Limits...
Identification of rice transcription factors associated with drought tolerance using the Ecotilling method.

Yu S, Liao F, Wang F, Wen W, Li J, Mei H, Luo L - PLoS ONE (2012)

Bottom Line: The results showed that three genes were associated with the DT index and that five genes were associated with the DT level.The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites.The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits.

View Article: PubMed Central - PubMed

Affiliation: Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, China.

ABSTRACT
The drought tolerance (DT) of plants is a complex quantitative trait. Under natural and artificial selection, drought tolerance represents the crop survival ability and production capacity under drought conditions (Luo, 2010). To understand the regulation mechanism of varied drought tolerance among rice genotypes, 95 diverse rice landraces or varieties were evaluated within a field screen facility based on the 'line-source soil moisture gradient', and their resistance varied from extremely resistant to sensitive. The method of Ecotype Targeting Induced Local Lesions in Genomes (Ecotilling) was used to analyze the diversity in the promoters of 24 transcription factor families. The bands separated by electrophoresis using Ecotilling were converted into molecular markers. STRUCTURE analysis revealed a value of K = 2, namely, the population with two subgroups (i.e., indica and japonica), which coincided very well with the UPGMA clusters (NTSYS-pc software) using distance-based analysis and InDel markers. Then the association analysis between the promoter diversity of these transcription factors and the DT index/level of each variety was performed. The results showed that three genes were associated with the DT index and that five genes were associated with the DT level. The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites. The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits.

Show MeSH
Sequence complexity of associated genes from five varieties.Black lines represent an insertion. Broken lines represent the repeat of the insertion. The arrows indicate that one or more than one site of cis-acting regulatory DNA elements were inserted into the promoters. The abscissa represents the distance to the transcription start sites.
© Copyright Policy
Related In: Results  -  Collection


getmorefigures.php?uid=PMC3278407&req=5

pone-0030765-g003: Sequence complexity of associated genes from five varieties.Black lines represent an insertion. Broken lines represent the repeat of the insertion. The arrows indicate that one or more than one site of cis-acting regulatory DNA elements were inserted into the promoters. The abscissa represents the distance to the transcription start sites.

Mentions: The promoters of 8 genes associated with drought resistance in 5 varieties were sequenced. Regions of approximately 1 kb upstream of the transcription initiation sites were a high-incidence area of sequence polymorphisms (Figure 3). Among them, insertions of more than 50 bp occurred in the promoters of three genes (OsALF11, OsAE128 and OsZIM14 (Figure 3). There was a 58 bp repeat insertion in front of the transcription initiation site of the OsALF11 gene in Huhan3. PLACE analysis (http://www.dna.affrc.go.jp/PLACE) revealed that the sequence polymorphism altered the plant cis-acting regulatory DNA elements. Compared to Shenshuidao1, a cauliflower mosaic virus 35S site (TCTCTCTCT) was appended in the insertion fragment of the promoter of the OsALF11 gene in Huhan3. Then the site was moved to the −77 position in front of the transcription initiation site, while the site in other varieties was proximal to the transcription initiation site (Figure 3). In the OsAE128 and OsZIM14 genes, large fragment insertions also altered the binding sites of the transcription factors (Figure 3). Variations in cis-elements in associated genes from Huhan3 tended to enrich more stress-related cis-elements. For example, an ABRELATERD1 factor was located upstream of OsAE115 in Huhan3, which was induced by dehydration stress and dark-induced senescence [33]. In addition, more than one ARFAT factor was appended upstream of OsGRF8 in Huhan3, which was responsive to ABA and auxin [34]. An ELRECOREPCRP1 factor was found in the OsGRF5 promoter of Huhan3, which was involved in pathogen- and wound-induced signaling [35]. A new CBFHV factor and a GT1GMSCAM4 factor were added to the promoter of the OsNFYB12 gene, which was related to cold- or pathogen- and NaCl-induced expression [36], [37].


Identification of rice transcription factors associated with drought tolerance using the Ecotilling method.

