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Leonova IN, Ageeva EV, Shumny VK. Prospects for mineral biofortification of wheat: classical breeding and agronomy. Vavilovskii Zhurnal Genet Selektsii 2024; 28:523-535. [PMID: 39280848 PMCID: PMC11393657 DOI: 10.18699/vjgb-24-59] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 09/18/2024] Open
Abstract
Low intake of micro- and macroelements and vitamins in food negatively affects the health of more than two billion people around the world provoking chronic diseases. For the majority of the world's population, these are soft and durum wheats that provide beneficial nutrients, however their modern high-yielding varieties have a significantly depleted grain mineral composition that have reduced mineral intake through food. Biofortification is a new research trend, whose main goal is to improve the nutritional qualities of agricultural crops using a set of classical (hybridization and selection) methods as well and the modern ones employing gene/QTL mapping, bioinformatic analysis, transgenesis, mutagenesis and genome editing. Using the classical breeding methods, biofortified varieties have been bred as a part of various international programs funded by HarvestPlus, CIMMYT, ICARDA. Despite the promise of transgenesis and genome editing, these labor-intensive methods require significant investments, so these technologies, when applied to wheat, are still at the development stage and cannot be applied routinely. In recent years, the interest in wheat biofortification has increased due to the advances in mapping genes and QTLs for agronomically important traits. The new markers obtained from wheat genome sequencing and application of bioinformatic methods (GWAS, meta-QTL analysis) has expanded our knowledge on the traits that determine the grain mineral concentration and has identified the key gene candidates. This review describes the current research on genetic biofortification of wheat in the world and in Russia and provides information on the use of cultivated and wild-relative germplasms to expand the genetic diversity of modern wheat varieties.
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Affiliation(s)
- I N Leonova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E V Ageeva
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Krasnoobsk, Novosibirsk region, Russia
| | - V K Shumny
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Vishwakarma MK, Bhati PK, Kumar U, Singh RP, Kumar S, Govindan V, Mavi GS, Thiyagarajan K, Dhar N, Joshi AK. Genetic dissection of value-added quality traits and agronomic parameters through genome-wide association mapping in bread wheat ( T. aestivum L.). FRONTIERS IN PLANT SCIENCE 2024; 15:1419227. [PMID: 39228836 PMCID: PMC11368860 DOI: 10.3389/fpls.2024.1419227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/12/2024] [Indexed: 09/05/2024]
Abstract
Bread wheat (T. aestivum) is one of the world's most widely consumed cereals. Since micronutrient deficiencies are becoming more common among people who primarily depend upon cereal-based diets, a need for better-quality wheat varieties has been felt. An association panel of 154 T. aestivum lines was evaluated for the following quality traits: grain appearance (GA) score, grain hardness (GH), phenol reaction (PR) score, protein percent, sodium dodecyl sulfate (SDS) sedimentation value, and test weight (TWt). In addition, the panel was also phenotyped for grain yield and related traits such as days to heading, days to maturity, plant height, and thousand kernel weight for the year 2017-18 at the Borlaug Institute for South Asia (BISA) Ludhiana and Jabalpur sites. We performed a genome-wide association analysis on this panel using 18,351 genotyping-by-sequencing (GBS) markers to find marker-trait associations for quality and grain yield-related traits. We detected 55 single nucleotide polymorphism (SNP) marker trait associations (MTAs) for quality-related traits on chromosomes 7B (10), 1A (9), 2A (8), 3B (6), 2B (5), 7A (4), and 1B (3), with 3A, 4A, and 6D, having two and the rest, 4B, 5A, 5B, and 1D, having one each. Additionally, 20 SNP MTAs were detected for yield-related traits based on a field experiment conducted in Ludhiana on 7D (4) and 4D (3) chromosomes, while 44 SNP MTAs were reported for Jabalpur on chromosomes 2D (6), 7A (5), 2A (4), and 4A (4). Utilizing these loci in marker-assisted selection will benefit from further validation studies for these loci to improve hexaploid wheat for better yield and grain quality.
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Affiliation(s)
| | | | - Uttam Kumar
- Astralyan Agro (OPC) Pvt. Ltd, Shamli, Uttar Pradesh, India
| | - Ravi P. Singh
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Sundeep Kumar
- Indian Council of Agricultural Research (ICAR)-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Gurvinder Singh Mavi
- Department of Plant breeding and genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | | | - Narain Dhar
- Borlaug Institute for South Asia (BISA), New Delhi, India
| | - Arun K. Joshi
- Borlaug Institute for South Asia (BISA), New Delhi, India
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
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Burridge AJ, Winfield M, Przewieslik‐Allen A, Edwards KJ, Siddique I, Barral‐Arca R, Griffiths S, Cheng S, Huang Z, Feng C, Dreisigacker S, Bentley AR, Brown‐Guedira G, Barker GL. Development of a next generation SNP genotyping array for wheat. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:2235-2247. [PMID: 38520342 PMCID: PMC11258986 DOI: 10.1111/pbi.14341] [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: 12/07/2023] [Revised: 03/05/2024] [Accepted: 03/06/2024] [Indexed: 03/25/2024]
Abstract
High-throughput genotyping arrays have provided a cost-effective, reliable and interoperable system for genotyping hexaploid wheat and its relatives. Existing, highly cited arrays including our 35K Wheat Breeder's array and the Illumina 90K array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in wheat sequencing has given us access to a vast pool of SNP diversity, whilst technological improvements have allowed us to fit significantly more probes onto a 384-well format Axiom array than previously possible. Here we describe a novel Axiom genotyping array, the 'Triticum aestivum Next Generation' array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins 'Core Collection'. We used a novel haplotype optimization approach to select SNPs with the highest combined varietal discrimination and a design iteration step to test and replace SNPs which failed to convert to reliable markers. The final design with 43 372 SNPs contains a combination of haplotype-optimized novel SNPs and legacy cross-platform markers. We show that this design has an improved distribution of SNPs compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous array. We also demonstrate the improved performance of TaNGv1.1 for Genome-wide association studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available with supporting marker annotations and initial genotyping results freely available.
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Affiliation(s)
| | - Mark Winfield
- School of Biological SciencesUniversity of BristolBristolUK
| | | | | | - Imteaz Siddique
- Thermo Fisher Scientific3450 Central ExpresswaySanta ClaraCAUSA
| | | | | | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Zejian Huang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | - Cong Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenChina
| | | | | | - Gina Brown‐Guedira
- Plant Science Research UnitUSDA Agricultural Research ServiceRaleighNCUSA
| | - Gary L. Barker
- School of Biological SciencesUniversity of BristolBristolUK
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Kumar J, Saini DK, Kumar A, Kumari S, Gahlaut V, Rahim MS, Pandey AK, Garg M, Roy J. Biofortification of Triticum species: a stepping stone to combat malnutrition. BMC PLANT BIOLOGY 2024; 24:668. [PMID: 39004715 PMCID: PMC11247745 DOI: 10.1186/s12870-024-05161-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/16/2024] [Indexed: 07/16/2024]
Abstract
BACKGROUND Biofortification represents a promising and sustainable strategy for mitigating global nutrient deficiencies. However, its successful implementation poses significant challenges. Among staple crops, wheat emerges as a prime candidate to address these nutritional gaps. Wheat biofortification offers a robust approach to enhance wheat cultivars by elevating the micronutrient levels in grains, addressing one of the most crucial global concerns in the present era. MAIN TEXT Biofortification is a promising, but complex avenue, with numerous limitations and challenges to face. Notably, micronutrients such as iron (Fe), zinc (Zn), selenium (Se), and copper (Cu) can significantly impact human health. Improving Fe, Zn, Se, and Cu contents in wheat could be therefore relevant to combat malnutrition. In this review, particular emphasis has been placed on understanding the extent of genetic variability of micronutrients in diverse Triticum species, along with their associated mechanisms of uptake, translocation, accumulation and different classical to advanced approaches for wheat biofortification. CONCLUSIONS By delving into micronutrient variability in Triticum species and their associated mechanisms, this review underscores the potential for targeted wheat biofortification. By integrating various approaches, from conventional breeding to modern biotechnological interventions, the path is paved towards enhancing the nutritional value of this vital crop, promising a brighter and healthier future for global food security and human well-being.
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Affiliation(s)
- Jitendra Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali-140306, Mohali, Punjab, India.
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, 141004, India
| | - Ashish Kumar
- National Agri-Food Biotechnology Institute (NABI), Mohali-140306, Mohali, Punjab, India
| | - Supriya Kumari
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, 110078, India
| | - Vijay Gahlaut
- Department of Biotechnology, University Center for Research and Development Chandigarh University, Gharuan, Mohali, Punjab, 140413, India
| | - Mohammed Saba Rahim
- CSIR - Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, 176061, India
| | - Ajay Kumar Pandey
- National Agri-Food Biotechnology Institute (NABI), Mohali-140306, Mohali, Punjab, India
| | - Monika Garg
- National Agri-Food Biotechnology Institute (NABI), Mohali-140306, Mohali, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Mohali-140306, Mohali, Punjab, India.
