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Tsukuba, Japan

Yamamoto T.,National Institute of Fruit Tree Science | Terakami S.,National Institute of Fruit Tree Science | Moriya S.,Apple Inc | Hosaka F.,National Institute of Fruit Tree Science | And 5 more authors.
Acta Horticulturae | Year: 2013

We performed random shotgun sequencing to obtain genome sequences from Japanese pear 'Housui' (Pyrus pyrifolia) for use in developing molecular markers. Nearly 2.7 million single-read sequences were obtained, with an average read length of 374 bases. More than 990 Mb of nucleotide sequence were recovered, which is equivalent to twice the size of the Japanese pear genome. We designed 237 simple sequence repeat (SSR) markers with motifs of 4, 5, or 10-14 nucleotides based on more than 50,000 SSR sequences. Out of these 237 markers, 128 loci could be added to at least one of three genetic linkage maps: European pears (P. communis) 'Bartlett' and 'La France', and Japanese pear 'Housui'. 86 of the 144 tested expressed sequence tag (EST)-SSR markers from apple (Malus × domestica) were mapped in one or more of the pear cultivars. The new genetic linkage map of 'Bartlett' consisted of 485 loci from SSR and single-nucleotide polymorphism markers, covering 17 linkage groups with a total length of 965 cM. The linkage map of 'La France' contained 370 loci in 17 linkage groups, with a total length of 1160 cM, and that of 'Housui' contained 415 loci in 20 linkage groups, with a total length of 1177 cM. The information obtained from this study will help us develop genome-wide markers and perform marker-assisted selection in pear breeding programs.

Kim H.,National Institute of Fruit Tree Science | Kim H.,Plant Biotechnology Institute | Terakami S.,National Institute of Fruit Tree Science | Nishitani C.,National Institute of Fruit Tree Science | And 6 more authors.
Breeding Science | Year: 2012

We developed retrotransposon-based insertional polymorphism (RBIP) markers based on the long terminal repeat (LTR) sequences of copia-like retrotransposon Ppcrt4 and flanking genome sequences, which were derived from 454 sequencing data from Japanese pear (Pyrus pyrifolia) 'Hosui'. Out of 40 sequences including both LTR and flanking genome regions, we developed 22 RBIP markers and used them for DNA profiling of 80 pear cultivars: 64 Japanese, 10 Chinese (Pyrus ussuriensis) and 6 European (Pyrus communis). Three RBIP markers were enough to differentiate 'Hosui' from the other Japanese pear cultivars. The 22 RBIP markers could also distinguish 61 of the 64 Japanese pear cultivars. European pears showed almost no amplification of the 22 RBIP markers, which might suggest that retrotransposons had transposed during Asian pear evolution or reflect the genetic relationship between Asian and European pears. Sixteen of the RBIP markers could be positioned on a genetic linkage map of 'Hosui'. The RBIP loci were distributed in 10 linkage groups, and some loci were very closely located within the same linkage group. The information obtained will be applicable to developing cultivar-specific RBIP marker sets in plants.

Suzuki K.,STAFF Institute | Suzuki K.,Animal Genome Research Program | Kobayashi E.,National Livestock Breeding Center | Yamashita H.,Tokai University | And 7 more authors.
Animal Genetics | Year: 2012

The chicken major histocompatibility complex (MHC-B locus) has a strong association with resistance and susceptibility to numerous diseases. We have found a B haplotype designated WLA that associated with the regression of tumours caused by Rous sarcoma virus J strain (RSV-J). Haplotype WLA was identical to the regressive B6 haplotype when partial genotyping was performed (Poultry Science, 89, 2010, 651). We then constructed a bacterial artificial chromosome (BAC) library from a WLA homozygote chicken to evaluate the structure of this regression haplotype and compared it to those of the B6 haplotype. Comparison between WLA and B6 above 59 kb within the 167 kb, including 14 genes from BG1 to BF2, revealed 75 SNPs and 14 indels. However, several genes were identical between WLA and B6, including the BF1 and BF2 genes, which encode a class I molecule previously suggested to be related to the regression phenotype. The BLB2 gene encoding the MHC class II beta chain showed the greatest diversity, with 19 non-synonymous SNPs. A comparison of WLA and B6 haplotpyes that are associated with tumour regression and RIRa and B24 haplotypes associated with tumour progression suggests that DMA1, DMA2, BRD2, TAPBP and BLB2 genes are not involved in the intensity of RSV J tumour regression. © 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.

She K.-C.,Tokyo University of Science | Kusano H.,Tokyo University of Science | Kusano H.,RIKEN | Koizumi K.,Tokyo University of Science | And 23 more authors.
Plant Cell | Year: 2010

Rice (Oryza sativa) endosperm accumulates a massive amount of storage starch and storage proteins during seed development. However, little is known about the regulatory system involved in the production of storage substances. The rice flo2 mutation resulted in reduced grain size and starch quality. Map-based cloning identified FLOURY ENDOSPERM2 (FLO2), a member of a novel gene family conserved in plants, as the gene responsible for the rice flo2 mutation. FLO2 harbors a tetratricopeptide repeat motif, considered to mediate a protein-protein interactions. FLO2 was abundantly expressed in developing seeds coincident with production of storage starch and protein, as well as in leaves, while abundant expression of its homologs was observed only in leaves. The flo2 mutation decreased expression of genes involved in production of storage starch and storage proteins in the endosperm. Differences between cultivars in their responsiveness of FLO2 expression during high-temperature stress indicated that FLO2 may be involved in heat tolerance during seed development. Over expression of FLO2 enlarged the size of grains significantly. These results suggest that FLO2 plays a pivotal regulatory role in rice grain size and starch quality by affecting storage substance accumulation in the endosperm. © 2010 American Society of Plant Biologists.

Burgos-Paz W.,Autonomous University of Barcelona | Souza C.A.,Autonomous University of Barcelona | Souza C.A.,EMBRAPA - Empresa Brasileira de Pesquisa Agropecuaria | Castello A.,Autonomous University of Barcelona | And 9 more authors.
Animal Genetics | Year: 2013

The phylogeography of the porcine X chromosome has not been studied despite the unique characteristics of this chromosome. Here, we genotyped 59 single nucleotide polymorphisms (SNPs) in 312 pigs from around the world, representing 39 domestic breeds and wild boars in 30 countries. Overall, widespread commercial breeds showed the highest heterozygosity values, followed by African and American populations. Structuring, as inferred from FST and analysis of molecular variance, was consistently larger in the non-pseudoautosomal (NPAR) than in the pseudoautosomal regions (PAR). Our results show that genetic relationships between populations can vary widely between the NPAR and the PAR, underscoring the fact that their genetic trajectories can be quite different. NPAR showed an increased commercial-like genetic component relative to the PAR, probably because human selection processes to obtain individuals with high productive parameters were mediated by introgressing boars rather than sows. © 2012 The Authors.

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