Identification, expression analysis and molecular modeling of <i>Iron deficiency specific clone 3</i> (<i>Ids3</i>) like gene in hexaploid wheat

Mathpal, Priyanka; Kumar, Upendra; Kumar, Anuj; Kumar, Sanjay; Malik, Sachin; Kumar, Naveen; Dhaliwal, H. S.; Kumar, Sunil

doi:10.1101/244392

Cited by 2 publications

(3 citation statements)

References 39 publications

(34 reference statements)

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“…As wheat is a hexaploid with three homeologous genomes there is a high chance that similar genes on the respective homeologous chromosomes would be found. An elaborate study of iron deficiency-specific clone 3 (Ids3)-like genes in hexaploid wheat was conducted by Mathpal et al, 2018. The authors found an ortholog on the telomeric region of chromosome 7A and its homolog ranged from 78% to 88% on chromosomes 7D and 7B.…”

Section: Discussionmentioning

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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Section: Discussionmentioning

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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“…Modeled 3D structures from the SWISS-MODEL server were used as the initial configuration of all simulations. The MD simulations were conducted as per the protocol previously described in Gajula et al (2016); Kumar et al (2016Kumar et al ( , 2018aKumar et al ( , and 2018b; Mathpal et al (2018);and Gautam et al (2019). A minimum of 10 Å distance was used between the protein surfaces and the simulation box edges.…”

Section: Molecular Dynamics Simulationmentioning

confidence: 99%

“…Phylogenetic analysis was performed by using sequences of predicted proteins associated with flag leaf development through Mega-X software (Kumar S. et al, 2018). A phylogenetic tree was constructed using the neighbor-joining method with 1,000 bootstraps for inferring evolutionary relationships.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Structural and functional insights into the candidate genes associated with different developmental stages of flag leaf in bread wheat (Triticum aestivum L.)

et al. 2022

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Grain yield is one of the most important aims for combating the needs of the growing world population. The role of development and nutrient transfer in flag leaf for higher yields at the grain level is well known. It is a great challenge to properly exploit this knowledge because all the processes, starting from the emergence of the flag leaf to the grain filling stages of wheat (Triticum aestivum L.), are very complex biochemical and physiological processes to address. This study was conducted with the primary goal of functionally and structurally annotating the candidate genes associated with different developmental stages of flag leaf in a comprehensive manner using a plethora of in silico tools. Flag leaf-associated genes were analyzed for their structural and functional impacts using a set of bioinformatics tools and algorithms. The results revealed the association of 17 candidate genes with different stages of flag leaf development in wheat crop. Of these 17 candidate genes, the expression analysis results revealed the upregulation of genes such as TaSRT1-5D, TaPNH1-7B, and TaNfl1-2B and the downregulation of genes such as TaNAP1-7B, TaNOL-4D, and TaOsl2-2B can be utilized for the generation of high-yielding wheat varieties. Through MD simulation and other in silico analyses, all these proteins were found to be stable. Based on the outcome of bioinformatics and molecular analysis, the identified candidate genes were found to play principal roles in the flag leaf development process and can be utilized for higher-yield wheat production.

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Identification, expression analysis and molecular modeling of Iron deficiency specific clone 3 (Ids3) like gene in hexaploid wheat

Abstract: 2 6

Cited by 2 publications

References 39 publications

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

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

Structural and functional insights into the candidate genes associated with different developmental stages of flag leaf in bread wheat (Triticum aestivum L.)

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