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Manjunath KK, Krishna H, Devate NB, Sunilkumar VP, Patil SP, Chauhan D, Singh S, Kumar S, Jain N, Singh GP, Singh PK. QTL mapping: insights into genomic regions governing component traits of yield under combined heat and drought stress in wheat. Front Genet 2024; 14:1282240. [PMID: 38269367 PMCID: PMC10805833 DOI: 10.3389/fgene.2023.1282240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/15/2023] [Indexed: 01/26/2024] Open
Abstract
Drought and heat frequently co-occur during crop growth leading to devastating yield loss. The knowledge of the genetic loci governing component traits of yield under combined drought and heat stress is essential for enhancing the climate resilience. The present study employed a mapping population of 180 recombinant inbred lines (RILs) derived from a cross between GW322 and KAUZ to identify quantitative trait loci (QTLs) governing the component traits of yield under heat and combined stress conditions. Phenotypic evaluation was conducted across two consecutive crop seasons (2021-2022 and 2022-2023) under late sown irrigation (LSIR) and late sown restricted irrigation (LSRI) conditions at the Indian Council of Agricultural Research Institute-Indian Agricultural Research Institute (ICAR-IARI), New Delhi. Various physiological and agronomic traits of importance were measured. Genotyping was carried out with 35K SNP Axiom breeder's genotyping array. The linkage map spanned a length of 6769.45 cM, ranging from 2.28 cM/marker in 1A to 14.21 cM/marker in 5D. A total of 35 QTLs were identified across 14 chromosomes with 6B containing the highest (seven) number of QTLs. Out of 35 QTLs, 16 were major QTLs explaining the phenotypic variance greater than 10%. The study identified eight stable QTLs along with two hotspots on chromosomes 6B and 5B. Five QTLs associated with traits thousand-grain weight (TGW), normalized difference vegetation index (NDVI), and plant height (PH) were successfully validated. Candidate genes encoding antioxidant enzymes, transcription factors, and growth-related proteins were identified in the QTL regions. In silico expression analysis highlighted higher expression of transcripts TraesCS2D02G021000.1, TraesCS2D02G031000, TraesCS6A02G247900, and TraesCS6B02G421700 under stress conditions. These findings contribute to a deeper understanding of the genetic architecture underlying combined heat and drought tolerance in wheat, providing valuable insights for wheat improvement strategies under changing climatic conditions.
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Affiliation(s)
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Narayana Bhat Devate
- 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
| | - Sahana Police Patil
- 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
| | - Sudhir Kumar
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, 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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Ramappa S, Joshi MA, Krishna H, Dunna V, Jain N, Sreevathsa R, Devate NB. Unravelling the Genetic Basis of Moisture Deficit Stress Tolerance in Wheat for Seedling Vigour-Related Traits and Root Traits Using Genome-Wide Association Study. Genes (Basel) 2023; 14:1902. [PMID: 37895250 PMCID: PMC10606372 DOI: 10.3390/genes14101902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
A key abiotic stress that negatively affects seed germination, plant development, and crop yield is moisture deficit stress. Achieving higher vigour and uniform germination under stress conditions is essential for crop establishment and productivity and to enhance the yield. Hence, revealing wheat's capacity to withstand moisture deficit stress during seed germination and early growth stages is fundamental in improving its overall performance. However, the genetic regulation of moisture deficit stress tolerance during the seed germination phase remains largely unexplored. In this study, a total of 193 wheat genotypes were subjected to simulated moisture deficit stress using PEG-6000 (-0.4 MPa) during the seed germination stage. The induced moisture deficit stress significantly reduced various seedling-vigour-related traits. The genetic regions linked to these traits were found using a genome-wide association study (GWAS). The analysis identified 235 MTAs with a significance -log10(p) value of >4. After applying the Bonferroni correction, the study identified 47 unique single nucleotide polymorphisms (SNPs) that are linked to candidate genes important for the trait of interest. The current study emphasises the effectiveness of genome-wide association studies (GWAS) in identifying promising candidate genes, improving wheat seedling vigour and root traits, and offering essential information for the development of wheat cultivars tolerant to moisture deficit stress.
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Affiliation(s)
- S Ramappa
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Monika A. Joshi
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Vijay Dunna
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Neelu Jain
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Rohini Sreevathsa
- Division of Molecular Biology and Biotechnology, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Narayana Bhat Devate
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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Taria S, Arora A, Krishna H, Manjunath KK, Meena S, Kumar S, Singh B, Krishna P, Malakondaiah AC, Das R, Alam B, Kumar S, Singh PK. Multivariate analysis and genetic dissection of staygreen and stem reserve mobilisation under combined drought and heat stress in wheat ( Triticum aestivum L.). Front Genet 2023; 14:1242048. [PMID: 37705611 PMCID: PMC10496116 DOI: 10.3389/fgene.2023.1242048] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 08/14/2023] [Indexed: 09/15/2023] Open
Abstract
Introduction: Abiotic stresses significantly reduce crop yield by adversely affecting many physio-biochemical processes. Several physiological traits have been targeted and improved for yield enhancement in limiting environmental conditions. Amongst them, staygreen and stem reserve mobilisation are two important mutually exclusive traits contributing to grain filling under drought and heat stress in wheat. Henceforth, the present study was carried out to identify the QTLs governing these traits and to identify the superiors' lines through multi-trait genotype-ideotype distance index (MGIDI) Methods: A mapping population consisting of 166 recombinant inbred lines (RILs) developed from a cross between HD3086 and HI1500 was utilized in this study. The experiment was laid down in alpha lattice design in four environmental conditions viz. Control, drought, heat and combined stress (heat and drought). Genotyping of parents and RILs was carried out with 35 K Axiom® array (Wheat breeder array). Results and Discussion: Medium to high heritability with a moderate to high correlation between traits was observed. Principal component analysis (PCA) was performed to derive latent variables in the original set of traits and the relationship of these traits with latent variables.From this study, 14 QTLs were identified, out of which 11, 2, and 1 for soil plant analysis development (SPAD) value, leaf senescence rate (LSR), and stem reserve mobilisation efficiency (SRE) respectively. Quantitative trait loci (QTLs) for SPAD value harbored various genes like Dirigent protein 6-like, Protein FATTY ACID EXPORT 3, glucan synthase-3 and Ubiquitin carboxyl-terminal hydrolase, whereas QTLs for LSR were found to contain various genes like aspartyl protease family protein, potassium transporter, inositol-tetrakisphosphate 1-kinase, and DNA polymerase epsilon subunit D-like. Furthermore, the chromosomal region for SRE was found to be associated with serine-threonine protein kinase. Serine-threonine protein kinases are involved in many signaling networks such as ABA mediated ROS signaling and acclimation to environmental stimuli. After the validation of QTLs in multilocation trials, these QTLs can be used for marker-assisted selection (MAS) in breeding programs.
