Contrasting cDNA-AFLP profiles between crown and leaf tissues of cold-acclimated wheat plants indicate differing regulatory circuitries for low temperature tolerance

Ganeshan, S.; Sharma, Pallavi; Young, Lester; Kumar, Ashwani; Fowler, D. B.; Chibbar, Ravindra N.

doi:10.1007/s11103-011-9734-8

Cited by 17 publications

(11 citation statements)

References 98 publications

(123 reference statements)

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“…Although the leaves would have been a more convenient tissue to use, recent experiments have shown that the low-temperature response of the leaves to cold treatment is different from that of the crown at the molecular level [9,20-22]. In overwintering wheat, it is the crown that survives to reestablish the plant roots and leaves in spring following high stress winters when sub-lethal tissue damage has been incurred.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.)

Laudencia‐Chingcuanco¹,

Ganeshan

You

et al. 2011

BMC Genomics

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BackgroundTo identify the genes involved in the development of low temperature (LT) tolerance in hexaploid wheat, we examined the global changes in expression in response to cold of the 55,052 potentially unique genes represented in the Affymetrix Wheat Genome microarray. We compared the expression of genes in winter-habit (winter Norstar and winter Manitou) and spring-habit (spring Manitou and spring Norstar)) cultivars, wherein the locus for the vernalization gene Vrn-A1 was swapped between the parental winter Norstar and spring Manitou in the derived near-isogenic lines winter Manitou and spring Norstar. Global expression of genes in the crowns of 3-leaf stage plants cold-acclimated at 6°C for 0, 2, 14, 21, 38, 42, 56 and 70 days was examined.ResultsAnalysis of variance of gene expression separated the samples by genetic background and by the developmental stage before or after vernalization saturation was reached. Using gene-specific ANOVA we identified 12,901 genes (at p < 0.001) that change in expression with respect to both genotype and the duration of cold-treatment. We examined in more detail a subset of these genes (2,771) where expression was highly influenced by the interaction between these two main factors. Functional assignments using GO annotations showed that genes involved in transport, oxidation-reduction, and stress response were highly represented. Clustering based on the pattern of transcript accumulation identified genes that were up or down-regulated by cold-treatment. Our data indicate that the cold-sensitive lines can up-regulate known cold-responsive genes comparable to that of cold-hardy lines. The levels of expression of these genes were highly influenced by the initial rate and the duration of the gene's response to cold. We show that the Vrn-A1 locus controls the duration of gene expression but not its initial rate of response to cold treatment. Furthermore, we provide evidence that Ta.Vrn-A1 and Ta.Vrt1 originally hypothesized to encode for the same gene showed different patterns of expression and therefore are distinct.ConclusionThis study provides novel insight into the underlying mechanisms that regulate the expression of cold-responsive genes in wheat. The results support the developmental model of LT tolerance gene regulation and demonstrate the complex genotype by environment interactions that determine LT adaptation in winter annual cereals.

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Section: Resultsmentioning

confidence: 99%

Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.)

Laudencia‐Chingcuanco¹,

Ganeshan

You

et al. 2011

BMC Genomics

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“…Phenotypic variations in general result from alterations in gene activities; therefore, it is likely that the differentially expressed TDFs formed genetic variations causing natural phenotypic variations. Since genome or transcriptome data are not available for Physalis , cDNA-AFLP technology, which is an efficient method of global transcriptional analysis for any species without a reference transcriptome (Ganeshan et al ., 2011; Yu et al ., 2011; Yang et al , 2012), was exploited to search for genes causing natural variation in the observed organ size. The 263 cloned differentially expressed TDFs have complicated expression patterns and they encode regulatory factors, protein kinases, protein phosphatase, and various enzymes, which contribute to the complexity of the genetic basis for the different floral phenotypes.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome-wide mining of the differentially expressed transcripts for natural variation of floral organ size in Physalis philadelphica

