Takato Koba

S Locus F-Box Brothers: Multiple and Pollen-Specific F-Box Genes With S Haplotype-Specific Polymorphisms in Apple and Japanese Pear

Although recent findings suggest that the F-box genes SFB/SLF control pollen-part S specificity in the S-RNase-based gametophytic self-incompatibility (GSI) system, how these genes operate in the system is unknown, and functional variation of pollen S genes in different species has been reported. Here, we analyzed the S locus of two species of Maloideae: apple (Malus domestica) and Japanese pear (Pyrus pyrifolia). The sequencing of a 317-kb region of the apple S9 haplotype revealed two similar F-box genes. Homologous sequences were isolated from different haplotypes of apple and Japanese pear, and they were found to be polymorphic genes derived from the S locus. Since each S haplotype contains two or three related genes, the genes were named SFBB for S locus F-box brothers. The SFBB genes are specifically expressed in pollen, and variable regions of the SFBB genes are under positive selection. In a style-specific mutant S haplotype of Japanese pear, the SFBB genes are retained. Apart from their multiplicity, SFBB genes meet the expected characteristics of pollen S. The unique multiplicity of SFBB genes as the pollen S candidate is discussed in the context of mechanistic variation in the S-RNase-based GSI system.

Isolation, identification and characterization of disomic and translocated barley chromosome addition lines of common wheat

Two disomic barley chromosome addition lines and five translocated chromosome addition lines of common wheat cultivar Shinchunaga were isolated. They were derived from a hybrid plant between Shinchunaga and cultivated barley Nyugoruden (New Golden) by backcrossing with wheat and self pollination. Barley chromosomes added to chromosome arms involved in the translocated chromosomes were identified by C-banding method and by crossing these lines with Chinese Spring/Betzes addition lines. Two disomic addition lines were identified to have chromosome 6 and 7 of barley, respectively. Two of the five translocated chromosome addition lines were clarified to have same chromosome constitution, 42 wheat chromosomes and a pair of translocated chromosomes constituted with a long arm of chromosome 5B of wheat and a short arm of chromosome 7 of barley. The other three lines could not be identified due to chromosome rearrangement. Performances of these seven lines on agronomic characters were examined. Addition of barley chromosome 7 induced early heading, and chromosome 6 showed lated heading. Almost all of the lines except that of chromosome 6 showed short culm length and all showed reduced number of tillers, spikelets and grains per ear, and low seed fertility. These lines would be useful for genetic analyses in wheat and barley and for induction of useful genes of barley into wheat.

Duplication of a well-conserved homeodomain-leucine zipper transcription factor gene in barley generates a copy with more specific functions

Three spikelets are formed at each rachis node of the cultivated barley (Hordeum vulgare ssp. vulgare) spike. In two-rowed barley, the central one is fertile and the two lateral ones are sterile, whereas in the six-rowed type, all three are fertile. This characteristic is determined by the allelic constitution at the six-rowed spike 1 (vrs1) locus on the long arm of chromosome 2H, with the recessive allele (vrs1) being responsible for the six-rowed phenotype. The Vrs1 (HvHox1) gene encodes a homeodomain-leucine zipper (HD-Zip) transcription factor. Here, we show that the Vrs1 gene evolved in the Poaceae via a duplication, with a second copy of the gene, HvHox2, present on the short arm of chromosome 2H. Micro-collinearity and polypeptide sequences were both well conserved between HvHox2 and its Poaceae orthologs, but Vrs1 is unique to the barley tribe. The Vrs1 gene product lacks a motif which is conserved among the HvHox2 orthologs. A phylogenetic analysis demonstrated that Vrs1 and HvHox2 must have diverged after the separation of Brachypodium distachyon from the Pooideae and suggests that Vrs1 arose following the duplication of HvHox2, and acquired its new function during the evolution of the barley tribe. HvHox2 was expressed in all organs examined but Vrs1 was predominantly expressed in immature inflorescence.

Linkage analysis among loci for RAPDs, isozymes and some agronomic traits in Brassica campestris L.

