Abstract
Sex form is one of the most important characteristics in papaya cultivation in which hermaphrodite is the preferable form. Self-pollination of H*-TSS No.7, an inbred line derived from a rare X chromosome mutant SR*, produced all-hermaphrodite progeny. The recessive lethal allele controlling the all-hermaphrodite phenomenon was proposed to be the recessive Germination suppressor (gs) locus. This study employed next-generation sequencing technology and genome comparison to identify the candidate Gs gene. One specific gene, monodehydroascorbate reductase 4 (MDAR4) harboring a unique polymorphic 3 bp deletion in H*-TSS No.7 was identified. The function of MDAR4 is known to be involved in the hydrogen peroxide (H2O2) scavenging pathway and is associated with seed germination. Furthermore, MDAR4 showed higher expression in the imbibed seeds than that in the dry seeds indicating its potential role in the seed germination. Perhaps this is the very first report providing the evidences that MDAR4 is the candidate of Gs locus in H*-TSS No.7. In addition, Gs allele-specific markers were developed which would be facilitated for breeding all-hermaphrodite lines.
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Data availability
The raw NGS read of TSS No. 7 genomic sequences are available in DDBJ Sequence Read Archive accession no. DRA009805. The patent of the newly developed gs-allele specific marker is under submission; however, the primers sequence data is available here for the scientific community.
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Acknowledgements
The authors thank Prof. Anne Frary, a native English speaker, for critically reviewing and editing the manuscript.
Funding
This work was partial supported to C.-C. Liu (100AS-1.1.8-SS-X4) and J.-R. Chen (105AS-9.7.2-SS-X1) by grants from Council of Agriculture. This work was also financially supported (in part) to Hsin-Mei Ku (MOST 109-2313-B-005-022-MY3) by the grant the Ministry of Science and Technology (MOST) in Taiwan.
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J.-R.C. and H.M. conceived of the experimental design, performed the experiments, data analysis and original manuscript writing. H.U., N.U. and K.T. conducted for bioformation analysis. C.-Y.L., F.-C.C., S.-W.C., C.-C.L., and C.-T.C. prepared plant materials and NGS sequencing. J.-Y.L. and C.-Y.L. prepared breeding materials and MAS. H.-M.K. is the project supervisor and responsible for conducting the project, manuscript writing and submission. All authors read and approved the final version of the manuscript.
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438_2021_1822_MOESM1_ESM.jpg
Multiple sequence alignment of 3 bp Indel (GGTAGT/GGT) polymorphism within MDAR4 gene among H*-TSS No. 7 and 48 papaya lines (KR699083-KR699130) located in the X chromosome. Arrows indicate tri-nucleotide Indel polymorphic sites. ‘*’ indicates conserved residue and ‘-’ indicate no consensus (JPG 1499 KB).
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Chen, JR., Ueno, H., Matsumura, H. et al. Genomic characterization of a rare Carica papaya X chromosome mutant reveals a candidate monodehydroascorbate reductase 4 gene involved in all-hermaphrodite phenomenon. Mol Genet Genomics 296, 1323–1335 (2021). https://doi.org/10.1007/s00438-021-01822-w
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DOI: https://doi.org/10.1007/s00438-021-01822-w