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Fernandez i Marti A, Castro S, DeJong TM, Dodd RS. Evaluation of the S-locus in Prunus domestica, characterization, phylogeny and 3D modelling. PLoS One 2021; 16:e0251305. [PMID: 33983990 PMCID: PMC8118244 DOI: 10.1371/journal.pone.0251305] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/23/2021] [Indexed: 11/18/2022] Open
Abstract
Self-compatibility has become the primary objective of most prune (Prunus domestica) breeding programs in order to avoid the problems related to the gametophytic self-incompatibility (GSI) system present in this crop. GSI is typically under the control of a specific locus., known as the S-locus., which contains at least two genes. The first gene encodes glycoproteins with RNase activity in the pistils., and the second is an SFB gene expressed in the pollen. There is limited information on genetics of SI/SC in prune and in comparison., with other Prunus species, cloning., sequencing and discovery of different S-alleles is very scarce. Clear information about S-alleles can be used for molecular identification and characterization of the S-haplotypes. We determined the S-alleles of 36 cultivars and selections using primers that revealed 17 new alleles. In addition, our study describes for the first time the association and design of a molecular marker for self-compatibility in P. domestica. Our phylogenetic tree showed that the S-alleles are spread across the phylogeny, suggesting that like previous alleles detected in the Rosaceae., they were of trans-specific origin. We provide for the first time 3D models for the P. domestica SI RNase alleles as well as in other Prunus species, including P. salicina (Japanese plum), P. avium (cherry), P. armeniaca (apricot), P. cerasifera and P. spinosa.
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Affiliation(s)
- Angel Fernandez i Marti
- Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
- * E-mail:
| | - Sarah Castro
- Plant Science, University of California, Davis, California, United States of America
| | - Theodore M. DeJong
- Plant Science, University of California, Davis, California, United States of America
| | - Richard S. Dodd
- Environmental Science, Policy and Management, University of California, Berkeley, California, United States of America
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Li W, Yang Q, Gu Z, Wu C, Meng D, Yu J, Chen Q, Li Y, Yuan H, Wang D, Li T. Molecular and genetic characterization of a self-compatible apple cultivar, 'CAU-1'. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2016; 252:162-175. [PMID: 27717452 DOI: 10.1016/j.plantsci.2016.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 07/16/2016] [Accepted: 07/18/2016] [Indexed: 06/06/2023]
Abstract
In this study, we characterized a naturally occurring self-compatible apple cultivar, 'CAU-1' (S1S9), and studied the underlying mechanism that causes its compatibility. Analyses of both fruit set rate and seed number after self-pollination or cross-pollination with 'Fuji' (S1S9), and of pollen tube growth, demonstrated that 'CAU-1' is self-compatible. Genetic analysis by S-RNase PCR-typing of selfed progeny of 'CAU-1' revealed the presence of all progeny classes (S1S1, S1S9, and S9S9). Moreover, no evidence of S-allele duplication was found. These findings support the hypothesis that loss of function of an S-locus unlinked pollen-part mutation (PPM) expressed in pollen, rather than a natural mutation in the pollen-S gene (S1- and S9- haplotype), leads to SI breakdown in 'CAU-1'. In addition, there were no significant differences in pollen morphology or fertility between 'Fuji' and 'CAU-1'. However, we found that the effect of S1- and S9-RNase on the SI behavior of pollen could not be addressed better in 'CAU-1' than in 'Fuji'. Furthermore, we found that a pollen-expressed hexose transporter, MdHT1, interacted with S-RNases and showed significantly less expression in 'CAU-1' than in 'Fuji' pollen tubes. These findings support the hypothesis that MdHT1 may participate in S-RNase internalization during the SI process, and decrease of MdHT1 expression in 'CAU-1' hindered the release of self S-RNase into the cytoplasm of pollen tubes, thereby protecting pollen from the cytotoxicity of S-RNase, finally probably resulting in self-compatibility. Together, these findings indicate that S-locus external factors are required for gametophytic SI in the Rosaceae subtribe Pyrinae.
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Affiliation(s)
- Wei Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Qing Yang
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Zhaoyu Gu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Chuanbao Wu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Dong Meng
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Jie Yu
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Qiuju Chen
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Yang Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China
| | - Hui Yuan
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Dongmei Wang
- Institute of Pomology, Liaoning Academy of Agricultural Sciences, Yingkou 115009, China
| | - Tianzhong Li
- Laboratory of Fruit Cell and Molecular Breeding, China Agricultural University, Beijing 100193, China.
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Do Canto J, Studer B, Lubberstedt T. Overcoming self-incompatibility in grasses: a pathway to hybrid breeding. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1815-29. [PMID: 27577253 DOI: 10.1007/s00122-016-2775-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/24/2016] [Indexed: 05/24/2023]
Abstract
Allogamous grasses exhibit an effective two-locus gametophytic self-incompatibility (SI) system, limiting the range of breeding techniques applicable for cultivar development. Current breeding methods based on populations are characterized by comparably low genetic gains for important traits such as biomass yield. To implement more efficient breeding schemes, the overall understanding of the SI system is crucial as are the mechanisms involved in the breakdown of SI. Self-fertile variants in outcrossing grasses have been studied, and the current level of knowledge includes approximate gene locations, linked molecular markers and first hypotheses on their mode of action. Environmental conditions increasing seed set upon self-pollination have also been described. Even though some strategies were proposed to take advantage of self-fertility, there have, so far, not been changes in the methods applied in cultivar development for allogamous grasses. In this review, we describe the current knowledge about self-fertility in allogamous grasses and outline strategies to incorporate this trait for implementation in synthetic and hybrid breeding schemes.