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Wright H, Devos KM. Finger millet: a hero in the making to combat food insecurity. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:139. [PMID: 38771345 PMCID: PMC11108925 DOI: 10.1007/s00122-024-04637-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/26/2024] [Indexed: 05/22/2024]
Abstract
Climate change and population growth pose challenges to food security. Major crops such as maize, wheat, and rice are expected to face yield reductions due to warming in the coming years, highlighting the need for incorporating climate-resilient crops in agricultural production systems. Finger millet (Eleusine coracana (L.) Gaertn) is a nutritious cereal crop adapted to arid regions that could serve as an alternative crop for sustaining the food supply in low rainfall environments where other crops routinely fail. Despite finger millet's nutritional qualities and climate resilience, it is deemed an "orphan crop," neglected by researchers compared to major crops, which has hampered breeding efforts. However, in recent years, finger millet has entered the genomics era. Next-generation sequencing resources, including a chromosome-scale genome assembly, have been developed to support trait characterization. This review discusses the current genetic and genomic resources available for finger millet while addressing the gaps in knowledge and tools that are still needed to aid breeders in bringing finger millet to its full production potential.
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Affiliation(s)
- Hallie Wright
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Katrien M Devos
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA.
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA.
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Kartseva T, Aleksandrov V, Alqudah AM, Arif MAR, Kocheva K, Doneva D, Prokopova K, Börner A, Misheva S. GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight. PLANTS (BASEL, SWITZERLAND) 2024; 13:1084. [PMID: 38674493 PMCID: PMC11054703 DOI: 10.3390/plants13081084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 04/03/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024]
Abstract
Genetic enhancement of grain production and quality is a priority in wheat breeding projects. In this study, we assessed two key agronomic traits-grain protein content (GPC) and thousand kernel weight (TKW)-across 179 Bulgarian contemporary and historic varieties and landraces across three growing seasons. Significant phenotypic variation existed for both traits among genotypes and seasons, and no discernible difference was evident between the old and modern accessions. To understand the genetic basis of the traits, we conducted a genome-wide association study with MLM using phenotypic data from the crop seasons, best linear unbiased estimators, and genotypic data from the 25K Infinium iSelect array. As a result, we detected 16 quantitative trait nucleotides (QTNs) associated with GPC and 15 associated with TKW, all of which passed the false discovery rate threshold. Seven loci favorably influenced GPC, resulting in an increase of 1.4% to 8.1%, while four loci had a positive impact on TKW with increases ranging from 1.9% to 8.4%. While some loci confirmed previously published associations, four QTNs linked to GPC on chromosomes 2A, 7A, and 7B, as well as two QTNs related to TKW on chromosomes 1B and 6A, may represent novel associations. Annotations for proteins involved in the senescence-associated nutrient remobilization and in the following buildup of resources required for seed germination have been found for selected putative candidate genes. These include genes coding for storage proteins, cysteine proteases, cellulose-synthase, alpha-amylase, transcriptional regulators, and F-box and RWP-RK family proteins. Our findings highlight promising genomic regions for targeted breeding programs aimed at improving grain yield and protein content.
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Affiliation(s)
- Tania Kartseva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Vladimir Aleksandrov
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Ahmad M. Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha P.O. Box 2713, Qatar;
| | - Mian Abdur Rehman Arif
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Jhang Road, Faisalabad 38000, Pakistan;
| | - Konstantina Kocheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Dilyana Doneva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Katelina Prokopova
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK Gatersleben), OT Gatersleben, Corrensstraße 3, 06466 Seeland, Germany;
| | - Svetlana Misheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.)
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Sehgal D, Rathan ND, Özdemir F, Keser M, Akin B, Dababat AA, Koc E, Dreisigacker S, Morgounov A. Genomic wide association study and selective sweep analysis identify genes associated with improved yield under drought in Turkish winter wheat germplasm. Sci Rep 2024; 14:8431. [PMID: 38600135 PMCID: PMC11006659 DOI: 10.1038/s41598-024-57469-1] [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: 06/26/2023] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
A panel comprising of 84 Turkish winter wheat landraces (LR) and 73 modern varieties (MV) was analyzed with genome wide association study (GWAS) to identify genes/genomic regions associated with increased yield under favorable and drought conditions. In addition, selective sweep analysis was conducted to detect signatures of selection in the winter wheat genome driving the differentiation between LR and MV, to gather an understanding of genomic regions linked to adaptation and yield improvement. The panel was genotyped with 25 K wheat SNP array and phenotyped for agronomic traits for two growing seasons (2018 and 2019) in Konya, Turkey. Year 2018 was treated as drought environment due to very low precipitation prior to heading whereas year 2019 was considered as a favorable season. GWAS conducted with SNPs and haplotype blocks using mixed linear model identified 18 genomic regions in the vicinities of known genes i.e., TaERF3-3A, TaERF3-3B, DEP1-5A, FRIZZY PANICLE-2D, TaSnRK23-1A, TaAGL6-A, TaARF12-2A, TaARF12-2B, WAPO1, TaSPL16-7D, TaTGW6-A1, KAT-2B, TaOGT1, TaSPL21-6B, TaSBEIb, trs1/WFZP-A, TaCwi-A1-2A and TaPIN1-7A associated with grain yield (GY) and yield related traits. Haplotype-based GWAS identified five haplotype blocks (H1A-42, H2A-71, H4A-48, H7B-123 and H7B-124), with the favorable haplotypes showing a yield increase of > 700 kg/ha in the drought season. SNP-based GWAS, detected only one larger effect genomic region on chromosome 7B, in common with haplotype-based GWAS. On an average, the percentage variation (PV) explained by haplotypes was 8.0% higher than PV explained by SNPs for all the investigated traits. Selective sweep analysis detected 39 signatures of selection between LR and MV of which 15 were within proximity of known functional genes controlling flowering (PRR-A1, PPR-D1, TaHd1-6B), GY and GY components (TaSus2-2B, TaGS2-B1, AG1-1A/WAG1-1A, DUO-A1, DUO-B1, AG2-3A/WAG2-3A, TaLAX1, TaSnRK210-4A, FBP, TaLAX1, TaPIL1 and AP3-1-7A/WPA3-7A) and 10 regions underlying various transcription factors and regulatory genes. The study outcomes contribute to utilization of LR in breeding winter wheat.
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Affiliation(s)
- Deepmala Sehgal
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mex-Veracruz, El Batan, CP 56237, Veracruz, Mexico.
- Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, RG42 6EY, UK.
| | | | - Fatih Özdemir
- Bahri Dagdas International Agricultural Research Institute, Konya, Turkey
| | - Mesut Keser
- International Center for Agricultural Research in Dry Areas (ICARDA), Ankara, Turkey
| | - Beyhan Akin
- International Maize and Wheat Improvement Center (CIMMYT), Ankara, Turkey
| | | | - Emrah Koc
- International Maize and Wheat Improvement Center (CIMMYT), Ankara, Turkey
| | - Susanne Dreisigacker
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera Mex-Veracruz, El Batan, CP 56237, Veracruz, Mexico
| | - Alexey Morgounov
- Scientific Production Center of Grain, Shortandy, Astana reg., 010000, Kazakhstan.
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8
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Gudi S, Halladakeri P, Singh G, Kumar P, Singh S, Alwutayd KM, Abd El-Moneim D, Sharma A. Deciphering the genetic landscape of seedling drought stress tolerance in wheat ( Triticum aestivum L.) through genome-wide association studies. FRONTIERS IN PLANT SCIENCE 2024; 15:1351075. [PMID: 38510445 PMCID: PMC10952099 DOI: 10.3389/fpls.2024.1351075] [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: 12/06/2023] [Accepted: 02/12/2024] [Indexed: 03/22/2024]
Abstract
Wheat is an important cereal crop constrained by several biotic and abiotic stresses including drought stress. Understating the effect of drought stress and the genetic basis of stress tolerance is important to develop drought resilient, high-yielding wheat cultivars. In this study, we investigated the effects of drought stress on seedling characteristics in an association panel consisting of 198 germplasm lines. Our findings revealed that drought stress had a detrimental effect on all the seedling characteristics under investigation with a maximum effect on shoot length (50.94% reduction) and the minimum effect on germination percentage (7.9% reduction). To gain a deeper understanding, we conducted a genome-wide association analysis using 12,511 single nucleotide polymorphisms (SNPs), which led to the identification of 39 marker-trait associations (MTAs). Of these 39 MTAs, 13 were particularly noteworthy as they accounted for >10% of the phenotypic variance with a LOD score >5. These high-confidence MTAs were further utilized to extract 216 candidate gene (CGs) models within 1 Mb regions. Gene annotation and functional characterization identified 83 CGs with functional relevance to drought stress. These genes encoded the WD40 repeat domain, Myb/SANT-like domain, WSD1-like domain, BTB/POZ domain, Protein kinase domain, Cytochrome P450, Leucine-rich repeat domain superfamily, BURP domain, Calmodulin-binding protein60, Ubiquitin-like domain, etc. Findings from this study hold significant promise for wheat breeders as they provide direct assistance in selecting lines harboring favorable alleles for improved drought stress tolerance. Additionally, the identified SNPs and CGs will enable marker-assisted selection of potential genomic regions associated with enhanced drought stress tolerance in wheat.
