The genome sequence of sweet cherry (Prunus avium) for use in genomics-assisted breeding.

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)).

The evolution of sex-independent transmission ratio distortion involving multiple allelic interactions at a single locus in rice.

Transmission ratio distortion (TRD) is frequently observed in inter- and intraspecific hybrids of plants, leading to a violation of Mendelian inheritance. Sex-independent TRD (siTRD) was detected in a hybrid between Asian cultivated rice and its wild ancestor. Here we examined how siTRD caused by an allelic interaction at a specific locus arose in Asian rice species. The siTRD is controlled by the S6 locus via a mechanism in which the S6 allele acts as a gamete eliminator, and both the male and female gametes possessing the opposite allele (S6a) are aborted only in heterozygotes (S6/S6a). Fine mapping revealed that the S6 locus is located near the centromere of chromosome 6. Testcross experiments using near-isogenic lines (NILs) carrying either the S6 or S6a alleles revealed that Asian rice strains frequently harbor an additional allele (S6n) the presence of which, in heterozygotic states (S6/S6n and S6a/S6n), does not result in siTRD. A prominent reduction in the nucleotide diversity of S6 or S6a carriers relative to that of S6n carriers was detected in the chromosomal region. These results suggest that the two incompatible alleles (S6 and S6a) arose independently from S6n and established genetically discontinuous relationships between limited constituents of the Asian rice population.