Wang

2012

Journal of Experimental Botany

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Natural phenotypic variation, a result of genetic variation, developed during evolution in response to environmental selections. Physalis philadelphica, known as tomatillo in the Solanaceae, is rich in floral and post-floral organ size diversity. However, its genetic variation is unknown. Here P. philadelphica was classified into three groups with large, intermediate, and small reproductive organ size, and a positive correlation was observed between floral organ and berry sizes. Through cDNA-amplified fragment length polymorphism (AFLP) analyses, 263 differentially expressed transcript-derived fragments (TDFs) were isolated from two accessions with different floral organ sizes. The genes encode various transcription factors, protein kinases, and enzymes, and they displayed multiple expression patterns during floral development, indicating a complexity in the genetic basis of phenotypic variation. Detailed expression analyses revealed that they were differentially expressed during floral and post-floral development, implying that they have roles in the development of flowers and fruits. Expression of three genes was further monitored in 26 accessions, and in particular the expression variation of Pp30, encoding an AP2-like transcription factor, correlates well with the observed phenotypic variations, which strongly supports an essential role for the gene in the natural variation of floral and post-floral organ size in Physalis. The results suggest that alteration in the expression pattern of a few key regulatory genes in the developmental process may be an important source of genetic variations that lead to natural variation in morphological traits.

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“…From a gene expression perspective, it has been shown that cold acclimation is associated with the significant upregulation or downregulation of hundreds to thousands of wheat genes (Gulick et al 2005; Monroy et al 2007; Laudencia-Chingcuanco et al 2011; Ganeshan et al 2011; Winfield et al 2009, 2010). Additional genes respond when acclimated plants are exposed to freezing temperatures (Herman et al 2006; Skinner 2009, 2015), leading to greater tolerance of subsequent, potentially damaging freezing events (Herman et al 2006; Skinner and Bellinger 2010).…”

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Genomic Regions Associated with Tolerance to Freezing Stress and Snow Mold in Winter Wheat

Kruse

Carle

Wen

et al. 2017

G3 Genes|Genomes|Genetics

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Plants grown through the winter are subject to selective pressures that vary with each year’s unique conditions, necessitating tolerance of numerous abiotic and biotic stress factors. The objective of this study was to identify molecular markers in winter wheat (Triticum aestivum L.) associated with tolerance of two of these stresses, freezing temperatures and snow mold—a fungal disease complex active under snow cover. A population of 155 F2:5 recombinant inbred lines from a cross between soft white wheat cultivars “Finch” and “Eltan” was evaluated for snow mold tolerance in the field, and for freezing tolerance under controlled conditions. A total of 663 molecular markers was used to construct a genetic linkage map and identify marker-trait associations. One quantitative trait locus (QTL) associated with both freezing and snow mold tolerance was identified on chromosome 5A. A second, distinct, QTL associated with freezing tolerance also was found on 5A, and a third on 4B. A second QTL associated with snow mold tolerance was identified on chromosome 6B. The QTL on 5A associated with both traits was closely linked with the Fr-A2 (Frost-Resistance A2) locus; its significant association with both traits may have resulted from pleiotropic effects, or from greater low temperature tolerance enabling the plants to better defend against snow mold pathogens. The QTL on 4B associated with freezing tolerance, and the QTL on 6B associated with snow mold tolerance have not been reported previously, and may be useful in the identification of sources of tolerance for these traits.

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Contrasting cDNA-AFLP profiles between crown and leaf tissues of cold-acclimated wheat plants indicate differing regulatory circuitries for low temperature tolerance

Cited by 17 publications

References 98 publications

Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.)

Genome-wide gene expression analysis supports a developmental model of low temperature tolerance gene regulation in wheat (Triticum aestivum L.)

Transcriptome-wide mining of the differentially expressed transcripts for natural variation of floral organ size in Physalis philadelphica

Genomic Regions Associated with Tolerance to Freezing Stress and Snow Mold in Winter Wheat

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