PCR-RFLP of S locus for identification of breeding lines in cruciferous vegetables

S haplotype collection in Brassicaceae crops-an updated list of S haplotypes

Self-incompatibility is the system that inhibits pollen germination and pollen tube growth by self-pollen. This trait is important for the breeding of Brassica and Raphanus species. In these species, self-incompatibility is governed by the S locus, which contains three linked genes (a set called the S haplotype), i.e., S-locus receptor kinase, S-locus cysteine-rich protein/S-locus protein 11, and S-locus glycoprotein. A large number of S haplotypes have been identified in Brassica oleracea, B. rapa, and Raphanus sativus to date, and the nucleotide sequences of their many alleles have also been registered. In this state, it is important to avoid confusion between S haplotypes, i.e., an identical S haplotype with different names and a different S haplotype with an identical S haplotype number. To mitigate this issue, we herein constructed a list of S haplotypes that are easily accessible to the latest nucleotide sequences of S-haplotype genes, together with revisions to and an update of S haplotype information. Furthermore, the histories of the S-haplotype collection in the three species are reviewed, the importance of the collection of S haplotypes as a genetic resource is discussed, and the management of information on S haplotypes is proposed.

An Identification System Targeting the SRK Gene for Selecting S-Haplotypes and Self-Compatible Lines in Cabbage

Cabbage (Brassica oleracea L. var. capitata) self-incompatibility is important for heterosis. However, the seed production of elite hybrid cannot be facilitated by honey bees due to the cross-incompatibility of the two parents. In this study, the self-compatibility of 58 winter cabbage inbred lines was identified by open-flower self-pollination (OS) and molecular techniques. Based on the NCBI database, a new class I S-haplotype-specific marker, PKC6F/PKC6R, was developed. Verification analyses revealed 9 different S-haplotypes in the 58 cabbage inbred lines; of these lines, 46 and 12 belonged to class I (S6, S7, S12, S14, S33, S45, S51, S68) and class II (S15) S-haplotypes, respectively. The coincidence rate between the self-compatibility index and S-haplotype was 91%. This study developed a Tri-Primer-PCR amplification method to rapidly select plants with specific S-haplotypes in biased segregated S-locus populations. Furthermore, it established an S-haplotype identification system based on these nine S-haplotypes. To overcome parental cross-incompatibility (18-503 and 18-512), an inbred line (18-2169) with the S15 haplotype was selected from the sister lines of self-incompatible 18-512 (S68, class I S-haplotype). The inbred line (18-2169) showed self-compatibility and cross-compatibility with 18-503. This study provides guidance for self-compatibility breeding in cabbage and predicts parental cross-incompatibility in elite combinations.

Characterization of self-incompatible Brassica napus lines lacking SP11 expression

Recognition of self-incompatibility (SI) is regulated by the SRK and SP11 genes in Brassicaceae. Brassica rapa and B. oleracea are self-incompatible, while most cultivated species of B. napus, which arose from hybridization between B. rapa and B. oleracea, are self-compatible. Various studies of the SRK and SP11 genes in self-compatible B. napus have been reported, but details of the mechanism in different B. napus lines are not fully understood. In this study, we confirmed the S haplotypes, SI phenotypes and SP11 expression in 10 representative lines of B. napus, and identified two SI lines (N110 and N343) lacking SP11 expression. In N343 (with BnS¹ and BnS⁶ haplotypes), we confirmed that there is a 3.6-kb insertion in the promoter region of BnSP11-1, and that BnSP11-1 and BnSP11-6 are not expressed, as reported previously (expression of BnSP11-6 is suppressed by the BnS¹ haplotype), although this line is self-incompatible. Similarly, in N110, with two novel S haplotypes (BnS⁸ and BnS⁹) in addition to BnS⁶, a 4.3-kb insertion was identified in the promoter region of BnSP11-9, and expression levels of BnSP11-6, BnSP11-8 and BnSP11-9 were all suppressed (BnSP11-6 and BnSP11-8 may be suppressed by BnS⁸ and BnS⁹, respectively), although the phenotype was self-incompatible. This observation of an SI phenotype without SP11 expression suggests the existence of unknown factor(s) that induce pollen-stigma incompatibility in B. napus.

Self-incompatibility in Brassicaceae crops: lessons for interspecific incompatibility

Most wild plants and some crops of the Brassicaceae express self-incompatibility, which is a mechanism that allows stigmas to recognize and discriminate against "self" pollen, thus preventing self-fertilization and inbreeding. Self-incompatibility in this family is controlled by a single S locus containing two multiallelic genes that encode the stigma-expressed S-locus receptor kinase and its pollen coat-localized ligand, the S-locus cysteine-rich protein. Physical interaction between receptor and ligand encoded in the same S locus activates the receptor and triggers a signaling cascade that results in inhibition of "self" pollen. Sequence information for many S-locus haplotypes in Brassica species has spurred studies of dominance relationships between S haplotypes and of S-locus structure, as well as the development of methods for S genotyping. Furthermore, molecular genetic studies have begun to identify genes that encode putative components of the self-incompatibility signaling pathway. In parallel, standard genetic analysis and QTL analysis of the poorly understood interspecific incompatibility phenomenon have been initiated to identify genes responsible for the inhibition of pollen from other species by the stigma. Herewith, we review recent studies of self-incompatibility and interspecific incompatibility, and we propose a model in which a universal pollen-inhibition pathway is shared by these two incompatibility systems.

Assessment of genetic diversity of accessions in Brassicaceae genetic resources by frequency distribution analysis of S haplotypes

Plant genetic resources are important sources of genetic variation for improving crop varieties as breeding materials. Conservation of such resources of allogamous species requires maintenance of the genetic diversity within each accession to avoid inbreeding depression and loss of rare alleles. For assessment of genetic diversity in the self-incompatibility locus (S locus), which is critically involved in the chance of mating, we developed a dot-blot genotyping method for self-incompatibility (S) haplotypes and applied it to indigenous, miscellaneous landraces of Brassica rapa, provided by the IPK Gene Bank (Gatersleben, Germany) and the Tohoku University Brassica Seed Bank (Sendai, Japan), in which landraces are maintained using different population sizes. This method effectively determined S genotypes of more than 500 individuals from the focal landraces. Although our results suggest that these landraces might possess sufficient numbers of S haplotypes, the strong reduction of frequencies of recessive S haplotypes occurred, probably owing to genetic drift. Based on these results, we herein discuss an appropriate way to conserve genetic diversity of allogamous plant resources in a gene bank.

Identification of S haplotypes in Brassica by dot-blot analysis of SP11 alleles

A self-incompatibility system is used for F(1) hybrid breeding in Brassicaceae vegetables. The determinants of recognition specificity of self-incompatibility in Brassica are SRK in the stigma and SP11/SCR in the pollen. Nucleotide sequences of SP11 alleles are more highly variable than those of SRK. We analyzed the S haplotype specificity of SP11 DNA by Southern-blot analysis and dot-blot analysis using 16 S haplotypes in Brassica oleracea, and found that DNA fragments of a mature protein region of SP11 cDNA, SP11(m), of eight S haplotypes can detect only the SP11 alleles of the same S haplotypes. This specificity makes these methods useful for S haplotype identification. Therefore, we developed two methods of dot-blot analysis for SP11. One is dot blotting of DNA samples, i.e. plant genomic DNA probed with labeled SP11(m), and the other is dot blotting of SP11(m) DNA fragments probed with labeled DNA samples, i.e. the SP11 coding region labeled by PCR using a template of plant genomic DNA. The former is useful for testing many plant materials. The latter is suitable, if there is no previous information on the S haplotypes of plant materials.