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Affiliation(s)
- Javier Do Canto
- Department of Agronomy, Iowa State University, 2104 Agronomy Hall, Ames, IA, 50011-1010, USA.
- National Institute of Agricultural Research, INIA, Route 5 km 386, Tacuarembo, Uruguay.
| | - Bruno Studer
- Forage Crop Genetics, Institute of Agricultural Sciences, ETH Zurich, LFW Building, University Street 2, Zurich, 8092, Switzerland
| | - Thomas Lubberstedt
- Department of Agronomy, Iowa State University, 2104 Agronomy Hall, Ames, IA, 50011-1010, USA
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Fernández i Martí A, Gradziel TM, Socias i Company R. Methylation of the S f locus in almond is associated with S-RNase loss of function. PLANT MOLECULAR BIOLOGY 2014; 86:681-9. [PMID: 25326263 DOI: 10.1007/s11103-014-0258-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 10/10/2014] [Indexed: 05/25/2023]
Abstract
Self-compatibility in almond (Prunus dulcis) is attributed to the presence of the S f haplotype, allelic to and dominant over the series of S-alleles controlling self-incompatibility. Some forms of the S f haplotype, however, are phenotypically self-incompatible even though their nucleotide sequences are identical. DNA from leaves and styles from genetically diverse almond samples was cloned and sequenced and then analyzed for changes affecting S f -RNase variants. Epigenetic changes in several cytosine residues were detected in a fragment of 4,700 bp of the 5' upstream region of all self-compatible samples of the S f -RNases, differentiating them from all self-incompatible samples of S f -RNases analyzed. This is the first report of DNA methylation in a Rosaceae species and appears to be strongly associated with inactivation of the S f allele. Results facilitate an understanding of the evolution of self-compatibility/self-incompatibility in almond and other Prunus species, and suggest novel approaches for future crop improvement.
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Affiliation(s)
- Angel Fernández i Martí
- Unidad de Hortofruticultura, Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Av. Montañana 930, 50059, Saragossa, Spain,
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Wang PP, Gao ZH, Ni ZJ, Zhang Z, Cai BH. Self-compatibility in 'Zaohong' Japanese apricot is associated with the loss of function of pollen S genes. Mol Biol Rep 2013; 40:6485-93. [PMID: 24062077 PMCID: PMC3824209 DOI: 10.1007/s11033-013-2765-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 09/14/2013] [Indexed: 11/02/2022]
Abstract
While most Japanese apricot (Prunus mume Sieb. et Zucc.) cultivars display typical S-RNase-based gametophytic self-incompatibility, some self-compatible (SC) cultivars have also been identified. In this study, we confirmed SC of 'Zaohong' through replicated self-pollination tests. Cross-pollination tests showed that SC of 'Zaohong' was caused by a loss of pollen function, so we determined that the S-genotype of 'Zaohong' was S 2 S 15 . Sequence analysis of the S-haplotypes of 'Zaohong' showed no mutations which were likely to alter gene function. Furthermore, expression analysis based on RT-PCR of S-locus genes revealed no differences at the transcript level when compared with 'Xiyeqing', a self-incompatible cultivar with the same S haplotypes. In addition, except for S-locus genes, a new type of F-box gene encoding a previously uncharacterised protein with high sequence similarity (61.03-64.65 %) to Prunus SFB genes was identified. Putative structural regions of PmF-box genes have been described, corresponding to regions in PmSFB alleles, but with some sequence variations. These results suggest that SC in 'Zaohong' occurs in pollen, and that other factors outside the S-locus, including PmF-box genes, might be associated with the loss of function of pollen S genes.
