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Parmar S, Janila P, Gangurde SS, Variath MT, Sharma V, Bomireddy D, Manohar SS, Varshney RK, Singam P, Pandey MK. Genetic mapping identified major main-effect and three co-localized quantitative trait loci controlling high iron and zinc content in groundnut. THE PLANT GENOME 2023; 16:e20361. [PMID: 37408143 DOI: 10.1002/tpg2.20361] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 07/07/2023]
Abstract
Malnutrition is a major challenge globally, and groundnut is a highly nutritious self-pollinated legume crop blessed with ample genomic resources, including the routine deployment of genomic-assisted breeding. This study aimed to identify genomic regions and candidate genes for high iron (Fe) and zinc (Zn) content, utilizing a biparental mapping population (ICGV 00440 × ICGV 06040;). Genetic mapping and quantitative trait locus (QTL) analysis (474 mapped single-nucleotide polymorphism loci; 1536.33 cM) using 2 seasons of phenotypic data together with genotypic data identified 5 major main-effect QTLs for Fe content. These QTLs exhibited log-of-odds (LOD) scores ranging from 6.5 to 7.4, explaining phenotypic variation (PVE) ranging from 22% (qFe-Ah01) to 30.0% (qFe-Ah14). Likewise, four major main effect QTLs were identified for Zn content, with LOD score ranging from 4.4 to 6.8 and PVE ranging from 21.8% (qZn-Ah01) to 32.8% (qZn-Ah08). Interestingly, three co-localized major and main effect QTLs (qFe-Ah01, qZn-Ah03, and qFe-Ah11) were identified for both Fe and Zn contents. These genomic regions harbored key candidate genes, including zinc/iron permease transporter, bZIP transcription factor, and vacuolar iron transporter which likely play pivotal roles in the accumulation of Fe and Zn contents in seeds. The findings of this study hold potential for fine mapping and diagnostic marker development for high Fe and Zn contents in groundnut.
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Affiliation(s)
- Sejal Parmar
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Pasupuleti Janila
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Sunil S Gangurde
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Murali T Variath
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vinay Sharma
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Deekshitha Bomireddy
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Surendra S Manohar
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev K Varshney
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Prashant Singam
- Department of Genetics, Osmania University, Hyderabad, India
| | - Manish K Pandey
- International, Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Singh B, Singh S, Mahato AK, Dikshit HK, Tripathi K, Bhatia S. Delineation of novel genomic loci and putative candidate genes associated with seed iron and zinc content in lentil (Lens culinaris Medik.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 335:111787. [PMID: 37419329 DOI: 10.1016/j.plantsci.2023.111787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/23/2023] [Accepted: 07/04/2023] [Indexed: 07/09/2023]
Abstract
The use of molecular breeding approaches for development of lentil genotypes biofortified with essential micro-nutrients such as iron and zinc, could serve as a promising solution to address the problem of global malnutrition. Thus, genome-wide association study (GWAS) strategy was adopted in this study to identify the genomic regions associated with seed iron and zinc content in lentil. A panel of 95 diverse lentil genotypes, grown across three different geographical locations and evaluated for seed iron and zinc content, exhibited a wide range of variation. Genotyping-by-sequencing (GBS) analysis of the panel identified 33,745 significant single nucleotide polymorphisms (SNPs) that were distributed across all the 7 lentil chromosomes. Association mapping revealed 23 SNPs associated with seed iron content that were distributed across all the chromosomes except chromosome 3. Similarly, 14 SNPs associated with seed zinc content were also identified that were distributed across chromosomes 1, 2, 4, 5 and 6. Further, 80 genes were identified in the proximity of iron associated markers and 36 genes were identified in the proximity of zinc associated markers. Functional annotation of these genes revealed their putative involvement in iron and zinc metabolism. For seed iron content, two highly significant SNPs were found to be located within two putative candidate genes namely iron-sulfur cluster assembly (ISCA) and flavin binding monooxygenase (FMO) respectively. For zinc content, a highly significant SNP was detected in a gene encoding UPF0678 fatty acid-binding protein. Expression analysis of these genes and their putative interacting partners suggests their involvement in iron and zinc metabolism in lentil. Overall, in this study we have identified markers, putative candidate genes and predicted putative interacting protein partners significantly associated with iron and zinc metabolism that could be utilized in future breeding studies of lentil for nutrient biofortification.
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Affiliation(s)
- Baljinder Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi 110067, India
| | - Sangeeta Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi 110067, India
| | - Ajay Kumar Mahato
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, PO Box No. 10531, New Delhi 110067, India
| | - Harsh Kumar Dikshit
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kuldeep Tripathi
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, 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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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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Huertas R, Karpinska B, Ngala S, Mkandawire B, Maling'a J, Wajenkeche E, Kimani PM, Boesch C, Stewart D, Hancock RD, Foyer CH. Biofortification of common bean ( Phaseolus vulgaris L.) with iron and zinc: Achievements and challenges. Food Energy Secur 2023; 12:e406. [PMID: 38440694 PMCID: PMC10909572 DOI: 10.1002/fes3.406] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 06/01/2022] [Accepted: 06/08/2022] [Indexed: 03/06/2024] Open
Abstract
Micronutrient deficiencies (hidden hunger), particularly in iron (Fe) and zinc (Zn), remain one of the most serious public health challenges, affecting more than three billion people globally. A number of strategies are used to ameliorate the problem of micronutrient deficiencies and to improve the nutritional profile of food products. These include (i) dietary diversification, (ii) industrial food fortification and supplements, (iii) agronomic approaches including soil mineral fertilisation, bioinoculants and crop rotations, and (iv) biofortification through the implementation of biotechnology including gene editing and plant breeding. These efforts must consider the dietary patterns and culinary preferences of the consumer and stakeholder acceptance of new biofortified varieties. Deficiencies in Zn and Fe are often linked to the poor nutritional status of agricultural soils, resulting in low amounts and/or poor availability of these nutrients in staple food crops such as common bean. This review describes the genes and processes associated with Fe and Zn accumulation in common bean, a significant food source in Africa that plays an important role in nutritional security. We discuss the conventional plant breeding, transgenic and gene editing approaches that are being deployed to improve Fe and Zn accumulation in beans. We also consider the requirements of successful bean biofortification programmes, highlighting gaps in current knowledge, possible solutions and future perspectives.
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Affiliation(s)
- Raul Huertas
- Environmental and Biochemical SciencesThe James Hutton InstituteDundeeUK
| | - Barbara Karpinska
- School of Biosciences, College of Life and Environmental SciencesUniversity of BirminghamEdgbastonUK
| | - Sophia Ngala
- Department of Plant Science and Crop Protection, College of Agriculture and Veterinary SciencesUniversity of NairobiNairobiKenya
| | - Bertha Mkandawire
- The Food, Agriculture and Natural Resources Policy Analysis Network (FANRPAN)PretoriaSouth Africa
| | - Joyce Maling'a
- Kenya Agriculture and Livestock Research Organization (KALRO)Food Crops Research InstituteKitaleKenya
| | - Elizabeth Wajenkeche
- Kenya Agriculture and Livestock Research Organization (KALRO)Food Crops Research InstituteKitaleKenya
| | - Paul M. Kimani
- Department of Plant Science and Crop Protection, College of Agriculture and Veterinary SciencesUniversity of NairobiNairobiKenya
| | | | - Derek Stewart
- Environmental and Biochemical SciencesThe James Hutton InstituteDundeeUK
- School of Engineering and Physical SciencesHeriot‐Watt UniversityEdinburghUK
| | | | - Christine H. Foyer
- School of Biosciences, College of Life and Environmental SciencesUniversity of BirminghamEdgbastonUK
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Dwivedi SL, Garcia-Oliveira AL, Govindaraj M, Ortiz R. Biofortification to avoid malnutrition in humans in a changing climate: Enhancing micronutrient bioavailability in seed, tuber, and storage roots. FRONTIERS IN PLANT SCIENCE 2023; 14:1119148. [PMID: 36794214 PMCID: PMC9923027 DOI: 10.3389/fpls.2023.1119148] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/12/2023] [Indexed: 06/18/2023]
Abstract
Malnutrition results in enormous socio-economic costs to the individual, their community, and the nation's economy. The evidence suggests an overall negative impact of climate change on the agricultural productivity and nutritional quality of food crops. Producing more food with better nutritional quality, which is feasible, should be prioritized in crop improvement programs. Biofortification refers to developing micronutrient -dense cultivars through crossbreeding or genetic engineering. This review provides updates on nutrient acquisition, transport, and storage in plant organs; the cross-talk between macro- and micronutrients transport and signaling; nutrient profiling and spatial and temporal distribution; the putative and functionally characterized genes/single-nucleotide polymorphisms associated with Fe, Zn, and β-carotene; and global efforts to breed nutrient-dense crops and map adoption of such crops globally. This article also includes an overview on the bioavailability, bioaccessibility, and bioactivity of nutrients as well as the molecular basis of nutrient transport and absorption in human. Over 400 minerals (Fe, Zn) and provitamin A-rich cultivars have been released in the Global South. Approximately 4.6 million households currently cultivate Zn-rich rice and wheat, while ~3 million households in sub-Saharan Africa and Latin America benefit from Fe-rich beans, and 2.6 million people in sub-Saharan Africa and Brazil eat provitamin A-rich cassava. Furthermore, nutrient profiles can be improved through genetic engineering in an agronomically acceptable genetic background. The development of "Golden Rice" and provitamin A-rich dessert bananas and subsequent transfer of this trait into locally adapted cultivars are evident, with no significant change in nutritional profile, except for the trait incorporated. A greater understanding of nutrient transport and absorption may lead to the development of diet therapy for the betterment of human health.
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Affiliation(s)
| | - Ana Luísa Garcia-Oliveira
- International Maize and Wheat Research Center, Centro Internacional de Mejoramiento de Maíz. y Trigo (CIMMYT), Nairobi, Kenya
- Department of Molecular Biology, College of Biotechnology, CCS Haryana Agricultural University, Hissar, India
| | - Mahalingam Govindaraj
- HarvestPlus Program, Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Rodomiro Ortiz
- Swedish University of Agricultural Sciences, Lomma, Sweden
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Genetic variation for grain protein, Fe and Zn content traits in chickpea reference set. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Asati R, Tripathi MK, Tiwari S, Yadav RK, Tripathi N. Molecular Breeding and Drought Tolerance in Chickpea. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111846. [PMID: 36430981 PMCID: PMC9698494 DOI: 10.3390/life12111846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/05/2022] [Accepted: 11/07/2022] [Indexed: 11/16/2022]
Abstract
Cicer arietinum L. is the third greatest widely planted imperative pulse crop worldwide, and it belongs to the Leguminosae family. Drought is the utmost common abiotic factor on plants, distressing their water status and limiting their growth and development. Chickpea genotypes have the natural ability to fight drought stress using certain strategies viz., escape, avoidance and tolerance. Assorted breeding methods, including hybridization, mutation, and marker-aided breeding, genome sequencing along with omics approaches, could be used to improve the chickpea germplasm lines(s) against drought stress. Root features, for instance depth and root biomass, have been recognized as the greatest beneficial morphological factors for managing terminal drought tolerance in the chickpea. Marker-aided selection, for example, is a genomics-assisted breeding (GAB) strategy that can considerably increase crop breeding accuracy and competence. These breeding technologies, notably marker-assisted breeding, omics, and plant physiology knowledge, underlined the importance of chickpea breeding and can be used in future crop improvement programmes to generate drought-tolerant cultivars(s).
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Affiliation(s)
- Ruchi Asati
- 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
- Correspondence: (M.K.T.); (N.T.)
| | - 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
| | - Rakesh Kumar Yadav
- Department of Genetics & Plant Breeding, College of Agriculture, Rajmata Vijayaraje Scindia Krishi Vishwa Vidyalaya, Gwalior 474002, India
| | - Niraj Tripathi
- Directorate of Research Services, Jawaharlal Nehru Agricultural University, Jabalpur 482004, India
- Correspondence: (M.K.T.); (N.T.)
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Jha R, Yadav HK, Raiya R, Singh RK, Jha UC, Sathee L, Singh P, Thudi M, Singh A, Chaturvedi SK, Tripathi S. Integrated breeding approaches to enhance the nutritional quality of food legumes. FRONTIERS IN PLANT SCIENCE 2022; 13:984700. [PMID: 36161025 PMCID: PMC9490089 DOI: 10.3389/fpls.2022.984700] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 07/26/2022] [Indexed: 05/31/2023]
Abstract
Global food security, both in terms of quantity and quality remains as a challenge with the increasing population. In parallel, micronutrient deficiency in the human diet leads to malnutrition and several health-related problems collectively known as "hidden hunger" more prominent in developing countries around the globe. Biofortification is a potential tool to fortify grain legumes with micronutrients to mitigate the food and nutritional security of the ever-increasing population. Anti-nutritional factors like phytates, raffinose (RFO's), oxalates, tannin, etc. have adverse effects on human health upon consumption. Reduction of the anti-nutritional factors or preventing their accumulation offers opportunity for enhancing the intake of legumes in diet besides increasing the bioavailability of micronutrients. Integrated breeding methods are routinely being used to exploit the available genetic variability for micronutrients through modern "omic" technologies such as genomics, transcriptomics, ionomics, and metabolomics for developing biofortified grain legumes. Molecular mechanism of Fe/Zn uptake, phytate, and raffinose family oligosaccharides (RFOs) biosynthesis pathways have been elucidated. Transgenic, microRNAs and genome editing tools hold great promise for designing nutrient-dense and anti-nutrient-free grain legumes. In this review, we present the recent efforts toward manipulation of genes/QTLs regulating biofortification and Anti-nutrient accumulation in legumes using genetics-, genomics-, microRNA-, and genome editing-based approaches. We also discuss the success stories in legumes enrichment and recent advances in development of low Anti-nutrient lines. We hope that these emerging tools and techniques will expedite the efforts to develop micronutrient dense legume crop varieties devoid of Anti-nutritional factors that will serve to address the challenges like malnutrition and hidden hunger.