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Affiliation(s)
- Santosh Gudi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Priyanka Halladakeri
- Department of Genetics and Plant Breeding, Anand Agricultural University, Anand, India
| | - Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
- Texas A&M University, AgriLife Research Center, Beaumont, TX, United States
| | - Pradeep Kumar
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD, United States
| | - Satinder Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Khairiah Mubarak Alwutayd
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | - Diaa Abd El-Moneim
- Department of Plant Production (Genetic Branch), Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt
| | - Achla Sharma
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, India
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9
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Sachdeva S, Singh R, Maurya A, Singh VK, Singh UM, Kumar A, Singh GP. New insights into QTNs and potential candidate genes governing rice yield via a multi-model genome-wide association study. BMC PLANT BIOLOGY 2024; 24:124. [PMID: 38373874 PMCID: PMC10877931 DOI: 10.1186/s12870-024-04810-5] [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: 12/15/2023] [Accepted: 02/08/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Rice (Oryza sativa L.) is one of the globally important staple food crops, and yield-related traits are prerequisites for improved breeding efficiency in rice. Here, we used six different genome-wide association study (GWAS) models for 198 accessions, with 553,229 single nucleotide markers (SNPs) to identify the quantitative trait nucleotides (QTNs) and candidate genes (CGs) governing rice yield. RESULTS Amongst the 73 different QTNs in total, 24 were co-localized with already reported QTLs or loci in previous mapping studies. We obtained fifteen significant QTNs, pathway analysis revealed 10 potential candidates within 100kb of these QTNs that are predicted to govern plant height, days to flowering, and plot yield in rice. Based on their superior allelic information in 20 elite and 6 inferior genotypes, we found a higher percentage of superior alleles in the elite genotypes in comparison to inferior genotypes. Further, we implemented expression analysis and enrichment analysis enabling the identification of 73 candidate genes and 25 homologues of Arabidopsis, 19 of which might regulate rice yield traits. Of these candidate genes, 40 CGs were found to be enriched in 60 GO terms of the studied traits for instance, positive regulator metabolic process (GO:0010929), intracellular part (GO:0031090), and nucleic acid binding (GO:0090079). Haplotype and phenotypic variation analysis confirmed that LOC_OS09G15770, LOC_OS02G36710 and LOC_OS02G17520 are key candidates associated with rice yield. CONCLUSIONS Overall, we foresee that the QTNs, putative candidates elucidated in the study could summarize the polygenic regulatory networks controlling rice yield and be useful for breeding high-yielding varieties.
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Grants
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
- BT/PR32853/AGIII/103/1159/2019 Department of Biotechnology, Ministry of Science and Technology, India
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Affiliation(s)
- Supriya Sachdeva
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India.
| | - Avantika Maurya
- Division of Genomic Resources, ICAR-NBPGR, Pusa, New Delhi, India
| | - Vikas K Singh
- International Rice Research Institute (IRRI), South Asia Hub, ICRISAT, Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI), South Asia Regional Centre (ISARC), Varanasi, India
| | - Arvind Kumar
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana, India
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10
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Jaiswal V, Bandyopadhyay T, Singh RK, Gahlaut V, Muthamilarasan M, Prasad M. Multi-environment GWAS identifies genomic regions underlying grain nutrient traits in foxtail millet (Setaria italica). PLANT CELL REPORTS 2023; 43:6. [PMID: 38127149 DOI: 10.1007/s00299-023-03127-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 12/03/2023] [Indexed: 12/23/2023]
Abstract
KEY MESSAGE A total of 104 foxtail millet accessions were evaluated for 11 nutrients in three environments and 67 high-confidence marker-trait associations (MTAs) were identified. Six SNPs showed pleiotropic effect and associated with two or more nutrients, whereas 24 candidate genes were identified for 28 MTAs involving seven traits. Millets are known for their better nutritional profiles compared to major cereals. Foxtail millet (Setaria italica) is rich in nutrients essential to circumvent malnutrition and hidden hunger. However, the genetic determinants underlying this trait remain elusive. In this context, we evaluated 104 diverse foxtail millet accessions in three different environments (E1, E2, and E3) for 11 nutrients and genotyped with 30K SNPs. The genome-wide association study showed 67 high-confidence (Bonferroni-corrected) marker-trait associations (MTAs) for the nutrients except for phosphorus. Six pleiotropic SNPs were also identified, which were associated with two or more nutrients. Around 24 candidate genes (CGs) were identified for 28 MTAs involving seven nutrients. A total of 17 associated SNPs were present within the gene region, and five (5) were mapped in the exon of the CGs. Significant SNPs, desirable alleles and CGs identified in the present study will be useful in breeding programmes for trait improvement.
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Affiliation(s)
- Vandana Jaiswal
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India.
| | | | | | - Vijay Gahlaut
- Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, India
- Department of Biotechnology, University Center for Research and Development, Chandigarh University, Gharuan, Mohali, India
| | - Mehanathan Muthamilarasan
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India.
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, Telangana, India.
- Department of Genetics, University of Delhi South Campus, New Delhi, India.
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11
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Kaur H, Sharma P, Kumar J, Singh VK, Vasistha NK, Gahlaut V, Tyagi V, Verma SK, Singh S, Dhaliwal HS, Sheikh I. Genetic analysis of iron, zinc and grain yield in wheat-Aegilops derivatives using multi-locus GWAS. Mol Biol Rep 2023; 50:9191-9202. [PMID: 37776411 DOI: 10.1007/s11033-023-08800-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 09/05/2023] [Indexed: 10/02/2023]
Abstract
BACKGROUND Wheat is a major staple crop and helps to reduce worldwide micronutrient deficiency. Investigating the genetics that control the concentrations of iron (Fe) and zinc (Zn) in wheat is crucial. Hence, we undertook a comprehensive study aimed at elucidating the genomic regions linked to the contents of Fe and Zn in the grain. METHODS AND RESULTS We performed the multi-locus genome-wide association (ML-GWAS) using a panel of 161 wheat-Aegilops substitution and addition lines to dissect the genomic regions controlling grain iron (GFeC), and grain zinc (GZnC) contents. The wheat panel was genotyped using 10,825 high-quality SNPs and phenotyped in three different environments (E1-E3) during 2017-2019. A total of 111 marker-trait associations (MTAs) (at p-value < 0.001) were detected that belong to all three sub-genomes of wheat. The highest number of MTAs were identified for GFeC (58), followed by GZnC (44) and yield (9). Further, six stable MTAs were identified for these three traits and also two pleiotropic MTAs were identified for GFeC and GZnC. A total of 1291 putative candidate genes (CGs) were also identified for all three traits. These CGs encode a diverse set of proteins, including heavy metal-associated (HMA), bZIP family protein, AP2/ERF, and protein previously associated with GFeC, GZnC, and grain yield. CONCLUSIONS The significant MTAs and CGs pinpointed in this current study are poised to play a pivotal role in enhancing both the nutritional quality and yield of wheat, utilizing marker-assisted selection (MAS) techniques.
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Affiliation(s)
- Harneet Kaur
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
| | - Prachi Sharma
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
| | - Jitendra Kumar
- National Agri-Food Biotechnology Institute, Sector-81, Mohali, Punjab, 140306, India
| | - Vikas Kumar Singh
- Department of Genetics and Plant Breeding, Ch. Charan Singh University, Meerut, U.P., 250004, India
| | - Neeraj Kumar Vasistha
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
- Department of Genetics and Plant Breeding, Rajiv Gandhi University, Itanagar, India
| | - Vijay Gahlaut
- Department of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India.
- University Center for Research and Development, Chandigarh University, Gharuan, Mohali, Punjab, 140413, India.
| | - Vikrant Tyagi
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
| | | | - Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), El Batan, Texcoco, Mexico
- USDA-ARS, Southeast Area, Subtropical Horticulture Research Station, 13601 Old Cutler Road, Miami, FL, 33158, USA
| | - H S Dhaliwal
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India
| | - Imran Sheikh
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmaur, 173101, India.
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12
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Tadesse W, Gataa ZE, Rachdad FE, Baouchi AE, Kehel Z, Alemu A. Single- and multi-trait genomic prediction and genome-wide association analysis of grain yield and micronutrient-related traits in ICARDA wheat under drought environment. Mol Genet Genomics 2023; 298:1515-1526. [PMID: 37851098 PMCID: PMC10657311 DOI: 10.1007/s00438-023-02074-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023]
Abstract
Globally, over 2 billion people suffer from malnutrition due to inadequate intake of micronutrients. Genomic-assisted breeding is identified as a valuable method to facilitate developing new improved plant varieties targeting grain yield and micronutrient-related traits. In this study, a genome-wide association study (GWAS) and single- and multi-trait-based genomic prediction (GP) analysis was conducted using a set of 252 elite wheat genotypes from the International Center for Agricultural Research in Dry Areas (ICARDA). The objective was to identify linked SNP markers, putative candidate genes and to evaluate the genomic estimated breeding values (GEBVs) of grain yield and micronutrient-related traits.. For this purpose, a field trial was conducted at a drought-prone station, Merchouch, Morocco for 2 consecutive years (2018 and 2019) followed by GWAS and genomic prediction analysis with 10,173 quality SNP markers. The studied genotypes exhibited a significant genotypic variation in grain yield and micronutrient-related traits. The GWAS analysis identified highly significantly associated markers and linked putative genes on chromosomes 1B and 2B for zinc (Zn) and iron (Fe) contents, respectively. The genomic predictive ability of selenium (Se) and Fe traits with the multi-trait-based GP GBLUP model was 0.161 and 0.259 improving by 6.62 and 4.44%, respectively, compared to the corresponding single-trait-based models. The identified significantly linked SNP markers, associated putative genes, and developed GP models could potentially facilitate breeding programs targeting to improve the overall genetic gain of wheat breeding for grain yield and biofortification of micronutrients via marker-assisted (MAS) and genomic selection (GS) methods.
