Genome-wide association mapping for component traits of drought and heat tolerance in wheat

Devate, Narayana Bhat; Krishna, Hari; Parmeshwarappa, Sunil Kumar V.; Manjunath, Karthik Kumar; Chauhan, Divya; Singh, Shweta; Singh, Jang Bahadur; Kumar, M. B. Arun; Patil, Ravindra; Khan, Hanif; Jain, Neelu; Singh, Gyanendra; Singh, Pradeep Kumar

doi:10.3389/fpls.2022.943033

Cited by 26 publications

(33 citation statements)

References 104 publications

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“…The GWAS panel under study had two subpopulations based on STRUCTURE and PCA scatter plots. Linkage-disequilibrium Frontiers in Genetics frontiersin.org (LD) decay block size was shown to be 5.24, 5.26, and 9.22 MB for the A, B, and D genomes, respectively, and a block of 7.15 MB was observed for the whole genome (Devate et al, 2022). The effect of the population structure of the association panel on the GWAS analysis is addressed by taking them as a covariate to ensure true association.…”

Section: Resultsmentioning

confidence: 99%

“…The GWAS mapping panel consists of 295 advanced breeding lines developed from popular Indian and exotic varieties as described in Devate et al (2022). All the materials were evaluated at the IARI, New Delhi (Indian Agricultural Research Institute, research farm located at 28 °38′30.5″N, 77 °09′58.2″E, 228 m AMSL) with three conditions, viz., timely sown irrigated (IR), timely sown drought (RI), and late-sown condition (LS).…”

Section: Plant Materials and Field Layoutmentioning

confidence: 99%

“…Population structure based on STRUCTURE software and molecular marker-based PCA analysis was conducted. Also, pairwise r 2 values between markers and Linkage Disequilibrium decay plots were drawn as described in Devate et al (2022).…”

Section: Phenotypingmentioning

confidence: 99%

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Identification of genomic regions of wheat associated with grain Fe and Zn content under drought and heat stress using genome-wide association study

Devate

Krishna²,

Sunilkumar³

et al. 2022

Front. Genet.

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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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Section: Resultsmentioning

confidence: 99%

Section: Plant Materials and Field Layoutmentioning

confidence: 99%

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Identification of genomic regions of wheat associated with grain Fe and Zn content under drought and heat stress using genome-wide association study

Devate

Krishna²,

Sunilkumar³

et al. 2022

Front. Genet.

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“…MABB is considered as one of the reliable methods to improve a crop variety by incorporating the desired gene(s)/QTLs that govern the trait expression in which the variety is essentially deficient. Numerous reports are available on molecular markers linked with the expression of QTLs for heat-stress tolerance (Devate et al, 2022;Khan et al, 2022;Pinto et al, 2010;Gupta et al, 2012;Gupta et al, 2017) but their use in wheat-breeding programs is still rare. The present study is an attempt of the transfer of QTLs associated with heat stress in to the background of high-yielding wheat varieties using MABB.…”

Section: Discussionmentioning

confidence: 99%

Marker-assisted backcross breeding for heat tolerance in bread wheat (Triticum aestivum L.)

Bellundagi

Ramya²,

Krishna³

et al. 2022

Front. Genet.

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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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“…Recent improvements in high-throughput genotyping and phenotyping have boosted the feasibility of discovering the genetic basis of complex traits ( Devate et al., 2022a ), such as grain nutrient content. This has led to the popularization of whole-genome-marker-based techniques such as Quantitative trait loci (QTL) mapping, genome-wide association studies (GWASs), and genomic selection ( Krishnappa et al., 2021 ; Anilkumar et al., 2022 ; Harikrishna et al., 2022 ).…”

Section: Introductionmentioning

confidence: 99%

Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and drought stress conditions in wheat

et al. 2023

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IntroductionWheat 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.MethodsA 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 DiscussionThree 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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Genome-wide association mapping for component traits of drought and heat tolerance in wheat

Cited by 26 publications

References 104 publications

Identification of genomic regions of wheat associated with grain Fe and Zn content under drought and heat stress using genome-wide association study

Identification of genomic regions of wheat associated with grain Fe and Zn content under drought and heat stress using genome-wide association study

Marker-assisted backcross breeding for heat tolerance in bread wheat (Triticum aestivum L.)

Genetic dissection of marker trait associations for grain micro-nutrients and thousand grain weight under heat and drought stress conditions in wheat

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