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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] [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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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.). FRONTIERS IN PLANT SCIENCE 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] [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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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] [Abstract] [Key Words] [Grants] [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
| | - 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
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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. FRONTIERS IN PLANT SCIENCE 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] [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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