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Jha UC, Nayyar H, Thudi M, Beena R, Vara Prasad PV, Siddique KHM. Unlocking the nutritional potential of chickpea: strategies for biofortification and enhanced multinutrient quality. FRONTIERS IN PLANT SCIENCE 2024; 15:1391496. [PMID: 38911976 PMCID: PMC11190093 DOI: 10.3389/fpls.2024.1391496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 05/20/2024] [Indexed: 06/25/2024]
Abstract
Chickpea (Cicer arietinum L.) is a vital grain legume, offering an excellent balance of protein, carbohydrates, fats, fiber, essential micronutrients, and vitamins that can contribute to addressing the global population's increasing food and nutritional demands. Chickpea protein offers a balanced source of amino acids with high bioavailability. Moreover, due to its balanced nutrients and affordable price, chickpea is an excellent alternative to animal protein, offering a formidable tool for combating hidden hunger and malnutrition, particularly prevalent in low-income countries. This review examines chickpea's nutritional profile, encompassing protein, amino acids, carbohydrates, fatty acids, micronutrients, vitamins, antioxidant properties, and bioactive compounds of significance in health and pharmaceutical domains. Emphasis is placed on incorporating chickpeas into diets for their myriad health benefits and nutritional richness, aimed at enhancing human protein and micronutrient nutrition. We discuss advances in plant breeding and genomics that have facilitated the discovery of diverse genotypes and key genomic variants/regions/quantitative trait loci contributing to enhanced macro- and micronutrient contents and other quality parameters. Furthermore, we explore the potential of innovative breeding tools such as CRISPR/Cas9 in enhancing chickpea's nutritional profile. Envisioning chickpea as a nutritionally smart crop, we endeavor to safeguard food security, combat hunger and malnutrition, and promote dietary diversity within sustainable agrifood systems.
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Affiliation(s)
- Uday Chand Jha
- Indian Council of Agricultural Research (ICAR) – Indian Institute of Pulses Research (IIPR), Kanpur, Uttar Pradesh, India
- Department of Agronomy, Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, KS, United States
| | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Mahender Thudi
- College of Agriculture, Family Sciences and Technology, Fort Valley State University, Fort Valley, GA, United States
| | - Radha Beena
- Department of Plant Physiology, College of Agriculture, Vellayani, Kerala Agriculture University, Thiruvananthapuram, Kerala, India
| | - P. V. Vara Prasad
- Department of Agronomy, Feed the Future Innovation Lab for Collaborative Research on Sustainable Intensification, Kansas State University, Manhattan, KS, United States
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Danakumara T, Kumar N, Patil BS, Kumar T, Bharadwaj C, Jain PK, Nimmy MS, Joshi N, Parida SK, Bindra S, Kole C, Varshney RK. Unraveling the genetics of heat tolerance in chickpea landraces ( Cicer arietinum L.) using genome-wide association studies. FRONTIERS IN PLANT SCIENCE 2024; 15:1376381. [PMID: 38590753 PMCID: PMC10999645 DOI: 10.3389/fpls.2024.1376381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/11/2024] [Indexed: 04/10/2024]
Abstract
Chickpea, being an important grain legume crop, is often confronted with the adverse effects of high temperatures at the reproductive stage of crop growth, drastically affecting yield and overall productivity. The current study deals with an extensive evaluation of chickpea genotypes, focusing on the traits associated with yield and their response to heat stress. Notably, we observed significant variations for these traits under both normal and high-temperature conditions, forming a robust basis for genetic research and breeding initiatives. Furthermore, the study revealed that yield-related traits exhibited high heritability, suggesting their potential suitability for marker-assisted selection. We carried out single-nucleotide polymorphism (SNP) genotyping using the genotyping-by-sequencing (GBS) method for a genome-wide association study (GWAS). Overall, 27 marker-trait associations (MTAs) linked to yield-related traits, among which we identified five common MTAs displaying pleiotropic effects after applying a stringent Bonferroni-corrected p-value threshold of <0.05 [-log10(p) > 4.95] using the BLINK (Bayesian-information and linkage-disequilibrium iteratively nested keyway) model. Through an in-depth in silico analysis of these markers against the CDC Frontier v1 reference genome, we discovered that the majority of the SNPs were located at or in proximity to gene-coding regions. We further explored candidate genes situated near these MTAs, shedding light on the molecular mechanisms governing heat stress tolerance and yield enhancement in chickpeas such as indole-3-acetic acid-amido synthetase GH3.1 with GH3 auxin-responsive promoter and pentatricopeptide repeat-containing protein, etc. The harvest index (HI) trait was associated with marker Ca3:37444451 encoding aspartic proteinase ortholog sequence of Oryza sativa subsp. japonica and Medicago truncatula, which is known for contributing to heat stress tolerance. These identified MTAs and associated candidate genes may serve as valuable assets for breeding programs dedicated to tailoring chickpea varieties resilient to heat stress and climate change.