F2 populations from a hybrid between an inbred line of Chinese cabbage (Brassica campestris L. var. pekinensis, 2n = 20) and an inbred line of Mizu-na (B. campestris L. var. japonica 2n = 20) were grown in two seasons, and were analyzed with RAPD and isozyme markers to construct a linkage map following our previous linkage analyses for 19 isozyme loci. A total of 52 RAPD markers were integrated into ten linkage groups, which is the same as the haploid chromosome number of B. campestris. Genes for morphological traits, such as leaf shape, period to bolting, leaf hairiness, the self-incompatibility (the S-glycoprotein) and the NS-glycoprotein which has a high degree of structural homology with the S-glycoprotein, were found to link to the RAPD markers by QTL or linkage analyses. Leaf shape was found to be controlled by multiple genes in two linkage groups. Leaf hairiness seemed to be controlled by a single gene and to be linked to a group of RAPD markers. The period to bolting was found to be controlled by at least two independent loci in the genome. A RAPD marker showing linkage to the self-incompatibility locus showed a recombination value of 20.2%. The NS-glycoprotein locus was linked to the ACP-1 isozyme locus. Linkages between markers and traits are useful for developing marker-assisted selection of important traits.

Divergence of expression pattern contributed to neofunctionalization of duplicated HD‐Zip I transcription factor in barley

Barley (Hordeum vulgare) spikes are developmentally switched from two-rowed to six-rowed by a single recessive gene, six-rowed spike 1 (vrs1), which encodes a homeodomain-leucine zipper I class transcription factor. Vrs1 is a paralog of HvHox2 and both were generated by duplication of an ancestral gene. HvHox2 is conserved among cereals, whereas Vrs1 acquired its current function during the evolution of barley. It was unclear whether divergence of expression pattern or protein function accounted for the functionalization of Vrs1. Here, we conducted a comparative analysis of protein functions and gene expression between HvHox2 and Vrs1 to clarify the functionalization mechanism. We revealed that the transcriptional activation activity of HvHOX2 and VRS1 was conserved. In situ hybridization analysis showed that HvHox2 is localized in vascular bundles in developing spikes, whereas Vrs1 is expressed exclusively in the pistil, lemma, palea and lodicule of lateral spikelets. The transcript abundance of Vrs1 was > 10-fold greater than that of HvHox2 during the pistil developmental stage, suggesting that the essential function of Vrs1 is to inhibit gynoecial development. We demonstrated the quantitative function of Vrs1 using RNAi transgenic plants and Vrs1 expression variants. Expression analysis of six-rowed spike mutants that are nonallelic to vrs1 showed that Vrs1 expression was up-regulated by Vrs4, whereas HvHox2 expression was not. These data demonstrate that the divergence of gene expression pattern contributed to the neofunctionalization of Vrs1.

Polymorphism of SFBB −γ and its use for S genotyping in Japanese pear (Pyrus pyrifolia)

Japanese pear (Pyrus pyrifolia) exhibits the S-RNase-based gametophytic self-incompatibility where the pollen-part determinant, pollen S, had long remained elusive. Recent identification of S locus F-box brothers (SFBB) in Japanese pear and apple suggested that the multiple F-box genes are the pollen S candidates as they exhibited pollen specific expression, S haplotype-specific polymorphisms and linkage to the S locus. In Japanese pear, three SFBBs were identified from a single S haplotype, and they were more homologous to other haplotype genes of the same group (i.e., α-, β- and γ-groups). In this study, we isolated new seven PpSFBB−γ genes from different S genotypes of Japanese pear. These genes showed S haplotype-specific polymorphisms, however, sequence similarities among them were very high. Based on the sequence polymorphisms of the PpSFBB−γ genes, we developed a CAPS/dCAPS system for S genotyping of the Japanese pear cultivars. This new S genotyping system was found to not only be able to discriminate the S1–S9, but also be suitable for identification of the mutant S4sm haplotype for the breeding of self-compatible cultivars, and detection of new S haplotypes such as Sk.