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Affiliation(s)
- Sukumar Taria
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- ICAR-Central Agroforestry Research Institute, Jhansi, Uttar Pradesh, India
| | - Ajay Arora
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Shashi Meena
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Sudhir Kumar
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Biswabiplab Singh
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pavithra Krishna
- Division of Plant Physiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | - Ritwika Das
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Badre Alam
- ICAR-Central Agroforestry Research Institute, Jhansi, Uttar Pradesh, India
| | - Sushil Kumar
- ICAR-Central Agroforestry Research Institute, Jhansi, Uttar Pradesh, India
| | - Pradeep Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
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TS A, Srivastava A, Tomar BS, Behera TK, Krishna H, Jain PK, Pandey R, Singh B, Gupta R, Mangal M. Genetic analysis of heat tolerance in hot pepper: insights from comprehensive phenotyping and QTL mapping. Front Plant Sci 2023; 14:1232800. [PMID: 37692444 PMCID: PMC10491018 DOI: 10.3389/fpls.2023.1232800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 07/31/2023] [Indexed: 09/12/2023]
Abstract
High temperatures present a formidable challenge to the cultivation of hot pepper, profoundly impacting not only vegetative growth but also leading to flower and fruit abscission, thereby causing a significant reduction in yield. To unravel the intricate genetic mechanisms governing heat tolerance in hot pepper, an F2 population was developed through the crossing of two distinct genotypes exhibiting contrasting heat tolerance characteristics: DLS-161-1 (heat tolerant) and DChBL-240 (heat susceptible). The F2 population, along with the parental lines, was subjected to comprehensive phenotyping encompassing diverse morphological, physiological, and biochemical heat-related traits under high temperature conditions (with maximum temperature ranging from 31 to 46.5°C and minimum temperature from 15.4 to 30.5°C). Leveraging the Illumina Nova Seq-6000 platform, Double digest restriction-site associated DNA sequencing (ddRAD-seq) was employed to generate 67.215 Gb data, with subsequent alignment of 218.93 million processed reads against the reference genome of Capsicum annuum. Subsequent variant calling and ordering resulted in 5806 polymorphic SNP markers grouped into 12 LGs. Further QTL analysis identified 64 QTLs with LOD values ranging from 2.517 to 11.170 and explained phenotypic variance ranging from 4.05 to 19.39%. Among them, 21 QTLs, explaining more than 10% phenotypic variance, were identified as major QTLs controlling 9 morphological, 3 physiological, and 2 biochemical traits. Interestingly, several QTLs governing distinct parameters were found to be colocalized, suggesting either a profound correlation between the QTLs regulating these traits or their significant genomic proximity. In addition to the QTLs, we also identified 368380 SSR loci within the identified QTL regions, dinucleotides being the most abundant type (211,381). These findings provide valuable insights into the genetics of heat tolerance in hot peppers. The identified QTLs and SSR markers offer opportunities to develop heat-tolerant varieties, ensuring better crop performance under high-temperature conditions.
