Dataset Information

The fate of drought-related genes after polyploidization in Arachis hypogaea cv. Tifrunner.

ABSTRACT: Drought stress affects plant growth and development. Cultivated peanut (Arachis hypogaea) was formed by a cross between A. duranensis and A. ipaensis. The drought tolerance of A. duranensis and A. ipaensis is reportedly stronger than that of cultivated peanut. However, there has been little study of drought tolerance genes in Arachis. In this study, we compared drought tolerance genes between A. hypogaea cv. Tifrunner and its diploid donors. We have observed that polyploidization does not generate more drought tolerance genes in A. hypogaea cv. Tifrunner but promotes the loss of many ancient drought tolerance genes. Although putative drought tolerance genes occurred on gene duplication events in A. hypogaea cv. Tifrunner, most copies lacked drought tolerance. These findings suggest that the loss of drought tolerance genes in A. hypogaea cv. Tifrunner could possibly result in weaker drought tolerance. In addition, we have observed that the three Arachis species stochastically lost putative drought tolerance genes. The evolution of drought tolerance genes could possibly have correlated with environmental changes. Our results enhance the current understanding of drought tolerance and polyploidy evolution in Arachis species.

Supplementary information

The online version contains supplementary material available at 10.1007/s12298-022-01198-0.

SUBMITTER: Zhang Y

PROVIDER: S-EPMC9334475 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature

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The fate of drought-related genes after polyploidization in Arachis hypogaea cv. Tifrunner.

Zhang Yongli Y Chai Maofeng M Zhang Xiaojun X Yang Guofeng G Yao Xiang X Song Hui H

Physiology and molecular biology of plants : an international journal of functional plant biology 20220613 6

Drought stress affects plant growth and development. Cultivated peanut (Arachis hypogaea) was formed by a cross between A. duranensis and A. ipaensis. The drought tolerance of A. duranensis and A. ipaensis is reportedly stronger than that of cultivated peanut. However, there has been little study of drought tolerance genes in Arachis. In this study, we compared drought tolerance genes between A. hypogaea cv. Tifrunner and its diploid donors. We ha ...[more]

PMID: 35910439

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Project description:BackgroundCultivated peanut (Arachis hypogaea, AABB genome), an allotetraploid from a cross between A. duranensis (AA genome) and A. ipaensis (BB genome), is an important oil and protein crop with released genome and RNA-seq sequence datasets. These datasets provide the molecular foundation for studying gene expression and evolutionary patterns. However, there are no reports on the proteomic data of A. hypogaea cv. Tifrunner, which limits understanding of its gene function and protein level evolution.ResultsThis study sequenced the A. hypogaea cv. Tifrunner leaf and root proteome using the tandem mass tag technology. A total of 4803 abundant proteins were identified. The 364 differentially abundant proteins were estimated by comparing protein abundances between leaf and root proteomes. The differentially abundant proteins enriched the photosystem process. The number of biased abundant homeologs between the two sub-genomes A (87 homeologs in leaf and root) and B (69 and 68 homeologs in leaf and root, respectively) was not significantly different. However, homeologous proteins with biased abundances in different sub-genomes enriched different biological processes. In the leaf, homeologs biased to sub-genome A enriched biosynthetic and metabolic process, while homeologs biased to sub-genome B enriched iron ion homeostasis process. In the root, homeologs with biased abundance in sub-genome A enriched inorganic biosynthesis and metabolism process, while homeologs with biased abundance in sub-genome B enriched organic biosynthesis and metabolism process. Purifying selection mainly acted on paralogs and homeologs. The selective pressure values were negatively correlated with paralogous protein abundance. About 77.42% (24/31) homeologous and 80% (48/60) paralogous protein pairs had asymmetric abundance, and several protein pairs had conserved abundances in the leaf and root tissues.ConclusionsThis study sequenced the proteome of A. hypogaea cv. Tifrunner using the leaf and root tissues. Differentially abundant proteins were identified, and revealed functions. Paralog abundance divergence and homeolog bias abundance was elucidated. These results indicate that divergent abundance caused retention of homologs in A. hypogaea cv. Tifrunner.

Project description:Nitrogen is an important plant nutrient that has a significant role in crop yield. Hence, to fulfill the needs of sustainable agriculture, it is necessary to improve biological nitrogen fixation in leguminous crops. Nod inducing gene families plays a crucial role in the interaction between rhizobia and legumes, leading to biological nitrogen fixation. However, nod inducing genes identification and characterization has not yet been performed in Arachis hypogaea. In this study, identification and genome-wide analysis of nod inducing genes are performed so that to explore their potential functions in the Arachis hypogaea for the first time. Nod genes were comprehensively analyzed by phylogenetic clustering analysis, gene structure determination, detection of conserved motifs, subcellular localization, conserved motifs, cis-acting elements and promoter region analysis. This study identified 42 Nod inducing genes in Arachis hypogaea, their sequences were submitted to NCBI and accession numbers were obtained. Potential involvement of these genes in biological nitrogen fixation has been unraveled, such as, phylogenetic analysis revealed that nod inducing genes evolved independently in Arachis hypogaea, the amino acid structures exhibited 20 highly conserved motifs, the proteins are present at different locations in cells and the gene structures revealed that all the genes are full-length genes with upstream intronic regions. Further, the promoter analysis determined a large number of cis-regulatory elements involved in nodulation. Moreover, this study not only provides identification and characterization of genes underlying developmental and functional stages of nodulation and biological nitrogen fixation but also lays the foundation for further revelation of nod inducing gene family. Besides, identification and structural analysis of these genes in Arachis hypogaea may provide a theoretical basis for the study of evolutionary relationships in future analysis.

Dataset Information

The fate of drought-related genes after polyploidization in Arachis hypogaea cv. Tifrunner.

Supplementary information

Publications

The fate of drought-related genes after polyploidization in <i>Arachis hypogaea</i> cv. Tifrunner.

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