Identifying citrus self-incompatibility genotypes (S-genotypes) and discovering self-compatible mutants

Abstract

Utilizing 32 previously identified S ribonuclease ( S- RNase) gene sequences and abundant citrus resources, this study designed specific primers for 10 S- RNase genes. A total of 32 pairs of primers were used to analyze the self-incompatibility genotypes ( S-genotypes) of 241 citrus resources, encompassing 105 mandarins, 47 pummelos, 69 oranges, and 20 lemons and citrons. These results provide theoretical guidance for parent selection in production and breeding programs. Among the 215 samples analyzed, two normal S-genotypes were identified, while no S-genotypes were detected in three samples. Notably, 21 samples, primarily citrons, exhibited amplification of only one S-genotype. Additionally, two pummelo samples showed amplification of three S-genotypes each. The integration of S-genotype and selfing phenotype identification revealed five newly discovered self-compatible mutated materials: Changsha ‘Shatian’ pummelo, large-fruited red pummelo, slender leaf ‘Mangshanyegan’, ‘Shatangju’, and W. Murcott. These findings provide valuable resources for investigating the self-compatibility mechanism in citrus.

Keywords

Citrus / Self-incompatibility / S-genotype; self-compatibility mutation

References

[1]	Aguiar B, Vieira J, Cunha AE, Fonseca NA, Reboiro-Jato D, Reboiro-Jato M, et al. Patterns of evolution at the gametophytic self-incompatibility Sorbus aucuparia (Pyrinae) S pollen genes support the non-self recognition by multiple factors model. J Exp Bot. 2013;64:2423–34. https://doi.org/10.1093/jxb/ert098.
[2]	Chai L, Biswas MK, Ge X, Deng X. Isolation, characterization, and expression analysis of an SKP1-like gene from ‘Shatian’ Pummelo (Citrus grandis Osbeck). Plant Mol Biol Rep. 2010;28:569–77. https://doi.org/10.1007/s11105-010-0184-2.
[3]	Chai L, Ge X, Xu Q, Deng X. CgSL2, an S-like RNase gene in ‘Zigui shatian’ pummelo (Citrus grandis Osbeck), is involved in ovary senescence. Mol Biol Rep. 2011;38:1–8. https://doi.org/10.1007/s11033-010-0070-x.
[4]	Cheng Y, De Vicente MC, Meng H, Guo W, Tao N, Deng X. A set of primers for analyzing chloroplast DNA diversity in citrus and related genera. Tree Physiol. 2005;25:661–72. https://doi.org/10.1093/treephys/25.6.661.
[5]	De Nettancourt D. Incompatibility in angiosperms. Sex Plant Reprod. 1997;10:185–99. https://doi.org/10.1007/s004970050087.
[6]	Emerson S. A preliminary survey of the oenothera organensis population. Genetics. 1939;24:524–37. https://doi.org/10.1093/genetics/24.4.524.
[7]	Foote HCC, Ride JP, Franklin-Tong VE, Walker EA, Lawrence MJ, Franklin FCH. Cloning and expression of a distinctive class of self-incompatibility (S) gene from Papaver rhoeas L. Proc Natl Acad Sci USA. 1994;91:2265–9. https://doi.org/10.1073/pnas.91.6.2265.
[8]	Honsho C, Ushijima K, Anraku M, Ishimura S, Yu Q, Gmitter FG, et al. Association of T2/S-RNase with self-incompatibility of Japanese citrus accessions examined by transcriptomic, phylogenetic, and genetic approaches. Front Plant Sci. 2021;12:638321. https://doi.org/10.3389/fpls.2021.638321.
[9]	Hu J, Xu Q, Liu C, Liu B, Deng C, Chen C, et al. Downregulated expression of S(2)-RNase attenuates self-incompatibility in “Guiyou No. 1” pummelo. Hortic Res. 2021;8:199. https://doi.org/10.1038/s41438-021-00634-8.
[10]	Hu J, Liu C, Du Z, Guo F, Song D, Wang N, et al. Transposable elements cause the loss of self-incompatibility in citrus. Plant Biotechnol J. 2023;12:1113–31. https://doi.org/10.1111/pbi.14250.
