We determined the genome sequence of sweet cherry (Prunus avium) using next-generation sequencing technology. The total length of the assembled sequences was 272.4 Mb, consisting of 10,148 scaffold sequences with an N50 length of 219.6 kb. The sequences covered 77.8% of the 352.9 Mb sweet cherry genome, as estimated by k-mer analysis, and included >96.0% of the core eukaryotic genes. We predicted 43,349 complete and partial protein-encoding genes. A high-density consensus map with 2,382 loci was constructed using double-digest restriction site–associated DNA sequencing. Comparing the genetic maps of sweet cherry and peach revealed high synteny between the two genomes; thus the scaffolds were integrated into pseudomolecules using map- and synteny-based strategies. Whole-genome resequencing of six modern cultivars found 1,016,866 SNPs and 162,402 insertions/deletions, out of which 0.7% were deleterious. The sequence variants, as well as simple sequence repeats, can be used as DNA markers. The genomic information helps us to identify agronomically important genes and will accelerate genetic studies and breeding programs for sweet cherries. Further information on the genomic sequences and DNA markers is available in DBcherry (http://cherry.kazusa.or.jp (8 May 2017, date last accessed)).

Transmission ratio distortion (TRD) is frequently observed in inter-and intraspecific hybrids of plants, leading to a violation of Mendelian inheritance. Sex-independent TRD (si TRD) was detected in a hybrid between Asian cultivated rice and its wild ancestor. Here we examined how si TRD caused by an allelic interaction at a specific locus arose in Asian rice species. The si TRD is controlled by the S 6 locus via a mechanism in which the S 6 allele acts as a gamete eliminator, and both the male and female gametes possessing the opposite allele (S 6 a ) are aborted only in heterozygotes (S 6 /S 6 a ). Fine mapping revealed that the S 6 locus is located near the centromere of chromosome 6. Testcross experiments using near-isogenic lines (NILs) carrying either the S 6 or S 6 a alleles revealed that Asian rice strains frequently harbor an additional allele (S 6 n ) the presence of which, in heterozygotic states (S 6 /S 6 n and S 6 a /S 6 n ), does not result in si TRD. A prominent reduction in the nucleotide diversity of S 6 or S 6 a carriers relative to that of S 6 n carriers was detected in the chromosomal region. These results suggest that the two incompatible alleles (S 6 and S 6 a ) arose independently from S 6 n and established genetically discontinuous relationships between limited constituents of the Asian rice population.

Transmission ratio distortion (TRD), in which one allele is transmitted more frequently than the opposite allele, is presumed to act as a driving force in the emergence of a reproductive barrier. TRD acting in a sex-specific manner has been frequently observed in interspecific and intraspecific hybrids across a broad range of organisms. In contrast, sex-independent TRD (siTRD), which results from preferential transmission of one of the two alleles in the heterozygote through both sexes, has been detected in only a few plant species. We previously reported an S 6 locus-mediated siTRD, in which the S 6 allele from an Asian wild rice strain (Oryza rufipogon) was transmitted more frequently than the S 6 a allele from an Asian cultivated rice strain (O. sativa) through both male and female gametes in heterozygous plants. Here, we report on the effect of a difference in genetic background on S 6 locus-mediated siTRD, based on the analysis using near-isogenic lines and the original wild strain as a parental strain for crossing. We found that the degree of TRD through the male gametes varied depending on the genetic background of the female (pistil) plants. Despite the occurrence of TRD through both male and female gametes, abnormality was detected in ovules, but not in pollen grains, in the heterozygote. These results suggest the involvement of unlinked modifiers and developmentally distinct, sex-specific genetic mechanisms in S 6 locus-mediated siTRD, raising the possibility that siTRD driven by a single locus may be affected by multiple genetic factors harbored in natural populations.

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Cross-incompatibility caused by endosperm abortion was found in advanced generations of backcrossing between the Asian wild (W593) and cultivated (T65wx) rice strains. The near isogenic line, T65WxS 6 (W593), carrying a segment of chromosome 6 from W593 showed a low seed setting when pollinated with pollen grains of T65wx in spite of the fact that the reciprocal cross gave a high seed setting. The unidirectional or asymmetric crossing barrier was previously explained by an interaction between Cif and cim, both of which acted sporophytically, resulting in the cross-incompatibility reactions in the female (CIF) and male (CIM), respectively. In the genetic model, endosperm abortion is induced only when CIF gametes are fertilized with CIM gametes. This predicted that the double homozygote for Cif and cim might be self-incompatible since the plant expresses both CIF and CIM simultaneously. However, we failed to obtain such a self-incompatible plant by transferring Cif into a cim plant. The present results showed that CIF is controlled not only by Cif but also by an additional gene(s) loosely linked with it. We propose here that Cif 1 (formerly named as Cif) and Cif 2 determine CIF. In addition, Cif 2 and Cim were not separated due to restriction of recombination, which might explain why it is difficult to obtain a self-incompatible rice plant expressing both CIF and CIM.