Functional genomic approaches to improve crop plant heat stress tolerance

Singh, Baljeet; Salaria, Neha; Thakur, Kajal; Kukreja, Sarvjeet; Gautam, Shristy; Goutam, Umesh

doi:10.12688/f1000research.19840.1

Cited by 36 publications

(18 citation statements)

References 94 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…As global warming continues, HS is expected to become more frequent and more severe (Reinman, 2013). Consequently, substantial worldwide efforts are being devoted to study and improve the genetic basis underlying HS tolerance (HST) in crop plants (Driedonks et al ., 2016; Singh et al ., 2019). As a typical cool season crop, wheat ( Triticum aestivum , AABBDD) is vulnerable to HS, particularly at the flowering and grain‐filling stages (Asseng et al ., 2015; Cossani and Reynolds, 2012; Kaur et al ., 2019; Stratonovitch and Semenov, 2015; Zampieri et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Wheat heat tolerance is impaired by heightened deletions in the distal end of 4AL chromosomal arm

Zhai

Jiang

Zhao

et al. 2021

Plant Biotechnology Journal

View full text Add to dashboard Cite

Heat stress (HS) causes substantial damages to worldwide crop production. As a cool season crop, wheat (Triticum aestivum) is sensitive to HS-induced damages. To support the genetic improvement of wheat HS tolerance (HST), we conducted fine mapping of TaHST1, a locus required for maintaining wheat vegetative and reproductive growth under elevated temperatures. TaHST1 was mapped to the distal terminus of 4AL chromosome arm using genetic populations derived from two BC 6 F 6 breeding lines showing tolerance (E6015-4T) or sensitivity (E6015-3S) to HS. The 4AL region carrying TaHST1 locus was approximately 0.949 Mbp and contained the last 19 high confidence genes of 4AL according to wheat reference genome sequence. Resequencing of E6015-3S and E6015-4T and haplotype analysis of 3087 worldwide wheat accessions revealed heightened deletion polymorphisms in the distal 0.949 Mbp region of 4AL, which was confirmed by the finding of frequent gene losses in this region in eight genomesequenced hexaploid wheat cultivars. The great majority (86.36%) of the 3087 lines displayed different degrees of nucleotide sequence deletions, with only 13.64% of them resembling E6015-4T in this region. These deletions can impair the presence and/or function of TaHST1 and surrounding genes, thus rendering global wheat germplasm vulnerable to HS or other environmental adversities. Therefore, conscientious and urgent efforts are needed in global wheat breeding programmes to optimize the structure and function of 4AL distal terminus by ensuring the presence of TaHST1 and surrounding genes. The new information reported here will help to accelerate the ongoing global efforts in improving wheat HST.

show abstract

Section: Introductionmentioning

confidence: 99%

Wheat heat tolerance is impaired by heightened deletions in the distal end of 4AL chromosomal arm

Zhai

Jiang

Zhao

et al. 2021

Plant Biotechnology Journal

View full text Add to dashboard Cite

show abstract

“…From a crop improvement perspective, it is possible to develop increasingly heat-resistant rice cultivars. For this, it is important to understand the responses that allow rice to tolerate heat [ 11 ].…”

Section: Introductionmentioning

confidence: 99%

Reading between the Lines: RNA-seq Data Mining Reveals the Alternative Message of the Rice Leaf Transcriptome in Response to Heat Stress

Vitoriano

Calixto

2021

Plants

View full text Add to dashboard Cite

Rice (Oryza sativa L.) is a major food crop but heat stress affects its yield and grain quality. To identify mechanistic solutions to improve rice yield under rising temperatures, molecular responses of thermotolerance must be understood. Transcriptional and post-transcriptional controls are involved in a wide range of plant environmental responses. Alternative splicing (AS), in particular, is a widespread mechanism impacting the stress defence in plants but it has been completely overlooked in rice genome-wide heat stress studies. In this context, we carried out a robust data mining of publicly available RNA-seq datasets to investigate the extension of heat-induced AS in rice leaves. For this, datasets of interest were subjected to filtering and quality control, followed by accurate transcript-specific quantifications. Powerful differential gene expression (DE) and differential AS (DAS) identified 17,143 and 2162 heat response genes, respectively, many of which are novel. Detailed analysis of DAS genes coding for key regulators of gene expression suggests that AS helps shape transcriptome and proteome diversity in response to heat. The knowledge resulting from this study confirmed a widespread transcriptional and post-transcriptional response to heat stress in plants, and it provided novel candidates for rapidly advancing rice breeding in response to climate change.

show abstract

“…Globally, web-based databases are an important resource for plant genomics, specifically detecting stress-reactive genes [ 4 ]. Functional genomics has helped to detect stress-related genes in crops [ 5 , 6 ]. Accessibility to the whole genome sequence of numerous plant species and recent developments in genomic approaches promise to deliver methods for locating stress-responsive genes at the genome-wide level.…”

Section: Introductionmentioning

confidence: 99%

Omics and CRISPR-Cas9 Approaches for Molecular Insight, Functional Gene Analysis, and Stress Tolerance Development in Crops

Razzaq

Aleem

Mansoor

et al. 2021

IJMS

View full text Add to dashboard Cite

Plants are regularly exposed to biotic and abiotic stresses that adversely affect agricultural production. Omics has gained momentum in the last two decades, fueled by statistical methodologies, computational capabilities, mass spectrometry, nucleic-acid sequencing, and peptide-sequencing platforms. Functional genomics—especially metabolomics, transcriptomics, and proteomics—have contributed substantially to plant molecular responses to stress. Recent progress in reverse and forward genetics approaches have mediated high-throughput techniques for identifying stress-related genes. Furthermore, web-based genetic databases have mediated bioinformatics techniques for detecting families of stress-tolerant genes. Gene ontology (GO) databases provide information on the gene product’s functional features and help with the computational estimation of gene function. Functional omics data from multiple platforms are useful for positional cloning. Stress-tolerant plants have been engineered using stress response genes, regulatory networks, and pathways. The genome-editing tool, CRISPR-Cas9, reveals the functional features of several parts of the plant genome. Current developments in CRISPR, such as de novo meristem induction genome-engineering in dicots and temperature-tolerant LbCas12a/CRISPR, enable greater DNA insertion precision. This review discusses functional omics for molecular insight and CRISPR-Cas9-based validation of gene function in crop plants. Omics and CRISPR-Cas9 are expected to garner knowledge on molecular systems and gene function and stress-tolerant crop production.

show abstract

Functional genomic approaches to improve crop plant heat stress tolerance

Cited by 36 publications

References 94 publications

Wheat heat tolerance is impaired by heightened deletions in the distal end of 4AL chromosomal arm

Wheat heat tolerance is impaired by heightened deletions in the distal end of 4AL chromosomal arm

Reading between the Lines: RNA-seq Data Mining Reveals the Alternative Message of the Rice Leaf Transcriptome in Response to Heat Stress

Omics and CRISPR-Cas9 Approaches for Molecular Insight, Functional Gene Analysis, and Stress Tolerance Development in Crops

Contact Info

Product

Resources

About