The Landscape of the Genomic Distribution and the Expression of the F-Box Genes Unveil Genome Plasticity in Hexaploid Wheat during Grain Development and in Response to Heat and Drought Stress

Guérin, Claire; Mouzeyar, Saïd; Roche, Jane

doi:10.3390/ijms22063111

Cited by 10 publications

(6 citation statements)

References 88 publications

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“…For example, the MAD-box and NAC families of transcription factors contain 201 and 488 genes respectively, which have probably expanded in wheat through tandem duplication, retrotransposition and small-scale duplications [ 25 , 26 ]. The same observation has been made for the F-box family, which include 3670 members in bread wheat [ 27 ].…”

Section: Discussionsupporting

confidence: 67%

In silico analysis of the Seven IN Absentia (SINA) genes in bread wheat sheds light on their structure in plants

Roche,

Guérin,

Dupuits

et al. 2023

PLoS ONE

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Seven IN Absentia (SINA) is a small family of genes coding for ubiquitin-ligases that play major roles in regulating various plant growth and developmental processes, as well as in plant response to diverse biotic and abiotic stresses. Here, we studied the SINA genes family in bread wheat Triticum aestivum which is a culture of major importance for food security worldwide. One hundred and forty-one SINA family genes have been identified in bread wheat and showed that their number is very high compared to other plant species such as A. thaliana or rice. The expansion of this family seems to have been more important in monocots than in eudicots. In bread wheat, the chromosome 3 distal region is the site of a massive amplification of the SINA family, since we found that 83 of the 141 SINA genes are located on this chromosome in the Chinese Spring variety. This amplification probably occurred as a result of local duplications, followed by sequences divergence. The study was then extended to 4856 SINA proteins from 97 plant species. Phylogenetic and structural analyses identified a group of putative ancestral SINA proteins in plants containing a 58 aminoacid specific signature. Based on sequence homology and the research of that “Ancestral SINA motif” of 58 amino acids, a methodological process has been proposed and lead to the identification of functional SINA genes in a large family such as the Triticae that might be used for other species. Finally, tis paper gives a comprehensive overview of wheat gene family organization and functionalization taken the SINA genes as an example.

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Section: Discussionsupporting

confidence: 67%

In silico analysis of the Seven IN Absentia (SINA) genes in bread wheat sheds light on their structure in plants

Roche,

Guérin,

Dupuits

et al. 2023

PLoS ONE

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“…Functional relevance of the genes/gene families listed above in category (iii) with thermotolerance has also been documented previously (Park et al 2014;Agarwal et al 2018;Chen et al 2018;Pandian et al 2020;Kumar et al 2021;Guérin et al 2021;). Following are some examples, (i) a mitogen-activated protein kinase (MAPK) was recently shown to be associated with oxidative stress tolerance and carbon assimilation in wheat under terminal heat stress (Kumar et al 2021); (ii) F-box-like proteins are known to play a major role in plant responses to diverse developmental and stress conditions in wheat (Guérin et al 2021); (iii) Cytochrome P450s are the largest enzyme family involved in O 2 and/or NADPH dependent hydroxylation reactions. The expressions of cytochrome P450…”

Section: Mqtls Co-located With Known Genes For Thermotolerancesupporting

confidence: 70%

Meta-QTLs, ortho-MQTLs and candidate genes for thermotolerance in wheat (Triticum aestivum L.)

Kumar

Singh

Saini

et al. 2021

Preprint

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Meta-QTL analysis for thermotolerance in wheat was conducted to identify robust meta-QTLs (MQTLs). In this study, 441 QTLs related to 31 heat-responsive traits were projected on the consensus map saturated with 50,310 markers. This exercise resulted in the identification of 85 MQTLs with confidence interval (CI) ranging from 0.11 to 34.9 cM with an average of 5.6 cM. This amounted to a 2.96 fold reduction relative to the mean CI (16.5 cM) of the QTLs used. Seventy-seven (77) of these MQTLs were also verified with the results of recent genome-wide association studies (GWAS). These MQTLs included seven MQTLs that are particularly useful for breeding purposes (we called them Breeders’ MQTLs). Seven ortho-MQTLs between wheat and rice genomes were also identified using synteny and collinearity. The MQTLs were used for the identification of 1,704 candidate genes (CGs). In silico expression analysis of these CGs permitted identification of 182 differentially expressed genes (DEGs), which included 36 high-confidence candidate genes (CGs) with known functions previously reported to be important for thermotolerance. These high confidence CGs encoded proteins belonging to the following families: protein kinase, WD40 repeat, glycosyltransferase, ribosomal protein, SNARE associated Golgi protein, GDSL lipase/esterase, SANT/Myb domain, K homology domain, etc. Thus, the present study resulted in the identification of MQTLs (including breeders’ MQTLs), ortho-MQTLs, and underlying CGs, which could prove useful not only for molecular breeding for the development of thermotolerant wheat cultivars but also for future studies focused on understanding the molecular basis of thermotolerance.

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“…For the loci on chromosome 5A (383.4–385.0 Mb and 595.4–597.7 Mb), candidate genes ( TraesCS5A01G182500 and TraesCS5A01G406800 ) for F-box proteins were identified. F-box proteins play crucial roles in cell-cycle progression, transcriptional regulation, flower formation, signal transduction, and many other cellular processes ( El-Sharkawy et al, 2021 ; Guérin et al, 2021 ). Of these, a cytokinin riboside 5′-monophosphate phosphoribohydrolase ( TraesCS1A01G362500 ) was identified in the LD decay of the loci on chromosome 1A (556.0–587.4 Mb).…”

Section: Discussionmentioning

confidence: 99%

Genetic analysis of morphological traits in spring wheat from the Northeast of China by a genome-wide association study

et al. 2022

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Identification of the gene for agronomic traits is important for the wheat marker-assisted selection (MAS) breeding. To identify the new and stable loci for agronomic traits, including flag leaf length (FLL), flag leaf width (FLW), uppermost internode length (UIL), and plant morphology (PM, including prostrate, semi-prostrate, and erect). A total of 251 spring wheat accessions collected from the Northeast of China were used to conduct genome-wide association study (GWAS) by 55K SNP arrays. A total of 30 loci for morphological traits were detected, and each explained 4.8–17.9% of the phenotypic variations. Of these, 13 loci have been reported by previous studies, and the other 17 are novel. We have identified seven genes involved in the signal transduction, cell-cycle progression, and plant development pathway as candidate genes. This study provides new insights into the genetic basis of morphological traits. The associated SNPs and accessions with more of favorable alleles identified in this study could be used to promote the wheat breeding progresses.

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The Landscape of the Genomic Distribution and the Expression of the F-Box Genes Unveil Genome Plasticity in Hexaploid Wheat during Grain Development and in Response to Heat and Drought Stress

Cited by 10 publications

References 88 publications

In silico analysis of the Seven IN Absentia (SINA) genes in bread wheat sheds light on their structure in plants

In silico analysis of the Seven IN Absentia (SINA) genes in bread wheat sheds light on their structure in plants

Meta-QTLs, ortho-MQTLs and candidate genes for thermotolerance in wheat (Triticum aestivum L.)

Genetic analysis of morphological traits in spring wheat from the Northeast of China by a genome-wide association study

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