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Affiliation(s)
- Wuletaw Tadesse
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Zakaria El Gataa
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Fatima Ezzahra Rachdad
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Adil El Baouchi
- AgroBioSciences, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Zakaria Kehel
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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13
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Alomari DZ, Schierenbeck M, Alqudah AM, Alqahtani MD, Wagner S, Rolletschek H, Borisjuk L, Röder MS. Wheat Grains as a Sustainable Source of Protein for Health. Nutrients 2023; 15:4398. [PMID: 37892473 PMCID: PMC10609835 DOI: 10.3390/nu15204398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 10/09/2023] [Accepted: 10/11/2023] [Indexed: 10/29/2023] Open
Abstract
Protein deficiency is recognized among the major global health issues with an underestimation of its importance. Genetic biofortification is a cost-effective and sustainable strategy to overcome global protein malnutrition. This study was designed to focus on protein-dense grains of wheat (Triticum aestivum L.) and identify the genes governing grain protein content (GPC) that improve end-use quality and in turn human health. Genome-wide association was applied using the 90k iSELECT Infinium and 35k Affymetrix arrays with GPC quantified by using a proteomic-based technique in 369 wheat genotypes over three field-year trials. The results showed significant natural variation among bread wheat genotypes that led to detecting 54 significant quantitative trait nucleotides (QTNs) surpassing the false discovery rate (FDR) threshold. These QTNs showed contrasting effects on GPC ranging from -0.50 to +0.54% that can be used for protein content improvement. Further bioinformatics analyses reported that these QTNs are genomically linked with 35 candidate genes showing high expression during grain development. The putative candidate genes have functions in the binding, remobilization, or transport of protein. For instance, the promising QTN AX-94727470 on chromosome 6B increases GPC by +0.47% and is physically located inside the gene TraesCS6B02G384500 annotated as Trehalose 6-phosphate phosphatase (T6P), which can be employed to improve grain protein quality. Our findings are valuable for the enhancement of protein content and end-use quality in one of the major daily food resources that ultimately improve human nutrition.
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Affiliation(s)
- Dalia Z. Alomari
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan
| | - Matías Schierenbeck
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
- CONICET CCT La Plata, La Plata 1900, Buenos Aires, Argentina
| | - Ahmad M. Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha P.O. Box 2713, Qatar;
| | - Mashael Daghash Alqahtani
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia;
| | - Steffen Wagner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
| | - Hardy Rolletschek
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
| | - Ljudmilla Borisjuk
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
| | - Marion S. Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, OT Gatersleben, D-06466 Seeland, Germany; (S.W.); (H.R.); (L.B.); (M.S.R.)
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14
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Bukomarhe CB, Kimwemwe PK, Githiri SM, Mamati EG, Kimani W, Mutai C, Nganga F, Nguezet PMD, Mignouna J, Civava RM, Fofana M. Association Mapping of Candidate Genes Associated with Iron and Zinc Content in Rice ( Oryza sativa L.) Grains. Genes (Basel) 2023; 14:1815. [PMID: 37761955 PMCID: PMC10530939 DOI: 10.3390/genes14091815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 08/22/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Micronutrient deficiencies, particularly of iron (Fe) and zinc (Zn), in the diet contribute to health issues and hidden hunger. Enhancing the Fe and Zn content in globally staple food crops like rice is necessary to address food malnutrition. A Genome-Wide Association Study (GWAS) was conducted using 85 diverse rice accessions from the Democratic Republic of Congo (DRC) to identify genomic regions associated with grain Fe and Zn content. The Fe content ranged from 0.95 to 8.68 mg/100 g on a dry weight basis (dwb) while Zn content ranged from 0.87 to 3.8 mg/100 g (dwb). Using MLM and FarmCPU models, we found 10 significant SNPs out of which one SNP on chromosome 11 was associated with the variation in Fe content and one SNP on chromosome 4 was associated with the Zn content, and both were commonly detected by the two models. Candidate genes belonging to transcription regulator activities, including the bZIP family genes and MYB family genes, as well as transporter activities involved in Fe and Zn homeostasis were identified in the vicinity of the SNP markers and selected. The identified SNP markers hold promise for marker-assisted selection in rice breeding programs aimed at enhancing Fe and Zn content in rice. This study provides valuable insights into the genetic factors controlling Fe and Zn uptake and their transport and accumulation in rice, offering opportunities for developing biofortified rice varieties to combat malnutrition among rice consumers.
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Affiliation(s)
- Chance Bahati Bukomarhe
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya; (P.K.K.); (S.M.G.); (E.G.M.)
- Olusegun O. Research Campus, International Institute of Tropical Agriculture (IITA), Bukavu P.O. Box 1222, Democratic Republic of the Congo; (J.M.); (M.F.)
- Institut National Pour l’Etude et la Recherche Agronomiques (INERA), Kinshasa P.O. Box 2037, Democratic Republic of the Congo;
| | - Paul Kitenge Kimwemwe
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya; (P.K.K.); (S.M.G.); (E.G.M.)
- Olusegun O. Research Campus, International Institute of Tropical Agriculture (IITA), Bukavu P.O. Box 1222, Democratic Republic of the Congo; (J.M.); (M.F.)
- Institut National Pour l’Etude et la Recherche Agronomiques (INERA), Kinshasa P.O. Box 2037, Democratic Republic of the Congo;
- Faculty of Agriculture and Environmental Sciences, Université de Kalemie (UNIKAL), Kalemie P.O. Box 570, Democratic Republic of the Congo
| | - Stephen Mwangi Githiri
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya; (P.K.K.); (S.M.G.); (E.G.M.)
| | - Edward George Mamati
- Department of Horticulture and Food Security, Jomo Kenyatta University of Agriculture and Technology (JKUAT), Nairobi P.O. Box 62000-00200, Kenya; (P.K.K.); (S.M.G.); (E.G.M.)
| | - Wilson Kimani
- International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709-00100, Kenya; (C.M.); (F.N.)
| | - Collins Mutai
- International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709-00100, Kenya; (C.M.); (F.N.)
| | - Fredrick Nganga
- International Livestock Research Institute (ILRI), Nairobi P.O. Box 30709-00100, Kenya; (C.M.); (F.N.)
| | - Paul-Martin Dontsop Nguezet
- International Institute of Tropical Agriculture (IITA), Kalemie P.O. Box 570, Democratic Republic of the Congo;
| | - Jacob Mignouna
- Olusegun O. Research Campus, International Institute of Tropical Agriculture (IITA), Bukavu P.O. Box 1222, Democratic Republic of the Congo; (J.M.); (M.F.)
| | - René Mushizi Civava
- Institut National Pour l’Etude et la Recherche Agronomiques (INERA), Kinshasa P.O. Box 2037, Democratic Republic of the Congo;
- Faculty of Agriculture and Environmental Sciences, Université Evangélique en Afrique (UEA), Bukavu P.O. Box 3323, Democratic Republic of the Congo
| | - Mamadou Fofana
- Olusegun O. Research Campus, International Institute of Tropical Agriculture (IITA), Bukavu P.O. Box 1222, Democratic Republic of the Congo; (J.M.); (M.F.)
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15
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Potapova NA, Timoshchuk AN, Tiys ES, Vinichenko NA, Leonova IN, Salina EA, Tsepilov YA. Multivariate Genome-Wide Association Study of Concentrations of Seven Elements in Seeds Reveals Four New Loci in Russian Wheat Lines. PLANTS (BASEL, SWITZERLAND) 2023; 12:3019. [PMID: 37687266 PMCID: PMC10489822 DOI: 10.3390/plants12173019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/11/2023] [Accepted: 08/19/2023] [Indexed: 09/10/2023]
Abstract
Wheat is a cereal grain that plays an important role in the world's food industry. The identification of the loci that change the concentration of elements in wheat seeds is an important challenge nowadays especially for genomic selection and breeding of novel varieties. In this study, we performed a multivariate genome-wide association study (GWAS) of the seven traits-concentrations of Zn, Mg, Mn, Ca, Cu, Fe, and K in grain-of the Russian collection of common wheat Triticum aestivum (N = 149 measured in two years in two different fields). We replicated one known locus associated with the concentration of Zn (IAAV1375). We identified four novel loci-BS00022069_51 (associated with concentrations of Ca and K), RFL_Contig6053_3082 (associated with concentrations of Fe and Mn), Kukri_rep_c70864_329 (associated with concentrations of all elements), and IAAV8416 (associated with concentrations of Fe and Mn)-three of them were located near the genes TraesCS6A02G375400, TraesCS7A02G094800, and TraesCS5B02G325400. Our result adds novel information on the loci involved in wheat grain element contents and may be further used in genomic selection.