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Affiliation(s)
- Pei-Pei Wang
- College of Horticulture, Nanjing Agricultural University, No.1 Weigang, Nanjing City, 210095, Jiangsu Province, People's Republic of China
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An S-locus independent pollen factor confers self-compatibility in 'Katy' apricot. PLoS One 2013; 8:e53947. [PMID: 23342044 PMCID: PMC3544744 DOI: 10.1371/journal.pone.0053947] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Accepted: 12/06/2012] [Indexed: 11/19/2022] Open
Abstract
Loss of pollen-S function in Prunus self-compatible cultivars has been mostly associated with deletions or insertions in the S-haplotype-specific F-box (SFB) genes. However, self-compatible pollen-part mutants defective for non-S-locus factors have also been found, for instance, in the apricot (Prunus armeniaca) cv. ‘Canino’. In the present study, we report the genetic and molecular analysis of another self-compatible apricot cv. termed ‘Katy’. S-genotype of ‘Katy’ was determined as S1S2 and S-RNase PCR-typing of selfing and outcrossing populations from ‘Katy’ showed that pollen gametes bearing either the S1- or the S2-haplotype were able to overcome self-incompatibility (SI) barriers. Sequence analyses showed no SNP or indel affecting the SFB1 and SFB2 alleles from ‘Katy’ and, moreover, no evidence of pollen-S duplication was found. As a whole, the obtained results are compatible with the hypothesis that the loss-of-function of a S-locus unlinked factor gametophytically expressed in pollen (M’-locus) leads to SI breakdown in ‘Katy’. A mapping strategy based on segregation distortion loci mapped the M’-locus within an interval of 9.4 cM at the distal end of chr.3 corresponding to ∼1.29 Mb in the peach (Prunus persica) genome. Interestingly, pollen-part mutations (PPMs) causing self-compatibility (SC) in the apricot cvs. ‘Canino’ and ‘Katy’ are located within an overlapping region of ∼273 Kb in chr.3. No evidence is yet available to discern if they affect the same gene or not, but molecular markers seem to indicate that both cultivars are genetically unrelated suggesting that every PPM may have arisen independently. Further research will be necessary to reveal the precise nature of ‘Katy’ PPM, but fine-mapping already enables SC marker-assisted selection and paves the way for future positional cloning of the underlying gene.
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Zuriaga E, Molina L, Badenes ML, Romero C. Physical mapping of a pollen modifier locus controlling self-incompatibility in apricot and synteny analysis within the Rosaceae. PLANT MOLECULAR BIOLOGY 2012; 79:229-242. [PMID: 22481163 DOI: 10.1007/s11103-012-9908-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2011] [Accepted: 03/23/2012] [Indexed: 05/31/2023]
Abstract
S-locus products (S-RNase and F-box proteins) are essential for the gametophytic self-incompatibility (GSI) specific recognition in Prunus. However, accumulated genetic evidence suggests that other S-locus unlinked factors are also required for GSI. For instance, GSI breakdown was associated with a pollen-part mutation unlinked to the S-locus in the apricot (Prunus armeniaca L.) cv. 'Canino'. Fine-mapping of this mutated modifier gene (M-locus) and the synteny analysis of the M-locus within the Rosaceae are here reported. A segregation distortion loci mapping strategy, based on a selectively genotyped population, was used to map the M-locus. In addition, a bacterial artificial chromosome (BAC) contig was constructed for this region using overlapping oligonucleotides probes, and BAC-end sequences (BES) were blasted against Rosaceae genomes to perform micro-synteny analysis. The M-locus was mapped to the distal part of chr.3 flanked by two SSR markers within an interval of 1.8 cM corresponding to ~364 Kb in the peach (Prunus persica L. Batsch) genome. In the integrated genetic-physical map of this region, BES were mapped against the peach scaffold_3 and BACs were anchored to the apricot map. Micro-syntenic blocks were detected in apple (Malus × domestica Borkh.) LG17/9 and strawberry (Fragaria vesca L.) FG6 chromosomes. The M-locus fine-scale mapping provides a solid basis for self-compatibility marker-assisted selection and for positional cloning of the underlying gene, a necessary goal to elucidate the pollen rejection mechanism in Prunus. In a wider context, the syntenic regions identified in peach, apple and strawberry might be useful to interpret GSI evolution in Rosaceae.
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Affiliation(s)
- Elena Zuriaga
- Instituto Valenciano de Investigaciones Agrarias-IVIA, Apartado Oficial, 46113 Moncada, Valencia, Spain.
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Cachi AM, Wünsch A. Characterization and mapping of non-S gametophytic self-compatibility in sweet cherry (Prunus avium L.). JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:1847-56. [PMID: 21127024 DOI: 10.1093/jxb/erq374] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Self-incompatibility in Prunus (Rosaceae) species, such as sweet cherry, is controlled by a multiallelic locus (S), in which two tightly linked genes, S-RNase and SFB (S haplotype-specific F-box), determine the specificity of the pollen and the style. Fertilization in these species occurs only if the S-specificities expressed in the pollen and the pistils are different. However, modifier genes have been proposed to be necessary for a full manifestation of the self-incompatibility response. 'Cristobalina' is a spontaneous self-compatible sweet cherry cultivar that originated in Eastern Spain. Previous studies with this genotype suggested that pollen modifier gene(s), not linked to the S-locus, may be the cause of self-incompatibility breakdown. In this work, an F(1) population from 'Cristobalina' that segregates for this trait was used to identify molecular markers linked to self-compatibility by bulked segregant analysis. One simple sequence repeat (SSR) locus (EMPaS02) was found to be linked to self-compatibility in this population at 3.2 cM. Two additional populations derived from 'Cristobalina' were used to confirm the linkage of this marker to self-compatibility. Since EMPaS02 has been mapped to the sweet cherry linkage group 3, other markers located on the same linkage group were analysed in these populations to confirm the location of the self-compatibility locus.
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Affiliation(s)
- A M Cachi
- Centro de Investigación y Tecnología Agroalimentaria de Aragón (CITA), Avda. Montañana 930, 50059 Zaragoza, Spain
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