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Genome-wide survey and expression analysis of F-box genes in chickpea.

Gupta S, Garg V, Kant C, Bhatia S - BMC Genomics (2015)

Bottom Line: Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis.Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India. shefaligupta.14@gmail.com.

ABSTRACT

Background: The F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. However, little is known about the F-box genes in the important legume crop, chickpea. The available draft genome sequence of chickpea allowed us to conduct a genome-wide survey of the F-box gene family in chickpea.

Results: A total of 285 F-box genes were identified in chickpea which were classified based on their C-terminal domain structures into 10 subfamilies. Thirteen putative novel motifs were also identified in F-box proteins with no known functional domain at their C-termini. The F-box genes were physically mapped on the 8 chickpea chromosomes and duplication events were investigated which revealed that the F-box gene family expanded largely due to tandem duplications. Phylogenetic analysis classified the chickpea F-box genes into 9 clusters. Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis. Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.

Conclusions: The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

Show MeSH
Relative expression levels of F-box genes in different chickpea tissues. Total RNA was extracted from seed, flower, leaf and root. For each gene, the relative expression levels were obtained by normalization with chickpea EF1α. The error bars indicate standard deviations.
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Fig7: Relative expression levels of F-box genes in different chickpea tissues. Total RNA was extracted from seed, flower, leaf and root. For each gene, the relative expression levels were obtained by normalization with chickpea EF1α. The error bars indicate standard deviations.

Mentions: To validate the expression patterns, several candidate genes were selected for quantitative RT-PCR (Figure 7). The transcript accumulation patterns were analysed in root, leaf, flower and seed of chickpea. The results were fairly similar to the RPKM data. For example, Ca_12512 showed preferential expression in root. Ca_06676 showed predominant transcript accumulation in seed and flower while Ca_02030 expressed ubiquitously in all the tissues with comparatively less expression in leaf.Figure 7


Genome-wide survey and expression analysis of F-box genes in chickpea.

Gupta S, Garg V, Kant C, Bhatia S - BMC Genomics (2015)

Relative expression levels of F-box genes in different chickpea tissues. Total RNA was extracted from seed, flower, leaf and root. For each gene, the relative expression levels were obtained by normalization with chickpea EF1α. The error bars indicate standard deviations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4340835&req=5

Fig7: Relative expression levels of F-box genes in different chickpea tissues. Total RNA was extracted from seed, flower, leaf and root. For each gene, the relative expression levels were obtained by normalization with chickpea EF1α. The error bars indicate standard deviations.
Mentions: To validate the expression patterns, several candidate genes were selected for quantitative RT-PCR (Figure 7). The transcript accumulation patterns were analysed in root, leaf, flower and seed of chickpea. The results were fairly similar to the RPKM data. For example, Ca_12512 showed preferential expression in root. Ca_06676 showed predominant transcript accumulation in seed and flower while Ca_02030 expressed ubiquitously in all the tissues with comparatively less expression in leaf.Figure 7

Bottom Line: Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis.Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

View Article: PubMed Central - PubMed

Affiliation: National Institute of Plant Genome Research, Aruna Asaf Ali Marg, Post Box No. 10531, New Delhi, 110067, India. shefaligupta.14@gmail.com.

ABSTRACT

Background: The F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. However, little is known about the F-box genes in the important legume crop, chickpea. The available draft genome sequence of chickpea allowed us to conduct a genome-wide survey of the F-box gene family in chickpea.

Results: A total of 285 F-box genes were identified in chickpea which were classified based on their C-terminal domain structures into 10 subfamilies. Thirteen putative novel motifs were also identified in F-box proteins with no known functional domain at their C-termini. The F-box genes were physically mapped on the 8 chickpea chromosomes and duplication events were investigated which revealed that the F-box gene family expanded largely due to tandem duplications. Phylogenetic analysis classified the chickpea F-box genes into 9 clusters. Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis. Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.

Conclusions: The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.

Show MeSH