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Affiliation(s)
- Nadezhda A. Potapova
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, 127051 Moscow, Russia
| | - Anna N. Timoshchuk
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
- MSU Institute for Artificial Intelligence, Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Evgeny S. Tiys
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Natalia A. Vinichenko
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Irina N. Leonova
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Elena A. Salina
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Yakov A. Tsepilov
- Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
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16
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Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [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: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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17
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Sinkovič L, Pipan B, Neji M, Rakszegi M, Meglič V. Influence of Hulling, Cleaning and Brushing/Polishing of (Pseudo)Cereal Grains on Compositional Characteristics. Foods 2023; 12:2452. [PMID: 37444190 DOI: 10.3390/foods12132452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/15/2023] [Accepted: 06/21/2023] [Indexed: 07/15/2023] Open
Abstract
(Pseudo)cereal grains have been the basis of human nutrition for thousands of years. The various types of cereals are usually harvested by grain harvesters and must be technologically processed in different ways before consumption. In addition to genotype and growing conditions, the compositional characteristics of the (pseudo)cereal grains are highly dependent on the processes used. In the present study, the effects of hulling, cleaning and brushing/polishing wheat, spelt, oat, barley, common and Tartary buckwheat grains and their fractions on physical parameters (thousand kernel weight, kernel width, fractional yield) and nutritional characteristics (protein, fat, β-glucan, macro- and microelements) were investigated. Grain samples contained 22.7-148.5 mg/g protein, 4.5-69.6 mg/g fat and 0.5-54.4 mg/g β-glucan. The content of macro- (K, Mg, P, S, Ca) and microelements (Mn, Fe, Zn, Na, Cu, Cr, Mo) varied considerably among the studied (pseudo)cereals and their grain fractions. Analysis of variance showed that species and fractions significantly influenced most of the analyzed characteristics. However, the composition of the edible fractions was not significantly dependent on the brushing/polishing process.
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Affiliation(s)
- Lovro Sinkovič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia
| | - Barbara Pipan
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia
| | - Mohamed Neji
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia
| | - Marianna Rakszegi
- Cereal Breeding Department, Agricultural Institute, Centre for Agricultural Research, Brunszvik u. 2, 2462 Martonvásár, Hungary
| | - Vladimir Meglič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia
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18
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Pradhan AK, Budhlakoti N, Chandra Mishra D, Prasad P, Bhardwaj SC, Sareen S, Sivasamy M, Jayaprakash P, Geetha M, Nisha R, Shajitha P, Peter J, Kaur A, Kaur S, Vikas VK, Singh K, Kumar S. Identification of Novel QTLs/Defense Genes in Spring Wheat Germplasm Panel for Seedling and Adult Plant Resistance to Stem Rust and Their Validation Through KASP Marker Assays. PLANT DISEASE 2023:PDIS09222242RE. [PMID: 37311158 DOI: 10.1094/pdis-09-22-2242-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Stem rust is one of the major diseases threatening wheat production globally. To identify novel resistance quantitative trait loci (QTLs), we performed 35K Axiom Array SNP genotyping assays on an association mapping panel of 400 germplasm accessions, including Indian landraces, in conjunction with phenotyping for stem rust at seedling and adult plant stages. Association analyses using three genome wide association study (GWAS) models (CMLM, MLMM, and FarmCPU) revealed 20 reliable QTLs for seedling and adult plant resistance. Among these 20 QTLs, five QTLs were found consistent with three models, i.e., four QTLs on chromosome 2AL, 2BL, 2DL, and 3BL for seedling resistance and one QTL on chromosome 7DS for adult plant resistance. Further, we identified a total of 21 potential candidate genes underlying QTLs using gene ontology analysis, including a leucine rich repeat receptor (LRR) and P-loop nucleoside triphosphate hydrolase, which have a role in pathogen recognition and disease resistance. Furthermore, four QTLs (Qsr.nbpgr-3B_11, QSr.nbpgr-6AS_11, QSr.nbpgr-2AL_117-6, and QSr.nbpgr-7BS_APR) were validated through KASP located on chromosomes 3B, 6A, 2A, and 7B. Out of these QTLs, QSr.nbpgr-7BS_APR was identified as a novel QTL for stem rust resistance which has been found effective in both seedling as well as the adult plant stages. Identified novel genomic regions and validated QTLs have the potential to be deployed in wheat improvement programs to develop disease resistant varieties for stem rust and can diversify the genetic basis of resistance.
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Affiliation(s)
| | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | | | - Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh 171002, India
| | - S C Bhardwaj
- ICAR-Indian Institute of Wheat and Barley Research, Flowerdale, Shimla, Himachal Pradesh 171002, India
| | - Sindhu Sareen
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - M Sivasamy
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - P Jayaprakash
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - M Geetha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - R Nisha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - P Shajitha
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - John Peter
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - Amandeep Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana 141004, India
| | - V K Vikas
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington 643 231, India
| | - Kuldeep Singh
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana 502324, India
| | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
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Kartseva T, Alqudah AM, Aleksandrov V, Alomari DZ, Doneva D, Arif MAR, Börner A, Misheva S. Nutritional Genomic Approach for Improving Grain Protein Content in Wheat. Foods 2023; 12:1399. [PMID: 37048220 PMCID: PMC10093644 DOI: 10.3390/foods12071399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Grain protein content (GPC) is a key aspect of grain quality, a major determinant of the flour functional properties and grain nutritional value of bread wheat. Exploiting diverse germplasms to identify genes for improving crop performance and grain nutritional quality is needed to enhance food security. Here, we evaluated GPC in a panel of 255 Triticum aestivum L. accessions from 27 countries. GPC determined in seeds from three consecutive crop seasons varied from 8.6 to 16.4% (11.3% on average). Significant natural phenotypic variation in GPC among genotypes and seasons was detected. The population was evaluated for the presence of the trait-linked single nucleotide polymorphism (SNP) markers via a genome-wide association study (GWAS). GWAS analysis conducted with calculated best linear unbiased estimates (BLUEs) of phenotypic data and 90 K SNP array using the fixed and random model circulating probability unification (FarmCPU) model identified seven significant genomic regions harboring GPC-associated markers on chromosomes 1D, 3A, 3B, 3D, 4B and 5A, of which those on 3A and 3B shared associated SNPs with at least one crop season. The verified SNP-GPC associations provide new promising genomic signals on 3A (SNPs: Excalibur_c13709_2568 and wsnp_Ku_c7811_13387117) and 3B (SNP: BS00062734_51) underlying protein improvement in wheat. Based on the linkage disequilibrium for significant SNPs, the most relevant candidate genes within a 4 Mbp-window included genes encoding a subtilisin-like serine protease; amino acid transporters; transcription factors; proteins with post-translational regulatory functions; metabolic proteins involved in the starch, cellulose and fatty acid biosynthesis; protective and structural proteins, and proteins associated with metal ions transport or homeostasis. The availability of molecular markers within or adjacent to the sequences of the detected candidate genes might assist a breeding strategy based on functional markers to improve genetic gains for GPC and nutritional quality in wheat.
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Affiliation(s)
- Tania Kartseva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.); (D.D.)
| | - Ahmad M. Alqudah
- Biological Science Program, Department of Biological and Environmental Sciences, College of Art and Science, Qatar University, Doha P.O. Box 2713, Qatar;
| | - Vladimir Aleksandrov
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.); (D.D.)
| | - Dalia Z. Alomari
- Department of Clinical Nutrition and Dietetics, Faculty of Applied Medical Sciences, The Hashemite University, P.O. Box 330127, Zarqa 13133, Jordan;
| | - Dilyana Doneva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.); (D.D.)
| | - Mian Abdur Rehman Arif
- Wheat Breeding Group, Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Faisalabad 38000, Pakistan;
| | - Andreas Börner
- Leibniz Institute of Plant Genetics and Crop Plants Research (IPK Gatersleben), Corrensstraße 3, OT Gatersleben, 06466 Seeland, Germany;
| | - Svetlana Misheva
- Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Acad. G. Bonchev Str., Block 21, 1113 Sofia, Bulgaria; (T.K.); (V.A.); (D.D.)
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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: 5] [Impact Index Per Article: 5.0] [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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Yannam VRR, Lopes M, Guzman C, Soriano JM. Uncovering the genetic basis for quality traits in the Mediterranean old wheat germplasm and phenotypic and genomic prediction assessment by cross-validation test. FRONTIERS IN PLANT SCIENCE 2023; 14:1127357. [PMID: 36778676 PMCID: PMC9911887 DOI: 10.3389/fpls.2023.1127357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The release of new wheat varieties is based on two main characteristics, grain yield and quality, to meet the consumer's demand. Identifying the genetic architecture for yield and key quality traits has wide attention for genetic improvement to meet the global requirement. In this sense, the use of landraces represents an impressive source of natural allelic variation. In this study, a genome-wide association analysis (GWAS) with PCA and kinship matrix was performed to detect QTLs in bread wheat for fifteen quality and agronomic traits using 170 diverse landraces from 24 Mediterranean countries in two years of field trials. A total of 53 QTL hotspots containing 165 significant marker-trait associations (MTAs) were located across the genome for quality and agronomical traits except for chromosome 2D. The major specific QTL hotspots for quality traits were QTL_3B.3 (13 MTAs with a mean PVE of 8.2%) and QTL_4A.3 (15 MTAs, mean PVE of 11.0%), and for yield-related traits were QTL_2B.1 (8 MTAs, mean PVE of 7.4%) and QTL_4B.2 (5 MTAs, mean PVE of 10.0%). A search for candidate genes (CG) identified 807 gene models within the QTL hotspots. Ten of these CGs were expressed specifically in grain supporting the role of identified QTLs in Landraces, associated to bread wheat quality traits and grain formation. A cross-validation approach within the collection was performed to calculate the accuracies of genomic prediction for quality and agronomical traits, ranging from -0.03 to 0.64 for quality and 0.46 to 0.65 for agronomic traits. In addition, five prediction equations using the phenotypic data were developed to predict bread loaf volume in landraces. The prediction ability varied from 0.67 to 0.82 depending on the complexity of the traits considered to predict loaf volume.