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Affiliation(s)
- Rintu Jha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Hemant Kumar Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rahul Raiya
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Rajesh Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Uday Chand Jha
- Crop Improvement Division, ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
| | - Lekshmy Sathee
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Prashant Singh
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Mahendar Thudi
- Department of Agricultural Biotechnology and Molecular Biology, Dr. Rajendra Prasad Central Agricultural University, Samastipur, India
- Shandong Academy of Agricultural Sciences, Jinan, China
- Center for Crop Health, University of Southern Queensland, Toowmba, QLD, Australia
| | - Anshuman Singh
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
| | - Sushil Kumar Chaturvedi
- College of Agriculture, Rani Lakshmi Bai Central Agricultural University, Jhansi, Uttar Pradesh, India
| | - Shailesh Tripathi
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Fayaz H, Tyagi S, Wani AA, Pandey R, Akhtar S, Bhat MA, Chitikineni A, Varshney RK, Thudi M, Kumar U, Mir RR. Genome-wide association analysis to delineate high-quality SNPs for seed micronutrient density in chickpea (Cicer arietinum L.). Sci Rep 2022; 12:11357. [PMID: 36064952 PMCID: PMC9445022 DOI: 10.1038/s41598-022-14487-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Accepted: 06/07/2022] [Indexed: 11/16/2022] Open
Abstract
Chickpea is the most important nutrient-rich grain legume crop in the world. A diverse core set of 147 chickpea genotypes was genotyped with a Axiom(®)50K CicerSNP array and trait phenotyped in two different environments for four seed micronutrients (Zn, Cu, Fe and Mn). The trait data and high-throughput 50K SNP genotypic data were used for the genome-wide association study (GWAS). The study led to the discovery of genes/QTLs for seed Zn, Cu, Fe and Mn, concentrations in chickpea. The analysis of seed micronutrient data revealed significant differences for all four micronutrient concentrations (P ≤ 0.05). The mean concentrations of seed Zn, Cu, Fe and Mn pooled over the 2 years were 45.9 ppm, 63.8 ppm 146.1 ppm, and 27.0 ppm, respectively. The analysis of results led to the identification of 35 SNPs significantly associated with seed Zn, Cu, Fe and Mn concentrations. Among these 35 marker-trait associations (MTAs), 5 were stable (consistently identified in different environments), 6 were major (explaining more than 15% of the phenotypic variation for an individual trait) and 3 were both major and stable MTAs. A set of 6 MTAs, MTAs (3 for Mn, 2 for Fe, and 1 for Cu) reported by us during the present study have been also reported in the same/almost same genomic regions in earlier studies and therefore declared as validated MTAs. The stable, major and validated MTAs identified during the present study will prove useful in future chickpea molecular breeding programs aimed at enhancing the seed nutrient density of chickpea.
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Affiliation(s)
- Humara Fayaz
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences & Technology (SKUAST)-Kashmir, Wadura Campus, Sopore, India.,Cytogenetics and Reproductive Biology Laboratory, Department of Botany, University of Kashmir, Srinagar, India
| | - Sandhya Tyagi
- Division of Plant Physiology, Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Aijaz A Wani
- Cytogenetics and Reproductive Biology Laboratory, Department of Botany, University of Kashmir, Srinagar, India
| | - Renu Pandey
- Division of Plant Physiology, Indian Agricultural Research Institute (IARI), New Delhi, India
| | - Sabina Akhtar
- College of Education, American University in the Emirates, Dubai, UAE
| | - Mohd Ashraf Bhat
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences & Technology (SKUAST)-Kashmir, Wadura Campus, Sopore, India
| | - Annapurna Chitikineni
- Center of Excellence in Genomics & Systems Biology (CEGSB), Iinternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 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
| | - 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, India. .,University of Southern Queensland (USQ), Toowoomba, Australia.
| | - Upendra Kumar
- Department of Molecular Biology, Biotechnology and Bioinformatics, College of Biotechnology, CCS Haryana Agricultural University, Hisar, 125004, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), Sher-e-Kashmir University of Agricultural Sciences & Technology (SKUAST)-Kashmir, Wadura Campus, Sopore, India.
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11
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Srungarapu R, Mahendrakar MD, Mohammad LA, Chand U, Jagarlamudi VR, Kondamudi KP, Kudapa H, Samineni S. Genome-Wide Association Analysis Reveals Trait-Linked Markers for Grain Nutrient and Agronomic Traits in Diverse Set of Chickpea Germplasm. Cells 2022; 11:cells11152457. [PMID: 35954301 PMCID: PMC9367858 DOI: 10.3390/cells11152457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/22/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Chickpea is an inexpensive source of protein, minerals, and vitamins to the poor people living in arid and semi-arid regions of Southern Asia and Sub-Saharan Africa. New chickpea cultivars with enhanced levels of protein, Fe and Zn content are a medium-term strategy for supplying essential nutrients for human health and reducing malnutrition. In the current study, a chickpea reference set of 280 accessions, including landraces, breeding lines, and advanced cultivars, was evaluated for grain protein, Fe, Zn content and agronomic traits over two seasons. Using a mid-density 5k SNP array, 4603 highly informative SNPs distributed across the chickpea genome were used for GWAS analysis. Population structure analysis revealed three subpopulations (K = 3). Linkage disequilibrium (LD) was extensive, and LD decay was relatively low. A total of 20 and 46 marker-trait associations (MTAs) were identified for grain nutrient and agronomic traits, respectively, using FarmCPU and BLINK models. Of which seven SNPs for grain protein, twelve for Fe, and one for Zn content were distributed on chromosomes 1, 4, 6, and 7. The marker S4_4477846 on chr4 was found to be co-associated with grain protein over seasons. The markers S1_11613376 and S1_2772537 co-associated with grain Fe content under NSII and pooled seasons and S7_9379786 marker under NSI and pooled seasons. The markers S4_31996956 co-associated with grain Fe and days to maturity. SNP annotation of associated markers were found to be related to gene functions of metal ion binding, transporters, protein kinases, transcription factors, and many more functions involved in plant metabolism along with Fe and protein homeostasis. The identified significant MTAs has potential use in marker-assisted selection for developing nutrient-rich chickpea cultivars after validation in the breeding populations.
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Affiliation(s)
- Rajasekhar Srungarapu
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
- Department of Molecular Biology and Biotechnology, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Mahesh Damodhar Mahendrakar
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Lal Ahamed Mohammad
- Department of Genetics and Plant Breeding, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Uttam Chand
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Venkata Ramana Jagarlamudi
- Department of Genetics and Plant Breeding, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Kiran Prakash Kondamudi
- Department of Statistics and Computer Applications, Acharya N.G. Ranga Agricultural University, Guntur 522034, India
| | - Himabindu Kudapa
- Genomics, Pre-Breeding and Bioinformatics, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
| | - Srinivasan Samineni
- Accelerated Crop Improvement, Chickpea Breeding, International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
- Correspondence:
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12
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Singh RK, Singh C, Chandana BS, Mahto RK, Patial R, Gupta A, Gahlaut V, Hamwieh A, Upadhyaya HD, Kumar R. Exploring Chickpea Germplasm Diversity for Broadening the Genetic Base Utilizing Genomic Resourses. Front Genet 2022; 13:905771. [PMID: 36035111 PMCID: PMC9416867 DOI: 10.3389/fgene.2022.905771] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/24/2022] [Indexed: 12/01/2022] Open
Abstract
Legume crops provide significant nutrition to humans as a source of protein, omega-3 fatty acids as well as specific macro and micronutrients. Additionally, legumes improve the cropping environment by replenishing the soil nitrogen content. Chickpeas are the second most significant staple legume food crop worldwide behind dry bean which contains 17%–24% protein, 41%–51% carbohydrate, and other important essential minerals, vitamins, dietary fiber, folate, β-carotene, anti-oxidants, micronutrients (phosphorus, calcium, magnesium, iron, and zinc) as well as linoleic and oleic unsaturated fatty acids. Despite these advantages, legumes are far behind cereals in terms of genetic improvement mainly due to far less effort, the bottlenecks of the narrow genetic base, and several biotic and abiotic factors in the scenario of changing climatic conditions. Measures are now called for beyond conventional breeding practices to strategically broadening of narrow genetic base utilizing chickpea wild relatives and improvement of cultivars through advanced breeding approaches with a focus on high yield productivity, biotic and abiotic stresses including climate resilience, and enhanced nutritional values. Desirable donors having such multiple traits have been identified using core and mini core collections from the cultivated gene pool and wild relatives of Chickpea. Several methods have been developed to address cross-species fertilization obstacles and to aid in inter-specific hybridization and introgression of the target gene sequences from wild Cicer species. Additionally, recent advances in “Omics” sciences along with high-throughput and precise phenotyping tools have made it easier to identify genes that regulate traits of interest. Next-generation sequencing technologies, whole-genome sequencing, transcriptomics, and differential genes expression profiling along with a plethora of novel techniques like single nucleotide polymorphism exploiting high-density genotyping by sequencing assays, simple sequence repeat markers, diversity array technology platform, and whole-genome re-sequencing technique led to the identification and development of QTLs and high-density trait mapping of the global chickpea germplasm. These altogether have helped in broadening the narrow genetic base of chickpeas.
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Affiliation(s)
| | - Charul Singh
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | - B S Chandana
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Rohit K Mahto
- Indian Agricultural Research Institute (ICAR), New Delhi, India
| | - Ranjana Patial
- Department of Agricultural Sciences, Chandigarh University, Mohali, India
| | - Astha Gupta
- School of Agricultural Sciences, Sharda University, Greater Noida, India
| | - Vijay Gahlaut
- Institute of Himalayan Bioresource Technology (CSIR), Pālampur, India
| | - Aladdin Hamwieh
- International Center for Agriculture Research in the Dry Areas (ICARDA), Giza, Egypt
| | - H D Upadhyaya
- Department of Entomology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
| | - Rajendra Kumar
- Indian Agricultural Research Institute (ICAR), New Delhi, India
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13
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Gupta OP, Singh AK, Singh A, Singh GP, Bansal KC, Datta SK. Wheat Biofortification: Utilizing Natural Genetic Diversity, Genome-Wide Association Mapping, Genomic Selection, and Genome Editing Technologies. Front Nutr 2022; 9:826131. [PMID: 35938135 PMCID: PMC9348810 DOI: 10.3389/fnut.2022.826131] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 06/06/2022] [Indexed: 01/11/2023] Open
Abstract
Alleviating micronutrients associated problems in children below five years and women of childbearing age, remains a significant challenge, especially in resource-poor nations. One of the most important staple food crops, wheat attracts the highest global research priority for micronutrient (Fe, Zn, Se, and Ca) biofortification. Wild relatives and cultivated species of wheat possess significant natural genetic variability for these micronutrients, which has successfully been utilized for breeding micronutrient dense wheat varieties. This has enabled the release of 40 biofortified wheat cultivars for commercial cultivation in different countries, including India, Bangladesh, Pakistan, Bolivia, Mexico and Nepal. In this review, we have systematically analyzed the current understanding of availability and utilization of natural genetic variations for grain micronutrients among cultivated and wild relatives, QTLs/genes and different genomic regions regulating the accumulation of micronutrients, and the status of micronutrient biofortified wheat varieties released for commercial cultivation across the globe. In addition, we have also discussed the potential implications of emerging technologies such as genome editing to improve the micronutrient content and their bioavailability in wheat.
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Affiliation(s)
- Om Prakash Gupta
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | | | | | - Swapan K. Datta
- Department of Botany, University of Calcutta, Kolkata, India
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14
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Xu J, Xu W, Chen X, Zhu H, Fu X, Yu F. Genome-Wide Association Analysis Reveals the Genetic Basis of Iron-Deficiency Stress Tolerance in Maize. FRONTIERS IN PLANT SCIENCE 2022; 13:878809. [PMID: 35720580 PMCID: PMC9202619 DOI: 10.3389/fpls.2022.878809] [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: 02/18/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
Abstract
Iron (Fe) is an essential trace element for almost all organisms and is often the major limiting nutrient for normal growth. Fe deficiency is a worldwide agricultural problem, which affects crop productivity and product quality. Understanding the Fe-deficiency response in plants is necessary for improving both plant health and the human diet. In this study, Fe-efficient (Ye478) and Fe-inefficient maize inbred lines (Wu312) were used to identify the genotypic difference in response to low Fe stress during different developmental stages and to further determine the optimal Fe-deficient Fe(II) supply level which leads to the largest phenotypic difference between Ye478 and Wu312. Then, genome-wide association analysis was performed to further identify candidate genes associated with the molecular mechanisms under different Fe nutritional statuses. Three candidate genes involved in Fe homeostasis of strategy II plants (strategy II genes) were identified, including ZmDMAS1, ZmNAAT1, and ZmYSL11. Furthermore, candidate genes ZmNAAT1, ZmDMAS1, and ZmYSL11 were induced in Fe-deficient roots and shoots, and the expression of ZmNAAT1 and ZmDMAS1 responded to Fe deficiency more in shoots than in roots. Beyond that, several genes that may participate in Fe homeostasis of strategy I plants (strategy I genes) were identified, which were either encoding Fe transporters (ZmIRT1 and ZmZIP4), or acting as essential ethylene signal transducers (ZmEBF1). Interestingly, ZmIRT1, ZmZIP4, and ZmEBF1 were significantly upregulated under low Fe stress, suggesting that these genes may be involved in Fe-deficiency tolerance in maize which is considered as strategy II plant. This study demonstrates the use of natural variation in the association population to identify important genes associated with Fe-deficiency tolerance and may further provide insights for understanding the molecular mechanism underlying the tolerance to Fe-deficiency stress in maize.