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Affiliation(s)
- Aruna TS
- Division of Vegetable Science, Indian Agricultural Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Arpita Srivastava
- Division of Vegetable Science, Indian Agricultural Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Bhoopal Singh Tomar
- Division of Vegetable Science, Indian Agricultural Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Tusar Kanti Behera
- Indian Council of Agricultural Research-Indian Institute of Vegetable Research (IIVR), Indian Council of Agricultural Research (ICAR), Varanasi, India
| | - Hari Krishna
- Division of Genetics, Indian Agricultural Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Pradeep Kumar Jain
- National Institute of Plant Biotechnology, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Renu Pandey
- Division of Plant Physiology, Indian Agricultural Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Bhupinder Singh
- Division of Environment Science, Indian Agricultural Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
| | - Ruchi Gupta
- Department of Computer Sciences, Jamia Milia Islamia, New Delhi, India
| | - Manisha Mangal
- Division of Vegetable Science, Indian Agricultural Research Institute, Indian Council of Agricultural Research (ICAR), New Delhi, India
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Sunilkumar VP, Krishna H, Devate NB, Manjunath KK, Chauhan D, Singh S, Sinha N, Singh JB, T. L. P, Pal D, Sivasamy M, Jain N, Singh GP, Singh PK. Marker-assisted selection for transfer of QTLs to a promising line for drought tolerance in wheat ( Triticum aestivum L.). Front Plant Sci 2023; 14:1147200. [PMID: 37546261 PMCID: PMC10401266 DOI: 10.3389/fpls.2023.1147200] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023]
Abstract
Wheat crop is subjected to various biotic and abiotic stresses, which affect crop productivity and yield. Among various abiotic stresses, drought stress is a major problem considering the current global climate change scenario. A high-yielding wheat variety, HD3086, has been released for commercial cultivation under timely sown irrigated conditions for the North Western Plain Zone (NWPZ) and North Eastern Plain Zone NEPZ of India. Presently, HD3086 is one of the highest breeder seed indented wheat varieties and has a stable yield over the years. However, under moisture deficit conditions, its potential yield cannot be achieved. The present study was undertaken to transfer drought-tolerant QTLs in the background of the variety HD3086 using marker-assisted backcross breeding. QTLs governing Biomass (BIO), Canopy Temperature (CT), Thousand Kernel Weight (TKW), Normalized Difference Vegetation Index (NDVI), and Yield (YLD) were transferred to improve performance under moisture deficit conditions. In BC1F1, BC2F1, and BC2F2 generations, the foreground selection was carried out to identify the plants with positive QTLs conferring drought tolerance and linked to traits NDVI, CT, TKW, and yield. The positive homozygous lines for targeted QTLs were advanced from BC2F2 to BC2F4 via the pedigree-based phenotypic selection method. Background analysis was carried out in BC2F5 and obtained 78-91% recovery of the recurrent parent genome in the improved lines. Furthermore, the advanced lines were evaluated for 2 years under drought stress to assess improvement in MABB-derived lines. Increased GWPS, TKW, and NDVI and reduced CT was observed in improved lines. Seven improved lines were identified with significantly higher yields in comparison to HD3086 under stress conditions.
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Affiliation(s)
| | - Hari Krishna
- Indian Agricultural Research Institute, ICAR, New Delhi, India
| | | | | | - Divya Chauhan
- Indian Agricultural Research Institute, ICAR, New Delhi, India
| | - Shweta Singh
- Indian Agricultural Research Institute, ICAR, New Delhi, India
| | - Nivedita Sinha
- Indian Agricultural Research Institute, ICAR, New Delhi, India
| | | | - Prakasha T. L.
- Indian Agricultural Research Institute, ICAR, New Delhi, India
| | - Dharam Pal
- Indian Agricultural Research Institute, ICAR, New Delhi, India
| | - M. Sivasamy
- Indian Agricultural Research Institute, ICAR, New Delhi, India
| | - Neelu Jain
- Indian Agricultural Research Institute, ICAR, New Delhi, India
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Singh B, Kumar S, Elangovan A, Vasht D, Arya S, Duc NT, Swami P, Pawar GS, Raju D, Krishna H, Sathee L, Dalal M, Sahoo RN, Chinnusamy V. Phenomics based prediction of plant biomass and leaf area in wheat using machine learning approaches. Front Plant Sci 2023; 14:1214801. [PMID: 37448870 PMCID: PMC10337996 DOI: 10.3389/fpls.2023.1214801] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/07/2023] [Indexed: 07/15/2023]
Abstract
Introduction Phenomics has emerged as important tool to bridge the genotype-phenotype gap. To dissect complex traits such as highly dynamic plant growth, and quantification of its component traits over a different growth phase of plant will immensely help dissect genetic basis of biomass production. Based on RGB images, models have been developed to predict biomass recently. However, it is very challenging to find a model performing stable across experiments. In this study, we recorded RGB and NIR images of wheat germplasm and Recombinant Inbred Lines (RILs) of Raj3765xHD2329, and examined the use of multimodal images from RGB, NIR sensors and machine learning models to predict biomass and leaf area non-invasively. Results The image-based traits (i-Traits) containing geometric features, RGB based indices, RGB colour classes and NIR features were categorized into architectural traits and physiological traits. Total 77 i-Traits were selected for prediction of biomass and leaf area consisting of 35 architectural and 42 physiological traits. We have shown that different biomass related traits such as fresh weight, dry weight and shoot area can be predicted accurately from RGB and NIR images using 16 machine learning models. We applied the models on two consecutive years of experiments and found that measurement accuracies were similar suggesting the generalized nature of models. Results showed that all biomass-related traits could be estimated with about 90% accuracy but the performance of model BLASSO was relatively stable and high in all the traits and experiments. The R2 of BLASSO for fresh weight prediction was 0.96 (both year experiments), for dry weight prediction was 0.90 (Experiment 1) and 0.93 (Experiment 2) and for shoot area prediction 0.96 (Experiment 1) and 0.93 (Experiment 2). Also, the RMSRE of BLASSO for fresh weight prediction was 0.53 (Experiment 1) and 0.24 (Experiment 2), for dry weight prediction was 0.85 (Experiment 1) and 0.25 (Experiment 2) and for shoot area prediction 0.59 (Experiment 1) and 0.53 (Experiment 2). Discussion Based on the quantification power analysis of i-Traits, the determinants of biomass accumulation were found which contains both architectural and physiological traits. The best predictor i-Trait for fresh weight and dry weight prediction was Area_SV and for shoot area prediction was projected shoot area. These results will be helpful for identification and genetic basis dissection of major determinants of biomass accumulation and also non-invasive high throughput estimation of plant growth during different phenological stages can identify hitherto uncovered genes for biomass production and its deployment in crop improvement for breaking the yield plateau.