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Affiliation(s)
- Venkata Rami Reddy Yannam
- Sustainable Field Crops Program, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Marta Lopes
- Sustainable Field Crops Program, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
| | - Carlos Guzman
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Universidad de Córdoba, Córdoba, Spain
| | - Jose Miguel Soriano
- Sustainable Field Crops Program, Institute for Food and Agricultural Research and Technology (IRTA), Lleida, Spain
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Jadon V, Sharma S, Krishna H, Krishnappa G, Gajghate R, Devate NB, Panda KK, Jain N, Singh PK, Singh GP. Molecular Mapping of Biofortification Traits in Bread Wheat ( Triticum aestivum L.) Using a High-Density SNP Based Linkage Map. Genes (Basel) 2023; 14:221. [PMID: 36672962 PMCID: PMC9859277 DOI: 10.3390/genes14010221] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 01/05/2023] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
A set of 188 recombinant inbred lines (RILs) derived from a cross between a high-yielding Indian bread wheat cultivar HD2932 and a synthetic hexaploid wheat (SHW) Synthetic 46 derived from tetraploid Triticum turgidum (AA, BB 2n = 28) and diploid Triticum tauschii (DD, 2n = 14) was used to identify novel genomic regions associated in the expression of grain iron concentration (GFeC), grain zinc concentration (GZnC), grain protein content (GPC) and thousand kernel weight (TKW). The RIL population was genotyped using SNPs from 35K Axiom® Wheat Breeder's Array and 34 SSRs and phenotyped in two environments. A total of nine QTLs including five for GPC (QGpc.iari_1B, QGpc.iari_4A, QGpc.iari_4B, QGpc.iari_5D, and QGpc.iari_6B), two for GFeC (QGfec.iari_5B and QGfec.iari_6B), and one each for GZnC (QGznc.iari_7A) and TKW (QTkw.iari_4B) were identified. A total of two stable and co-localized QTLs (QGpc.iari_4B and QTkw.iari_4B) were identified on the 4B chromosome between the flanking region of Xgwm149-AX-94559916. In silico analysis revealed that the key putative candidate genes such as P-loop containing nucleoside triphosphatehydrolase, Nodulin-like protein, NAC domain, Purine permease, Zinc-binding ribosomal protein, Cytochrome P450, Protein phosphatase 2A, Zinc finger CCCH-type, and Kinesin motor domain were located within the identified QTL regions and these putative genes are involved in the regulation of iron homeostasis, zinc transportation, Fe, Zn, and protein remobilization to the developing grain, regulation of grain size and shape, and increased nitrogen use efficiency. The identified novel QTLs, particularly stable and co-localized QTLs are useful for subsequent use in marker-assisted selection (MAS).
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Affiliation(s)
- Vasudha Jadon
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
- Amity Institute of Biotechnology, Amity University, Noida 201313, India
| | - Shashi Sharma
- Amity Institute of Biotechnology, Amity University, Noida 201313, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Gopalareddy Krishnappa
- ICAR-Sugarcane Breeding Institute, Coimbatore 641007, India
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
| | - Rahul Gajghate
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | | | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Pradeep Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Gyanendra Pratap Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal 132001, India
- National Bureau of Plant Genetic Resources, New Delhi 110012, India
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Sahoo DK, Hegde C, Bhattacharyya MK. Identification of multiple novel genetic mechanisms that regulate chilling tolerance in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 13:1094462. [PMID: 36714785 PMCID: PMC9878698 DOI: 10.3389/fpls.2022.1094462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Cold stress adversely affects the growth and development of plants and limits the geographical distribution of many plant species. Accumulation of spontaneous mutations shapes the adaptation of plant species to diverse climatic conditions. METHODS The genome-wide association study of the phenotypic variation gathered by a newly designed phenomic platform with the over six millions single nucleotide polymorphic (SNP) loci distributed across the genomes of 417 Arabidopsis natural variants collected from various geographical regions revealed 33 candidate cold responsive genes. RESULTS Investigation of at least two independent insertion mutants for 29 genes identified 16 chilling tolerance genes governing diverse genetic mechanisms. Five of these genes encode novel leucine-rich repeat domain-containing proteins including three nucleotide-binding site-leucine-rich repeat (NBS-LRR) proteins. Among the 16 identified chilling tolerance genes, ADS2 and ACD6 are the only two chilling tolerance genes identified earlier. DISCUSSION The 12.5% overlap between the genes identified in this genome-wide association study (GWAS) of natural variants with those discovered previously through forward and reverse genetic approaches suggests that chilling tolerance is a complex physiological process governed by a large number of genetic mechanisms.
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Affiliation(s)
- Dipak Kumar Sahoo
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Chinmay Hegde
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, United States
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Rathan ND, Krishnappa G, Singh AM, Govindan V. Mapping QTL for Phenological and Grain-Related Traits in a Mapping Population Derived from High-Zinc-Biofortified Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:220. [PMID: 36616350 PMCID: PMC9823887 DOI: 10.3390/plants12010220] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/27/2022] [Accepted: 12/29/2022] [Indexed: 06/17/2023]
Abstract
Genomic regions governing days to heading (DH), days to maturity (DM), plant height (PH), thousand-kernel weight (TKW), and test weight (TW) were investigated in a set of 190 RILs derived from a cross between a widely cultivated wheat-variety, Kachu (DPW-621-50), and a high-zinc variety, Zinc-Shakti. The RIL population was genotyped using 909 DArTseq markers and phenotyped in three environments. The constructed genetic map had a total genetic length of 4665 cM, with an average marker density of 5.13 cM. A total of thirty-seven novel quantitative trait loci (QTL), including twelve for PH, six for DH, five for DM, eight for TKW and six for TW were identified. A set of 20 stable QTLs associated with the expression of DH, DM, PH, TKW, and TW were identified in two or more environments. Three novel pleiotropic genomic-regions harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the DArTseq markers were located on important putative candidate genes such as MLO-like protein, Phytochrome, Zinc finger and RING-type, Cytochrome P450 and pentatricopeptide repeat, involved in the regulation of pollen maturity, the photoperiodic modulation of flowering-time, abiotic-stress tolerance, grain-filling duration, thousand-kernel weight, seed morphology, and plant growth and development. The identified novel QTLs, particularly stable and co-localized QTLs, will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).
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Affiliation(s)
| | | | | | - Velu Govindan
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco 56237, Mexico
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Ma J, Ye M, Liu Q, Yuan M, Zhang D, Li C, Zeng Q, Wu J, Han D, Jiang L. Genome-wide association study for grain zinc concentration in bread wheat ( Triticum aestivum L.). FRONTIERS IN PLANT SCIENCE 2023; 14:1169858. [PMID: 37077637 PMCID: PMC10106671 DOI: 10.3389/fpls.2023.1169858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Introduction Zinc (Zn) deficiency causes serious diseases in people who rely on cereals as their main food source. However, the grain zinc concentration (GZnC) in wheat is low. Biofortification is a sustainable strategy for reducing human Zn deficiency. Methods In this study, we constructed a population of 382 wheat accessions and determined their GZnC in three field environments. Phenotype data was used for a genome-wide association study (GWAS) using a 660K single nucleotide polymorphism (SNP) array, and haplotype analysis identified an important candidate gene for GZnC. Results We found that GZnC of the wheat accessions showed an increasing trend with their released years, indicating that the dominant allele of GZnC was not lost during the breeding process. Nine stable quantitative trait loci (QTLs) for GZnC were identified on chromosomes 3A, 4A, 5B, 6D, and 7A. And an important candidate gene for GZnC, namely, TraesCS6D01G234600, and GZnC between the haplotypes of this gene showed, significant difference (P ≤ 0.05) in three environments. Discussion A novel QTL was first identified on chromosome 6D, this finding enriches our understanding of the genetic basis of GZnC in wheat. This study provides new insights into valuable markers and candidate genes for wheat biofortification to improve GZnC.
