Tyagi
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K. Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Jamalabadi JG, Saidi A, Karami E, Kharkesh M, Talebi R. Molecular mapping and characterization of genes governing time to flowering, seed weight, and plant height in an intraspecific genetic linkage map of chickpea (Cicer arietinum). Biochem Genet 2013; 51:387-97. [PMID: 23371372 DOI: 10.1007/s10528-013-9571-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2012] [Accepted: 11/06/2012] [Indexed: 10/27/2022]
Abstract
Drought is the major constraint to chickpea productivity worldwide. Utilizing early flowering genotypes and larger seed size have been suggested as strategies for breeding in drought zones. Therefore, this study aimed to identify potential markers linked to days-to-flowering, 100-seed weight, and plant height in a chickpea intraspecific F(2:3) population derived from the cross ILC3279 × ICCV2. A closely linked marker (TA117) on linkage group LG3 was identified for the days-to-flowering trait, explaining 33% of the variation. In relation to plant height, a quantitative trait loci (QTL) was located in LG3, close to the Ts5 marker, that explained 29% of phenotypic variation. A QTL for 100-seed weight located in LG4, close to TA176, explained 51% of variation. The identification of a locus linked both to high 100-seed weight and days-to-flowering may account for the correlation observed between these traits in this and other breeding attempts.
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Affiliation(s)
- Javad Ghorbani Jamalabadi
- Department of Biotechnology, College of New Technologies and Energy Engineering, Shahid Beheshti University, Tehran, Iran
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Agarwal G, Jhanwar S, Priya P, Singh VK, Saxena MS, Parida SK, Garg R, Tyagi AK, Jain M. Comparative analysis of kabuli chickpea transcriptome with desi and wild chickpea provides a rich resource for development of functional markers. PLoS One 2012; 7:e52443. [PMID: 23300670 PMCID: PMC3531472 DOI: 10.1371/journal.pone.0052443] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 11/13/2012] [Indexed: 11/25/2022] Open
Abstract
Chickpea (Cicer arietinum L.) is an important crop legume plant with high nutritional value. The transcriptomes of desi and wild chickpea have already been sequenced. In this study, we sequenced the transcriptome of kabuli chickpea, C. arietinum (genotype ICCV2), having higher commercial value, using GS-FLX Roche 454 and Illumina technologies. The assemblies of both Roche 454 and Illumina datasets were optimized using various assembly programs and parameters. The final optimized hybrid assembly generated 43,389 transcripts with an average length of 1065 bp and N50 length of 1653 bp representing 46.2 Mb of kabuli chickpea transcriptome. We identified a total of 5409 simple sequence repeats (SSRs) in these transcript sequences. Among these, at least 130 and 493 SSRs were polymorphic with desi (ICC4958) and wild (PI489777) chickpea, respectively. In addition, a total of 1986 and 37,954 single nucleotide polymorphisms (SNPs) were predicted in kabuli/desi and kabuli/wild genotypes, respectively. The SNP frequency was 0.043 SNP per kb for kabuli/desi and 0.821 SNP per kb for kabuli/wild, reflecting very low genetic diversity in chickpea. Further, SSRs and SNPs present in tissue-specific and transcription factor encoding transcripts have been identified. The experimental validation of a selected set of polymorphic SSRs and SNPs exhibited high intra-specific polymorphism potential between desi and kabuli chickpea, suggesting their utility in large-scale genotyping applications. The kabuli chickpea gene index assembled, and SSRs and SNPs identified in this study will serve as useful genomic resource for genetic improvement of chickpea.
