Transcriptomic Insights into Phenological Development and Cold Tolerance of Wheat Grown in the Field

Li, Qiang; Byrns, Brook; Badawi, Mohamed Yousef; Diallo, Abdoulaye Baniré; Danyluk, Jean; Sarhan, Fathey; Laudencia‐Chingcuanco, Debbie; Zou, Jitao; Fowler, D. B.

doi:10.1104/pp.17.01311

Cited by 41 publications

(49 citation statements)

References 87 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The silencing of VRN2 was consistent with the observation that the expression of VRN2 could be significantly repressed by vernalization 72 . Meanwhile, VRN3 , a homologous gene of Arabidopsis FT that was expressed in leaves and its protein was transported to the shoot apical meristem, was also not detected in young spike in a recent study 57 . The Ppd-D1 gene was expressed higher during the stage when spikelets were differentiated (Fig.…”

Section: Discussionmentioning

confidence: 89%

See 1 more Smart Citation

A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat

Zhao

et al. 2018

Sci Rep

View full text Add to dashboard Cite

Wheat spike development is a coordinated process of cell proliferation and differentiation with distinctive phases and architecture changes. However, the dynamic alteration of gene expression in this process remains enigmatic. Here, we characterized and dissected bread wheat spike into six developmental stages, and used genome-wide gene expression profiling, to investigate the underlying regulatory mechanisms. High gene expression correlations between any two given stages indicated that wheat early spike development is controlled by a small subset of genes. Throughout, auxin signaling increased, while cytokinin signaling decreased. Besides, many genes associated with stress responses highly expressed during the double ridge stage. Among the differentially expressed genes (DEGs), were identified 375 transcription factor (TF) genes, of which some homologs in rice or Arabidopsis are proposed to function in meristem maintenance, flowering time, meristem initiation or transition, floral organ development or response to stress. Gene expression profiling demonstrated that these genes had either similar or distinct expression pattern in wheat. Several genes regulating spike development were expressed in the early spike, of which Earliness per se 3 (Eps-3) was found might function in the initiation of spikelet meristem. Our study helps uncover important genes associated with apical meristem morphology and development in wheat.

show abstract

Section: Discussionmentioning

confidence: 89%

“…According to a recent study, VRN-A1 , VRN-B1 and VRN-D1 corresponded to Traes_5AL_13E2DEC48 , Traes_5BL_5D2D22E67 and Traes_5DL_9CC4EC839 in bread wheat, respectively 57 . The transcriptome analysis result showed that all the three VRN1 genes were highly expressed from KNIV to KNVI (Fig.…”

Section: Resultsmentioning

confidence: 95%

A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat

Zhao

et al. 2018

Sci Rep

View full text Add to dashboard Cite

show abstract

“…For RNA‐Seq analyses, developing crowns of Norstar and Manitou wheat grown under field conditions were collected at five time points in 2010 as described by Li et al (2018). Two biological replicates were collected for each sampling date and immediately frozen in liquid nitrogen and stored at '80°C for analysis.…”

Section: Methodsmentioning

confidence: 99%

Genome‐Wide Identification and Characterization of the Wheat Remorin (TaREM) Family during Cold Acclimation

et al. 2019

Self Cite

View full text Add to dashboard Cite

Core Ideas Twenty different wheat remorin (TaREM) genes were identified and classified into six phylogenetic groups. TaREM gene expression was measured in plants grown under both field and controlled cold conditions and in response to hormone treatment. Twelve TaREM were regulated during cold acclimation in four different tissues (roots, crowns, stems, and leaves). Several TaREM genes are implicated in cold response and tolerance. Eight genes were induced in response to abscisic acid and methyl jasmonate treatment. Remorins (REMs) are plant‐specific proteins that play an essential role in plant–microbe interactions. However, their roles in vernalization and abiotic stress responses remain speculative. Most remorins have a variable proline‐rich N‐half and a more conserved C‐half that is predicted to form coils. A search of the wheat (Triticum aestivum L.) database revealed the existence of 20 different REM genes, which we classified into six groups on the basis of whether they shared a common phylogenetic and structural origin. Analysis of the physical genomic distributions demonstrated that REM genes are dispersed in the wheat genome and have one to seven introns. Promoter analysis of TaREM genes revealed the presence of putative cis‐elements related to diverse functions like development, hormonal regulation, and biotic and abiotic stress responsiveness. Expression levels of TaREM genes were measured in plants grown under field and controlled conditions and in response to hormone treatment. Our analyses revealed that 12 members of the REM family are regulated during cold acclimation in wheat in four different tissues (roots, crowns, stems, and leaves), with the highest expression in roots. Differential gene expression was found between wheat cultivars with contrasting degrees of cold tolerance, suggesting the implication of TaREM genes in cold response and tolerance. Additionally, eight genes were induced in response to abscisic acid and methyl jasmonate treatment. This genome‐wide analysis of TaREM genes provides valuable resources for functional analysis aimed at understanding their role in stress adaptation.

