Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (<i>Gossypium hirsutum</i>)

Zaidi, Syed Shan-e-Ali; Naqvi, Rubab Zahra; Asif, Muhammad; Strickler, Susan R.; Shakir, Sara; Shafiq, Muhammad; Khan, Ayesha; Amin, Imran; Mishra, Bharat; Mukhtar, M. Shahid; Scheffler, Brian E.; Scheffler, Jodi A.; Mueller, Lukas A.; Mansoor, Shahid

doi:10.1111/pbi.13236

Cited by 51 publications

(32 citation statements)

References 95 publications

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“…Weighted gene co‐expression network analysis (WGCNA) can discern such relationships and generate an undirected weighted network with scale‐free topology. The network contains modules comprised by a cohort of genes with similar expression patterns in response to a given stimulus or physiological condition (Zaidi et al ., 2019). The DEGs were subjected to a WGCNA.…”

Section: Resultsmentioning

confidence: 99%

Deciphering transcriptional regulators of banana fruit ripening by regulatory network analysis

Kuang

Guo

et al. 2020

Plant Biotechnology Journal

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Summary Fruit ripening is a critical phase in the production and marketing of fruits. Previous studies have indicated that fruit ripening is a highly coordinated process, mainly regulated at the transcriptional level, in which transcription factors play essential roles. Thus, identifying key transcription factors regulating fruit ripening as well as their associated regulatory networks promises to contribute to a better understanding of fruit ripening. In this study, temporal gene expression analyses were performed to investigate banana fruit ripening with the aim to discern the global architecture of gene regulatory networks underlying fruit ripening. Eight time points were profiled covering dynamic changes of phenotypes, the associated physiology and levels of known ripening marker genes. Combining results from a weighted gene co‐expression network analysis (WGCNA) as well as cis‐motif analysis and supported by EMSA, Y1H, tobacco‐, banana‐transactivation experimental results, the regulatory network of banana fruit ripening was constructed, from which 25 transcription factors were identified as prime candidates to regulate the ripening process by modulating different ripening‐related pathways. Our study presents the first global view of the gene regulatory network involved in banana fruit ripening, which may provide the basis for a targeted manipulation of fruit ripening to attain higher banana and loss‐reduced banana commercialization.

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Section: Resultsmentioning

confidence: 99%

Deciphering transcriptional regulators of banana fruit ripening by regulatory network analysis

Kuang

Guo

et al. 2020

Plant Biotechnology Journal

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“…Begomoviruses, transmitted by white ies, have emerged as serious limitations to the cultivation of a wide variety of crops worldwide (Navas-Castillo et al, 2011;Rojas et al 2018). This has motivated researchers and breeders to identify begomovirus resistant sources and to conduct genetic mapping of resistance loci in various crops such as tomato, pepper, melon (Cucumis melo), squash (Cucurbita moschata), common bean (Phaseolus vulgaris), cassava (Manihot esculenta), and cotton (Gossypium hirsutum) (Blair and Morales 2008;Lapidot and Levin 2017;Sáez et al 2017Sáez et al , 2020Beam and Ascencio-Ibáñez 2020;Thakur et al 2020;Zaidi et al 2020). To the best of our knowledge, tomato Ty-1/Ty-3/Ty-3a (encoding RDR), Ty-2 (encoding an NB-LRR protein), and ty-5 (encoding Pelota) are the only begomovirus resistance genes cloned to date (Verlaan et al 2013;Lapdot et al 2015;Yamaguchi et al 2018).…”

Section: Discussionmentioning

confidence: 99%

A recessive gene pepy-1 encoding Pelota confers resistance to begomovirus isolates of PepYLCIV and PepYLCAV in Capsicum annuum

et al. 2021

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Pepper yellow leaf curl disease caused by begomoviruses seriously affects pepper (Capsicum spp.) production in a number of regions around the world. Ty genes of tomato, which confer resistance to the tomato yellow leaf curl virus, are the only begomovirus resistance genes cloned to date. In this study, we focused on the identi cation of begomovirus resistance genes in Capsicum annuum. BaPep-5 was identi ed as a novel source of resistance against pepper yellow leaf curl Indonesia virus (PepYLCIV) and pepper yellow leaf curl Aceh virus (PepYLCAV). A single recessive locus, which we named as pepper yellow leaf curl disease virus resistance 1 (pepy-1), responsible for PepYLCAV resistance in BaPep-5 was identi ed on chromosome 5 in an F 2 population derived from a cross between BaPep-5 and the begomovirus susceptible accession BaPep-4. In the target region spanning 34 kb, a single candidate gene, the messenger RNA surveillance factor Pelota, was identi ed. Whole-genome resequencing of BaPep-4 and BaPep-5 and comparison of their genomic DNA sequences revealed a single nucleotide polymorphism (A to G) located at the splice site of the 9th intron of CaPelota in BaPep-5, which caused the insertion of the 9th intron into the transcript, resulting in the addition of 28 amino acids to CaPelota protein without causing a frameshift. Virus-induced gene silencing of CaPelota in the begomovirus susceptible pepper No.218 resulted in the gain of resistance against PepYLCIV, a phenotype consistent with BaPep-5. The DNA marker developed in this study will greatly facilitate marker-assisted breeding of begomovirus resistance in peppers.

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“…The reason behind this is the difficulty in the selection of candidate genes for functional validation due to a large set of genes. This could be addressed by using modern statistical tools to study the association of key DEGs with target traits that will refine the search for key candidate genes, as described in these studies [ 154 , 155 ].…”

Section: Limitations In Crop Improvementmentioning

confidence: 99%

Thermal Stresses in Maize: Effects and Management Strategies

Waqas

Wang

Zafar

et al. 2021

Plants

106

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Climate change can decrease the global maize productivity and grain quality. Maize crop requires an optimal temperature for better harvest productivity. A suboptimal temperature at any critical stage for a prolonged duration can negatively affect the growth and yield formation processes. This review discusses the negative impact of temperature extremes (high and low temperatures) on the morpho-physiological, biochemical, and nutritional traits of the maize crop. High temperature stress limits pollen viability and silks receptivity, leading to a significant reduction in seed setting and grain yield. Likewise, severe alterations in growth rate, photosynthesis, dry matter accumulation, cellular membranes, and antioxidant enzyme activities under low temperature collectively limit maize productivity. We also discussed various strategies with practical examples to cope with temperature stresses, including cultural practices, exogenous protectants, breeding climate-smart crops, and molecular genomics approaches. We reviewed that identified quantitative trait loci (QTLs) and genes controlling high- and low temperature stress tolerance in maize could be introgressed into otherwise elite cultivars to develop stress-tolerant cultivars. Genome editing has become a key tool for developing climate-resilient crops. Moreover, challenges to maize crop improvement such as lack of adequate resources for breeding in poor countries, poor communication among the scientists of developing and developed countries, problems in germplasm exchange, and high cost of advanced high-throughput phenotyping systems are discussed. In the end, future perspectives for maize improvement are discussed, which briefly include new breeding technologies such as transgene-free clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas)-mediated genome editing for thermo-stress tolerance in maize.

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Molecular insight into cotton leaf curl geminivirus disease resistance in cultivated cotton (Gossypium hirsutum)

Cited by 51 publications

References 95 publications

Deciphering transcriptional regulators of banana fruit ripening by regulatory network analysis

Deciphering transcriptional regulators of banana fruit ripening by regulatory network analysis

A recessive gene pepy-1 encoding Pelota confers resistance to begomovirus isolates of PepYLCIV and PepYLCAV in Capsicum annuum

Thermal Stresses in Maize: Effects and Management Strategies

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