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Affiliation(s)
- Gaurav Agarwal
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Shalu Jhanwar
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Pushp Priya
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Vikash K. Singh
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Maneesha S. Saxena
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Swarup K. Parida
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Rohini Garg
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Akhilesh K. Tyagi
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Mukesh Jain
- Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
- * E-mail:
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Gaur R, Azam S, Jeena G, Khan AW, Choudhary S, Jain M, Yadav G, Tyagi AK, Chattopadhyay D, Bhatia S. High-throughput SNP discovery and genotyping for constructing a saturated linkage map of chickpea (Cicer arietinum L.). DNA Res 2012; 19:357-73. [PMID: 22864163 PMCID: PMC3473369 DOI: 10.1093/dnares/dss018] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The present study reports the large-scale discovery of genome-wide single-nucleotide polymorphisms (SNPs) in chickpea, identified mainly through the next generation sequencing of two genotypes, i.e. Cicer arietinum ICC4958 and its wild progenitor C. reticulatum PI489777, parents of an inter-specific reference mapping population of chickpea. Development and validation of a high-throughput SNP genotyping assay based on Illumina's GoldenGate Genotyping Technology and its application in building a high-resolution genetic linkage map of chickpea is described for the first time. In this study, 1022 SNPs were identified, of which 768 high-confidence SNPs were selected for designing the custom Oligo Pool All (CpOPA-I) for genotyping. Of these, 697 SNPs could be successfully used for genotyping, demonstrating a high success rate of 90.75%. Genotyping data of the 697 SNPs were compiled along with those of 368 co-dominant markers mapped in an earlier study, and a saturated genetic linkage map of chickpea was constructed. One thousand and sixty-three markers were mapped onto eight linkage groups spanning 1808.7 cM (centiMorgans) with an average inter-marker distance of 1.70 cM, thereby representing one of the most advanced maps of chickpea. The map was used for the synteny analysis of chickpea, which revealed a higher degree of synteny with the phylogenetically close Medicago than with soybean. The first set of validated SNPs and map resources developed in this study will not only facilitate QTL mapping, genome-wide association analysis and comparative mapping in legumes but also help anchor scaffolds arising out of the whole-genome sequencing of chickpea.
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Affiliation(s)
- Rashmi Gaur
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box 10531, New Delhi 110067, India
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Jhanwar S, Priya P, Garg R, Parida SK, Tyagi AK, Jain M. Transcriptome sequencing of wild chickpea as a rich resource for marker development. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:690-702. [PMID: 22672127 DOI: 10.1111/j.1467-7652.2012.00712.x] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The transcriptome of cultivated chickpea (Cicer arietinum L.), an important crop legume, has recently been sequenced. Here, we report sequencing of the transcriptome of wild chickpea, C. reticulatum (PI489777), the progenitor of cultivated chickpea, by GS-FLX 454 technology. The optimized assembly of C. reticulatum transcriptome generated 37 265 transcripts in total with an average length of 946 bp. A total of 4072 simple sequence repeats (SSRs) could be identified in these transcript sequences, of which at least 561 SSRs were polymorphic between C. arietinum and C. reticulatum. In addition, a total of 36 446 single-nucleotide polymorphisms (SNPs) were identified after optimization of probability score, quality score, read depth and consensus base ratio. Several of these SSRs and SNPs could be associated with tissue-specific and transcription factor encoding transcripts. A high proportion (92-94%) of polymorphic SSRs and SNPs identified between the two chickpea species were validated successfully. Further, the estimation of synonymous substitution rates of orthologous transcript pairs suggested that the speciation event for divergence of C. arietinum and C. reticulatum may have happened approximately 0.53 million years ago. The results of our study provide a rich resource for exploiting genetic variations in chickpea for breeding programmes.
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Affiliation(s)
- Shalu Jhanwar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
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Babaei N, Abdullah NAP, Saleh G, Abdullah TL. Isolation and characterization of microsatellite markers and analysis of genetic variability in Curculigo latifolia Dryand. Mol Biol Rep 2012; 39:9869-77. [PMID: 22752726 PMCID: PMC3459080 DOI: 10.1007/s11033-012-1853-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2012] [Accepted: 06/11/2012] [Indexed: 11/26/2022]
Abstract
Curculin, a sweet protein found in Curculigo latifolia fruit has great potential for the pharmaceutical industry. This protein interestingly has been found to have both sweet taste and taste-modifying capacities comparable with other natural sweeteners. According to our knowledge this is the first reported case on the isolation of microsatellite loci in this genus. Hence, the current development of microsatellite markers for C. latifolia will facilitate future population genetic studies and breeding programs for this valuable plant. In this study 11 microsatellite markers were developed using 3' and 5' ISSR markers. The primers were tested on 27 accessions from all states of Peninsular Malaysia. The number of alleles per locus ranged from three to seven, with allele size ranging from 141 to 306 bp. The observed and expected heterozygosity ranged between 0.00-0.65 and 0.38-0.79, respectively. The polymorphic information content ranged from 0.35 to 0.74 and the Shannon's information index ranged from 0.82 to 1.57. These developed polymorphic microsatellites were used for constructing a dendrogram by unweighted pair group method with arithmetic mean cluster analysis using the Dice's similarity coefficient. Accessions association according to their geographical origin was observed. Based on characteristics of isolated microsatellites for C. latifolia accessions all genotype can be distinguished using these 11 microsatellite markers. These polymorphic markers could also be applied to studies on uniformity determination and somaclonal variation of tissue culture plantlets, varieties identification, genetic diversity, analysis of phylogenetic relationship, genetic linkage maps and quantitative trait loci in C. latifolia.