[11]	Huang S, Lee HS, Karunanandaa B, Kao TH. Ribonuclease activity of Petunia inflata S proteins is essential for rejection of self-pollen. Plant Cell. 1994;6:1021–8. https://doi.org/10.1105/tpc.6.7.1021.
[12]	Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9. https://doi.org/10.1093/molbev/msy096.
[13]	Liang M, Yang W, Su S, Fu L, Yi H, Chen C, et al. Genome-wide identification and functional analysis of S-RNase involved in the self-incompatibility of citrus. Mol Genet Genomics. 2017;292:325–41. https://doi.org/10.1007/s00438-016-1279-8.
[14]	Liang M, Cao Z, Zhu A, Liu Y, Tao M, Yang H, et al. Evolution of self-compatibility by a mutant S(m)-RNase in citrus. Nat Plants. 2020;6:131–42. https://doi.org/10.1038/s41477-020-0597-3.
[15]	Long S, Li M, Han Z, Wang K, Li T. Characterization of three new S-alleles and development of an S-allele-specific PCR system for rapidly identifying the S-genotype in apple cultivars. Tree Genet Genomes. 2010;6:161–8. https://doi.org/10.1007/s11295-009-0237-6.
[16]	Sassa H, Hirano H, Nishio T, Koba T. Style-specific self-compatible mutation caused by deletion of the S-RNase gene in Japanese pear (Pyrus serotina). Plant J. 1997;12:223–7. https://doi.org/10.1046/j.1365-313X.1997.12010223.x.
[17]	Stein JC, Howlett B, Boyes DC, Nasrallah ME, Nasrallah JB. Molecular cloning of a putative receptor protein kinase gene encoded at the self-incompatibility locus of Brassica oleracea. Proc Natl Acad Sci USA. 1991;88:8816–20. https://doi.org/10.1073/pnas.88.19.8816.
[18]	Takayama S, Isogai A. Self-incompatibility in plants. Annu Rev Plant Biol. 2005;56:467–89. https://doi.org/10.1146/annurev.arplant.56.032604.144249.
[19]	Takayama S, Shiba H, Iwano M, Shimosato H, Che FS, Kai N, et al. The pollen determinant of self-incompatibility in brassica campestris. Proc Natl Acad Sci USA. 2000;97:1920–5. https://doi.org/10.1073/pnas.040556397.
[20]	Verdoodt L, Van Haute A, Goderis IJ, De Witte K, Keulemans J, Broothaerts W. Use of the multi-allelic self-incompatibility gene in apple to assess homozygocity in shoots obtained through haploid induction. Theor Appl Genet. 1998;96:294–300. https://doi.org/10.1007/s001220050739.
[21]	Wei Z, Wei S, Chen P, Hu J, Tang Y, Ye J, et al. Identification of self-incompatibility genotypes (S-genotypes) of 63 pummelo germplasm resources. Acta Hortic Sin. 2022;49:1111–20. https://www.ahs.ac.cn/CN/10.16420/j.issn.0513-353x.2021-0260.
[22]	Wheeler MJ, de Graaf BHJ, Hadjiosif N, Perry RM, Poulter NS, Osman K, et al. Identification of the pollen self-incompatibility determinant in Papaver rhoeas. Nature. 2009;459:992–5. https://doi.org/10.1038/nature08027.
[23]	Wu J, Li M, Li T. Genetic features of the spontaneous self-compatible mutant, ‘Jin Zhui’ (Pyrus bretschneideri Rehd.). PLoS One. 2013;8:e76509. https://doi.org/10.1371/journal.pone.0076509.
[24]	Xue Y, Carpenter R, Dickinson HG, Coen ES. Origin of allelic diversity in antirrhinum S locus RNases. Plant Cell. 1996;8:805–14. https://doi.org/10.1105/tpc.8.5.805.

Funding

Key Research and Development Program of Guangdong Province(2022B0202070002); National Natural Science Foundation of China(32072523); National Modern Agricultural (Citrus) Industry Technology System(CARS-27); Special Project for the Construction of Innovative Provinces in Hunan Province(2022SK2140); Natural Science Foundation of Changsha(kq2208136)