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Affiliation(s)
- Biswabiplab Singh
- Division of Plant Physiology and Nanaji Deshmukh Plant Phenomics Centre (NDPPC), Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sudhir Kumar
- Division of Plant Physiology and Nanaji Deshmukh Plant Phenomics Centre (NDPPC), Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Allimuthu Elangovan
- Division of Plant Physiology and Nanaji Deshmukh Plant Phenomics Centre (NDPPC), Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Devendra Vasht
- Division of Plant Physiology and Nanaji Deshmukh Plant Phenomics Centre (NDPPC), Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Sunny Arya
- Division of Plant Physiology and Nanaji Deshmukh Plant Phenomics Centre (NDPPC), Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Nguyen Trung Duc
- Division of Plant Physiology and Nanaji Deshmukh Plant Phenomics Centre (NDPPC), Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
- Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Pooja Swami
- Division of Plant Physiology and Nanaji Deshmukh Plant Phenomics Centre (NDPPC), Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Godawari Shivaji Pawar
- Division of Agricultural Botany, Vasantrao Naik Marathwada Krishi Vidyapeeth, Parbhani, India
| | - Dhandapani Raju
- Division of Plant Physiology and Nanaji Deshmukh Plant Phenomics Centre (NDPPC), Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Lekshmy Sathee
- Division of Plant Physiology and Nanaji Deshmukh Plant Phenomics Centre (NDPPC), Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
| | - Monika Dalal
- ICAR-National Institute for Plant Biotechnology, New Delhi, India
| | - Rabi Narayan Sahoo
- Division of Agricultural Physics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Viswanathan Chinnusamy
- Division of Plant Physiology and Nanaji Deshmukh Plant Phenomics Centre (NDPPC), Indian Council of Agricultural Research (ICAR)-Indian Agricultural Research Institute, New Delhi, India
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Gurumurthy S, Arora A, Krishna H, Chinnusamy V, Hazra KK. Genotypic capacity of post-anthesis stem reserve mobilization in wheat for yield sustainability under drought and heat stress in the subtropical region. Front Genet 2023; 14:1180941. [PMID: 37408776 PMCID: PMC10318140 DOI: 10.3389/fgene.2023.1180941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/23/2023] [Indexed: 07/07/2023] Open
Abstract
Wheat productivity is severely affected by drought and heat stress conditions worldwide. Currently, stem reserve mobilization (SRM) is receiving increased attention as a trait that can sustain wheat yields under adverse environments. However, the significance of SRM in sustaining wheat yields under drought and heat stress conditions remains uncertain in the tropical climate of Indo-Gangetic Plain region. Therefore, this study aimed to investigate genotypic variations in SRM in wheat and their influence on yield sustainability under drought and heat stress environments. The experiment was designed in an alpha-lattice layout, accommodating 43 genotypes under four simulated environments [timely sown and well irrigated (non-stress); timely sown and water-deficit/drought stress; late-sown and well-irrigated crop facing terminally high temperature; and late-sown and water-deficit stress (both water-deficit and heat stress)]. The water-deficit stress significantly increased SRM (16%-68%, p < 0.01) compared to the non-stress environment, while the heat stress conditions reduced SRM (12%-18%). Both SRM and stem reserve mobilization efficiency exhibited positive correlations with grain weight (grain weight spike-1) under all three different stress treatments (p < 0.05). Strong positive correlations between stem weight (at 12 days after anthesis) and grain weight were observed across the environments (p < 0.001); however, a significant positive correlation between stem weight and SRM was observed only with stress treatments. Results revealed that the SRM trait could effectively alleviate the impacts of water-deficit stress on yields. However, the SRM-mediated yield protection was uncertain under heat stress and combined water-deficit and heat stress treatments, possibly due to sink inefficiencies caused by high temperature during the reproductive period. Defoliated plants exhibited higher SRM than non-defoliated plants, with the highest increment observed in the non-stress treatment compared to all the stress treatments. Results revealed that wider genetic variability exists for the SRM trait, which could be used to improve wheat yield under drought stress conditions.
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Affiliation(s)
- S. Gurumurthy
- Division of Plant Physiology, ICAR–Indian Agricultural Research Institute, New Delhi, India
- School of Water Stress Management, ICAR–National Institute of Abiotic Stress Management, Baramati, Maharashtra, India
| | - A. Arora
- Division of Plant Physiology, ICAR–Indian Agricultural Research Institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, ICAR–Indian Agricultural Research Institute, New Delhi, India
| | - V. Chinnusamy
- Division of Plant Physiology, ICAR–Indian Agricultural Research Institute, New Delhi, India
| | - K. K. Hazra
- Crop Production Division, ICAR–Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
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Manjunath KK, Krishna H, Devate NB, Sunilkumar VP, Chauhan D, Singh S, Mishra CN, Singh JB, Sinha N, Jain N, Singh GP, Singh PK. Mapping of the QTLs governing grain micronutrients and thousand kernel weight in wheat ( Triticum aestivum L.) using high density SNP markers. Front Nutr 2023; 10:1105207. [PMID: 36845058 PMCID: PMC9950559 DOI: 10.3389/fnut.2023.1105207] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/27/2023] [Indexed: 02/12/2023] Open
Abstract
Biofortification is gaining importance globally to improve human nutrition through enhancing the micronutrient content, such as vitamin A, iron, and zinc, in staple food crops. The present study aims to identify the chromosomal regions governing the grain iron concentration (GFeC), grain zinc concentration (GZnC), and thousand kernel weight (TKW) using recombinant inbred lines (RILs) in wheat, developed from a cross between HD3086 and HI1500. The experiment was conducted in four different production conditions at Delhi viz., control, drought, heat, and combined heat and drought stress and at Indore under drought stress. Grain iron and zinc content increased under heat and combined stress conditions, while thousand kernel weight decreased. Medium to high heritability with a moderate correlation between grain iron and zinc was observed. Out of 4,106 polymorphic markers between the parents, 3,407 SNP markers were used for linkage map construction which spanned over a length of 14791.18 cm. QTL analysis identified a total of 32 chromosomal regions governing the traits under study, which includes 9, 11, and 12 QTLs for GFeC, GZnC, and TKW, respectively. A QTL hotspot was identified on chromosome 4B which is associated with grain iron, grain zinc, and thousand kernel weight explaining the phenotypic variance of 29.28, 10.98, and 17.53%, respectively. Similarly, common loci were identified on chromosomes 4B and 4D for grain iron, zinc, and thousand kernel weight. In silico analysis of these chromosomal regions identified putative candidate genes that code for proteins such as Inositol 1,3,4-trisphosphate 5/6-kinase, P-loop containing nucleoside triphosphate hydrolase, Pleckstrin homology (PH) domains, Serine-threonine/tyrosine-protein kinase and F-box-like domain superfamily proteins which play role in many important biochemical or physiological process. The identified markers linked to QTLs can be used in MAS once successfully validated.