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Affiliation(s)
- Nahid Babaei
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | | | - Ghizan Saleh
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor Malaysia
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Madrid E, Rajesh PN, Rubio J, Gil J, Millán T, Chen W. Characterization and genetic analysis of an EIN4-like sequence (CaETR-1) located in QTL(AR1) implicated in ascochyta blight resistance in chickpea. PLANT CELL REPORTS 2012; 31:1033-1042. [PMID: 22238063 DOI: 10.1007/s00299-011-1221-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 12/13/2011] [Accepted: 12/24/2011] [Indexed: 05/31/2023]
Abstract
Two alleles of a chickpea (Cicer arietinum L.) ethylene receptor-like sequence (CaETR-1) were sequence-characterized using synteny analysis with genome sequences of Medicago truncatula L. The full length of the sequence obtained in the accession FLIP84-92C resistant to ascochyta blight (CaETR-1a) span 4,428 bp, including the polyadenylation signal in the 3'-untranslated region (UTR), whereas it has a 730 bp deletion in the 3'-UTR region in the susceptible accession PI359075 (CaETR-1b). The deduced protein belongs to subfamily II of the ethylene receptors and contains all the domains that define EIN4 homologs in Arabidopsis. The EIN4-like sequence (CaETR-1) has been mapped using a recombinant inbred line (RIL) population derived from an intraspecific cross between ILC3279 and WR315, resistant and susceptible to blight, respectively. The locus was located in LGIVa of the genetic map, flanked by markers NCPGR91 and GAA47 (at distances of 11.3 and 17.9 cM, respectively). This is the first potentially functional sequence identified under a QTL peak for ascochyta blight resistance in chickpea (QTL(AR1)). This EIN4-like (CaETR-1) sequence explained up to 33.8% of the total phenotypic variation. This sequence could be directly related to blight resistance, together with other QTLs that have been found to be involved in resistance to this major chickpea disease.
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Affiliation(s)
- E Madrid
- Departamento de Genética, Universidad de Córdoba, Campus Rabanales, Edif. C5, 14071 Córdoba, Spain.
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Choudhary S, Gaur R, Gupta S. EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1449-62. [PMID: 22301907 DOI: 10.1007/s00122-012-1800-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Accepted: 01/05/2012] [Indexed: 05/17/2023]
Abstract
Well-saturated linkage maps especially those based on expressed sequence tag (EST)-derived genic molecular markers (GMMs) are a pre-requisite for molecular breeding. This is especially true in important legumes such as chickpea where few simple sequence repeats (SSR) and even fewer GMM-based maps have been developed. Therefore, in this study, 2,496 ESTs were generated from chickpea seeds and utilized for the development of 487 novel EST-derived functional markers which included 125 EST-SSRs, 151 intron targeted primers (ITPs), 109 expressed sequence tag polymorphisms (ESTPs), and 102 single nucleotide polymorphisms (SNPs). Whereas ESTSSRs, ITPs, and ESTPs were developed by in silico analysis of the developed EST sequences, SNPs were identified by allele resequencing and their genotyping was performedusing the Illumina GoldenGate Assay. Parental polymorphism was analyzed between C. arietinum ICC4958 and C. reticulatum PI489777, parents of the reference chickpea mapping population, using a total of 872 markers: 487 new gene-based markers developed in this study along with 385 previously published markers, of which 318 (36.5%) were found to be polymorphic and were used for genotyping. The genotypic data were integrated with the previously published data of 108 markers and an advanced linkage map was generated that contained 406 loci distributed on eight linkage groups that spanned 1,497.7 cM. The average marker density was 3.68 cM and the average number of markers per LG was 50.8. Among the mapped markers, 303 new genomic locations were defined that included 177 gene-based and 126 gSSRs (genomic SSRs) thereby producing the most advanced gene-rich map of chickpea solely based on co-dominant markers.
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Affiliation(s)
- Shalu Choudhary
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No 10531, New Delhi 110067, India
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