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Affiliation(s)
- Jianqin Xu
- Key Laboratory of Plant-Soil Interaction (MOE), Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Weiya Xu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Xulei Chen
- Key Laboratory of Plant-Soil Interaction (MOE), Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Huaqing Zhu
- Key Laboratory of Plant-Soil Interaction (MOE), Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
| | - Xiuyi Fu
- Key Laboratory of Maize DNA Fingerprinting and Molecular Breeding, Maize Research Center, Beijing Academy of Agriculture and Forestry Science (BAAFS), Beijing, China
| | - Futong Yu
- Key Laboratory of Plant-Soil Interaction (MOE), Centre for Resources, Environment and Food Security, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China
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15
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Nazir M, Mahajan R, Mansoor S, Rasool S, Mir RA, Singh R, Thakral V, Kumar V, Sofi PA, El-Serehy HA, Hefft DI, Zargar SM. Identification of QTLs/ Candidate Genes for Seed Mineral Contents in Common Bean (Phaseolus vulgaris L.) Through Genotyping-by-Sequencing. Front Genet 2022; 13:750814. [PMID: 35391791 PMCID: PMC8982075 DOI: 10.3389/fgene.2022.750814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Accepted: 01/17/2022] [Indexed: 11/13/2022] Open
Abstract
Throughout the ages, the common bean has been consumed by humanity as an important food staple crop and source of nutrition on a global scale. Since its domestication, a wide spectrum of phenotypic and genotypic investigations have been carried out to unravel the potential of this crop and to understand the process of nutrient accumulation along with other desirable characteristics. The common bean is one of the essential legume crops due to its high protein and micronutrient content. The balance in micronutrients is critical for the growth and development of plants as well as humans. Iron (Fe), Zinc (Zn), Copper (Cu), Manganese (Mn), Magnesium (Mg), Calcium (Ca), and Molybdenum (Mo) are some of the important micronutrients present in legumes. Thus, we aimed to investigate the quantitative trait loci’s (QTLs)/single nucleotide polymorphisms (SNPs) to identify the candidate genes associated with micronutrients through genotyping by sequencing (GBS). In our investigation, through GBS we identified SNPs linked with traits and assessed seven micronutrients in 96 selected common bean genotypes for screening nutritionally rich genotypes. Among 96399 SNPs total identified through GBS, 113 SNPs showed significant phenotypic variance, ranging from 13.50 to 21.74%. SNPs associated with most of the seed micronutrients (Mg, Mn, Fe, Ca, Cu) were found on chr3 & chr11 (Mg, Mn, Mo, Ca, Zn). The findings from this study could be used for haplotype-based selection of nutritionally rich genotypes and for marker-assisted genetic enhancement of the common bean. Further, the identified SNPs for candidate genes/transporters associated with micronutrient content may pave the way for the enrichment of seeds by employing genomics-assisted breeding programs.
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Affiliation(s)
- Muslima Nazir
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Reetika Mahajan
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Sheikh Mansoor
- Division of Biochemistry, FBSc, Sher-e Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Sheezan Rasool
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | | | - Ravinder Singh
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Vandana Thakral
- National Agr Food Biotechnology Institute (NABI), Mohali, India
| | - Virender Kumar
- National Agr Food Biotechnology Institute (NABI), Mohali, India
| | - Parvaze A. Sofi
- Division of Genetics and Plant Breeding, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Hamed A. El-Serehy
- Department of Zoology, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Daniel Ingo Hefft
- University Centre Reaseheath, Reaseheath College, Nantwich, United Kingdom
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
- *Correspondence: Sajad Majeed Zargar,
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16
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Wang H, Jia J, Cai Z, Duan M, Jiang Z, Xia Q, Ma Q, Lian T, Nian H. Identification of quantitative trait loci (QTLs) and candidate genes of seed Iron and zinc content in soybean [Glycine max (L.) Merr.]. BMC Genomics 2022; 23:146. [PMID: 35183125 PMCID: PMC8857819 DOI: 10.1186/s12864-022-08313-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 01/13/2022] [Indexed: 01/04/2023] Open
Abstract
BACKGROUND Deciphering the hereditary mechanism of seed iron (Fe) and zinc (Zn) content in soybean is important and sustainable to address the "hidden hunger" that presently affects approximately 2 billion people worldwide. Therefore, in order to detect genomic regions related to soybean seed Fe and Zn content, a recombinant inbred line (RIL) population with 248 lines was assessed in four environments to detect Quantitative Trait Loci (QTLs) related to soybean seed Fe and Zn content. RESULT Wide variation was found in seed Fe and Zn content in four environments, and genotype, environment, and genotype × environment interactions had significant influences on both the seed Fe and Zn content. A positive correlation was observed between seed Fe content and seed Zn content, and broad-sense heritability (H2) of seed Fe and Zn content were 0.73 and 0.75, respectively. In this study, five QTLs for seed Fe content were detected with 4.57 - 32.71% of phenotypic variation explained (PVE) and logarithm of odds (LOD) scores ranging from 3.60 to 33.79. Five QTLs controlling the seed Zn content were detected, and they individually explained 3.35 to 26.48% of the phenotypic variation, with LOD scores ranging from 3.64 to 20.4. Meanwhile, 409,541 high-quality single-nucleotide variants (SNVs) and 85,102 InDels (except intergenic regions) between two bi-parental lines were identified by whole genome resequencing. A total of 12 candidate genes were reported in one major QTL for seed Fe content and two major QTLs for seed Zn content, with the help of RNA-Seq analysis, gene ontology (GO) enrichment, gene annotation, and bi-parental whole genome sequencing (WGS) data. CONCLUSIONS Limited studies were performed about microelement of soybean, so these results may play an important role in the biofortification of Fe and Zn and accelerate the development of marker-assisted selection (MAS) for breeding soybeans fortified with iron and zinc.
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Affiliation(s)
- Huan Wang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, 510642 Guangzhou, Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
| | - Jia Jia
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, 510642 Guangzhou, Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
| | - Zhandong Cai
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, 510642 Guangzhou, Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
| | - Mingming Duan
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, 510642 Guangzhou, Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
| | - Ze Jiang
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, 510642 Guangzhou, Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
| | - Qiuju Xia
- Rice Molecular Breeding Institute, GRANLUX ASSOCIATED GRAINS, 518024 Shenzhen, Guangdong, People’s Republic of China
| | - Qibin Ma
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, 510642 Guangzhou, Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
| | - Tengxiang Lian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, 510642 Guangzhou, Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
| | - Hai Nian
- The State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
- Guangdong Laboratory for Lingnan Modern Agriculture, 510642 Guangzhou, Guangdong People’s Republic of China
- The Key Laboratory of Plant Molecular Breeding of Guangdong Province, College of Agriculture, South China Agricultural University, 510642 Guangzhou, Guangdong People’s Republic of China
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17
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Du S, Lu Q, Liu L, Wang Y, Li J. Rhodococcus qingshengii facilitates the phytoextraction of Zn, Cd, Ni, and Pb from soils by Sedum alfredii Hance. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127638. [PMID: 34801314 DOI: 10.1016/j.jhazmat.2021.127638] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
The enhanced heavy metal (HM) phytoextraction efficiency of hyperaccumulating plants via plant-growth-promoting microbes has been proposed as an effective strategy to remove HMs from contaminated soil. Nevertheless, it remains unclear whether catabolizing the abscisic acid (ABA) in hyperaccumulating plants via rhizobacteria can facilitate HM phytoextraction. In the present study, a hyperaccumulator, Sedum alfredii Hance, inoculated with an ABA-catabolizing bacterium Rhodococcus qingshengii, showed higher concentrations of Zn, Cd, Ni, and Pb in the contaminated paddy-grown plant shoots by 35%, 63%, 49%, and 49%, and in plants grown in mine soils by 112%, 105%, 46%, and 49%, respectively, than in the controlbacteria-free plants. However, no significant changes were observed in Cu content between these plants. Furthermore, parameters indicating phytoremediation potential, including the translocation factor (TF) and bioconcentration factor (BCF), revealed that bacterial inoculation could markedly increase the efficacy of Zn, Cd, Ni, and Pb phytoextraction from the soil. Notably, the bioavailabilities of HMs in soils were not influenced by R. qingshengii; however, the expression of transporters related to the uptake of these HMs, including SaIRT1, SaZIP1, SaZIP2, SaZIP3, SaNramp1, SaNramp3, SaNramp6, SaHMA2, and SaHMA3, was upregulated. These findings indicate that R. qingshengii inoculation could increase the HM-uptake ability of plants by catabolizing ABA and may provide a promising strategy for enhancing the phytoremediation efficacy in HM-contaminated soils.
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Affiliation(s)
- Shaoting Du
- Key Laboratory of Pollution Exposure and Health Intervention Technology, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou 310015, China.
| | - Qi Lu
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Lijuan Liu
- Key Laboratory of Pollution Exposure and Health Intervention Technology, Interdisciplinary Research Academy (IRA), Zhejiang Shuren University, Hangzhou 310015, China
| | - Yu Wang
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
| | - Jiaxin Li
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou 310018, China
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18
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Diaz S, Polania J, Ariza-Suarez D, Cajiao C, Grajales M, Raatz B, Beebe SE. Genetic Correlation Between Fe and Zn Biofortification and Yield Components in a Common Bean ( Phaseolus vulgaris L.). FRONTIERS IN PLANT SCIENCE 2022; 12:739033. [PMID: 35046970 PMCID: PMC8761845 DOI: 10.3389/fpls.2021.739033] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/08/2021] [Indexed: 05/05/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is the most important legume for direct human consumption worldwide. It is a rich and relatively inexpensive source of proteins and micronutrients, especially iron and zinc. Bean is a target for biofortification to develop new cultivars with high Fe/Zn levels that help to ameliorate malnutrition mainly in developing countries. A strong negative phenotypic correlation between Fe/Zn concentration and yield is usually reported, posing a significant challenge for breeders. The objective of this study was to investigate the genetic relationship between Fe/Zn. We used Quantitative Trait Loci (QTLs) mapping and Genome-Wide Association Studies (GWAS) analysis in three bi-parental populations that included biofortified parents, identifying genomic regions associated with yield and micromineral accumulation. Significant negative correlations were observed between agronomic traits (pod harvest index, PHI; pod number, PdN; seed number, SdN; 100 seed weight, 100SdW; and seed per pod, Sd/Pd) and micronutrient concentration traits (SdFe and SdZn), especially between pod harvest index (PHI) and SdFe and SdZn. PHI presented a higher correlation with SdN than PdN. Seventy-nine QTLs were identified for the three populations: 14 for SdFe, 12 for SdZn, 13 for PHI, 11 for SdN, 14 for PdN, 6 for 100SdW, and 9 for Sd/Pd. Twenty-three hotspot regions were identified in which several QTLs were co-located, of which 13 hotpots displayed QTL of opposite effect for yield components and Fe/Zn accumulation. In contrast, eight QTLs for SdFe and six QTLs for SdZn were observed that segregated independently of QTL of yield components. The selection of these QTLs will enable enhanced levels of Fe/Zn and will not affect the yield performance of new cultivars focused on biofortification.
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Affiliation(s)
| | | | | | | | | | | | - Stephen E. Beebe
- Bean Program, Crops for Health and Nutrition Area, Alliance Bioversity International – CIAT, Cali, Colombia
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Gore PG, Das A, Bhardwaj R, Tripathi K, Pratap A, Dikshit HK, Bhattacharya S, Nair RM, Gupta V. Understanding G × E Interaction for Nutritional and Antinutritional Factors in a Diverse Panel of Vigna stipulacea (Lam.) Kuntz Germplasm Tested Over the Locations. FRONTIERS IN PLANT SCIENCE 2021; 12:766645. [PMID: 34966400 PMCID: PMC8710513 DOI: 10.3389/fpls.2021.766645] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
Micronutrient malnutrition or hidden hunger is a serious challenge toward societal well-being. Vigna stipulacea (Lam.) Kuntz (known locally as Minni payaru), is an underutilized legume that has the potential to be a global food legume due to its rich nutrient profile. In the present study, 99 accessions of V. stipulacea were tested for iron (Fe), zinc (Zn), calcium (Ca), protein, and phytate concentrations over two locations for appraisal of stable nutrient-rich sources. Analysis of variance revealed significant effects of genotype for all the traits over both locations. Fe concentration ranged from 29.35-130.96 mg kg-1 whereas Zn concentration ranged from 19.44 to 74.20 mg kg-1 across both locations. The highest grain Ca concentration was 251.50 mg kg-1 whereas the highest grain protein concentration was recorded as 25.73%. In the case of grain phytate concentration, a genotype with the lowest value is desirable. IC622867 (G-99) was the lowest phytate containing accession at both locations. All the studied traits revealed highly significant genotypic variances and highly significant genotype × location interaction though less in magnitude than the genotypic variance. GGE Biplot analysis detected that, for grain Fe, Zn, and Ca concentration the 'ideal' genotypes were IC331457 (G-75), IC331610 (G-76), and IC553564 (G-60), respectively, whereas for grain protein concentration IC553521 (G-27) was the most "ideal type." For phytate concentration, IC351407 (G-95) and IC550523 (G-99) were considered as 'ideal' and 'desirable,' respectively. Based on the desirability index, Location 1 (Kanpur) was identified as ideal for Fe, Zn, Ca, and phytate, and for grain protein concentration, Location 2 (New Delhi) was the ideal type. A significant positive correlation was detected between grain Fe as well as grain Zn and protein concentration considering the pooled analysis over both the locations where as a significant negative association was observed between phytate and protein concentration over the locations. This study has identified useful donors and enhanced our knowledge toward the development of biofortified Vigna cultivars. Promoting domestication of this nutrient-rich semi-domesticated, underutilized species will boost sustainable agriculture and will contribute toward alleviating hidden hunger.