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Affiliation(s)
| | - Hari Krishna
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India,*Correspondence: Hari Krishna,
| | - Narayana Bhat Devate
- 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
| | - 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
| | - C. N. Mishra
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - J. B. Singh
- Regional Station, ICAR-Indian Agricultural Research Institute, Indore, India
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 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,*Correspondence: Hari Krishna,
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Devate NB, Krishna H, Mishra CN, Manjunath KK, Sunilkumar VP, Chauhan D, Singh S, Sinha N, Jain N, Singh GP, Singh PK. Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and drought stress conditions in wheat. Front Plant Sci 2023; 13:1082513. [PMID: 36726675 PMCID: PMC9885108 DOI: 10.3389/fpls.2022.1082513] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 12/15/2022] [Indexed: 06/18/2023]
Abstract
Introduction Wheat is grown and consumed worldwide, making it an important staple food crop for both its calorific and nutritional content. In places where wheat is used as a staple food, suboptimal micronutrient content levels, especially of grain iron (Fe) and zinc (Zn), can lead to malnutrition. Grain nutrient content is influenced by abiotic stresses, such as drought and heat stress. The best method for addressing micronutrient deficiencies is the biofortification of food crops. The prerequisites for marker-assisted varietal development are the identification of the genomic region responsible for high grain iron and zinc contents and an understanding of their genetics. Methods A total of 193 diverse wheat genotypes were evaluated under drought and heat stress conditions across the years at the Indian Agricultural Research Institute (IARI), New Delhi, under timely sown irrigated (IR), restricted irrigated (RI) and late sown (LS) conditions. Grain iron content (GFeC) and grain zinc content (GZnC) were estimated from both the control and treatment groups. Genotyping of all the lines under study was carried out with the single nucleotide polymorphisms (SNPs) from Breeder's 35K Axiom Array. Result and Discussion Three subgroups were observed in the association panel based on both principal component analysis (PCA) and dendrogram analysis. A large whole-genome linkage disequilibrium (LD) block size of 3.49 Mb was observed. A genome-wide association study identified 16 unique stringent marker trait associations for GFeC, GZnC, and 1000-grain weight (TGW). In silico analysis demonstrated the presence of 28 potential candidate genes in the flanking region of 16 linked SNPs, such as synaptotagmin-like mitochondrial-lipid-binding domain, HAUS augmin-like complex, di-copper center-containing domain, protein kinase, chaperonin Cpn60, zinc finger, NUDIX hydrolase, etc. Expression levels of these genes in vegetative tissues and grain were also found. Utilization of identified markers in marker-assisted breeding may lead to the rapid development of biofortified wheat genotypes to combat malnutrition.
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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
| | - 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
| | - Nivedita Sinha
- Division of Genetics, ICAR-Indian Agricultural research institute, New Delhi, 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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Kumar PKC, Bellundagi A, Krishna H, Mallikarjuna MG, Thimmappa RK, Rai N, Shashikumara P, Sinha N, Jain N, Singh PK, Singh GP, Prabhu KV. Development of bread wheat ( Triticum aestivum L) variety HD3411 following marker-assisted backcross breeding for drought tolerance. Front Genet 2023; 14:1046624. [PMID: 36911407 PMCID: PMC9998906 DOI: 10.3389/fgene.2023.1046624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 02/06/2023] [Indexed: 02/26/2023] Open
Abstract
Marker-assisted backcross breeding enables selective insertion of targeted traits into the genome to improve yield, quality, and stress resistance in wheat. In the current investigation, we transferred four drought tolerance quantitative trait loci (QTLs) controlling traits, viz canopy temperature, normalized difference vegetative index, chlorophyll content, and grain yield from the drought-tolerant donor line, C306, into a popular high-yielding, drought-sensitive variety, HD2733. Marker-assisted selection coupled with stringent phenotypic screening was used to advance each generation. This study resulted in 23 improved lines carrying combinations of four drought tolerance QTLs with a range of 85.35%-95.79% background recovery. The backcross-derived lines gave a higher yield under moisture-deficit stress conditions compared with the recipient parent. They also showed higher phenotypic mean values for physiological traits and stability characteristics of HD2733. A promising genotype, HD3411, derived from this cross was identified for release after national multi-location coordinating trials under the All India Coordinated Wheat Improvement Project. Our study is a prime example of the advantages of precision breeding using integrating markers and phenotypic selection to develop new cultivars with desirable traits like drought tolerance.
