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Genome-wide comparative transcriptome analysis of the A4-CMS line ICPA 2043 and its maintainer ICPB 2043 during the floral bud development of pigeonpea

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Abstract

Cytoplasmic male sterility (CMS) offers a unique system to understand cytoplasmic nuclear crosstalk, and is also employed for exploitation of hybrid vigor in various crops. Pigeonpea A4-CMS, a predominant source of male sterility, is being used for efficient hybrid seed production. The molecular mechanisms of CMS trait remain poorly studied in pigeonpea. We performed genome-wide transcriptome profiling of A4-CMS line ICPA 2043 and its isogenic maintainer ICPB 2043 at two different stages of floral bud development (stage S1 and stage S2). Consistent with the evidences from some other crops, we also observed significant difference in the expression levels of genes in the later stage, i.e., stage S2. Differential expression was observed for 143 and 55 genes within the two stages of ICPA 2043 and ICPB 2043, respectively. We obtained only 10 differentially expressed genes (DEGs) between the stage S1 of the two genotypes, whereas expression change was significant for 582 genes in the case of stage S2. The qRT-PCR assay of randomly selected six genes supported the differential expression of genes between ICPA 2043 and ICPB 2043. Further, GO and KEGG pathway mapping suggested a possible compromise in key bioprocesses during flower and pollen development. Besides providing novel insights into the functional genomics of CMS trait, our results were in strong agreement with the gene expression atlas of pigeonpea that implicated various candidate genes like sucrose-proton symporter 2 and an uncharacterized protein along with pectate lyase, pectinesterase inhibitors, l-ascorbate oxidase homolog, ATPase, β-galactosidase, polygalacturonase, and aldose 1-epimerase for pollen development of pigeonpea. The dataset presented here provides a rich genomic resource to improve understanding of CMS trait and its deployment in heterosis breeding in pigeonpea.

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Acknowledgements

AB acknowledges support from Centre for Agricultural Bioinformatics (CABin: AGENIASRICOP201501000047) scheme of Indian Council of Agricultural Research (ICAR), New Delhi.

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Authors and Affiliations

  1. ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur, 208024, India

    Abhishek Bohra, S. J. Satheesh Naik, Dibendu Dutta, Indra P. Singh, Farindra Singh, Meenal Rathore & Narendra P. Singh

  2. International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India

    Abhishek Rathore, Prasad Gandham, Rachit K. Saxena & Rajeev K. Varshney

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  1. Abhishek Bohra
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  2. Abhishek Rathore
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Contributions

AB conceptualized the idea and planned the experiments. AB, RKS, SNSJ, DD, and MR carried out the experiments. AR, PG, and AB performed the analysis and interpretation. AB prepared the original draft with support from PG, AT, MR, RKS, RKV, and NPS. FS and IPS contributed to field experimentation and sampling. RKV and NPS reviewed and edited the manuscript. All authors have read and approved the final manuscript.

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Correspondence to Abhishek Bohra.

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Supplementary Information

Supplementary Table 1

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Supplementary Table 2

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Supplementary Table 3

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Supplementary Figure 1

Sample-to-sample distance matrix. The image presents the relationships among biological replicates of the two stages (S1 and S2) and the two genotypes (ICPA 2043 and ICPB 2043B). (PNG 10 kb)

Supplementary Figure 2

The GO enrichment analysis using BiNGO. Enrichment of genes down-regulated in stage S2 of ICPB 2043 in comparison to stage S2 of ICPA 2043 in “Biological process” is shown. The colour depth and size of the nodes refer to the corrected p-values and genes corresponding to the ontologies. Significance threshold of 0.05 is considered. (PNG 1862 kb)

Supplementary Figure 3

KEGG pathway mapping of DEGs. As an example, enrichment of up-regulated genes (in stage 2 of ICPB 2043 in comparison to stage 2 of ICPA 2043) in “Metabolic pathways” is shown. Majority of the DEGs in the current dataset were associated with “Metabolic pathways”. (PNG 2429 kb)

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Bohra, A., Rathore, A., Gandham, P. et al. Genome-wide comparative transcriptome analysis of the A4-CMS line ICPA 2043 and its maintainer ICPB 2043 during the floral bud development of pigeonpea. Funct Integr Genomics 21, 251–263 (2021). https://doi.org/10.1007/s10142-021-00775-y

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