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Affiliation(s)
- Padmavati G. Gore
- Division of Plant Genetic Resources, Indian Council of Agricultural Research – Indian Agricultural Research Institute, New Delhi, India
- Indian Council of Agricultural Research – National Bureau of Plant Genetic Resources, New Delhi, India
| | - Arpita Das
- Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, India
| | - Rakesh Bhardwaj
- Indian Council of Agricultural Research – National Bureau of Plant Genetic Resources, New Delhi, India
| | - Kuldeep Tripathi
- Indian Council of Agricultural Research – National Bureau of Plant Genetic Resources, New Delhi, India
| | - Aditya Pratap
- Indian Council of Agricultural Research – Indian Institute of Pulses Research, Kanpur, India
| | - Harsh K. Dikshit
- Division of Genetics, Indian Council of Agricultural Research – Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Veena Gupta
- Indian Council of Agricultural Research – National Bureau of Plant Genetic Resources, New Delhi, India
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Zenda T, Liu S, Dong A, Li J, Wang Y, Liu X, Wang N, Duan H. Omics-Facilitated Crop Improvement for Climate Resilience and Superior Nutritive Value. FRONTIERS IN PLANT SCIENCE 2021; 12:774994. [PMID: 34925418 PMCID: PMC8672198 DOI: 10.3389/fpls.2021.774994] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 11/08/2021] [Indexed: 05/17/2023]
Abstract
Novel crop improvement approaches, including those that facilitate for the exploitation of crop wild relatives and underutilized species harboring the much-needed natural allelic variation are indispensable if we are to develop climate-smart crops with enhanced abiotic and biotic stress tolerance, higher nutritive value, and superior traits of agronomic importance. Top among these approaches are the "omics" technologies, including genomics, transcriptomics, proteomics, metabolomics, phenomics, and their integration, whose deployment has been vital in revealing several key genes, proteins and metabolic pathways underlying numerous traits of agronomic importance, and aiding marker-assisted breeding in major crop species. Here, citing several relevant examples, we appraise our understanding on the recent developments in omics technologies and how they are driving our quest to breed climate resilient crops. Large-scale genome resequencing, pan-genomes and genome-wide association studies are aiding the identification and analysis of species-level genome variations, whilst RNA-sequencing driven transcriptomics has provided unprecedented opportunities for conducting crop abiotic and biotic stress response studies. Meanwhile, single cell transcriptomics is slowly becoming an indispensable tool for decoding cell-specific stress responses, although several technical and experimental design challenges still need to be resolved. Additionally, the refinement of the conventional techniques and advent of modern, high-resolution proteomics technologies necessitated a gradual shift from the general descriptive studies of plant protein abundances to large scale analysis of protein-metabolite interactions. Especially, metabolomics is currently receiving special attention, owing to the role metabolites play as metabolic intermediates and close links to the phenotypic expression. Further, high throughput phenomics applications are driving the targeting of new research domains such as root system architecture analysis, and exploration of plant root-associated microbes for improved crop health and climate resilience. Overall, coupling these multi-omics technologies to modern plant breeding and genetic engineering methods ensures an all-encompassing approach to developing nutritionally-rich and climate-smart crops whose productivity can sustainably and sufficiently meet the current and future food, nutrition and energy demands.
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Affiliation(s)
- Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
- Department of Crop Science, Faculty of Agriculture and Environmental Science, Bindura University of Science Education, Bindura, Zimbabwe
| | - Songtao Liu
- Academy of Agriculture and Forestry Sciences, Hebei North University, Zhangjiakou, China
| | - Anyi Dong
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Jiao Li
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Yafei Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Xinyue Liu
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Nan Wang
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
| | - Huijun Duan
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
- Department of Crop Genetics and Breeding, College of Agronomy, Hebei Agricultural University, Baoding, China
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21
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Singh B, Goutam U, Kukreja S, Sharma J, Sood S, Bhardwaj V. Potato biofortification: an effective way to fight global hidden hunger. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:2297-2313. [PMID: 34744367 PMCID: PMC8526655 DOI: 10.1007/s12298-021-01081-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/16/2021] [Accepted: 09/22/2021] [Indexed: 06/03/2023]
Abstract
Hidden hunger is leading to extensive health problems in the developing world. Several strategies could be used to reduce the micronutrient deficiencies by increasing the dietary uptake of essential micronutrients. These include diet diversification, pharmaceutical supplementation, food fortification and crop biofortification. Among all, crop biofortification is the most sustainable and acceptable strategy to overcome the global issue of hidden hunger. Since most of the people suffering from micronutrient deficiencies, have monetary issues and are dependent on staple crops to fulfil their recommended daily requirements of various essential micronutrients. Therefore, increasing the micronutrient concentrations in cost effective staple crops seems to be an effective solution. Potato being the world's most consumed non-grain staple crop with enormous industrial demand appears to be an ideal candidate for biofortification. It can be grown in different climatic conditions, provide high yield, nutrition and dry matter in lesser time. In addition, huge potato germplasm have natural variations related to micronutrient concentrations, which can be utilized for its biofortification. This review discuss the current scenario of micronutrient malnutrition and various strategies that could be used to overcome it. The review also shed a light on the genetic variations present in potato germplasm and suggest effective ways to incorporate them into modern high yielding potato varieties.
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Affiliation(s)
- Baljeet Singh
- Division of Crop Improvement and Seed Technology, Central Potato Research Institute, Shimla, India
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Umesh Goutam
- School of Bioengineering and Biosciences, Lovely Professional University, Phagwara, India
| | - Sarvjeet Kukreja
- Department of Agronomy, Lovely Professional University, Phagwara, India
| | - Jagdev Sharma
- Division of Crop Production, Central Potato Research Institute, Shimla, India
| | - Salej Sood
- Division of Crop Improvement and Seed Technology, Central Potato Research Institute, Shimla, India
| | - Vinay Bhardwaj
- Division of Crop Improvement and Seed Technology, Central Potato Research Institute, Shimla, India
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Wang W, Guo H, Wu C, Yu H, Li X, Chen G, Tian J, Deng Z. Identification of novel genomic regions associated with nine mineral elements in Chinese winter wheat grain. BMC PLANT BIOLOGY 2021; 21:311. [PMID: 34210282 PMCID: PMC8252321 DOI: 10.1186/s12870-021-03105-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 06/14/2021] [Indexed: 05/08/2023]
Abstract
BACKGROUND Mineral elements are important for maintaining good human health besides heavy metals. Mining genes that control mineral elements are paramount for improving their accumulation in the wheat grain. Although previous studies have reported some loci for beneficial trace elements, they have mainly focused on Zn and Fe content. However, little information is available regarding the genetic loci differences in dissecting synchronous accumulation of multiple mineral elements in wheat grains, including beneficial and heavy elements. Therefore, a genome-wide association study (GWAS) was conducted on 205 wheat accessions with 24,355 single nucleotide polymorphisms (SNPs) to identify important loci and candidate genes for controlling Ca, Fe, Zn, Se, Cu, Mn, Cd, As, and Pb accumulation in wheat grains. RESULTS A total of 101 marker-trait associations (MTAs) (P < 10-5) loci affecting the content of nine mineral elements was identified on chromosomes 1B, 1D, 2A, 2B, 3A, 3B, 3D, 4A, 4B, 5A, 5B, 5D, 6B, 7A, 7B, and 7D. Among these, 17 major MTAs loci for the nine mineral elements were located, and four MTAs loci (P < 10-5) were found on chromosomes 1B, 6B, 7B, and 7D. Eight multi-effect MTAs loci were detected that are responsible for the control of more than one trait, mainly distributed on chromosomes 3B, 7B, and 5A. Furthermore, sixteen candidate genes controlling Ca, Fe, Zn, Se, Cd, and Pb were predicted, whose functions were primarily related to ion binding, including metals, Fe, Ca, Cu, Mg, and Zn, ATP binding, ATPase activity, DNA binding, RNA binding, and protein kinase activity. CONCLUSIONS Our study indicated the existence of gene interactions among mineral elements based on multi-effect MTAs loci and candidate genes. Meanwhile this study provided new insights into the genetic control of mineral element concentrations, and the important loci and genes identified may contribute to the rapid development of beneficial mineral elements and a reduced content of harmful heavy metals in wheat grain.
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Affiliation(s)
- Wei Wang
- State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271000, P.R. China
| | - Hong Guo
- State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271000, P.R. China
| | - Chongning Wu
- State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271000, P.R. China
| | - Hui Yu
- State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271000, P.R. China
| | - Xiaokang Li
- Handan Academy of Agricultural Sciences, Handan, Hebei, 056000, P.R. China
| | - Guangfeng Chen
- College of Ecology and Garden Architecture, Dezhou University, Dezhou, Shandong, 253023, P.R. China
| | - Jichun Tian
- State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271000, P.R. China
| | - Zhiying Deng
- State Key Laboratory of Crop Biology, Key Laboratory of Crop Biology of Shandong Province, Group of Wheat Quality and Molecular Breeding, College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271000, P.R. China.
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23
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Katuuramu DN, Wiesinger JA, Luyima GB, Nkalubo ST, Glahn RP, Cichy KA. Investigation of Genotype by Environment Interactions for Seed Zinc and Iron Concentration and Iron Bioavailability in Common Bean. FRONTIERS IN PLANT SCIENCE 2021; 12:670965. [PMID: 34040625 PMCID: PMC8141707 DOI: 10.3389/fpls.2021.670965] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 03/24/2021] [Indexed: 05/26/2023]
Abstract
Iron and zinc malnutrition are global public health concerns afflicting mostly infants, children, and women in low- and middle-income countries with widespread consumption of plant-based diets. Common bean is a widely consumed staple crop around the world and is an excellent source of protein, fiber, and minerals including iron and zinc. The development of nutrient-dense common bean varieties that deliver more bioavailable iron and zinc with a high level of trait stability requires a measurement of the contributions from genotype, environment, and genotype by environment interactions. In this research, we investigated the magnitude of genotype by environment interaction for seed zinc and iron concentration and seed iron bioavailability (FeBIO) using a set of nine test genotypes and three farmers' local check varieties. The research germplasm was evaluated for two field seasons across nine on-farm locations in three agro-ecological zones in Uganda. Seed zinc concentration ranged from 18.0 to 42.0 μg g-1 and was largely controlled by genotype, location, and the interaction between location and season [28.0, 26.2, and 14.7% of phenotypic variability explained (PVE), respectively]. Within a genotype, zinc concentration ranged on average 12 μg g-1 across environments. Seed iron concentration varied from 40.7 to 96.7 μg g-1 and was largely controlled by genotype, location, and the interaction between genotype, location, and season (25.7, 17.4, and 13.7% of PVE, respectively). Within a genotype, iron concentration ranged on average 28 μg g-1 across environments. Seed FeBIO ranged from 8 to 116% of Merlin navy control and was largely controlled by genotype (68.3% of PVE). The red mottled genotypes (Rozi Koko and Chijar) accumulated the most seed zinc and iron concentration, while the yellow (Ervilha and Cebo Cela) and white (Blanco Fanesquero) genotypes had the highest seed FeBIO and performed better than the three farmers' local check genotypes (NABE-4, NABE-15, and Masindi yellow). The genotypes with superior and stable trait performance, especially the Manteca seed class which combine high iron and zinc concentrations with high FeBIO, would serve as valuable parental materials for crop improvement breeding programs aimed at enhancing the nutritional value of the common bean.
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Affiliation(s)
- Dennis N. Katuuramu
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- USDA – ARS, U.S. Vegetable Laboratory, Charleston, SC, United States
| | - Jason A. Wiesinger
- USDA – ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Gabriel B. Luyima
- Legumes Research Program, National Crops Resources Research Institute, Kampala, Uganda
| | - Stanley T. Nkalubo
- Legumes Research Program, National Crops Resources Research Institute, Kampala, Uganda
| | - Raymond P. Glahn
- USDA – ARS, Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
| | - Karen A. Cichy
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
- USDA – ARS, Sugarbeet and Bean Research Unit, East Lansing, MI, United States
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Miller CN, Busch W. Using natural variation to understand plant responses to iron availability. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:2154-2164. [PMID: 33458759 PMCID: PMC7966951 DOI: 10.1093/jxb/erab012] [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: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 05/08/2023]
Abstract
Iron bioavailability varies dramatically between soil types across the globe. This has given rise to high levels of natural variation in plant iron responses, allowing members of even a single species to thrive across a wide range of soil types. In recent years we have seen the use of genome-wide association analysis to identify natural variants underlying plant responses to changes in iron availability in both Arabidopsis and important crop species. These studies have provided insights into which genes have been important in shaping local adaptation to iron availability in different plant species and have allowed the discovery of novel regulators and mechanisms, not previously identified using mutagenesis approaches. Furthermore, these studies have allowed the identification of markers that can be used to accelerate breeding of future elite varieties with increased resilience to iron stress and improved nutritional quality. The studies highlighted here show that, in addition to studying plant responses to iron alone, it is important to consider these responses within the context of plant nutrition more broadly and to also consider iron regulation in relation to additional traits of agronomic importance such as yield and disease resistance.
