To reveal the genetic regions controlling eating quality of japonica rice and to establish a system for markerassisted selection (MAS), we conducted a QTL analysis for eating quality of Koshihikari, a leading cultivar in Japan. We used a recombinant inbred population consisting of 92 lines derived from a cross between two closely related japonica cultivars, Moritawase (low eating quality) and Koshihikari. We evaluated overall eating quality (OE), glossiness (GL), taste (TA), stickiness (ST), and hardness (HD) of the lines over 3 years by sensory tests. QTL analysis revealed 43 QTLs on 16 regions across all chromosomes except chromosome 5. QTLs on chromosomes 1, 3, 6, 7, and 10 were detected in multiple years. The Koshihikari alleles at 37 QTLs increased the eating quality. Further QTL analysis revealed 8 QTLs for textural characteristics of cooked rice and 3 for the amino acid ratio of polished rice. Those on chromosomes 1, 3, 6, and 7 were located near the QTLs for eating quality.

In order to establish a system for marker assisted selection (MAS) to develop new rice cultivars with good eating quality, we conducted QTL analyses for physicochemical properties of rice by using a recombinant inbred (RI) population consisting of 92 lines derived from a cross between closely related japonica cultivars, Moritawase (a cutivar with low eating quality) and Koshihikari (a cultivar with good eating quality). We developed a linkage map with 119 simple sequence repeat (SSR) markers. Physicochemical properties of rice were evaluated two years by measuring protein content, amylose content and textural characteristics. QTL analysis for protein content revealed three QTLs on chromosome 2, 6 and 9. Four QTLs for amylose content were detected on chromosome 3, 7, 9 and 12. One QTL for texture characteristics were identified on chromosome 3. The DNA markers linked to these QTLs will be used for the MAS for good eating quality.

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Abstract:Retrotransposons have been used frequently for the development of 23 molecular markers by using their insertion polymorphisms among cultivars, because 24 multiple copies of these elements are dispersed throughout the genome and inserted 25 copies are inherited genetically. Although a large number of long terminal repeat 26 (LTR) retrotransposon families exist in the higher eukaryotic genomes, the 27 identification of families that show high insertion polymorphism has been challenging. 28Here, we performed an efficient screening of these retrotransposon families using an 29Illumina HiSeq2000 sequencing platform with comprehensive LTR library 30 construction based on the primer binding site (PBS), which is located adjacent to the 5 31 LTR and has a motif that is universal and conserved among LTR retrotransposon 32 families. The paired-end sequencing library of the fragments containing a large number 33 of LTR sequences and their insertion sites was sequenced for seven strawberry 34 cultivars (Fragaria x ananassa Duchesne) and one diploid wild species (F. vesca). 35Among them, we screened 24 families with a "unique" insertion site that appeared only 36 in one variety and not in any others, assuming that this type of insertion should have 37 occurred quite recently. Finally, we confirmed experimentally the selected LTR 38 families showed high insertion polymorphisms among closely related cultivars. 39 40

A strawberry Multi-parent Advanced Generation Intercrosses (MAGIC) population, derived from crosses using six strawberry cultivars was successfully developed. The population was composed of 338 individuals; genome conformation was evaluated by expressed sequence tag-derived simple short repeat (EST-SSR) markers. Cluster analysis and principal component analysis (PCA) based on EST-SSR marker polymorphisms revealed that the MAGIC population was a mosaic of the six founder cultivars and covered the genomic regions of the six founders evenly. Fruit quality related traits, including days to flowering (DTF), fruit weight (FW), fruit firmness (FF), fruit color (FC), soluble solid content (SC), and titratable acidity (TA), of the MAGIC population were evaluated over two years. All traits showed normal transgressive segregation beyond the founder cultivars and most traits, except for DTF, distributed normally. FC exhibited the highest correlation coefficient overall and was distributed normally regardless of differences in DTF, FW, FF, SC, and TA. These facts were supported by PCA using fruit quality related values as explanatory variables, suggesting that major genetic factors, which are not influenced by fluctuations in other fruit traits, could control the distribution of FC. This MAGIC population is a promising resource for genome-wide association studies and genomic selection for efficient strawberry breeding.