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Affiliation(s)
| | | | - Hari Krishna
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Neha Rai
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - P Shashikumara
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | - Nivedita Sinha
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Neelu Jain
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pradeep K Singh
- ICAR-Indian Agricultural Research Institute, New Delhi, India
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Bellundagi A, Ramya KT, Krishna H, Jain N, Shashikumara P, Singh PK, Singh GP, Prabhu KV. Marker-assisted backcross breeding for heat tolerance in bread wheat ( Triticum aestivum L.). Front Genet 2022; 13:1056783. [PMID: 36568399 PMCID: PMC9785257 DOI: 10.3389/fgene.2022.1056783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
Manipulation of flowering time for adaptation through natural or genetic approaches may combat heat-stress damage that occurs at the reproductive stages in production conditions. HD2733, a popular wheat variety of the eastern plains of India, is largely sensitive to heat stress. Therefore, the current study aims to improve heat tolerance of HD2733 by introgression of QTLs associated with early anthesis and high kernel weight linked to markers Xbarc186 and Xgwm190, respectively, through marker-assisted backcross breeding (MABB) from a tolerant donor, WH730. A total of 124 simple sequence repeat (SSR) markers distributed evenly across the genome were used for the background selection. The alleles of Xbarc186 and Xgwm190 were fixed in BC2F1 and BC1F2 generations by selecting individual plants heterozygous for both marker loci and backcrossed with HD2733 and simultaneously selfed to generate BC2F1 and BC1F2 populations, respectively. Furthermore, the selected BC1F2 were selfed to generate the BC1F4 population. By background screening, a total of 39 BC2F3 and 21 BC1F4 families homozygous for the targeted QTLs with 90.9-97.9% and 86.8-88.3% RPG recoveries were selected. The best performing 17 BC2F3 and 10 BC1F4 lines were evaluated for various morpho-physiological traits. Phenotypic evaluation and multi-location trials of the introgressed lines under late sown conditions led to the selection of three promising lines with early anthesis and higher grain yield. The improved lines will serve as an excellent genetic material for functional genomics and expression studies to understand the molecular mechanisms and pathways underlying the stress tolerance.
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Affiliation(s)
- Amasiddha Bellundagi
- ICAR-Indian Institute of Millets Research, Hyderabad, India,ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - K. T. Ramya
- ICAR-Indian Institute of Oilseeds Research, Hyderabad, India
| | - Hari Krishna
- ICAR-Indian Agricultural Research Institute, New Delhi, India,*Correspondence: Hari Krishna, ; Gyanendra Pratap Singh,
| | - Neelu Jain
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - P. Shashikumara
- ICAR-Indian Institute of Millets Research, Hyderabad, India,ICAR-Indian Grassland and Fodder Research Institute, Jhansi, India
| | | | - Gyanendra Pratap Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India,*Correspondence: Hari Krishna, ; Gyanendra Pratap Singh,
| | - Kumble Vinod Prabhu
- Protection of Plant Varieties and Farmers’ Rights Authority, Government of India, New Delhi, India
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Sunilkumar V, Krishna H, Devate NB, Manjunath KK, Chauhan D, Singh S, Sinha N, Singh JB, Prakasha TL, Pal D, Sivasamy M, Jain N, Singh GP, Singh PK. Marker assisted improvement for leaf rust and moisture deficit stress tolerance in wheat variety HD3086. Front Plant Sci 2022; 13:1035016. [PMID: 36352858 PMCID: PMC9638138 DOI: 10.3389/fpls.2022.1035016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
There is a significant yield reduction in the wheat crop as a result of different biotic and abiotic stresses, and changing climate, among them moisture deficit stress and leaf rust are the major ones affecting wheat worldwide. HD3086 is a high-yielding wheat variety that has been released for commercial cultivation under timely sown irrigated conditions in the Indo-Gangetic plains of India. Variety HD3086 provides a good, stable yield, and it is the choice of millions of farmers in India. It becomes susceptible to the most prevalent pathotypes 77-5 and 77-9 of Puccinia triticina (causing leaf rust) in the production environment and its potential yield cannot be realized under moisture deficit stress. The present study demonstrates the use of a marker-assisted back cross breeding approach to the successful transfer of leaf rust resistance gene Lr24 and QTLs linked to moisture deficit stress tolerance in the background of HD3086. The genotype HI1500 was used as a donor parent that possesses leaf rust-resistant gene Lr24, which confers resistance against the major pathotypes found in the production environment. It possesses inbuilt tolerance under abiotic stresses with superior quality traits. Foreground selection for gene Lr24 and moisture deficit stress tolerance QTLs linked to Canopy temperature (CT), Normal Differential Vegetation Index (NDVI) and Thousand Kernel Weight (TKW) in different generations of the backcrossing and selection. In BC2F2, foreground selection was carried out to identify homozygous lines based on the linked markers and were advanced following pedigree based phenotypic selection. The selected lines were evaluated against P. triticina pathotypes 77-5 and 77-9 under controlled conditions. Recurrent parent recovery of the selected lines ranged from 78-94%. The identified lines were evaluated for their tolerance to moisture stress under field conditions and their resistance to rust under artificial epiphytotic conditions for two years. In BC2F5 generation, eight positive lines for marker alleles were selected which showed resistance to leaf rust and recorded an improvement in component traits of moisture deficit stress tolerance such as CT, NDVI, TKW and yield compared to the recurrent parent HD3086. The derived line is named HD3471 and is nominated for national trials for testing and further release for commercial cultivation.