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Affiliation(s)
- Charlotte N Miller
- Salk Institute For Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Wolfgang Busch
- Salk Institute For Biological Studies, Plant Molecular and Cellular Biology Laboratory, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
- Correspondence:
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25
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Liu J, Huang L, Li T, Liu Y, Yan Z, Tang G, Zheng Y, Liu D, Wu B. Genome-Wide Association Study for Grain Micronutrient Concentrations in Wheat Advanced Lines Derived From Wild Emmer. FRONTIERS IN PLANT SCIENCE 2021; 12:651283. [PMID: 34054897 PMCID: PMC8160437 DOI: 10.3389/fpls.2021.651283] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/08/2021] [Indexed: 05/02/2023]
Abstract
Wheat is one of the important staple crops as the resources of both food and micronutrient for most people of the world. However, the levels of micronutrients (especially Fe and Zn) in common wheat are inherently low. Biofortification is an effective way to increase the micronutrient concentration of wheat. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, AABB, 2n = 4x = 28) is an important germplasm resource for wheat micronutrients improvement. In the present study, a genome-wide association study (GWAS) was performed to characterize grain iron, zinc, and manganese concentration (GFeC, GZnC, and GMnC) in 161 advanced lines derived from wild emmer. Using both the general linear model and mixed linear model, we identified 14 high-confidence significant marker-trait associations (MTAs) that were associated with GFeC, GZnC, and GMnC of which nine MTAs were novel. Six MTAs distributed on chromosomes 3B, 4A, 4B, 5A, and 7B were significantly associated with GFeC. Three MTAs on 1A and 2A were significantly associated with GZnC and five MTAs on 1B were significantly associated with GMnC. These MTAs show no negative effects on thousand kernel weight (TKW), implying the potential value for simultaneous improvement of micronutrient concentrations and TKW in breeding. Meanwhile, the GFeC, GZnC and GMnC are positively correlated, suggesting that these traits could be simultaneously improved. Genotypes containing high-confidence MTAs and 61 top genotypes with a higher concentration of grain micronutrients were recommended for wheat biofortification breeding. A total of 38 candidate genes related to micronutrient concentrations were identified. These candidates can be classified into four main groups: enzymes, transporter proteins, MYB transcription factor, and plant defense responses proteins. The MTAs and associated candidate genes provide essential information for wheat biofortification breeding through marker-assisted selection (MAS).
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Affiliation(s)
- Jia Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Tingxuan Li
- College of Resources, Sichuan Agricultural University, Wenjiang, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya'an, China
| | - Zehong Yan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya'an, China
| | - Guan Tang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya'an, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya'an, China
| | - Bihua Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, China
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, China
- Key Laboratory of Crop Genetic Resources and Improvement, Ministry of Education, Sichuan Agricultural University, Ya'an, China
- *Correspondence: Bihua Wu
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Roorkiwal M, Pandey S, Thavarajah D, Hemalatha R, Varshney RK. Molecular Mechanisms and Biochemical Pathways for Micronutrient Acquisition and Storage in Legumes to Support Biofortification for Nutritional Security. FRONTIERS IN PLANT SCIENCE 2021; 12:682842. [PMID: 34163513 PMCID: PMC8215609 DOI: 10.3389/fpls.2021.682842] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/06/2021] [Indexed: 05/10/2023]
Abstract
The world faces a grave situation of nutrient deficiency as a consequence of increased uptake of calorie-rich food that threaten nutritional security. More than half the world's population is affected by different forms of malnutrition. Unhealthy diets associated with poor nutrition carry a significant risk of developing non-communicable diseases, leading to a high mortality rate. Although considerable efforts have been made in agriculture to increase nutrient content in cereals, the successes are insufficient. The number of people affected by different forms of malnutrition has not decreased much in the recent past. While legumes are an integral part of the food system and widely grown in sub-Saharan Africa and South Asia, only limited efforts have been made to increase their nutrient content in these regions. Genetic variation for a majority of nutritional traits that ensure nutritional security in adverse conditions exists in the germplasm pool of legume crops. This diversity can be utilized by selective breeding for increased nutrients in seeds. The targeted identification of precise factors related to nutritional traits and their utilization in a breeding program can help mitigate malnutrition. The principal objective of this review is to present the molecular mechanisms of nutrient acquisition, transport and metabolism to support a biofortification strategy in legume crops to contribute to addressing malnutrition.
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Affiliation(s)
- Manish Roorkiwal
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Sarita Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Dil Thavarajah
- Plant and Environmental Sciences, Poole Agricultural Center, Clemson University, Clemson, SC, United States
| | - R. Hemalatha
- ICMR-National Institute of Nutrition (NIN), Hyderabad, India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- *Correspondence: Rajeev K. Varshney, ;
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Gupta PK, Balyan HS, Sharma S, Kumar R. Biofortification and bioavailability of Zn, Fe and Se in wheat: present status and future prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:1-35. [PMID: 33136168 DOI: 10.1007/s00122-020-03709-7] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/13/2020] [Indexed: 05/02/2023]
Abstract
Knowledge of genetic variation, genetics, physiology/molecular basis and breeding (including biotechnological approaches) for biofortification and bioavailability for Zn, Fe and Se will help in developing nutritionally improved wheat. Biofortification of wheat cultivars for micronutrients is a priority research area for wheat geneticists and breeders. It is known that during breeding of wheat cultivars for productivity and quality, a loss of grain micronutrient contents occurred, leading to decline in nutritional quality of wheat grain. Keeping this in view, major efforts have been made during the last two decades for achieving biofortification and bioavailability of wheat grain for micronutrients including Zn, Fe and Se. The studies conducted so far included evaluation of gene pools for contents of not only grain micronutrients as above, but also for phytic acid (PA) or phytate and phytase, so that, while breeding for the micronutrients, bioavailability is also improved. For this purpose, QTL interval mapping and GWAS were carried out to identify QTLs/genes and associated markers that were subsequently used for marker-assisted selection (MAS) during breeding for biofortification. Studies have also been conducted to understand the physiology and molecular basis of biofortification, which also allowed identification of genes for uptake, transport and storage of micronutrients. Transgenics using transgenes have also been produced. The breeding efforts led to the development of at least a dozen cultivars with improved contents of grain micronutrients, although land area occupied by these biofortified cultivars is still marginal. In this review, the available information on different aspects of biofortification and bioavailability of micronutrients including Zn, Fe and Se in wheat has been reviewed for the benefit of those, who plan to start work or already conducting research in this area.
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Affiliation(s)
- P K Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P, 250004, India.
| | - H S Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P, 250004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P, 250004, India
| | - Rahul Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, U.P, 250004, India
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Gaikwad KB, Rani S, Kumar M, Gupta V, Babu PH, Bainsla NK, Yadav R. Enhancing the Nutritional Quality of Major Food Crops Through Conventional and Genomics-Assisted Breeding. Front Nutr 2020; 7:533453. [PMID: 33324668 PMCID: PMC7725794 DOI: 10.3389/fnut.2020.533453] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Accepted: 09/03/2020] [Indexed: 01/14/2023] Open
Abstract
Nutritional stress is making over two billion world population malnourished. Either our commercially cultivated varieties of cereals, pulses, and oilseed crops are deficient in essential nutrients or the soils in which these crops grow are becoming devoid of minerals. Unfortunately, our major food crops are poor sources of micronutrients required for normal human growth. To overcome the problem of nutritional deficiency, greater emphasis should be laid on the identification of genes/quantitative trait loci (QTLs) pertaining to essential nutrients and their successful deployment in elite breeding lines through marker-assisted breeding. The manuscript deals with information on identified QTLs for protein content, vitamins, macronutrients, micro-nutrients, minerals, oil content, and essential amino acids in major food crops. These QTLs can be utilized in the development of nutrient-rich crop varieties. Genome editing technologies that can rapidly modify genomes in a precise way and will directly enrich the nutritional status of elite varieties could hold a bright future to address the challenge of malnutrition.
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Affiliation(s)
- Kiran B. Gaikwad
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sushma Rani
- Indian Council of Agricultural Research (ICAR)-National Institute for Plant Biotechnology, New Delhi, India
| | - Manjeet Kumar
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Vikas Gupta
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Prashanth H. Babu
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Naresh Kumar Bainsla
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Rajbir Yadav
- Division of Genetics, Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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Khandal H, Gupta SK, Dwivedi V, Mandal D, Sharma NK, Vishwakarma NK, Pal L, Choudhary M, Francis A, Malakar P, Singh NP, Sharma K, Sinharoy S, Singh NP, Sharma R, Chattopadhyay D. Root-specific expression of chickpea cytokinin oxidase/dehydrogenase 6 leads to enhanced root growth, drought tolerance and yield without compromising nodulation. PLANT BIOTECHNOLOGY JOURNAL 2020; 18:2225-2240. [PMID: 32181964 PMCID: PMC7589355 DOI: 10.1111/pbi.13378] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 01/16/2020] [Accepted: 01/20/2020] [Indexed: 05/11/2023]
Abstract
Cytokinin group of phytohormones regulate root elongation and branching during post-embryonic development. Cytokinin-degrading enzymes cytokinin oxidases/dehydrogenases (CKXs) have been deployed to investigate biological activities of cytokinin and to engineer root growth. We expressed chickpea cytokinin oxidase 6 (CaCKX6) under the control of a chickpea root-specific promoter of CaWRKY31 in Arabidopsis thaliana and chickpea having determinate and indeterminate growth patterns, respectively, to study the effect of cytokinin depletion on root growth and drought tolerance. Root-specific expression of CaCKX6 led to a significant increase in lateral root number and root biomass in Arabidopsis and chickpea without any penalty to vegetative and reproductive growth of shoot. Transgenic chickpea lines showed increased CKX activity in root. Soil-grown advanced chickpea transgenic lines exhibited higher root-to-shoot biomass ratio and enhanced long-term drought tolerance. These chickpea lines were not compromised in root nodulation and nitrogen fixation. The seed yield in some lines was up to 25% higher with no penalty in protein content. Transgenic chickpea seeds possessed higher levels of zinc, iron, potassium and copper. Our results demonstrated the potential of cytokinin level manipulation in increasing lateral root number and root biomass for agronomic trait improvement in an edible legume crop with indeterminate growth habit.
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Affiliation(s)
| | | | - Vikas Dwivedi
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Drishti Mandal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | | | | | - Lalita Pal
- National Institute of Plant Genome ResearchNew DelhiIndia
| | | | - Aleena Francis
- National Institute of Plant Genome ResearchNew DelhiIndia
| | - Paheli Malakar
- National Institute of Plant Genome ResearchNew DelhiIndia
| | | | - Kapil Sharma
- Repository of Tomato Genomics ResourcesDepartment of Plant SciencesUniversity of HyderabadHyderabadIndia
| | | | | | - Rameshwar Sharma
- Repository of Tomato Genomics ResourcesDepartment of Plant SciencesUniversity of HyderabadHyderabadIndia
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Reddy VRP, Das S, Dikshit HK, Mishra GP, Aski M, Meena SK, Singh A, Pandey R, Singh MP, Tripathi K, Gore PG, Priti, Bhagat TK, Kumar S, Nair R, Sharma TR. Genome-Wide Association Analysis for Phosphorus Use Efficiency Traits in Mungbean ( Vigna radiata L. Wilczek) Using Genotyping by Sequencing Approach. FRONTIERS IN PLANT SCIENCE 2020; 11:537766. [PMID: 33193476 PMCID: PMC7658405 DOI: 10.3389/fpls.2020.537766] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 09/18/2020] [Indexed: 10/10/2023]
Abstract
Mungbean (Vigna radiata L. Wilczek) is an annual grain legume crop affected by low availability of phosphorus. Phosphorus deficiency mainly affects the growth and development of plants along with changes in root morphology and increase in root-to-shoot ratio. Deciphering the genetic basis of phosphorus use efficiency (PUE) traits can benefit our understanding of mungbean tolerance to low-phosphorus condition. To address this issue, 144 diverse mungbean genotypes were evaluated for 12 PUE traits under hydroponics with optimum- and low-phosphorus levels. The broad sense heritability of traits ranged from 0.63 to 0.92 and 0.58 to 0.92 under optimum- and low-phosphorus conditions, respectively. This study, reports for the first time such a large number of genome wide Single nucleotide polymorphisms (SNPs) (76,160) in mungbean. Further, genome wide association study was conducted using 55,634 SNPs obtained by genotyping-by-sequencing method. The results indicated that total 136 SNPs shared by both GLM and MLM models were associated with tested PUE traits under different phosphorus regimes. We have identified SNPs with highest p value (-log10(p)) for some traits like, TLA and RDW with p value (-log10(p)) of more than 6.0 at LP/OP and OP condition. We have identified nine SNPs (three for TLA and six for RDW trait) which was found to be present in chromosomes 8, 4, and 7. One SNP present in Vradi07g06230 gene contains zinc finger CCCH domain. In total, 71 protein coding genes were identified, of which 13 genes were found to be putative candidate genes controlling PUE by regulating nutrient uptake and root architectural development pathways in mungbean. Moreover, we identified three potential candidate genes VRADI11G08340, VRADI01G05520, and VRADI04G10750 with missense SNPs in coding sequence region, which results in significant variation in protein structure at tertiary level. The identified SNPs and candidate genes provide the essential information for genetic studies and marker-assisted breeding program for improving low-phosphorus tolerance in mungbean.
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Affiliation(s)
| | - Shouvik Das
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Harsh Kumar Dikshit
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Gyan Prakash Mishra
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Muraleedhar Aski
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Surendra Kumar Meena
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Division of Basic Science, ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Akanksha Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
- Amity Institute of Organic Agriculture, Amity University, Noida, India
| | - Renu Pandey
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Madan Pal Singh
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Kuldeep Tripathi
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Padmavati Ganpat Gore
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Priti
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Shiv Kumar
- Biodiversity and Integrated Gene Management Program, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | | | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
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Karaca N, Ates D, Nemli S, Ozkuru E, Yilmaz H, Yagmur B, Kartal C, Tosun M, Ozdestan O, Otles S, Kahriman A, Chang P, Tanyolac MB. Identification of SNP Markers Associated with Iron and Zinc Concentrations in Cicer Seeds. Curr Genomics 2020; 21:212-223. [PMID: 33071615 PMCID: PMC7521033 DOI: 10.2174/1389202921666200413150951] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 03/18/2020] [Accepted: 03/27/2020] [Indexed: 12/30/2022] Open
Abstract
Background Cicer reticulatum L. is the wild progenitor of chickpea Cicer arietinum L., the fourth most important pulse crop in the world. Iron (Fe) and zinc (Zn) are vital micronutrients that play crucial roles in sustaining life by acting as co-factors for various proteins. Aims and Objectives
In order to improve micronutrient-dense chickpea lines, this study aimed to investigate variability and detect DNA markers associated with Fe and Zn concentrations in the seeds of 73 cultivated (C. arietinum L.) and 107 C. reticulatum genotypes. Methods
A set of 180 accessions was genotyped using 20,868 single nucleotide polymorphism (SNP) markers obtained from genotyping by sequencing analysis. Results
The results revealed substantial variation in the seed Fe and Zn concentration of the surveyed population. Using STRUCTURE software, the population structure was divided into two groups according to the principal component analysis and neighbor-joining tree analysis. A total of 23 and 16 associated SNP markers related to Fe and Zn concentrations, respectively were identified in TASSEL software by the mixed linear model method. Significant SNP markers found in more than two environments were accepted as more reliable than those that only existed in a single environment. Conclusion
The identified markers can be used in marker-assisted selection in chickpea breeding programs for the improvement of seed Fe and Zn concentrations in the chickpea.
