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

Laudencia-Chingcuanco D, Ganeshan S, You F, Fowler B, Chibbar R, Anderson O - BMC Genomics (2011)

Bottom Line: 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.Functional assignments using GO annotations showed that genes involved in transport, oxidation-reduction, and stress response were highly represented.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics and Gene Discovery Unit, USDA-ARS WRRC, Albany, CA 94710, USA. debbie.laudencia@ars.usda.gov

ABSTRACT

Background: To 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.

Results: Analysis 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.

Conclusion: This 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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Shoot apex development in winter Norstar and spring Manitou and the near isogenic lines spring Norstar and winter Manitou. Day 0 is the start of vernalization/acclimation at 6°C following 2 d growth at 4°C plus 13 d at 20 to 22°C (15 day pre-treatment). First number in each plate indicates the days the plants were grown at 6°C. Second number (10) indicates that the plants were grown an additional 10 days at 20°C before sampling for dissection e.g., 7 + 10 indicates 7 d at 6°C followed by 10 d at 20°C. Arrow indicates double ridge. The apices of samples that bracket the vegetative to reproductive phase transition for each genotype are shown. A) Manitou 0+10 SAM at stage-5; B) Manitou 7+10 SAM at stage-7; C) Winter Manitou 28+10 SAM at stage 0; D) Winter Manitou 35+10 SAM at early stage-5; E) Spring Norstar 0+10 SAM at stage-2 F) Spring Norstar 7+10 SAM at stage-5; G) Winter Norstar 49+10 SAM at stage-2 H) Winter Norstar 56+10 SAM at stage-5. DR, double ridge, was used as a marker of a reproductive meristem.
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Figure 2: Shoot apex development in winter Norstar and spring Manitou and the near isogenic lines spring Norstar and winter Manitou. Day 0 is the start of vernalization/acclimation at 6°C following 2 d growth at 4°C plus 13 d at 20 to 22°C (15 day pre-treatment). First number in each plate indicates the days the plants were grown at 6°C. Second number (10) indicates that the plants were grown an additional 10 days at 20°C before sampling for dissection e.g., 7 + 10 indicates 7 d at 6°C followed by 10 d at 20°C. Arrow indicates double ridge. The apices of samples that bracket the vegetative to reproductive phase transition for each genotype are shown. A) Manitou 0+10 SAM at stage-5; B) Manitou 7+10 SAM at stage-7; C) Winter Manitou 28+10 SAM at stage 0; D) Winter Manitou 35+10 SAM at early stage-5; E) Spring Norstar 0+10 SAM at stage-2 F) Spring Norstar 7+10 SAM at stage-5; G) Winter Norstar 49+10 SAM at stage-2 H) Winter Norstar 56+10 SAM at stage-5. DR, double ridge, was used as a marker of a reproductive meristem.

Mentions: The changes in the shoot apex morphology in response to cold treatment were also monitored by dissection after seedlings were grown under inductive conditions. As shown in Figure 2, spring Manitou shoot apex developed double ridges, without vernalization treatment, thus, was already competent to flower. However, even though it shares the same vernalization alleles as spring Manitou, double ridge formation was delayed in spring Norstar (Figure 2E), indicating that factors outside of the swapped Vrn-A1 locus are involved in the acceleration of competence to flower. In this instance spring Norstar had a minimum FLN that was greater than spring Manitou, which delayed the vegetative/reproductive transition independent of the vernalization gene. In contrast, the meristem of unvernalized winter habit lines remained in the vegetative stage for the duration of the experiment even when grown under inductive conditions (data not shown). It took about 35 days and 49 days of vernalization for the apical meristem of winter Manitou and winter Norstar, respectively, to reach vernalization saturation (Figure 1A).


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

Laudencia-Chingcuanco D, Ganeshan S, You F, Fowler B, Chibbar R, Anderson O - BMC Genomics (2011)

Shoot apex development in winter Norstar and spring Manitou and the near isogenic lines spring Norstar and winter Manitou. Day 0 is the start of vernalization/acclimation at 6°C following 2 d growth at 4°C plus 13 d at 20 to 22°C (15 day pre-treatment). First number in each plate indicates the days the plants were grown at 6°C. Second number (10) indicates that the plants were grown an additional 10 days at 20°C before sampling for dissection e.g., 7 + 10 indicates 7 d at 6°C followed by 10 d at 20°C. Arrow indicates double ridge. The apices of samples that bracket the vegetative to reproductive phase transition for each genotype are shown. A) Manitou 0+10 SAM at stage-5; B) Manitou 7+10 SAM at stage-7; C) Winter Manitou 28+10 SAM at stage 0; D) Winter Manitou 35+10 SAM at early stage-5; E) Spring Norstar 0+10 SAM at stage-2 F) Spring Norstar 7+10 SAM at stage-5; G) Winter Norstar 49+10 SAM at stage-2 H) Winter Norstar 56+10 SAM at stage-5. DR, double ridge, was used as a marker of a reproductive meristem.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Figure 2: Shoot apex development in winter Norstar and spring Manitou and the near isogenic lines spring Norstar and winter Manitou. Day 0 is the start of vernalization/acclimation at 6°C following 2 d growth at 4°C plus 13 d at 20 to 22°C (15 day pre-treatment). First number in each plate indicates the days the plants were grown at 6°C. Second number (10) indicates that the plants were grown an additional 10 days at 20°C before sampling for dissection e.g., 7 + 10 indicates 7 d at 6°C followed by 10 d at 20°C. Arrow indicates double ridge. The apices of samples that bracket the vegetative to reproductive phase transition for each genotype are shown. A) Manitou 0+10 SAM at stage-5; B) Manitou 7+10 SAM at stage-7; C) Winter Manitou 28+10 SAM at stage 0; D) Winter Manitou 35+10 SAM at early stage-5; E) Spring Norstar 0+10 SAM at stage-2 F) Spring Norstar 7+10 SAM at stage-5; G) Winter Norstar 49+10 SAM at stage-2 H) Winter Norstar 56+10 SAM at stage-5. DR, double ridge, was used as a marker of a reproductive meristem.
Mentions: The changes in the shoot apex morphology in response to cold treatment were also monitored by dissection after seedlings were grown under inductive conditions. As shown in Figure 2, spring Manitou shoot apex developed double ridges, without vernalization treatment, thus, was already competent to flower. However, even though it shares the same vernalization alleles as spring Manitou, double ridge formation was delayed in spring Norstar (Figure 2E), indicating that factors outside of the swapped Vrn-A1 locus are involved in the acceleration of competence to flower. In this instance spring Norstar had a minimum FLN that was greater than spring Manitou, which delayed the vegetative/reproductive transition independent of the vernalization gene. In contrast, the meristem of unvernalized winter habit lines remained in the vegetative stage for the duration of the experiment even when grown under inductive conditions (data not shown). It took about 35 days and 49 days of vernalization for the apical meristem of winter Manitou and winter Norstar, respectively, to reach vernalization saturation (Figure 1A).

Bottom Line: 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.Functional assignments using GO annotations showed that genes involved in transport, oxidation-reduction, and stress response were highly represented.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Genomics and Gene Discovery Unit, USDA-ARS WRRC, Albany, CA 94710, USA. debbie.laudencia@ars.usda.gov

ABSTRACT

Background: To 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.

Results: Analysis 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.

Conclusion: This 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.

Show MeSH