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Affiliation(s)
- V.P. Sunilkumar
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - Hari Krishna
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - Narayana Bhat Devate
- 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
| | - Nivedita Sinha
- 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
| | - T. L. Prakasha
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - Dharam Pal
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, India
| | - M. Sivasamy
- Division of Genetics, Icar- Indian Agricultural Research Institute, New Delhi, 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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [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
- *Correspondence: Gopalareddy Krishnappa, ; Gyanendra Pratap Singh,
| | - 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
| | - Gyanendra Pratap Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- *Correspondence: Gopalareddy Krishnappa, ; Gyanendra Pratap Singh,
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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. Front Plant Sci 2022; 13:943033. [PMID: 36061792 PMCID: PMC9429996 DOI: 10.3389/fpls.2022.943033] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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Sukumaran S, Krishna H, Singh K, Mottaleb KA, Reynolds M. Progress and Prospects of Developing Climate Resilient Wheat in South Asia Using Modern Pre-Breeding Methods. Curr Genomics 2021; 22:440-449. [PMID: 35340360 PMCID: PMC8886626 DOI: 10.2174/1389202922666210705125006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 04/10/2021] [Accepted: 05/03/2021] [Indexed: 11/22/2022] Open
Abstract
:
Developing climate-resilient wheat is a priority for South Asia since the effect of climate
change will be pronounced on the major crops that are staple to the region. South Asia must
produce >400 million metric tons (MMT) of wheat by 2050 to meet the demand. However, the current
average yield <3 t/ha is not sufficient to meet the requirement. In this review, we are addressing
how pre-breeding methods in wheat can address the gap in grain yield as well as reduce the
bottleneck of genetic diversity. Physiological pre-breeding which incorporates screening of diverse
germplasm from gene banks for physiological and agronomic traits, the strategic crossing of complementary
traits, high throughput phenotyping, molecular markers-based generation advancement,
genomic prediction, and validation of high-value heat and drought tolerant lines to South Asia can
help to alleviate the drastic effect of climate change on wheat production. There are several gene
banks, if utilized well, can play a major role in breeding for climate-resilient wheat. CIMMYT’s
wheat physiological pre-breeding has delivered several hundred lines via the Stress Adapted Trait
Yield Nursery (SATYN) to the NARS in many South Asian countries; India, Pakistan, Nepal,
Bangladesh, Afghanistan, and Iran. Some of these improved germplasms have resulted in varieties
for farmer's field. We conclude the review by pointing out the importance of collaborative interdisciplinary
translational research to alleviate the effects of climate change on wheat production in
South Asia.
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Affiliation(s)
- Sivakumar Sukumaran
- Global Wheat Program, International maize and wheat improvement Center (CIMMYT),Mexico
| | - Hari Krishna
- Division of Plant Breeding and Genetics, Indian Agricultural Research Institute, New Delhi,India
| | - Kuldeep Singh
- National Institute of Plant Genetic Resources (NIPGR), New Delhi,India
| | | | - Matthew Reynolds
- Global Wheat Program, International maize and wheat improvement Center (CIMMYT),Mexico
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Krishna H, Banerjee A, Singh S, Rani N. Unusual branching pattern of left gastric artery: a clinical interpretation. J ANAT SOC INDIA 2018. [DOI: 10.1016/j.jasi.2018.06.174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Dhungana BR, Deepika B, Atul S, Krishna H, Birendra C, Veena A. Improved Physical Endurance Activity of Fruit of <I>Beta vulgaris</I>. Journal of Pharmaceutical Research 2015. [DOI: 10.18579/jpcrkc/2015/0/0/79301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Sachan R, Yadavali S, Shirato N, Krishna H, Ramos V, Duscher G, Pennycook SJ, Gangopadhyay AK, Garcia H, Kalyanaraman R. Self-organized bimetallic Ag-Co nanoparticles with tunable localized surface plasmons showing high environmental stability and sensitivity. Nanotechnology 2012; 23:275604. [PMID: 22710488 DOI: 10.1088/0957-4484/23/27/275604] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
We demonstrate a promising synthesis route based on pulsed laser dewetting of bilayer films (Ag and Co) to make bimetallic nanoparticle arrays. By combining experiment and theory we establish a parameter space for the independent control of composition and diameter for the bimetallic nanoparticles. As a result, physical properties, such as the localized surface plasmon resonance (LSPR), that depend on particle size and composition can be readily tuned over a wavelength range one order of magnitude greater than for pure Ag nanoparticles. The LSPR detection sensitivity of the bimetallic nanoparticles with narrow size distribution was found to be high-comparable with pure Ag (∼60 nm/RIU). Moreover, they showed significantly higher long-term environmental stability over pure Ag.