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Affiliation(s)
- Jianhui Ma
- College of Life Science, Henan Normal University, Xinxiang, China
- *Correspondence: Lina Jiang, ; Jianhui Ma, ; Dejun Han,
| | - Miaomiao Ye
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Qianqian Liu
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Meng Yuan
- College of Life Science, Henan Normal University, Xinxiang, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shanxi, China
| | - Daijing Zhang
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Chunxi Li
- College of Life Science, Henan Normal University, Xinxiang, China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shanxi, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shanxi, China
| | - Dejun Han
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shanxi, China
- *Correspondence: Lina Jiang, ; Jianhui Ma, ; Dejun Han,
| | - Lina Jiang
- College of Life Science, Henan Normal University, Xinxiang, China
- *Correspondence: Lina Jiang, ; Jianhui Ma, ; Dejun Han,
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Kumar S, Pradhan AK, Kumar U, Dhillon GS, Kaur S, Budhlakoti N, Mishra DC, Singh AK, Singh R, Kumari J, Kumaran VV, Mishra VK, Bhati PK, Das S, Chand R, Singh K, Kumar S. Validation of Novel spot blotch disease resistance alleles identified in unexplored wheat (Triticum aestivum L.) germplasm lines through KASP markers. BMC PLANT BIOLOGY 2022; 22:618. [PMID: 36577935 PMCID: PMC9798658 DOI: 10.1186/s12870-022-04013-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND During the last few decades, the diverse sources of resistance, several genes and QTLs for spot blotch resistance have been identified. However, a large set of germplasm lines are still unexplored that have the potential to develop highly resistant wheat cultivars for the target environments. Therefore, the identification of new sources of resistance to spot blotch is essential for breeding programmes to develop spot blotch resistant cultivars and sustain wheat production. The association mapping panel of 294 diverse bread wheat accessions was used to explore new sources of spot blotch disease resistance and to identify genomic regions using genome wide association analysis (GWAS). The genotypes were tested in replicated trials for spot blotch disease at three major hot spots in India (Varanasi in UP, Pusa in Bihar, and Cooch Behar in West Bengal). The area under the disease progress curve (AUDPC) was calculated to assess the level of resistance in each genotype. RESULTS A total of 19 highly and 76 moderately resistant lines were identified. Three accessions (EC664204, IC534306 and IC535188) were nearly immune to spot blotch disease. The genotyping of all accessions resulted in a total of 16,787 high-quality polymorphic SNPs. The GWAS was performed using a Compressed Mixed Linear Model (CMLM) and a Mixed Linear Model (MLM). A total of seven significant MTAs, common in both the models and consistent across the environment, were further validated to develop KASP markers. Four MTAs (AX-94710084, AX-94865722, AX-95135556, and AX-94529408) on three chromosomes (2AL, 2BL, and 3BL) have been successfully validated through the KASP marker. CONCLUSIONS The new source of resistance was identified from unexplored germplasm lines. The genomic regions identified through GWAS were validated through KASP markers. The marker information and the highly resistant sources are valuable resources to rapidly develop immune or near immune wheat varieties.
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Affiliation(s)
- Suneel Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | | | - Uttam Kumar
- Borlaug Institute for South Asia, NASC Complex, DPS Marg, New Delhi, India.
| | | | - Satinder Kaur
- Punjab Agricultural University, Ludhiana, Punjab, India
| | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Rakesh Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Jyoti Kumari
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Vikas V Kumaran
- ICAR-Indian Agricultural Research Institute, Regional Station, Wellington, India
| | | | | | - Saikat Das
- Uttar Banga Krishi Vishwavidyalaya, Pundibari, Coochbehar, India
| | - Ramesh Chand
- Banaras Hindu University, Uttar Pradesh, Varanasi, India
| | - Kuldeep Singh
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India
| | - Sundeep Kumar
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, India.
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Zia MAB, Yousaf MF, Asim A, Naeem M. An overview of genome-wide association mapping studies in Poaceae species (model crops: wheat and rice). Mol Biol Rep 2022; 49:12077-12090. [DOI: 10.1007/s11033-022-08036-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
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Devate NB, Krishna H, Sunilkumar VP, Manjunath KK, Mishra CN, Jain N, Singh GP, Singh PK. Identification of genomic regions of wheat associated with grain Fe and Zn content under drought and heat stress using genome-wide association study. Front Genet 2022; 13:1034947. [PMID: 36338980 PMCID: PMC9634069 DOI: 10.3389/fgene.2022.1034947] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/07/2022] [Indexed: 09/10/2023] Open
Abstract
Wheat is the staple food crop of global importance for its grain nutrient quality. Grain iron and zinc content of the wheat grain is an important quantitatively inherited trait that is influenced by the environmental factors such as drought and heat stress. Phenotypic evaluation of 295 advanced breeding lines from the wheat stress breeding program of IARI was carried out under timely sown irrigated (IR), restricted irrigated, and late-sown conditions at New Delhi during the cropping season of 2020-21, and grain iron (GFeC) and zinc (GZnC) contents were estimated from both control and treatments. A statistically significant increase in GFeC and GZnC was observed under stress conditions compared to that of the control. Genotyping was carried out with the SNPs from the 35K Axiom Breeder's array, and marker-trait association was identified by GWAS analysis. Of the 23 MTAs identified, seven were linked with GFeC and sixteen were linked with GZnC. In silico analysis revealed a few important transcripts involved in various plant metabolism, growth, and development activities such as auxin response factor, root UVB sensitive proteins, potassium transporter, glycosyl transferase, COBRA, and F-box-like domain. The identified MTAs can be used for molecular breeding after validation and also for rapid development of micronutrient-rich varieties of wheat to mitigate hidden hunger.
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Affiliation(s)
- Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - V. P. Sunilkumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - C. N. Mishra
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - G. P. Singh
- ICAR- Indian Institute of Wheat and Barley Research, Karnal, India
| | - P. K. Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Saini P, Sheikh I, Saini DK, Mir RR, Dhaliwal HS, Tyagi V. Consensus genomic regions associated with grain protein content in hexaploid and tetraploid wheat. Front Genet 2022; 13:1021180. [PMID: 36246648 PMCID: PMC9554612 DOI: 10.3389/fgene.2022.1021180] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 09/13/2022] [Indexed: 11/13/2022] Open
Abstract
A meta-analysis of QTLs associated with grain protein content (GPC) was conducted in hexaploid and tetraploid wheat to identify robust and stable meta-QTLs (MQTLs). For this purpose, as many as 459 GPC-related QTLs retrieved from 48 linkage-based QTL mapping studies were projected onto the newly developed wheat consensus map. The analysis resulted in the prediction of 57 MQTLs and 7 QTL hotspots located on all wheat chromosomes (except chromosomes 1D and 4D) and the average confidence interval reduced 2.71-fold in the MQTLs and QTL hotspots compared to the initial QTLs. The physical regions occupied by the MQTLs ranged from 140 bp to 224.02 Mb with an average of 15.2 Mb, whereas the physical regions occupied by QTL hotspots ranged from 1.81 Mb to 36.03 Mb with a mean of 8.82 Mb. Nineteen MQTLs and two QTL hotspots were also found to be co-localized with 45 significant SNPs identified in 16 previously published genome-wide association studies in wheat. Candidate gene (CG) investigation within some selected MQTLs led to the identification of 705 gene models which also included 96 high-confidence CGs showing significant expressions in different grain-related tissues and having probable roles in GPC regulation. These significantly expressed CGs mainly involved the genes/gene families encoding for the following proteins: aminotransferases, early nodulin 93, glutamine synthetases, invertase/pectin methylesterase inhibitors, protein BIG GRAIN 1-like, cytochrome P450, glycosyl transferases, hexokinases, small GTPases, UDP-glucuronosyl/UDP-glucosyltransferases, and EamA, SANT/Myb, GNAT, thioredoxin, phytocyanin, and homeobox domains containing proteins. Further, eight genes including GPC-B1, Glu-B1-1b, Glu-1By9, TaBiP1, GSr, TaNAC019-A, TaNAC019-D, and bZIP-TF SPA already known to be associated with GPC were also detected within some of the MQTL regions confirming the efficacy of MQTLs predicted during the current study.
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Affiliation(s)
- Pooja Saini
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Imran Sheikh
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Dinesh Kumar Saini
- Department of Plant Breeding and Genetics, Punajb Agricultural University, Ludhiana, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture SKUAST-Kashmir, Srinagar, India
| | - Harcharan Singh Dhaliwal
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
| | - Vikrant Tyagi
- Department of Genetics-Plant Breeding and Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, India
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Padhy AK, Kaur P, Singh S, Kashyap L, Sharma A. Colored wheat and derived products: key to global nutritional security. Crit Rev Food Sci Nutr 2022; 64:1894-1910. [PMID: 36069286 DOI: 10.1080/10408398.2022.2119366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Ensuring food and nutritional security of fast-growing population will pose a huge challenge in future. An estimated one-half population who does not go hungry, nonetheless suffers the debilitating effects of unhealthy diets. In view of the nutritional awareness, when the major wheat breeding programs have started shifting to quality, instead of quantity in wheat, the colored wheats give a novel twist of targeting the malnutrition by enhancing the antioxidants such as anthocyanin, carotenoids, flavonoids, polyphenols etc. Moreover, changing consumer demands have picked the trend to prefer a nutritionally balanced diet over the conventional high energy diets and thus, colored wheat has opened up a hidden avenue for providing additional value to the wheat-based products. Besides providing nutrition, these pigments have the potential to replace the synthetic dyes and food colorants prevalent in the market. The review summarizes the genetics and biochemistry of the pigments of colored wheat along with their product development, nutritional status and consumer preference. The review also sheds light on the environmental effect on color accumulation and the effect of increased colorants on other quality traits of wheat.