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Affiliation(s)
| | - Neeraj Kumar
- ICAR- Indian Agricultural Research Institute, New Delhi, India
| | | | - Tapan Kumar
- International Centre for Agricultural Research in the Dry Areas, Amlaha, Madhya Pradesh, India
| | | | | | | | - Nilesh Joshi
- ICAR- Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Chittaranjan Kole
- Prof. Chittaranjan Kole Foundation for Science & Society, Kolkatta, India
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Istanbuli T, Nassar AE, Abd El-Maksoud MM, Tawkaz S, Alsamman AM, Hamwieh A. Genome-wide association study reveals SNP markers controlling drought tolerance and related agronomic traits in chickpea across multiple environments. FRONTIERS IN PLANT SCIENCE 2024; 15:1260690. [PMID: 38525151 PMCID: PMC10957531 DOI: 10.3389/fpls.2024.1260690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 02/06/2024] [Indexed: 03/26/2024]
Abstract
Chickpea, renowned for its exceptional nutritional value, stands as a crucial crop, serving as a dietary staple in various parts of the world. However, its productivity faces a significant challenge in the form of drought stress. This challenge highlights the urgent need to find genetic markers linked to drought tolerance for effective breeding programs. The primary objective of this study is to identify genetic markers associated with drought tolerance to facilitate effective breeding programs. To address this, we cultivated 185 chickpea accessions in two distinct locations in Lebanon over a two-year period, subjecting them to both irrigated and rain-fed environments. We assessed 11 drought-linked traits, including morphology, growth, yield, and tolerance score. SNP genotyping revealed 1344 variable SNP markers distributed across the chickpea genome. Genetic diversity across populations originating from diverse geographic locations was unveiled by the PCA, clustering, and structure analysis indicating that these genotypes have descend from five or four distinct ancestors. A genome-wide association study (GWAS) revealed several marker trait associations (MTAs) associated with the traits evaluated. Within the rainfed conditions, 11 significant markers were identified, each associated with distinct chickpea traits. Another set of 11 markers exhibited associations in both rainfed and irrigated environments, reflecting shared genetic determinants across these conditions for the same trait. The analysis of linkage disequilibrium (LD) highlighted two genomic regions with notably strong LD, suggesting significant interconnections among several investigated traits. This was further investigated by the correlation between major markers associated with these traits. Gene annotation of the identified markers has unveiled insights into 28 potential genes that play a role in influencing various chickpea drought-linked traits. These traits encompass crucial aspects such as blooming organ development, plant growth, seed weight, starch metabolism, drought regulation, and height index. Among the identified genes are CPN60-2, hsp70, GDSL(GELP), AHL16, NAT3, FAB1B, bZIP, and GL21. These genes collectively contribute to the multifaceted response of chickpea plants to drought stress. Our identified genetic factors exert their influence in both irrigated and rainfed environments, emphasizing their importance in shaping chickpea characteristics.
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Affiliation(s)
- Tawffiq Istanbuli
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon
| | - Ahmed E. Nassar
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | | | - Sawsan Tawkaz
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Alsamman M. Alsamman
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
- Genome Mapping Department, Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Aladdin Hamwieh
- Biotechnology Department, International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
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Naik S, Sudan J, Urwat U, Pakhtoon MM, Bhat B, Sharma V, Sofi PA, Shikari AB, Bhat BA, Sofi NR, Prasad PVV, Zargar SM. Genome-wide SNP discovery and genotyping delineates potential QTLs underlying major yield-attributing traits in buckwheat. THE PLANT GENOME 2024; 17:e20427. [PMID: 38239091 DOI: 10.1002/tpg2.20427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 11/07/2023] [Accepted: 12/22/2023] [Indexed: 03/22/2024]
Abstract
Buckwheat (Fagopyrum spp.) is an important nutritional and nutraceutical-rich pseudo-cereal crop. Despite its obvious potential as a functional food, buckwheat has not been fully harnessed due to its low yield, self-incompatibility, increased seed cracking, limited seed set, lodging, and frost susceptibility. The inadequate availability of genomics resources in buckwheat is one of the major reasons for this. In the present study, genome-wide association mapping (GWAS) was conducted to identify loci associated with various morphological and yield-related traits in buckwheat. High throughput genotyping by sequencing led to the identification of 34,978 single nucleotide polymorphisms that were distributed across eight chromosomes. Population structure analysis grouped the genotypes into three sub-populations. The genotypes were also characterized for various qualitative and quantitative traits at two diverse locations, the analysis of which revealed a significant difference in the mean values. The association analysis revealed a total of 71 significant marker-trait associations across eight chromosomes. The candidate genes were identified near 100 Kb of quantitative trait loci (QTLs), providing insights into several metabolic and biosynthetic pathways. The integration of phenology and GWAS in the present study is useful to uncover the consistent genomic regions, related markers associated with various yield-related traits, and potential candidate genes having implications for being utilized in molecular breeding for the improvement of economically important traits in buckwheat. Moreover, the identified QTLs will assist in tracking the desirable alleles of target genes within the buckwheat breeding populations/germplasm.