Identification and functional analysis of pistil self-incompatibility factor HT-B of Petunia

Gametophytic self-incompatibility (GSI) in Solanaceae, Rosaceae, and Plantaginaceae is controlled by a multiallelic S-locus. The specificities of pistil and pollen are controlled by separate S-locus genes, S-RNase and SLF/SFB, respectively. Although the S-specificity is determined by the S-locus genes, factors located outside the S-locus are also required for expression of GSI. HT-B is one of the pistil non-S-factors identified in Nicotiana and Solanum, and encodes a small asparagine/aspartate-rich extracellular protein with unknown biochemical function. Here, HT-B was cloned from Petunia and characterized. The structural features and expression pattern of Petunia HT-B were very similar to those of Nicotiana and Solanum. Unlike other solanaceous species, expression of HT-B was also observed in self-compatible Petunia species. RNA interference (RNAi)-mediated suppression of Petunia HT-B resulted in partial breakdown of GSI. Quantitative analysis of the HT-B mRNA accumulation in the transgenics showed that a 100-fold reduction is not sufficient and a >1000-fold reduction is required to achieve partial breakdown of GSI.

Effects of barley chromosome on heading characters in wheat-barley chromosome addition lines

Heading time in cereals is a composite character determined by vernalization requirement, photoperiodic sensitivity and narrow-sense earliness. To study the effects of added barley chromosomes on the heading characters in wheat, two sets of wheat-barley chromosome addition lines, i.e., ‘Betzes’ barley chromosomes 2H to 7H added to ’Chinese Spring‘ wheat (CS-Be2H to CS-Be7H) and ‘New Golden’ barley chromosomes 5H and 6H added to ‘Shinchunaga’ wheat (Shi-NG5H, Shi-NG6H), were examined for their heading characters. All barley chromosomes except Be6H affected vernalization requirement and/or narrow-sense earliness in CS or Shi. Be5H chromosome also slightly increased the photoperiodic sensitivity of CS. Shi-NG5H addition line showed significantly decreased vernalization requirement in comparison with Shi, whereas CS-Be5H did not show any difference from CS. The F1 hybrid of the cross, Shi-NG5H × CS-Be5H, exhibited the same level of vernalization insensitivity as the Shi-NG5H addition line, and plants with and without a vernalization requirement segregated in a 1 : 3 ratio in the F2 generation. These observations, together with previous reports, suggest that the decreased vernalization requirement in the Shi-NG5H addition line was caused by the presence of a major dominant gene for spring habit, Sh2, located on the NG5H barley chromosome. Furthermore, this study revealed that the Sh2 gene in barley has a similar but weaker effect than the wheat vernalization insensitive gene, Vrn1, on the vernalization response in wheat.

Determination of partial genomic sequences and development of a CAPS system of the S-RNase gene for the identification of 22 S haplotypes of apple (Malus × domestica Borkh.).

Information about self-incompatibility (S) genotypes of apple cultivars is important for the selection of pollen donors for fruit production and breeding. Although S genotyping systems using S haplotype-specific PCR of S-RNase, the pistil S gene, are useful, they are sometimes associated with false-positive/negative problems and are unable to identify new S haplotypes. The CAPS (cleaved amplified polymorphic sequences) system is expected to overcome these problems, however, the genomic sequences needed to establish this system are not available for many S-RNases. Here, we determined partial genomic sequences of eight S-RNases, and used the information to design new primer and to select 17 restriction enzymes for the discrimination of 22 S-RNases by CAPS. Using the system, the S genotypes of three cultivars were determined. The genomic sequence-based CAPS system would be useful for S genotyping and analyzing new S haplotypes of apple.

Structure, transcription and post-transcriptional regulation of the bread wheat orthologs of the barley cleistogamy gene Cly1

The majority of genes present in the hexaploid bread wheat genome are present as three homoeologs. Here, we describe the three homoeologous orthologs of the barley cleistogamy gene Cly1, a member of the AP2 gene family. As in barley, the wheat genes (designated TaAP2-A, -B and -D) map to the sub-telomeric region of the long arms of the group 2 chromosomes. The structure and pattern of transcription of the TaAP2 homoeologs were similar to those of Cly1. Transcript abundance was high in the florets, and particularly in the lodicule. The TaAP2 message was cleaved at its miR172 target sites. The set of homoeolog-specific PCR assays developed will be informative for identifying either naturally occurring or induced cleistogamous alleles at each of the three wheat homoeologs. By combining such alleles via conventional crossing, it should be possible to generate a cleistogamous form of bread wheat, which would be advantageous both with respect to improving the level of the crop’s resistance against the causative pathogen of fusarium head blight, and for controlling pollen-mediated gene flow to and from genetically modified cultivars.