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Affiliation(s)
- Nur Karaca
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Duygu Ates
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Seda Nemli
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Esin Ozkuru
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Hasan Yilmaz
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Bulent Yagmur
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Canan Kartal
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Muzaffer Tosun
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Ozgul Ozdestan
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Semih Otles
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Abdullah Kahriman
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Peter Chang
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
| | - Muhammed Bahattin Tanyolac
- 1Ege University, Department of Bioengineering, Bornova, Izmir35100, Turkey; 2Ege University, Faculty of Fisheries, Bornova, Izmir35100, Turkey; 3Ege University, Department of Soil Science and Plant Nutrition, Bornova, Izmir35100, Turkey; 4Ege University, Department of Food Engineering, Bornova, Izmir35100, Turkey; 5Department of Field Crops, Ege University, Bornova, Izmir35100, Turkey; 6Harran University, Department of Field Crops, 63000 Sanliurfa, Turkey; 7University of Southern California, Los Angeles, CA90007, USA
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Ullah A, Al-Sadi AM, Al-Subhi AM, Farooq M. Characterization of chickpea genotypes of Pakistani origin for genetic diversity and zinc grain biofortification. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2020; 100:4139-4149. [PMID: 32356568 DOI: 10.1002/jsfa.10453] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 02/27/2020] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Intake of food low in essential minerals, like zinc (Zn), is one of the major reasons of malnutrition. Development of genotypes with grains enriched in essential minerals may help to solve the issue of malnutrition. In this study, 16 chickpea genotypes (eight each of desi and kabuli types) of Pakistani origin were evaluated for genetic diversity and grain Zn biofortification potential with and without Zn fertilization. RESULTS A wide variation was noted for agronomic, physiological, agro-physiological, utilization, and apparent recovery efficiencies of Zn in the chickpea genotypes tested. Genotypes also differed for grain Zn concentration (37.5-48.6 mg kg-1 ), bioavailable Zn (3.72-4.42 mg day-1 ), and grain yield. The highest grain Zn concentration and bioavailable Zn were noted in genotypes NIAB-CH-2016 (47.1 mg kg-1 and 4.30 mg day-1 respectively) and Noor-2013 (48.6 mg kg-1 and 4.38 mg day-1 respectively) among the desi and kabuli types respectively. The same genotypes were the highest yielders. Cluster analysis showed that all (eight) kabuli genotypes grouped together, whereas most (six) of the desi genotypes clustered in a separate group. There was low to moderate genetic diversity (0.149 for desi and 0.104 for kabuli types) and a low level of genetic differentiation between the two chickpea types (0.098). CONCLUSION Two populations of chickpea had low to moderate genetic diversity, with consistent gene flow. This genetic diversity in both chickpea types allows the breeding gains for improving the grain yield and grain Zn biofortification potential of chickpea genotypes. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Aman Ullah
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoudh, Oman
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
| | - Abdullah M Al-Sadi
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoudh, Oman
| | - Ali M Al-Subhi
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoudh, Oman
| | - Muhammad Farooq
- Department of Crop Sciences, College of Agricultural and Marine Sciences, Sultan Qaboos University, Al Khoudh, Oman
- Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
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Wu X, Islam ASMF, Limpot N, Mackasmiel L, Mierzwa J, Cortés AJ, Blair MW. Genome-Wide SNP Identification and Association Mapping for Seed Mineral Concentration in Mung Bean ( Vigna radiata L.). Front Genet 2020; 11:656. [PMID: 32670356 PMCID: PMC7327122 DOI: 10.3389/fgene.2020.00656] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 05/29/2020] [Indexed: 01/27/2023] Open
Abstract
Mung bean (Vigna radiata L.) quality is dependent on seed chemical composition, which in turn determines the benefits of its consumption for human health and nutrition. While mung bean is rich in a range of nutritional components, such as protein, carbohydrates and vitamins, it remains less well studied than other legume crops in terms of micronutrients. In addition, mung bean genomics and genetic resources are relatively sparse. The objectives of this research were three-fold, namely: to develop a genome-wide marker system for mung bean based on genotyping by sequencing (GBS), to evaluate diversity of mung beans available to breeders in the United States and finally, to perform a genome-wide association study (GWAS) for nutrient concentrations based on a seven mineral analysis using inductively coupled plasma (ICP) spectroscopy. All parts of our research were performed with 95 cultivated mung bean genotypes chosen from the USDA core collection representing accessions from 13 countries. Overall, we identified a total of 6,486 high quality single nucleotide polymorphisms (SNPs) from the GBS dataset and found 43 marker × trait associations (MTAs) with calcium, iron, potassium, manganese, phosphorous, sulfur or zinc concentrations in mung bean grain produced in either of two consecutive years' field experiments. The MTAs were scattered across 35 genomic regions explaining on average 22% of the variation for each seed nutrient in each year. Most of the gene regions provided valuable candidate loci to use in future breeding of new varieties of mung bean and further the understanding of genetic control of nutritional properties in the crop. Other SNPs identified in this study will serve as important resources to enable marker-assisted selection (MAS) for nutritional improvement in mung bean and to analyze cultivars of mung bean.
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Affiliation(s)
- Xingbo Wu
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - A. S. M. Faridul Islam
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | | | - Lucas Mackasmiel
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Jerzy Mierzwa
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
| | - Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria AGROSAVIA, C.I. La Selva, Rionegro, Colombia
- Departamento de Ciencias Forestales, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia – Sede Medellín, Medellín, Colombia
| | - Matthew W. Blair
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, United States
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Roorkiwal M, Bharadwaj C, Barmukh R, Dixit GP, Thudi M, Gaur PM, Chaturvedi SK, Fikre A, Hamwieh A, Kumar S, Sachdeva S, Ojiewo CO, Tar'an B, Wordofa NG, Singh NP, Siddique KHM, Varshney RK. Integrating genomics for chickpea improvement: achievements and opportunities. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:1703-1720. [PMID: 32253478 PMCID: PMC7214385 DOI: 10.1007/s00122-020-03584-2] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 03/18/2020] [Indexed: 05/19/2023]
Abstract
Integration of genomic technologies with breeding efforts have been used in recent years for chickpea improvement. Modern breeding along with low cost genotyping platforms have potential to further accelerate chickpea improvement efforts. The implementation of novel breeding technologies is expected to contribute substantial improvements in crop productivity. While conventional breeding methods have led to development of more than 200 improved chickpea varieties in the past, still there is ample scope to increase productivity. It is predicted that integration of modern genomic resources with conventional breeding efforts will help in the delivery of climate-resilient chickpea varieties in comparatively less time. Recent advances in genomics tools and technologies have facilitated the generation of large-scale sequencing and genotyping data sets in chickpea. Combined analysis of high-resolution phenotypic and genetic data is paving the way for identifying genes and biological pathways associated with breeding-related traits. Genomics technologies have been used to develop diagnostic markers for use in marker-assisted backcrossing programmes, which have yielded several molecular breeding products in chickpea. We anticipate that a sequence-based holistic breeding approach, including the integration of functional omics, parental selection, forward breeding and genome-wide selection, will bring a paradigm shift in development of superior chickpea varieties. There is a need to integrate the knowledge generated by modern genomics technologies with molecular breeding efforts to bridge the genome-to-phenome gap. Here, we review recent advances that have led to new possibilities for developing and screening breeding populations, and provide strategies for enhancing the selection efficiency and accelerating the rate of genetic gain in chickpea.
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Affiliation(s)
- Manish Roorkiwal
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia.
| | | | - Rutwik Barmukh
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Department of Genetics, Osmania University, Hyderabad, India
| | - Girish P Dixit
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | - Mahendar Thudi
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Pooran M Gaur
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Asnake Fikre
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Addis Ababa, Ethiopia
| | - Aladdin Hamwieh
- International Center for Agriculture Research in the Dry Areas (ICARDA), Cairo, Egypt
| | - Shiv Kumar
- International Center for Agriculture Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Supriya Sachdeva
- ICAR-Indian Agricultural Research Institute (IARI), Delhi, India
| | - Chris O Ojiewo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Nairobi, Kenya
| | - Bunyamin Tar'an
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Canada
| | | | | | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India.
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia.
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Lu Q, Weng Y, You Y, Xu Q, Li H, Li Y, Liu H, Du S. Inoculation with abscisic acid (ABA)-catabolizing bacteria can improve phytoextraction of heavy metal in contaminated soil. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 257:113497. [PMID: 31733960 DOI: 10.1016/j.envpol.2019.113497] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 09/18/2019] [Accepted: 10/25/2019] [Indexed: 05/18/2023]
Abstract
Promotion of plant capacity for accumulation of heavy metals (HMs) is one of the key strategies in enhancing phytoremediation in contaminated soils. Here we report that, Rhodococcus qingshengii, an abscisic acid (ABA)-catabolizing bacteria, clearly boosts levels of Cd, Zn, and Ni in wild-type Arabidopsis by 47, 24, and 30%, respectively, but no increase in Cu was noted, when compared with non-inoculated Arabidopsis plants in contaminated growth substrate. Furthermore, when compared with wild-type plants, R.qingshengii-induced increases in Cd, Zn, and Ni concentrations were more pronounced in abi1/hab1/abi2 (ABA-sensitive mutant) strains of Arabidopsis, whereas little effect was observed in snrk2.2/2.3 (ABA insensitive mutant). This demonstrates that metabolizing ABA might be indispensable for R. qingshengii to improve metal accumulation in plants. Bacterial inoculation significantly elevated the expression of Cd, Zn, and Ni-related transporters; whereas the transcript levels of Cu transporters remained unchanged. This result may be a reasonable explanation for why the uptake of Cd, Zn, and Ni in plants was stimulated by bacterial inoculation, while no effect was observed on Cu levels. From our results, we clearly demonstrate that R. qingshengii can increase the accumulation of Cd, Zn, and Ni in plants via an ABA-mediated HM transporters-associated mechanism. Metabolizing ABA in the plants by ABA-catabolizing bacterial inoculation might be an alternative strategy to improve phytoremediation efficiency in HMs contaminated soil.
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Affiliation(s)
- Qi Lu
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Yineng Weng
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Yue You
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Qianru Xu
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Haiyue Li
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Yuan Li
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Huijun Liu
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China
| | - Shaoting Du
- College of Environmental Science and Engineering, Zhejiang Gongshang University, Hangzhou, 310018, China.
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Jha AB, Warkentin TD. Biofortification of Pulse Crops: Status and Future Perspectives. PLANTS (BASEL, SWITZERLAND) 2020; 9:E73. [PMID: 31935879 PMCID: PMC7020478 DOI: 10.3390/plants9010073] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 01/02/2020] [Accepted: 01/02/2020] [Indexed: 01/08/2023]
Abstract
Biofortification through plant breeding is a sustainable approach to improve the nutritional profile of food crops. The majority of the world's population depends on staple food crops; however, most are low in key micronutrients. Biofortification to improve the nutritional profile of pulse crops has increased importance in many breeding programs in the past decade. The key micronutrients targeted have been iron, zinc, selenium, iodine, carotenoids, and folates. In recent years, several biofortified pulse crops including common beans and lentils have been released by HarvestPlus with global partners in developing countries, which has helped in overcoming micronutrient deficiency in the target population. This review will focus on recent research advances and future strategies for the biofortification of pulse crops.
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Affiliation(s)
| | - Thomas D. Warkentin
- Crop Development Centre/Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada;
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Karaca N, Ates D, Nemli S, Ozkuru E, Yilmaz H, Yagmur B, Kartal C, Tosun M, Ocak OO, Otles S, Kahriman A, Tanyolac MB. Association mapping of magnesium and manganese concentrations in the seeds of C. arietinum and C. reticulatum. Genomics 2019; 112:1633-1642. [PMID: 31669504 DOI: 10.1016/j.ygeno.2019.09.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/05/2019] [Accepted: 09/16/2019] [Indexed: 12/30/2022]
Abstract
Chickpea (Cicer arietinum L.) is one of the oldest and most important pulse crops grown and consumed all over the world, especially in developing countries. Magnesium (Mg) and manganese (Mn) are essential plant nutrients in terms of human health and many health problems arise in their deficiencies. The objectives of this study were to characterize genetic variability in the seed Mg and Mn concentrations and identify single nucleotide polymorphism (SNP) markers associated with these traits in 107 Cicer reticulatum and 73C. arietinum genotypes, using a genome wide association study. The genotypes were grown in four environments, characterized for Mg and Mn concentrations, and genotyped with 121,841 SNP markers. The population showed three-fold and two-fold variation for the Mg and Mn concentrations, respectively. The population structure was identified using STRUCTURE software, which divided 180 genotypes into two (K = 2) groups. Principal component analysis and neighbor joining tree analysis confirmed the results of STRUCTURE. A total of 4 and 16 consistent SNPs were detected for the Mg and Mn concentrations, respectively. The identified markers can be utilized in breeding of chickpea to increase Mg and Mn levels in order to improve human and livestock nutrition.