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Affiliation(s)
- Samiullah Naik
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Jebi Sudan
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Uneeb Urwat
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Mohammad Maqbool Pakhtoon
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Basharat Bhat
- Division of Animal Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Varun Sharma
- Bioinformatics Division, NMC Genetics India Pvt. Ltd., Gurugram, India
| | - Parvaze A Sofi
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Asif B Shikari
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Bilal A Bhat
- Mountain Agriculture Research & Extension Station, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Najeebul Rehman Sofi
- Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - P V Vara Prasad
- Sustainable Intensification Innovation Lab, Kansas State University, Manhattan, Kansas, USA
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Faculty of Horticulture, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
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Salaria S, Boatwright JL, Johnson N, Madurapperumage A, Joshi P, Thavarajah P, Vandemark G, Thavarajah D. Fatty acid composition and genome-wide associations of a chickpea (Cicer arietinum L.) diversity panel for biofortification efforts. Sci Rep 2023; 13:14002. [PMID: 37635199 PMCID: PMC10460795 DOI: 10.1038/s41598-023-41274-3] [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: 02/10/2023] [Accepted: 08/24/2023] [Indexed: 08/29/2023] Open
Abstract
Chickpea is a nutritionally dense pulse crop with high levels of protein, carbohydrates, micronutrients and low levels of fats. Chickpea fatty acids are associated with a reduced risk of obesity, blood cholesterol, and cardiovascular diseases in humans. We measured four primary chickpea fatty acids; palmitic acid (PA), linoleic acid (LA), alpha-linolenic acid (ALA), and oleic acid (OA), which are crucial for human health and plant stress responses in a chickpea diversity panel with 256 accessions (Kabuli and desi types). A wide concentration range was found for PA (450.7-912.6 mg/100 g), LA (1605.7-3459.9 mg/100 g), ALA (416.4-864.5 mg/100 g), and OA (1035.5-1907.2 mg/100 g). The percent recommended daily allowances also varied for PA (3.3-6.8%), LA (21.4-46.1%), ALA (34.7-72%), and OA (4.3-7.9%). Weak correlations were found among fatty acids. Genome-wide association studies (GWAS) were conducted using genotyping-by-sequencing data. Five significant single nucleotide polymorphisms (SNPs) were identified for PA. Admixture population structure analysis revealed seven subpopulations based on ancestral diversity in this panel. This is the first reported study to characterize fatty acid profiles across a chickpea diversity panel and perform GWAS to detect associations between genetic markers and concentrations of selected fatty acids. These findings demonstrate biofortification of chickpea fatty acids is possible using conventional and genomic breeding techniques, to develop superior cultivars with better fatty acid profiles for improved human health and plant stress responses.
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Affiliation(s)
- Sonia Salaria
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - J Lucas Boatwright
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA
- Advanced Plant Technology, Clemson University, Clemson, SC, 29634, USA
| | - Nathan Johnson
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Amod Madurapperumage
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Priyanka Joshi
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - Pushparajah Thavarajah
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA
| | - George Vandemark
- Grain Legume Genetics and Physiology Research Unit, USDA-ARS, Washington State University, 303 Johnson Hall, Pullman, WA, 99164, USA
| | - Dil Thavarajah
- Plant and Environmental Sciences, Clemson University, 113 Biosystems Research Complex, Clemson, SC, 29634, USA.