show abstract

“…Similarly, in addition to the WRKY2 transcription factor on Miscanthus LG 11/ S. bicolor chromosome 6, another WRKY locus ( WRKY54 ) was located downstream of marker–trait association UIMiscanthus097991, which aligned to S. bicolor chromosome 8 (Table ). Similar to COR47 within the QTL on Miscanthus LG 8/ S. bicolor chromosome 6, another locus associated with protecting thylakoid membranes was identified, COR314 , which was located 0.07 Mb from UIMiscanthus012595 and aligned to S. bicolor chromosome 9 (Grundy, Stoker, & Carré, ; Li et al, ). Additionally, three marker–trait associations (UIMiscanthus118368 aligned to S. bicolor Chromosome 2, UIMiscanthus017647 aligned to S. bicolor Chromosome 3, and UIMiscanthus005328 aligned to S. bicolor Chromosome 4) were all located within or near MYB transcription factor genes (Table ).…”

Section: Discussionmentioning

confidence: 97%

Winter hardiness of Miscanthus (III): Genome‐wide association and genomic prediction for overwintering ability in Miscanthus sinensis

et al. 2019

View full text Add to dashboard Cite

Overwintering ability is an important selection criterion for Miscanthus breeding in temperate regions. Insufficient overwintering ability of the currently leading Miscanthus biomass cultivar, M. ×giganteus (M×g) ‘1993–1780', in regions where average annual minimum temperatures are −26.1°C (USDA hardiness zone 5) or lower poses a pressing need to develop new cultivars with superior cold tolerance. To facilitate breeding of Miscanthus, this study characterized phenotypic and genetic variation of overwintering ability in an M. sinensis germplasm panel consisting of 564 accessions, evaluated in field trials at three locations in North America and two in Asia. Genome‐wide association (GWA) and genomic prediction analyses were performed. The Korea/N China M. sinensis genetic group is a valuable gene pool for cold tolerance. The Yangtze‐Qinling, Southern Japan, and Northern Japan genetic groups were also potential sources of cold tolerance. A total of 73 marker–trait associations were detected for overwintering ability. Estimated breeding value for overwintering ability based on these 73 markers could explain 55% of the variation for first winter overwintering ability among M. sinensis. Average genomic prediction ability for overwintering ability across 50 fivefold cross‐validations was high (~0.73) after accounting for population structure. Common genomic regions for overwintering ability were detected by GWA analyses and a previous parallel QTL mapping study using three interconnected biparental F1 populations. One QTL on Miscanthus LG 8 encompassed five GWA hits and a known cold‐responsive gene, COR47. The other overwintering ability QTL on Miscanthus LG 11 contained two GWA hits and three known cold stress‐related genes, carboxylesterase 13 (CEX13), WRKY2 transcription factor, and cold shock domain (CSDP1). Miscanthus accessions collected from high latitude locations with cold winters had higher rates of overwintering, and more alleles for overwintering, than accessions collected from southern locations with mild winters.

show abstract

Transcriptomic Insights into Phenological Development and Cold Tolerance of Wheat Grown in the Field

Abstract: All authors contributed to the interpretation of results, read, edited, and approved the manuscript.

Cited by 41 publications

References 87 publications

A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat

A Genome-wide View of Transcriptome Dynamics During Early Spike Development in Bread Wheat

Genome‐Wide Identification and Characterization of the Wheat Remorin (TaREM) Family during Cold Acclimation

Winter hardiness of Miscanthus (III): Genome‐wide association and genomic prediction for overwintering ability in Miscanthus sinensis

Contact Info

Product

Resources

About