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Affiliation(s)
- Nur Karaca
- Ege University, Department of Bioengineering, 35040, Bornova, Izmir, Turkey
| | - Duygu Ates
- Ege University, Department of Bioengineering, 35040, Bornova, Izmir, Turkey
| | - Seda Nemli
- Ege University, Department of Bioengineering, 35040, Bornova, Izmir, Turkey
| | - Esin Ozkuru
- Ege University, Department of Bioengineering, 35040, Bornova, Izmir, Turkey
| | - Hasan Yilmaz
- Ege University, Department of Bioengineering, 35040, Bornova, Izmir, Turkey
| | - Bulent Yagmur
- Ege University, Department of Soil Sciences, 35040, Bornova, Izmir, Turkey
| | - Canan Kartal
- Ege University, Department of Food Engineering, 35040, Bornova, Izmir, Turkey
| | - Muzaffer Tosun
- Ege University, Department of Field Crops, 35040, Bornova, Izmir, Turkey
| | - Ozgul Ozdestan Ocak
- Ege University, Department of Food Engineering, 35040, Bornova, Izmir, Turkey
| | - Semih Otles
- Ege University, Department of Food Engineering, 35040, Bornova, Izmir, Turkey
| | - Abdullah Kahriman
- Harran University, Department of Field Crops, 64000 Sanli Urfa, Turkey
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Sharma A, Basu U, Malik N, Daware A, Thakro V, Narnoliya L, Bajaj D, Tripathi S, Hegde VS, Upadhyaya HD, Tyagi AK, Parida SK. Genome-wide cis-regulatory signatures for modulation of agronomic traits as exemplified by drought yield index (DYI) in chickpea. Funct Integr Genomics 2019; 19:973-992. [PMID: 31177403 DOI: 10.1007/s10142-019-00691-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 05/07/2019] [Accepted: 05/10/2019] [Indexed: 12/26/2022]
Abstract
Developing functional molecular tags from the cis-regulatory sequence components of genes is vital for their deployment in efficient genetic dissection of complex quantitative traits in crop plants including chickpea. The current study identified 431,194 conserved non-coding SNP (CNSNP) from the cis-regulatory element regions of genes which were annotated on a chickpea genome. These genome-wide CNSNP marker resources are made publicly accessible through a user-friendly web-database ( http://www.cnsnpcicarbase.com ). The CNSNP-based quantitative trait loci (QTL) and expression QTL (eQTL) mapping and genome-wide association study (GWAS) were further integrated with global gene expression landscapes, molecular haplotyping, and DNA-protein interaction study in the association panel and recombinant inbred lines (RIL) mapping population to decode complex genetic architecture of one of the vital seed yield trait under drought stress, drought yield index (DYI), in chickpea. This delineated two constituted natural haplotypes and alleles from a histone H3 protein-coding gene and its transcriptional regulator NAC transcription factor (TF) harboring the major QTLs and trans-acting eQTL governing DYI in chickpea. The effect of CNSNPs in TF-binding cis-element of a histone H3 gene in altering the binding affinity and transcriptional activity of NAC TF based on chromatin immunoprecipitation-quantitative PCR (ChIP-qPCR) assay was evident. The CNSNP-led promising molecular tags scanned will essentially have functional significance to decode transcriptional gene regulatory function and thus can drive translational genomic analysis in chickpea.
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Affiliation(s)
- Akash Sharma
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Udita Basu
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Virevol Thakro
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Laxmi Narnoliya
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Deepak Bajaj
- Genomics-Assisted Breeding and Crop Improvement Laboratory, 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
| | - V S Hegde
- 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, Telangana, 502324, India
| | - Akhilesh K Tyagi
- Genomics-Assisted Breeding and Crop Improvement Laboratory, 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
- Genomics-Assisted Breeding and Crop Improvement Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India.
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Dixit S, Singh UM, Abbai R, Ram T, Singh VK, Paul A, Virk PS, Kumar A. Identification of genomic region(s) responsible for high iron and zinc content in rice. Sci Rep 2019; 9:8136. [PMID: 31148549 PMCID: PMC6544658 DOI: 10.1038/s41598-019-43888-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 04/23/2019] [Indexed: 11/15/2022] Open
Abstract
Micronutrient especially iron and zinc-enriched rice hold immense promise for sustainable and cost-effective solutions to overcome malnutrition. In this context, BC2F5 population derived from cross between RP-Bio226 and Sampada was used to localize genomic region(s)/QTL(s) for grain Fe (iron) and Zn (zinc) content together with yield and yield-related traits. Genotyping of mapping population with 108 SSR markers resulted in a genetic map of 2317.5 cM with an average marker distance of 21.5 cM. Mean grain mineral content in the mapping population across the two seasons ranged from 10.5–17.5 ppm for Fe and 11.3–22.1 ppm for Zn. Based on the multi-season phenotypic data together with genotypic data, a total of two major QTLs for Fe (PVE upto 17.1%) and three for Zn (PVE upto 34.2%) were identified. Comparative analysis across the two seasons has revealed four consistent QTLs for Fe (qFe1.1, qFe1.2, qFe6.1 and qFe6.2) and two QTL for Zn content (qZn1.1 and qZn6.2). Additionally, based on the previous and current studies three meta-QTLs for grain Fe and two for grain Zn have been identified. In-silico analysis of the identified QTL regions revealed the presence of potential candidate gene(s) such as, OsPOT, OsZIP4, OsFDR3, OsIAA5 etc., that were previously reported to influence grain Fe and Zn content. The identified QTLs could be utilized in developing high yielding, Fe and Zn denser varieties by marker assisted selection (MAS).
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Affiliation(s)
- Shilpi Dixit
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT Campus, Hyderabad, 502324, India.,Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT Campus, Hyderabad, 502324, India
| | - Ragavendran Abbai
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT Campus, Hyderabad, 502324, India
| | - T Ram
- Indian Institute of Rice Research (IIRR), Hyderabad, 500030, India
| | - Vikas Kumar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT Campus, Hyderabad, 502324, India
| | - Amitava Paul
- Visva-Bharati University, Santiniketan, West Bengal, 731235, India
| | - P S Virk
- HarvestPlus, ICRISAT Campus, Hyderabad, 502324, India
| | - Arvind Kumar
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT Campus, Hyderabad, 502324, India. .,International Rice Research Institute, DAPO BOX 7777, Metro Manila, Philippines.
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de Camargo AC, Favero BT, Morzelle MC, Franchin M, Alvarez-Parrilla E, de la Rosa LA, Geraldi MV, Maróstica Júnior MR, Shahidi F, Schwember AR. Is Chickpea a Potential Substitute for Soybean? Phenolic Bioactives and Potential Health Benefits. Int J Mol Sci 2019; 20:E2644. [PMID: 31146372 PMCID: PMC6600242 DOI: 10.3390/ijms20112644] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 05/18/2019] [Accepted: 05/22/2019] [Indexed: 01/07/2023] Open
Abstract
Legume seeds are rich sources of protein, fiber, and minerals. In addition, their phenolic compounds as secondary metabolites render health benefits beyond basic nutrition. Lowering apolipoprotein B secretion from HepG2 cells and decreasing the level of low-density lipoprotein (LDL)-cholesterol oxidation are mechanisms related to the prevention of cardiovascular diseases (CVD). Likewise, low-level chronic inflammation and related disorders of the immune system are clinical predictors of cardiovascular pathology. Furthermore, DNA-damage signaling and repair are crucial pathways to the etiology of human cancers. Along CVD and cancer, the prevalence of obesity and diabetes is constantly increasing. Screening the ability of polyphenols in inactivating digestive enzymes is a good option in pre-clinical studies. In addition, in vivo studies support the role of polyphenols in the prevention and/or management of diabetes and obesity. Soybean, a well-recognized source of phenolic isoflavones, exerts health benefits by decreasing oxidative stress and inflammation related to the above-mentioned chronic ailments. Similar to soybeans, chickpeas are good sources of nutrients and phenolic compounds, especially isoflavones. This review summarizes the potential of chickpea as a substitute for soybean in terms of health beneficial outcomes. Therefore, this contribution may guide the industry in manufacturing functional foods and/or ingredients by using an undervalued feedstock.
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Affiliation(s)
- Adriano Costa de Camargo
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile.
| | - Bruno Trevenzoli Favero
- University of Copenhagen, Department of Plant and Environmental Sciences, 2630 Taastrup, Denmark.
| | - Maressa Caldeira Morzelle
- Department of Food and Nutrition, Faculty of Nutrition, Federal University of Mato Grosso, Fernando Correa Avenue, P.O. box 2367, Cuiabá, MT 78060-900, Brazil.
| | - Marcelo Franchin
- Department of Physiological Sciences, Piracicaba Dental School, University of Campinas, Piracicaba, SP 13414-903, Brazil.
| | - Emilio Alvarez-Parrilla
- Department of Chemical Biological Sciences, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo, s/n, Cd, Juárez, Chihuahua 32310, México.
| | - Laura A de la Rosa
- Department of Chemical Biological Sciences, Universidad Autónoma de Ciudad Juárez, Anillo Envolvente del Pronaf y Estocolmo, s/n, Cd, Juárez, Chihuahua 32310, México.
| | - Marina Vilar Geraldi
- Department of Food and Nutrition, University of Campinas-UNICAMP, Campinas, SP 13083-862, Brazil.
| | | | - Fereidoon Shahidi
- Department of Biochemistry, Memorial University of Newfoundland, St. John's, NL A1B 3X9, Canada.
| | - Andrés R Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Casilla 306-22, Santiago, Chile.
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41
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Wang R, Gangola MP, Irvine C, Gaur PM, Båga M, Chibbar RN. Co-localization of genomic regions associated with seed morphology and composition in a desi chickpea (Cicer arietinum L.) population varying in seed protein concentration. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1263-1281. [PMID: 30661107 DOI: 10.1007/s00122-019-03277-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 01/07/2019] [Indexed: 06/09/2023]
Abstract
Major QTL on LG 1 and 3 control seed filling and seed coat development, thereby affecting seed shape, size, color, composition and weight, key determinants of crop yield and quality. A chickpea (Cicer arietinum L.) population consisting of 189 recombinant inbred lines (RILs) derived from a cross between medium-protein ICC 995 and high-protein ICC 5912 genotypes of the desi market class was analyzed for seed properties. Seed from the parental lines and RILs was produced in four different environments for determination of seed shape (SS), 100-seed weight (100-SW), protein (PRO) and starch (STA) concentration. Polymorphic genetic markers for the population were identified by Genotyping by Sequencing and assembled into a 522.5 cM genetic map. Phenotype data from the different growth environments were analyzed by QTL mapping done by single and multi-environment analyses and in addition, single marker association mapping. The analyses identified in total 11 QTL, of which the most significant (P < 0.05) loci were located on LG 1 (q-1.1), LG 2 (q-2.1), LG 3 (q-3.2, q-3.3), LG 4 (q-4.2), and LG 5 (q-5.1). STA was mostly affected by q-1.1, which explained 19.0% of the phenotypic variance for the trait. The largest QTL effects were demonstrated by q-3.2 that explained 52.5% of the phenotypic variances for 100-SW, 44.3% for PRO, and 14.6% for SS. This locus was also highly associated with flower color (COL; 95.2% explained) and showed q-3.2 alleles from the ICC 5912 parent conferred the blue flower color and production of small, round seeds with relatively high protein concentration. Genes affecting seed filling at q-1.1 and seed coat development at q-3.2, respectively, were considered to underlie differences in seed composition and morphology in the RIL population.
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Affiliation(s)
- Runfeng Wang
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Manu P Gangola
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Craig Irvine
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Pooran M Gaur
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana, 502 324, India
| | - Monica Båga
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Ravindra N Chibbar
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada.
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42
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Basu U, Bajaj D, Sharma A, Malik N, Daware A, Narnoliya L, Thakro V, Upadhyaya HD, Kumar R, Tripathi S, Bharadwaj C, Tyagi AK, Parida SK. Genetic dissection of photosynthetic efficiency traits for enhancing seed yield in chickpea. PLANT, CELL & ENVIRONMENT 2019; 42:158-173. [PMID: 29676051 DOI: 10.1111/pce.13319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 04/03/2018] [Indexed: 06/08/2023]
Abstract
Understanding the genetic basis of photosynthetic efficiency (PE) contributing to enhanced seed yield per plant (SYP) is vital for genomics-assisted crop improvement of chickpea. The current study employed an integrated genomic strategy involving photosynthesis pathway gene-based association mapping, genome-wide association study, quantitative trait loci (QTL) mapping, and expression profiling. This identified 16 potential single nucleotide polymorphism loci linked to major QTLs underlying 16 candidate genes significantly associated with PE and SYP traits in chickpea. The allelic variants were tightly linked to positively interacting QTLs regulating both enhanced PE and SYP traits as exemplified by a chlorophyll A-B binding protein-coding gene. The leaf tissue-specific pronounced up-regulated expression of 16 associated genes in germplasm accessions and homozygous individuals of mapping population was evident. Such combinatorial genomic strategy coupled with gene haplotype-specific association and in silico protein-protein interaction study delineated natural alleles and superior haplotypes from a chlorophyll A-B binding (CAB) protein-coding gene and its interacting gene, Timing of CAB Expression 1 (TOC1), which appear to be most promising candidates in modulating chickpea PE and SYP traits. These functionally pertinent molecular signatures identified have efficacy to drive marker-assisted selection for developing PE-enriched cultivars with high seed yield in chickpea.