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Susmitha P, Kumar P, Yadav P, Sahoo S, Kaur G, Pandey MK, Singh V, Tseng TM, Gangurde SS. Genome-wide association study as a powerful tool for dissecting competitive traits in legumes. FRONTIERS IN PLANT SCIENCE 2023; 14:1123631. [PMID: 37645459 PMCID: PMC10461012 DOI: 10.3389/fpls.2023.1123631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 06/08/2023] [Indexed: 08/31/2023]
Abstract
Legumes are extremely valuable because of their high protein content and several other nutritional components. The major challenge lies in maintaining the quantity and quality of protein and other nutritional compounds in view of climate change conditions. The global need for plant-based proteins has increased the demand for seeds with a high protein content that includes essential amino acids. Genome-wide association studies (GWAS) have evolved as a standard approach in agricultural genetics for examining such intricate characters. Recent development in machine learning methods shows promising applications for dimensionality reduction, which is a major challenge in GWAS. With the advancement in biotechnology, sequencing, and bioinformatics tools, estimation of linkage disequilibrium (LD) based associations between a genome-wide collection of single-nucleotide polymorphisms (SNPs) and desired phenotypic traits has become accessible. The markers from GWAS could be utilized for genomic selection (GS) to predict superior lines by calculating genomic estimated breeding values (GEBVs). For prediction accuracy, an assortment of statistical models could be utilized, such as ridge regression best linear unbiased prediction (rrBLUP), genomic best linear unbiased predictor (gBLUP), Bayesian, and random forest (RF). Both naturally diverse germplasm panels and family-based breeding populations can be used for association mapping based on the nature of the breeding system (inbred or outbred) in the plant species. MAGIC, MCILs, RIAILs, NAM, and ROAM are being used for association mapping in several crops. Several modifications of NAM, such as doubled haploid NAM (DH-NAM), backcross NAM (BC-NAM), and advanced backcross NAM (AB-NAM), have also been used in crops like rice, wheat, maize, barley mustard, etc. for reliable marker-trait associations (MTAs), phenotyping accuracy is equally important as genotyping. Highthroughput genotyping, phenomics, and computational techniques have advanced during the past few years, making it possible to explore such enormous datasets. Each population has unique virtues and flaws at the genomics and phenomics levels, which will be covered in more detail in this review study. The current investigation includes utilizing elite breeding lines as association mapping population, optimizing the choice of GWAS selection, population size, and hurdles in phenotyping, and statistical methods which will analyze competitive traits in legume breeding.
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Affiliation(s)
- Pusarla Susmitha
- Regional Agricultural Research Station, Acharya N.G. Ranga Agricultural University, Andhra Pradesh, India
| | - Pawan Kumar
- Department of Genetics and Plant Breeding, College of Agriculture, Chaudhary Charan Singh (CCS) Haryana Agricultural University, Hisar, India
| | - Pankaj Yadav
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Rajasthan, India
| | - Smrutishree Sahoo
- Department of Genetics and Plant Breeding, School of Agriculture, Gandhi Institute of Engineering and Technology (GIET) University, Odisha, India
| | - Gurleen Kaur
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Manish K. Pandey
- Department of Genomics, Prebreeding and Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, India
| | - Varsha Singh
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Te Ming Tseng
- Department of Plant and Soil Sciences, Mississippi State University, Starkville, MS, United States
| | - Sunil S. Gangurde
- Department of Plant Pathology, University of Georgia, Tifton, GA, United States
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Koul B, Sharma K, Sehgal V, Yadav D, Mishra M, Bharadwaj C. Chickpea ( Cicer arietinum L.) Biology and Biotechnology: From Domestication to Biofortification and Biopharming. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212926. [PMID: 36365379 PMCID: PMC9654780 DOI: 10.3390/plants11212926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/13/2022] [Accepted: 10/25/2022] [Indexed: 05/13/2023]
Abstract
Chickpea (Cicer arietinum L.), the world's second most consumed legume crop, is cultivated in more than 50 countries around the world. It is a boon for diabetics and is an excellent source of important nutrients such as vitamins A, C, E, K, B1-B3, B5, B6, B9 and minerals (Fe, Zn, Mg and Ca) which all have beneficial effects on human health. By 2050, the world population can cross 9 billion, and in order to feed the teaming millions, chickpea production should also be increased, as it is a healthy alternative to wheat flour and a boon for diabetics. Moreover, it is an important legume that is crucial for food, nutrition, and health security and the livelihood of the small-scale farmers with poor resources, in developing countries. Although marvelous improvement has been made in the development of biotic and abiotic stress-resistant varieties, still there are many lacunae, and to fulfill that, the incorporation of genomic technologies in chickpea breeding (genomics-assisted breeding, high-throughput and precise-phenotyping and implementation of novel breeding strategies) will facilitate the researchers in developing high yielding, climate resilient, water use efficient, salt-tolerant, insect/pathogen resistant varieties, acceptable to farmers, consumers, and industries. This review focuses on the origin and distribution, nutritional profile, genomic studies, and recent updates on crop improvement strategies for combating abiotic and biotic stresses in chickpea.
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Affiliation(s)
- Bhupendra Koul
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
- Correspondence: (B.K.); (D.Y.); (M.M.)
| | - Komal Sharma
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
| | - Vrinda Sehgal
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
| | - Dhananjay Yadav
- Department of Life Science, Yeungnam University, Gyeongsan 38541, Korea
- Correspondence: (B.K.); (D.Y.); (M.M.)
| | - Meerambika Mishra
- Department of Infectious Diseases and Pathology, University of Florida, Gainesville, FL 32611, USA
- Correspondence: (B.K.); (D.Y.); (M.M.)
| | - Chellapilla Bharadwaj
- Division of Genetics, Indian Agricultural Research Institute (IARI), Pusa, New Delhi 110012, India
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