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Affiliation(s)
- R Sachan
- Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN 37996, USA
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Krishna H, Sachan R, Strader J, Favazza C, Khenner M, Kalyanaraman R. Thickness-dependent spontaneous dewetting morphology of ultrathin Ag films. Nanotechnology 2010; 21:155601. [PMID: 20299723 DOI: 10.1088/0957-4484/21/15/155601] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We show here that the morphological pathway of spontaneous dewetting of ultrathin Ag films on SiO2 under nanosecond laser melting is dependent on film thickness. For films with thickness h of 2 nm < or = h < or = 9.5 nm, the morphology during the intermediate stages of dewetting consisted of bicontinuous structures. For films with 11.5 nm < or = h < or = 20 nm, the intermediate stages consisted of regularly sized holes. Measurement of the characteristic length scales for different stages of dewetting as a function of film thickness showed a systematic increase, which is consistent with the spinodal dewetting instability over the entire thickness range investigated. This change in morphology with thickness is consistent with observations made previously for polymer films (Sharma and Khanna 1998 Phys. Rev. Lett. 81 3463-6; Seemann et al 2001 J. Phys.: Condens. Matter 13 4925-38). Based on the behavior of free energy curvature that incorporates intermolecular forces, we have estimated the morphological transition thickness for the intermolecular forces for Ag on SiO2. The theory predictions agree well with observations for Ag. These results show that it is possible to form a variety of complex Ag nanomorphologies in a consistent manner, which could be useful in optical applications of Ag surfaces, such as in surface enhanced Raman sensing.
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Affiliation(s)
- H Krishna
- Department of Physics, Washington University in St Louis, MO 63130, USA
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Krishna H, Shirato N, Favazza C, Kalyanaraman R. Energy driven self-organization in nanoscale metallic liquid films. Phys Chem Chem Phys 2009; 11:8136-43. [DOI: 10.1039/b906281p] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Krishna H, Wani AA, Behari S, Banerji D, Chhabra DK, Jain VK. Intracranial aneurysms in patients 18 years of age or under, are they different from aneurysms in adult population? Acta Neurochir (Wien) 2005; 147:469-76; discussion 476. [PMID: 15812597 DOI: 10.1007/s00701-005-0481-y] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
BACKGROUND Intracranial aneurysms are extremely uncommon in the first two decades of life. This study was undertaken to assess the clinicoradiological features and surgical outcome of intracranial aneurysms in patients less than or equal to 18 years of age; and, to highlight the differences between these and intracranial aneurysms seen in adult patients. METHODS AND MATERIAL Twenty-two patients, 18 years of age or under (male:female ratio=1.75:1; mean age 14.18+/-3.8 years, age range 5 to 18 years) and 451 adult patients aged older than 18 years (male:female ratio=1:1.05; mean age 48.21+/-12.71 years, age range, 19 to 81 years) were treated for intracranial aneurysms at our center between January 1991 and July 2003. The univariate statistical analysis was used to compare differences between the two groups. FINDINGS The patients under 18 years constituted 4.6% of the total patient population having intracranial aneurysms. The incidence of associated medical diseases was greater in patients under 18 years than in the adults (9% versus 0.26%, p<0.05). The incidence of seizures was more than double in patients under 18 years (36% versus 17%, p<0.05). The incidence of intracerebral haematoma (ICH; 41% versus 22.5%, p>0.05), intraventricular haemorrhage (IVH; 45% versus 34%, p>0.05), and hydrocephalus (36% versus 25%, p>0.05) were higher in patients under 18 years. In adult patients, anterior communicating artery (AcoA) and in children, ICA bifurcation were the most frequent sites of aneurysm formation respectively (p<0.05). The incidence of giant aneurysms was nearly double in children (13.6% versus 6.5%, p>0.05). The incidence of clinical vasospasm was almost the same in both groups. The overall outcome was favourable in 82% of patients under 18 years and 58.8% in adults. The management mortality in patients under 18 years was 9.1%, while in the adult patients, it was 19%. CONCLUSION In patients under 18 years of age, there was a definite male predominance; a higher incidence of seizures; and, the ICA bifurcation formed the most frequent site of intracranial aneurysms. In adults, AcoA a was the commonest site. Rebleeding and delayed ischaemic deficits were the major causes of morbidity. Favorable outcome after surgery in young patients was better in comparison to their adult counterparts.
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MESH Headings
- Adolescent
- Adult
- Age Distribution
- Age Factors
- Aged
- Aged, 80 and over
- Carotid Artery, Internal, Dissection/mortality
- Carotid Artery, Internal, Dissection/pathology
- Carotid Artery, Internal, Dissection/physiopathology
- Cerebral Arteries/pathology
- Cerebral Arteries/physiopathology
- Cerebral Hemorrhage/mortality
- Cerebral Hemorrhage/pathology
- Cerebral Hemorrhage/physiopathology
- Cerebral Ventricles/pathology
- Cerebral Ventricles/physiopathology
- Child
- Child, Preschool
- Comorbidity
- Female
- Humans
- Hydrocephalus/epidemiology
- Hydrocephalus/physiopathology
- Incidence
- Intracranial Aneurysm/mortality
- Intracranial Aneurysm/pathology
- Intracranial Aneurysm/physiopathology
- Male
- Middle Aged
- Mortality
- Seizures/epidemiology
- Seizures/physiopathology
- Sex Factors
- Treatment Outcome
- Vasospasm, Intracranial/epidemiology
- Vasospasm, Intracranial/physiopathology
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Affiliation(s)
- H Krishna
- Department of Neurosurgery, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Raebareilly Road, Lucknow, UP, India
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Gaskin R, Murray R, Krishna H, Carpenter A. Effect of adjuvants on the retention of insecticide spray on cucumber and pea foliage. ACTA ACUST UNITED AC 2000. [DOI: 10.30843/nzpp.2000.53.3608] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Spray additives are often used to enhance the efficacy of agrochemicals in the management of pests and diseases in vegetables but their effects can vary widely and are not fully understood This study investigated the effects of adjuvants on the retention of a systemic insecticide spray on two contrasting plant species Adjuvants provided no benefits on easytowet cucumber foliage particularly with high volume application On waterrepellent pea foliage retention of spray was enhanced by adjuvants (P
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