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Affiliation(s)
- Udita Basu
- 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
| | - Akash Sharma
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Naveen Malik
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Anurag Daware
- 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
| | - Virevol Thakro
- 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, India
| | - Rajendra Kumar
- U.P. Council of Agricultural Research, Gomati Nagar, Lucknow, 226010, India
| | - Shailesh Tripathi
- Division of Genetics, Indian Agricultural Research Institute (IARI), New Delhi, 110012, India
| | - Chellapilla Bharadwaj
- 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
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, 110067, India
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Rehman HM, Cooper JW, Lam HM, Yang SH. Legume biofortification is an underexploited strategy for combatting hidden hunger. PLANT, CELL & ENVIRONMENT 2019; 42:52-70. [PMID: 29920691 DOI: 10.1111/pce.13368] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 06/07/2018] [Indexed: 05/03/2023]
Abstract
Legumes are the world's primary source of dietary protein and are particularly important for those in developing economies. However, the biofortification potential of legumes remains underexploited. Legumes offer a diversity of micronutrients and amino acids, exceeding or complementing the profiles of cereals. As such, the enhancement of legume nutritional composition presents an appealing target for addressing the "hidden hunger" of global micronutrient malnutrition. Affecting ~2 billion people, micronutrient malnutrition causes severe health effects ranging from stunted growth to reduced lifespan. An increased availability of micronutrient-enriched legumes, particularly to those in socio-economically deprived areas, would serve the dual functions of ameliorating hidden hunger and increasing the positive health effects associated with legumes. Here, we give an updated overview of breeding approaches for the nutritional improvement of legumes, and crucially, we highlight the importance of considering nutritional improvement in a wider ecological context. Specifically, we review the potential of the legume microbiome for agronomic trait improvement and highlight the need for increased genetic, biochemical, and environmental data resources. Finally, we state that such resources should be complemented by an international and multidisciplinary initiative that will drive crop improvement and, most importantly, ensure that research outcomes benefit those who need them most.
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Affiliation(s)
- Hafiz Mamoon Rehman
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, Korea
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - James William Cooper
- Institute of Molecular Cell and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow, Lanarkshire, G12 8QQ, UK
| | - Hon-Ming Lam
- Center for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Chonnam, Korea
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44
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Whole-Genome Association Mapping and Genomic Prediction for Iron Concentration in Wheat Grains. Int J Mol Sci 2018; 20:ijms20010076. [PMID: 30585193 PMCID: PMC6337276 DOI: 10.3390/ijms20010076] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 12/18/2018] [Accepted: 12/20/2018] [Indexed: 11/17/2022] Open
Abstract
Malnutrition of iron (Fe) affects two billion people worldwide. Therefore, enhancing grain Fe concentration (GFeC) in wheat (Triticum aestivum L.) is an important goal for breeding. Here we study the genetic factors underlying GFeC trait by genome-wide association studies (GWAS) and the prediction abilities using genomic prediction (GP) in a panel of 369 European elite wheat varieties which was genotyped with 15,523 mapped single-nucleotide polymorphism markers (SNP) and a subpanel of 183 genotypes with 44,233 SNP markers. The resulting means of GFeC from three field experiments ranged from 24.42 to 52.42 μg·g−1 with a broad-sense heritability (H2) equaling 0.59 over the years. GWAS revealed 41 and 137 significant SNPs in the whole and subpanel, respectively, including significant marker-trait associations (MTAs) for best linear unbiased estimates (BLUEs) of GFeC on chromosomes 2A, 3B and 5A. Putative candidate genes such as NAC transcription factors and transmembrane proteins were present on chromosome 2A (763,689,738–765,710,113 bp). The GP for a GFeC trait ranged from low to moderate values. The current study reported GWAS of GFeC for the first time in hexaploid wheat varieties. These findings confirm the utility of GWAS and GP to explore the genetic architecture of GFeC for breeding programs aiming at the improvement of wheat grain quality.
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Kumar A, Kaur G, Goel P, Bhati KK, Kaur M, Shukla V, Pandey AK. Genome-wide analysis of oligopeptide transporters and detailed characterization of yellow stripe transporter genes in hexaploid wheat. Funct Integr Genomics 2018; 19:75-90. [PMID: 30120602 DOI: 10.1007/s10142-018-0629-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Revised: 06/20/2018] [Accepted: 07/20/2018] [Indexed: 01/11/2023]
Abstract
Oligopeptide transporters (OPT) are integral cell membrane proteins that play a critical role in the transport of small peptides, secondary amino acids, glutathione conjugates, and mineral uptake. In the present study, 67 putative wheat yellow stripe-like transporter (YSL) proteins belonging to the subfamily of OPT transporters were identified. Phylogeny analysis resulted in the distribution of wheat YSLs into four discrete clades. The highest number of YSLs was present on the A genome and the chromosome 2 of hexaploid wheat. The identified wheat YSL genes showed differential expression in different tissues and during grain development suggesting the importance of this subfamily. Gene expression pattern of TaYSLs during iron starvation experiments suggested an early high transcript accumulation of TaYS1A, TaYS1B, TaYSL3, TaYSL5, and TaYSL6 in roots. In contrast, delayed expression was observed in shoots for TaYS1A, TaYS1B, TaYSL5, TaYSL12, and TaYSL19 as compared to control. Further, their expression under biotic and abiotic response emphasized their alternative functions during the plant growth and development. In conclusion, this work is the first comprehensive study of wheat YSL transporters and would be an important resource for prioritizing genes towards wheat biofortification.
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Affiliation(s)
- Anil Kumar
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Knowledge City, Mohali, Punjab, 140306, India.,Department of Biotechnology, Panjab University, Chandigarh, India
| | - Gazaldeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Knowledge City, Mohali, Punjab, 140306, India.,Department of Biotechnology, Panjab University, Chandigarh, India
| | - Parul Goel
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Knowledge City, Mohali, Punjab, 140306, India
| | - Kaushal Kumar Bhati
- Copenhagen Plant Science Centre, PLEN, University of Copenhagen, Thorvaldsensvej, 40, 1871, Frederiksberg C, Denmark
| | - Mandeep Kaur
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Knowledge City, Mohali, Punjab, 140306, India.,Department of Biotechnology, Panjab University, Chandigarh, India
| | - Vishnu Shukla
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Knowledge City, Mohali, Punjab, 140306, India
| | - Ajay Kumar Pandey
- Department of Biotechnology, National Agri-Food Biotechnology Institute, Sector 81, Knowledge City, Mohali, Punjab, 140306, India.
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Izquierdo P, Astudillo C, Blair MW, Iqbal AM, Raatz B, Cichy KA. Meta-QTL analysis of seed iron and zinc concentration and content in common bean (Phaseolus vulgaris L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1645-1658. [PMID: 29752522 DOI: 10.1007/s00122-018-3104-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 05/02/2018] [Indexed: 05/03/2023]
Abstract
Twelve meta-QTL for seed Fe and Zn concentration and/or content were identified from 87 QTL originating from seven population grown in sixteen field trials. These meta-QTL include 2 specific to iron, 2 specific to zinc and 8 that co-localize for iron and zinc concentrations and/or content. Common bean (Phaseolus vulgaris L.) is the most important legume for human consumption worldwide and it is an important source of microelements, especially iron and zinc. Bean biofortification breeding programs develop new varieties with high levels of Fe and Zn targeted for countries with human micronutrient deficiencies. Biofortification efforts thus far have relied on phenotypic selection of raw seed mineral concentrations in advanced generations. While numerous quantitative trait loci (QTL) studies have been conducted to identify genomic regions associated with increased Fe and Zn concentration in seeds, these results have yet to be employed for marker-assisted breeding. The objective of this study was to conduct a meta-analysis from seven QTL studies in Andean and Middle American intra- and inter-gene pool populations to identify the regions in the genome that control the Fe and Zn levels in seeds. Two meta-QTL specific to Fe and two meta-QTL specific to Zn were identified. Additionally, eight Meta QTL that co-localized for Fe and Zn concentration and/or content were identified across seven chromosomes. The Fe and Zn shared meta-QTL could be useful candidates for marker-assisted breeding to simultaneously increase seed Fe and Zn. The physical positions for 12 individual meta-QTL were identified and within five of the meta-QTL, candidate genes were identified from six gene families that have been associated with transport of iron and zinc in plants.
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Affiliation(s)
- Paulo Izquierdo
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Carolina Astudillo
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Matthew W Blair
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN, USA
| | - Asif M Iqbal
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA
| | - Bodo Raatz
- International Center for Tropical Agriculture, Cali, Colombia
| | - Karen A Cichy
- Department of Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI, USA.
- Sugarbeet and Bean Research Unit, USDA-ARS East Lansing, East Lansing, MI, USA.
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Jha UC. Current advances in chickpea genomics: applications and future perspectives. PLANT CELL REPORTS 2018; 37:947-965. [PMID: 29860584 DOI: 10.1007/s00299-018-2305-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 05/23/2018] [Indexed: 05/27/2023]
Abstract
Chickpea genomics promises to illuminate our understanding of genome organization, structural variations, evolutionary and domestication-related insights and fundamental biology of legume crops. Unprecedented advancements of next generation sequencing (NGS) technologies have enabled in decoding of multiple chickpea genome sequences and generating huge genomic resources in chickpea both at functional and structural level. This review is aimed to update the current progress of chickpea genomics ranging from high density linkage map development, genome-wide association studies (GWAS), functional genomics resources for various traits, emerging role of abiotic stress responsive coding and non-coding RNAs after the completion of draft chickpea genome sequences. Additionally, the current efforts of whole genome re-sequencing (WGRS) approach of global chickpea germplasm to capture the global genetic diversity existing in the historically released varieties across the world and increasing the resolution of the previously identified candidate gene(s) of breeding importance have been discussed. Thus, the outcomes of these genomics resources will assist in genomics-assisted selection and facilitate breeding of climate-resilient chickpea cultivars for sustainable agriculture.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, 208024, India.
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Tan GZH, Das Bhowmik SS, Hoang TML, Karbaschi MR, Long H, Cheng A, Bonneau JP, Beasley JT, Johnson AAT, Williams B, Mundree SG. Investigation of Baseline Iron Levels in Australian Chickpea and Evaluation of a Transgenic Biofortification Approach. FRONTIERS IN PLANT SCIENCE 2018; 9:788. [PMID: 29963065 PMCID: PMC6010650 DOI: 10.3389/fpls.2018.00788] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2018] [Accepted: 05/24/2018] [Indexed: 05/25/2023]
Abstract
Iron deficiency currently affects over two billion people worldwide despite significant advances in technology and society aimed at mitigating this global health problem. Biofortification of food staples with iron (Fe) represents a sustainable approach for alleviating human Fe deficiency in developing countries, however, biofortification efforts have focused extensively on cereal staples while pulses have been largely overlooked. In this study we describe a genetic engineering (GE) approach to biofortify the pulse crop, chickpea (Cicer arietinum L.), with Fe using a combination of the chickpea nicotianamine synthase 2 (CaNAS2) and soybean (Glycine max) ferritin (GmFER) genes which function in Fe transport and storage, respectively. This study consists of three main components: (1) the establishment for baseline Fe concentration of existing germplam, (2) the isolation and study of expression pattern of the novel CaNAS2 gene, and (3) the generation of GE chickpea overexpressing the CaNAS2 and GmFER genes. Seed of six commercial chickpea cultivars was collected from four different field locations in Australia and assessed for seed Fe concentration. The results revealed little difference between the cultivars assessed, and that chickpea seed Fe was negatively affected where soil Fe bioavailability is low. The desi cultivar HatTrick was then selected for further study. From it, the CaNAS2 gene was cloned and its expression in different tissues examined. The gene was found to be expressed in multiple vegetative tissues under Fe-sufficient conditions, suggesting that it may play a housekeeping role in systemic translocation of Fe. Two GE chickpea events were then generated and the overexpression of the CaNAS2 and GmFER transgenes confirmed. Analysis of nicotianamine (NA) and Fe levels in the GE seeds revealed that NA was nearly doubled compared to the null control while Fe concentration was not changed. Increased NA content in chickpea seed is likely to translate into increased Fe bioavailability and may thus overcome the effect of the bioavailability inhibitors found in pulses; however, further study is required to confirm this. This is the first known example of GE Fe biofortified chickpea; information gleaned from this study can feed into future pulse biofortification work to help alleviate global Fe deficiency.
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Affiliation(s)
- Grace Z. H. Tan
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Sudipta S. Das Bhowmik
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Thi M. L. Hoang
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Mohammad R. Karbaschi
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Hao Long
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Alam Cheng
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Julien P. Bonneau
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
| | - Jesse T. Beasley
- School of Biosciences, The University of Melbourne, Melbourne, VIC, Australia
| | | | - Brett Williams
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
| | - Sagadevan G. Mundree
- Centre for Tropical Crops and Biocommodities, Queensland University of Technology, Brisbane, QLD, Australia
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de Abreu E Lima F, Li K, Wen W, Yan J, Nikoloski Z, Willmitzer L, Brotman Y. Unraveling lipid metabolism in maize with time-resolved multi-omics data. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:1102-1115. [PMID: 29385634 DOI: 10.1111/tpj.13833] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 01/03/2018] [Accepted: 01/04/2018] [Indexed: 05/19/2023]
Abstract
Maize is the cereal crop with the highest production worldwide, and its oil is a key energy resource. Improving the quantity and quality of maize oil requires a better understanding of lipid metabolism. To predict the function of maize genes involved in lipid biosynthesis, we assembled transcriptomic and lipidomic data sets from leaves of B73 and the high-oil line By804 in two distinct time-series experiments. The integrative analysis based on high-dimensional regularized regression yielded lipid-transcript associations indirectly validated by Gene Ontology and promoter motif enrichment analyses. The co-localization of lipid-transcript associations using the genetic mapping of lipid traits in leaves and seedlings of a B73 × By804 recombinant inbred line population uncovered 323 genes involved in the metabolism of phospholipids, galactolipids, sulfolipids and glycerolipids. The resulting association network further supported the involvement of 50 gene candidates in modulating levels of representatives from multiple acyl-lipid classes. Therefore, the proposed approach provides high-confidence candidates for experimental testing in maize and model plant species.
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Affiliation(s)
| | - Kun Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Weiwei Wen
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Shizishan Lu 1, 430070, Hongshan, Wuhan, China
| | - Zoran Nikoloski
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam, Germany
| | - Lothar Willmitzer
- Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Yariv Brotman
- Department of Life Sciences, Ben Gurion University of the Negev, Beersheva, Israel
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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: 1.0] [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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