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Affiliation(s)
| | | | | | | | - Achla Sharma
- Punjab Agricultural University, Ludhiana, Punjab, India
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31
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Khan H, Krishnappa G, Kumar S, Mishra CN, Krishna H, Devate NB, Rathan ND, Parkash O, Yadav SS, Srivastava P, Biradar S, Kumar M, Singh GP. Genome-wide association study for grain yield and component traits in bread wheat ( Triticum aestivum L.). Front Genet 2022; 13:982589. [PMID: 36092913 PMCID: PMC9458894 DOI: 10.3389/fgene.2022.982589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association studies (GWAS) panel was genotyped using a 35K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 27 Bonferroni-corrected marker-trait associations (MTAs) on 15 chromosomes representing all three wheat subgenomes. The GFD showed the highest MTAs (8), followed by GWPS (7), GY (4), GNPS (3), PH (3), and DH (2). Furthermore, 20 MTAs were identified with more than 10% phenotypic variation. A total of five stable MTAs (AX-95024590, AX-94425015, AX-95210025 AX-94539354, and AX-94978133) were identified in more than one environment and associated with the expression of DH, GFD, GNPS, and GY. Similarly, two novel pleiotropic genomic regions with associated MTAs i.e. AX-94978133 (4D) and AX-94539354 (6A) harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the SNPs were located on important putative candidate genes such as F-box-like domain superfamily, Lateral organ boundaries, LOB, Thioredoxin-like superfamily Glutathione S-transferase, RNA-binding domain superfamily, UDP-glycosyltransferase family, Serine/threonine-protein kinase, Expansin, Patatin, Exocyst complex component Exo70, DUF1618 domain, Protein kinase domain involved in the regulation of grain size, grain number, growth and development, grain filling duration, and abiotic stress tolerance. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).
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Affiliation(s)
- Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Gopalareddy Krishnappa
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Hari Krishna
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Om Parkash
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sonu Singh Yadav
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Suma Biradar
- University of Agricultural Sciences, Dharwad, India
| | - Monu Kumar
- ICAR-Indian Agricultural Research Institute, Jharkhand, India
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Morgounov A, Li H, Shepelev S, Ali M, Flis P, Koksel H, Savin T, Shamanin V. Genetic Characterization of Spring Wheat Germplasm for Macro-, Microelements and Trace Metals. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11162173. [PMID: 36015476 PMCID: PMC9412593 DOI: 10.3390/plants11162173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 06/12/2023]
Abstract
Wheat as a staple food crop is the main source of micro- and macronutrients for most people of the world and is recognized as an attractive crop for biofortification. This study presents a comprehensive investigation of genomic regions governing grain micro- and macroelements concentrations in a panel of 135 diverse wheat accessions through a genome-wide association study. The genetic diversity panel was genotyped using the genotyping-by-sequencing (GBS) method and phenotyped in two environments during 2017−2018. Wide ranges of variation in nutrient element concentrations in grain were detected among the accessions. Based on 33,808 high-quality single nucleotide polymorphisms (SNPs), 2997 marker-element associations (MEAs) with −log10(p-value) > 3.5 were identified, representing all three subgenomes of wheat for 15-grain concentration elements. The highest numbers of MEAs were identified for Mg (499), followed by S (399), P (394), Ni (381), Cd (243), Ca (229), Mn (224), Zn (212), Sr (212), Cu (111), Rb (78), Fe (63), Mo (43), K (32) and Co (19). Further, MEAs associated with multiple elements and referred to as pleiotropic SNPs were identified for Mg, P, Cd, Mn, and Zn on chromosomes 1B, 2B, and 6B. Fifty MEAs were subjected to validation using KASIB multilocational trial at six sites in two years using 39 genotypes. Gene annotation of MEAs identified putative candidate genes that potentially encode different types of proteins related to disease, metal transportation, and metabolism. The MEAs identified in the present study could be potential targets for further validation and may be used in marker-assisted breeding to improve nutrient element concentrations in wheat grain.
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Affiliation(s)
- Alexey Morgounov
- Agronomy Department, Omsk State Agrarian University, 644008 Omsk, Russia
| | - Huihui Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences & CIMMYT-China, Beijing 100081, China
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya 572024, China
| | - Sergey Shepelev
- Agronomy Department, Omsk State Agrarian University, 644008 Omsk, Russia
| | - Mohsin Ali
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences & CIMMYT-China, Beijing 100081, China
- Nanfan Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Sanya 572024, China
| | - Paulina Flis
- Future Food Beacon of Excellence and the School of Biosciences, University of Nottingham, Nottingham LE12 5RD, UK
| | - Hamit Koksel
- Agronomy Department, Omsk State Agrarian University, 644008 Omsk, Russia
- Department of Nutrition and Dietetics, Istinye University, Istanbul 34010, Turkey
| | - Timur Savin
- Department of Research, S. Seifullin Kazakh Agro Technical University, Nur-Sultan 010011, Kazakhstan
| | - Vladimir Shamanin
- Agronomy Department, Omsk State Agrarian University, 644008 Omsk, Russia
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Devate NB, Krishna H, Parmeshwarappa SKV, Manjunath KK, Chauhan D, Singh S, Singh JB, Kumar M, Patil R, Khan H, Jain N, Singh GP, Singh PK. Genome-wide association mapping for component traits of drought and heat tolerance in wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:943033. [PMID: 36061792 PMCID: PMC9429996 DOI: 10.3389/fpls.2022.943033] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/25/2022] [Indexed: 06/01/2023]
Abstract
Identification of marker trait association is a prerequisite for marker-assisted breeding. To find markers linked with traits under heat and drought stress in bread wheat (Triticum aestivum L.), we performed a genome-wide association study (GWAS). GWAS mapping panel used in this study consists of advanced breeding lines from the IARI stress breeding programme produced by pairwise and complex crosses. Phenotyping was done at multi locations namely New Delhi, Karnal, Indore, Jharkhand and Pune with augmented-RCBD design under different moisture and heat stress regimes, namely timely sown irrigated (IR), timely sown restricted irrigated (RI) and late sown (LS) conditions. Yield and its component traits, viz., Days to Heading (DH), Days to Maturity (DM), Normalized Difference Vegetation Index (NDVI), Chlorophyll Content (SPAD), Canopy temperature (CT), Plant Height (PH), Thousand grain weight (TGW), Grain weight per spike (GWPS), Plot Yield (PLTY) and Biomass (BMS) were phenotyped. Analysis of variance and descriptive statistics revealed significant differences among the studied traits. Genotyping was done using the 35k SNP Wheat Breeder's Genotyping Array. Population structure and diversity analysis using filtered 10,546 markers revealed two subpopulations with sufficient diversity. A large whole genome LD block size of 7.15 MB was obtained at half LD decay value. Genome-wide association search identified 57 unique markers associated with various traits across the locations. Twenty-three markers were identified to be stable, among them nine pleiotropic markers were also identified. In silico search of the identified markers against the IWGSC ref genome revealed the presence of a majority of the SNPs at or near the gene coding region. These SNPs can be used for marker-assisted transfer of genes/QTLs after validation to develop climate-resilient cultivars.
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Affiliation(s)
- Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Divya Chauhan
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shweta Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Jang Bahadur Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Monu Kumar
- Division of Genetics and Plant Breeding, ICAR-Indian Agricultural Research Institute, Gauria Karma, India
| | - Ravindra Patil
- Genetics and Plant Breeding Group, Agharkar Research Institute, Pune, India
| | - Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Pradeep Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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Genetic dissection of grain iron and zinc, and thousand kernel weight in wheat (Triticum aestivum L.) using genome-wide association study. Sci Rep 2022; 12:12444. [PMID: 35858934 PMCID: PMC9300641 DOI: 10.1038/s41598-022-15992-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 07/04/2022] [Indexed: 01/13/2023] Open
Abstract
Genetic biofortification is recognized as a cost-effective and sustainable strategy to reduce micronutrient malnutrition. Genomic regions governing grain iron concentration (GFeC), grain zinc concentration (GZnC), and thousand kernel weight (TKW) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association (GWAS) panel was genotyped using 35 K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 17 Bonferroni-corrected marker-trait associations (MTAs) in nine chromosomes representing all the three wheat subgenomes. The TKW showed the highest MTAs (7), followed by GZnC (5) and GFeC (5). Furthermore, 14 MTAs were identified with more than 10% phenotypic variation. One stable MTA i.e. AX-95025823 was identified for TKW in both E4 and E5 environments along with pooled data, which is located at 68.9 Mb on 6A chromosome. In silico analysis revealed that the SNPs were located on important putative candidate genes such as Multi antimicrobial extrusion protein, F-box domain, Late embryogenesis abundant protein, LEA-18, Leucine-rich repeat domain superfamily, and C3H4 type zinc finger protein, involved in iron translocation, iron and zinc homeostasis, and grain size modifications. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection. The identified SNPs will be valuable in the rapid development of biofortified wheat varieties to ameliorate the malnutrition problems.
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