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Genome-wide analysis of homeobox gene family in legumes: identification, gene duplication and expression profiling.

Bhattacharjee A, Ghangal R, Garg R, Jain M - PLoS ONE (2015)

Bottom Line: Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family.Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization.The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development.

View Article: PubMed Central - PubMed

Affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.

ABSTRACT
Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development.

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Differential expression of chickpea homeobox genes under abiotic stress conditions.(A) Heat-map showing differential expression of chickpea homeobox genes under abiotic stress conditions in root and shoot tissues. The scale at the bottom represents log2 fold change, maximum value is displayed as dark red and minimum value is displayed as light green. Gene IDs are given on right side. (B) Real-time PCR analysis to validate the differential expression of representative chickpea homeobox genes during various abiotic stress conditions. The mRNA levels for each candidate gene were calculated relative to its expression in control root or shoot tissues. DS, desiccation stress; SS, salinity stress; CS, cold stress.
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pone.0119198.g006: Differential expression of chickpea homeobox genes under abiotic stress conditions.(A) Heat-map showing differential expression of chickpea homeobox genes under abiotic stress conditions in root and shoot tissues. The scale at the bottom represents log2 fold change, maximum value is displayed as dark red and minimum value is displayed as light green. Gene IDs are given on right side. (B) Real-time PCR analysis to validate the differential expression of representative chickpea homeobox genes during various abiotic stress conditions. The mRNA levels for each candidate gene were calculated relative to its expression in control root or shoot tissues. DS, desiccation stress; SS, salinity stress; CS, cold stress.

Mentions: Crop production is often adversely affected by several abiotic stress factors like desiccation, salinity and extremes of temperatures. Since homeobox genes are known to play an important role in abiotic stress responses, we analyzed the expression profile of chickpea homeobox genes in root and shoot tissues subjected to desiccation, salinity and cold stresses using RNA-seq data [35]. Out of 89 chickpea homeobox genes, 44 were found to be significantly differentially regulated in root and/or shoot tissues subjected to at least one of the abiotic stress conditions. Overall, more number of homeobox genes were up-regulated in root tissues subjected to salinity stress as compared to desiccation and cold stresses. All HD-Zip II members were reasonably up-regulated under salinity stress in root tissues, thereby suggesting their possible role in salinity stress responses (Fig. 6A). However, HD-Zip II genes showed no change in their expression pattern in root tissues under desiccation stress. Highest fold change in root tissue was recorded for Ca_08006, a member of PLINC class, when subjected to salinity stress. Cold stress did not alter the expression level of most homeobox genes. Only a few members showed differential expression in root tissues in response to cold. However, no considerable alteration in transcript levels could be detected in shoot tissues under cold stress. Under desiccation stress, HD-Zip I genes were highly up-regulated in shoot tissues as compared to root tissues (Fig. 6A). Similar observations have been made in Arabidopsis, where transcript levels of HD-Zip I members (ATHB7 and ATHB12) increased tremendously in response to desiccation stress [57]. However, Ca_06148 and Ca_00550 were found to be downregulated in response to all the abiotic stress conditions analyzed in either of the tissues. Highest upregulation in shoot tissue was recorded for Ca_19899, a member of HD-Zip I class, when subjected to desiccation stress. However, this gene was greatly up-regulated during salinity stress as compared to desiccation stress in root tissues (Fig. 6A). It has been reported that a cotton homeobox gene, GhHB1, is specifically expressed in root tissues and gets up-regulated under exogenous salinity treatment [58]. Similarly, differential expression of many homeobox genes during abiotic stress conditions has been reported in various plant species [10,24,35,59]. We performed qRT-PCR analysis of six randomly selected differentially expressed homeobox genes in root and shoot tissues of chickpea during desiccation, salinity and cold stress conditions to validate the results obtained from RNA-seq data (Fig. 6B). The qRT-PCR analysis revealed similar differential expression patterns of all the selected genes as observed in RNA-seq data showing good correlation between the results of qRT-PCR and RNA-seq data analysis. These results suggest that homeobox genes may prove to be suitable candidates for engineering abiotic stress tolerance in crop plants.


Genome-wide analysis of homeobox gene family in legumes: identification, gene duplication and expression profiling.