Yu S, Liao F, Wang F, Wen W, Li J, Mei H, Luo L - PLoS ONE (2012)

Sequence complexity of associated genes from five varieties.Black lines represent an insertion. Broken lines represent the repeat of the insertion. The arrows indicate that one or more than one site of cis-acting regulatory DNA elements were inserted into the promoters. The abscissa represents the distance to the transcription start sites.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3278407&req=5

pone-0030765-g003: Sequence complexity of associated genes from five varieties.Black lines represent an insertion. Broken lines represent the repeat of the insertion. The arrows indicate that one or more than one site of cis-acting regulatory DNA elements were inserted into the promoters. The abscissa represents the distance to the transcription start sites.
Mentions: The promoters of 8 genes associated with drought resistance in 5 varieties were sequenced. Regions of approximately 1 kb upstream of the transcription initiation sites were a high-incidence area of sequence polymorphisms (Figure 3). Among them, insertions of more than 50 bp occurred in the promoters of three genes (OsALF11, OsAE128 and OsZIM14 (Figure 3). There was a 58 bp repeat insertion in front of the transcription initiation site of the OsALF11 gene in Huhan3. PLACE analysis (http://www.dna.affrc.go.jp/PLACE) revealed that the sequence polymorphism altered the plant cis-acting regulatory DNA elements. Compared to Shenshuidao1, a cauliflower mosaic virus 35S site (TCTCTCTCT) was appended in the insertion fragment of the promoter of the OsALF11 gene in Huhan3. Then the site was moved to the −77 position in front of the transcription initiation site, while the site in other varieties was proximal to the transcription initiation site (Figure 3). In the OsAE128 and OsZIM14 genes, large fragment insertions also altered the binding sites of the transcription factors (Figure 3). Variations in cis-elements in associated genes from Huhan3 tended to enrich more stress-related cis-elements. For example, an ABRELATERD1 factor was located upstream of OsAE115 in Huhan3, which was induced by dehydration stress and dark-induced senescence [33]. In addition, more than one ARFAT factor was appended upstream of OsGRF8 in Huhan3, which was responsive to ABA and auxin [34]. An ELRECOREPCRP1 factor was found in the OsGRF5 promoter of Huhan3, which was involved in pathogen- and wound-induced signaling [35]. A new CBFHV factor and a GT1GMSCAM4 factor were added to the promoter of the OsNFYB12 gene, which was related to cold- or pathogen- and NaCl-induced expression [36], [37].

Bottom Line: The results showed that three genes were associated with the DT index and that five genes were associated with the DT level.The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites.The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits.

View Article: PubMed Central - PubMed

Affiliation: Shanghai Agrobiological Gene Center, Shanghai Academy of Agricultural Sciences, Shanghai, China.

ABSTRACT
The drought tolerance (DT) of plants is a complex quantitative trait. Under natural and artificial selection, drought tolerance represents the crop survival ability and production capacity under drought conditions (Luo, 2010). To understand the regulation mechanism of varied drought tolerance among rice genotypes, 95 diverse rice landraces or varieties were evaluated within a field screen facility based on the 'line-source soil moisture gradient', and their resistance varied from extremely resistant to sensitive. The method of Ecotype Targeting Induced Local Lesions in Genomes (Ecotilling) was used to analyze the diversity in the promoters of 24 transcription factor families. The bands separated by electrophoresis using Ecotilling were converted into molecular markers. STRUCTURE analysis revealed a value of K = 2, namely, the population with two subgroups (i.e., indica and japonica), which coincided very well with the UPGMA clusters (NTSYS-pc software) using distance-based analysis and InDel markers. Then the association analysis between the promoter diversity of these transcription factors and the DT index/level of each variety was performed. The results showed that three genes were associated with the DT index and that five genes were associated with the DT level. The sequences of these associated genes are complex and variable, especially at approximately 1000 bp upstream of the transcription initiation sites. The study illuminated that association analysis aimed at Ecotilling diversity of natural groups could facilitate the isolation of rice genes related to complex quantitative traits.

Show MeSH