MOESM1 of Sequence analysis of cultivated strawberry (Fragaria × ananassa Duch.) using microdissected single somatic chromosomes

Additional file 1: Table S1. Numbers and alignment rates of sequence reads obtained from single-chromosome samples

Bulletin de l'Alliance internationale des anciens de la cité universitaire de Paris

novembre 19911991/11 (N121)-1991/11

MOESM3 of Development of AhMITE1 markers through genome-wide analysis in peanut (Arachis hypogaea L.)

Additional file 3: Table S3. Genotype-specific AhMITE1 markers

MOESM2 of Development of AhMITE1 markers through genome-wide analysis in peanut (Arachis hypogaea L.)

Additional file 2: Table S2a. PCR components for AhMITE1 marker assay. Table S2b. PCR temperature profile used for AhMITE1 markers. Table S2c. PCR components for CAPS marker assay. Table S2d. PCR temperature profile used for CAPS markers. Table S2e. Restriction digestion components for CAPS assay

Navrhněte princip a realizaci kódové ochrany digitálního obrazu proti vlivu šumu při přenosu pomocí komunikační sítě

Import 20/04/2006Prezenční výpůjčkaVŠB - Technická univerzita Ostrava. Fakulta elektrotechniky a informatiky. Katedra (455) měřící a řídící technik

Additional file 5: of Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa)

Graphical view of syntenic relationship between the ‘Reikou’ linkage map and F. vesca genome (v2.0.a1) or F. iinumae linkage map [25]. Outer pink, green and yellow arks show the LGs of the ‘Reikou’ linkage map, the chromosomes of F. vesca, and the LGs of F. iinumae, respectively. Syntenic loci between the two species are connected by colored lines. Scales represent the genetic position on LGs (cM) or physical position on chromosomes (Mb). (TIFF 4364 kb

Additional file 4: of Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa)

Detailed summary statistics of the ‘Reikou’ linkage map. (XLSX 53 kb

DataSheet_1_A self-compatible pear mutant derived from γ-irradiated pollen carries an 11-Mb duplication in chromosome 17.zip

Self-compatibility is a highly desirable trait for pear breeding programs. Our breeding program previously developed a novel self-compatible pollen-part Japanese pear mutant (Pyrus pyrifolia Nakai), ‘415-1’, by using γ-irradiated pollen. ‘415-1’ carries the S-genotype S4dS5S5, with “d” indicating a duplication of S5 responsible for breakdown of self-incompatibility. Until now, the size and inheritance of the duplicated segment was undetermined, and a reliable detection method was lacking. Here, we examined genome duplications and their inheritance in 140 F1 seedlings resulting from a cross between ‘515-20’ (S1S3) and ‘415-1’. Amplicon sequencing of S-RNase and SFBB18 clearly detected S-haplotype duplications in the seedlings. Intriguingly, 30 partially triploid seedlings including genotypes S1S4dS5, S3S4dS5, S1S5dS5, S3S5dS5, and S3S4dS4 were detected among the 140 seedlings. Depth-of-coverage analysis using ddRAD-seq showed that the duplications in those individuals were limited to chromosome 17. Further analysis through resequencing confirmed an 11-Mb chromosome duplication spanning the middle to the end of chromosome 17. The duplicated segment remained consistent in size across generations. The presence of an S3S4dS4 seedling provided evidence for recombination between the duplicated S5 segment and the original S4haplotype, suggesting that the duplicated segment can pair with other parts of chromosome 17. This research provides valuable insights for improving pear breeding programs using partially triploid individuals.</p

Table_1_A self-compatible pear mutant derived from γ-irradiated pollen carries an 11-Mb duplication in chromosome 17.xlsx

Self-compatibility is a highly desirable trait for pear breeding programs. Our breeding program previously developed a novel self-compatible pollen-part Japanese pear mutant (Pyrus pyrifolia Nakai), ‘415-1’, by using γ-irradiated pollen. ‘415-1’ carries the S-genotype S4dS5S5, with “d” indicating a duplication of S5 responsible for breakdown of self-incompatibility. Until now, the size and inheritance of the duplicated segment was undetermined, and a reliable detection method was lacking. Here, we examined genome duplications and their inheritance in 140 F1 seedlings resulting from a cross between ‘515-20’ (S1S3) and ‘415-1’. Amplicon sequencing of S-RNase and SFBB18 clearly detected S-haplotype duplications in the seedlings. Intriguingly, 30 partially triploid seedlings including genotypes S1S4dS5, S3S4dS5, S1S5dS5, S3S5dS5, and S3S4dS4 were detected among the 140 seedlings. Depth-of-coverage analysis using ddRAD-seq showed that the duplications in those individuals were limited to chromosome 17. Further analysis through resequencing confirmed an 11-Mb chromosome duplication spanning the middle to the end of chromosome 17. The duplicated segment remained consistent in size across generations. The presence of an S3S4dS4 seedling provided evidence for recombination between the duplicated S5 segment and the original S4haplotype, suggesting that the duplicated segment can pair with other parts of chromosome 17. This research provides valuable insights for improving pear breeding programs using partially triploid individuals.</p

Rapid identification of candidate genes for resistance to tomato late blight disease using next-generation sequencing technologies

<div><p>Tomato late blight caused by <i>Phytophthora infestans</i> (Mont.) de Bary, also known as the Irish famine pathogen, is one of the most destructive plant diseases. Wild relatives of tomato possess useful resistance genes against this disease, and could therefore be used in breeding to improve cultivated varieties. In the genome of a wild relative of tomato, <i>Solanum habrochaites</i> accession LA1777, we identified a new quantitative trait locus for resistance against blight caused by an aggressive Egyptian isolate of <i>P</i>. <i>infestans</i>. Using double-digest restriction site–associated DNA sequencing (ddRAD-Seq) technology, we determined 6,514 genome-wide SNP genotypes of an F₂ population derived from an interspecific cross. Subsequent association analysis of genotypes and phenotypes of the mapping population revealed that a 6.8 Mb genome region on chromosome 6 was a candidate locus for disease resistance. Whole-genome resequencing analysis revealed that 298 genes in this region potentially had functional differences between the parental lines. Among of them, two genes with missense mutations, Solyc06g071810.1 and Solyc06g083640.3, were considered to be potential candidates for disease resistance. SNP and SSR markers linking to this region can be used in marker-assisted selection in future breeding programs for late blight disease, including introgression of new genetic loci from wild species. In addition, the approach developed in this study provides a model for identification of other genes for attractive agronomical traits.</p></div