Bhattacharjee A, Ghangal R, Garg R, Jain M - PLoS ONE (2015)

Differential expression of chickpea homeobox genes under abiotic stress conditions.(A) Heat-map showing differential expression of chickpea homeobox genes under abiotic stress conditions in root and shoot tissues. The scale at the bottom represents log2 fold change, maximum value is displayed as dark red and minimum value is displayed as light green. Gene IDs are given on right side. (B) Real-time PCR analysis to validate the differential expression of representative chickpea homeobox genes during various abiotic stress conditions. The mRNA levels for each candidate gene were calculated relative to its expression in control root or shoot tissues. DS, desiccation stress; SS, salinity stress; CS, cold stress.
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Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4352023&req=5

pone.0119198.g006: Differential expression of chickpea homeobox genes under abiotic stress conditions.(A) Heat-map showing differential expression of chickpea homeobox genes under abiotic stress conditions in root and shoot tissues. The scale at the bottom represents log2 fold change, maximum value is displayed as dark red and minimum value is displayed as light green. Gene IDs are given on right side. (B) Real-time PCR analysis to validate the differential expression of representative chickpea homeobox genes during various abiotic stress conditions. The mRNA levels for each candidate gene were calculated relative to its expression in control root or shoot tissues. DS, desiccation stress; SS, salinity stress; CS, cold stress.
Mentions: Crop production is often adversely affected by several abiotic stress factors like desiccation, salinity and extremes of temperatures. Since homeobox genes are known to play an important role in abiotic stress responses, we analyzed the expression profile of chickpea homeobox genes in root and shoot tissues subjected to desiccation, salinity and cold stresses using RNA-seq data [35]. Out of 89 chickpea homeobox genes, 44 were found to be significantly differentially regulated in root and/or shoot tissues subjected to at least one of the abiotic stress conditions. Overall, more number of homeobox genes were up-regulated in root tissues subjected to salinity stress as compared to desiccation and cold stresses. All HD-Zip II members were reasonably up-regulated under salinity stress in root tissues, thereby suggesting their possible role in salinity stress responses (Fig. 6A). However, HD-Zip II genes showed no change in their expression pattern in root tissues under desiccation stress. Highest fold change in root tissue was recorded for Ca_08006, a member of PLINC class, when subjected to salinity stress. Cold stress did not alter the expression level of most homeobox genes. Only a few members showed differential expression in root tissues in response to cold. However, no considerable alteration in transcript levels could be detected in shoot tissues under cold stress. Under desiccation stress, HD-Zip I genes were highly up-regulated in shoot tissues as compared to root tissues (Fig. 6A). Similar observations have been made in Arabidopsis, where transcript levels of HD-Zip I members (ATHB7 and ATHB12) increased tremendously in response to desiccation stress [57]. However, Ca_06148 and Ca_00550 were found to be downregulated in response to all the abiotic stress conditions analyzed in either of the tissues. Highest upregulation in shoot tissue was recorded for Ca_19899, a member of HD-Zip I class, when subjected to desiccation stress. However, this gene was greatly up-regulated during salinity stress as compared to desiccation stress in root tissues (Fig. 6A). It has been reported that a cotton homeobox gene, GhHB1, is specifically expressed in root tissues and gets up-regulated under exogenous salinity treatment [58]. Similarly, differential expression of many homeobox genes during abiotic stress conditions has been reported in various plant species [10,24,35,59]. We performed qRT-PCR analysis of six randomly selected differentially expressed homeobox genes in root and shoot tissues of chickpea during desiccation, salinity and cold stress conditions to validate the results obtained from RNA-seq data (Fig. 6B). The qRT-PCR analysis revealed similar differential expression patterns of all the selected genes as observed in RNA-seq data showing good correlation between the results of qRT-PCR and RNA-seq data analysis. These results suggest that homeobox genes may prove to be suitable candidates for engineering abiotic stress tolerance in crop plants.

Bottom Line: Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family.Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization.The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development.

View Article: PubMed Central - PubMed

Affiliation: Functional and Applied Genomics Laboratory, National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi, India.

ABSTRACT
Homeobox genes encode transcription factors that are known to play a major role in different aspects of plant growth and development. In the present study, we identified homeobox genes belonging to 14 different classes in five legume species, including chickpea, soybean, Medicago, Lotus and pigeonpea. The characteristic differences within homeodomain sequences among various classes of homeobox gene family were quite evident. Genome-wide expression analysis using publicly available datasets (RNA-seq and microarray) indicated that homeobox genes are differentially expressed in various tissues/developmental stages and under stress conditions in different legumes. We validated the differential expression of selected chickpea homeobox genes via quantitative reverse transcription polymerase chain reaction. Genome duplication analysis in soybean indicated that segmental duplication has significantly contributed in the expansion of homeobox gene family. The Ka/Ks ratio of duplicated homeobox genes in soybean showed that several members of this family have undergone purifying selection. Moreover, expression profiling indicated that duplicated genes might have been retained due to sub-functionalization. The genome-wide identification and comprehensive gene expression profiling of homeobox gene family members in legumes will provide opportunities for functional analysis to unravel their exact role in plant growth and development.

Show MeSH