Genotype Matrix Mapping: Searching for Quantitative Trait Loci Interactions in Genetic Variation in Complex Traits

In order to reveal quantitative trait loci (QTL) interactions and the relationship between various interactions in complex traits, we have developed a new QTL mapping approach, named genotype matrix mapping (GMM), which searches for QTL interactions in genetic variation. The central approach in GMM is the following. (1) Each tested marker is given a virtual matrix, named a genotype matrix (GM), containing intersecting lines and rows equal to the total allele number for that marker in the population analyzed. (2) QTL interactions are then estimated and compared through virtual networks among the GMs. To evaluate the contribution of marker combinations to a quantitative phenotype, the GMM method divides the samples into two non-overlapping subclasses, S0 and S1; the former contains the samples that have a specific genotype pattern to be evaluated, and the latter contains samples that do not. Based on this division, the F-measure is calculated as an index of significance. With the GMM method, we extracted significant marker combinations consisting of one to three interacting markers. The results indicated there were multiple QTL interactions affecting the phenotype (flowering date). GMM will be a valuable approach to identify QTL interactions in genetic variation of a complex trait within a variety of organisms

Chromosome-scale genome assembly of a Japanese chili pepper landrace, Capsicum annuum ‘Takanotsume’

日本を代表するトウガラシ「鷹の爪」の全ゲノムを解読 --多様なトウガラシを生み出すための基盤に--. 京都大学プレスリリース. 2023-01-12.Here, we report the genome sequence of a popular Japanese chili pepper landrace, Capsicum annuum ‘Takanotsume’. We used long-read sequencing and optical mapping, together with the genetic mapping technique, to obtain the chromosome-scale genome assembly of ‘Takanotsume’. The assembly consists of 12 pseudomolecules, which corresponds to the basic chromosome number of C. annuum, and is 3, 058.5 Mb in size, spanning 97.0% of the estimated genome size. A total of 34, 324 high-confidence genes were predicted in the genome, and 83.4% of the genome assembly was occupied by repetitive sequences. Comparative genomics of linked-read sequencing-derived de novo genome assemblies of two Capsicum chinense lines and whole-genome resequencing analysis of Capsicum species revealed not only nucleotide sequence variations but also genome structure variations (i.e., chromosomal rearrangements and transposon-insertion polymorphisms) between ‘Takanotsume’ and its relatives. Overall, the genome sequence data generated in this study will accelerate the pan-genomics and breeding of Capsicum, and facilitate the dissection of genetic mechanisms underlying the agronomically important traits of ‘Takanotsume’

Chromosome-level genome assembly of Japanese chestnut (Castanea crenata Sieb. et Zucc.) reveals conserved chromosomal segments in woody rosids

Japanese chestnut (Castanea crenata Sieb. et Zucc.), unlike other Castanea species, is resistant to most diseases and wasps. However, genomic data of Japanese chestnut that could be used to determine its biotic stress resistance mechanisms have not been reported to date. In this study, we employed long-read sequencing and genetic mapping to generate genome sequences of Japanese chestnut at the chromosome level. Long reads (47.7 Gb; 71.6× genome coverage) were assembled into 781 contigs, with a total length of 721.2 Mb and a contig N50 length of 1.6 Mb. Genome sequences were anchored to the chestnut genetic map, comprising 14,973 single nucleotide polymorphisms (SNPs) and covering 1,807.8 cM map distance, to establish a chromosome-level genome assembly (683.8 Mb), with 69,980 potential protein-encoding genes and 425.5 Mb repetitive sequences. Furthermore, comparative genome structure analysis revealed that Japanese chestnut shares conserved chromosomal segments with woody plants, but not with herbaceous plants, of rosids. Overall, the genome sequence data of Japanese chestnut generated in this study is expected to enhance not only its genetics and genomics but also the evolutionary genomics of woody rosids

シャカイ フクシ キョウイク ノ キソ リロン ト シテ ノ セイカツ ロン オ カンガエル

阿部志郎はかつて「福祉は生活を視座とする。いのちも生活も『ライフ』と訳せるが『ライフ』はなにより『人生』を意味する。人間は多面で複合的問題に逢着しながら人生を過ごす。」と指摘した。こうしたことを引きあいに出すまでもなく社会福祉の理論、政策、技術、実践などあらゆる角度からみて、「生活」は社会福祉の基本であり、福祉課題=生活課題と言えるくらい、社会福祉と生活は切り離せない深い関係にある。社会福祉の視点に立った「生活論」を社会福祉教育の基礎科目として位置づける必要があるのではないか。基本となる生活理論を共有することで人々の生活支援を技とする社会福祉の専門職教育の基盤が安定すると考えられる。この研究ノートはその第一歩としたい。Social welfare is based on people\u27s living; therefore, the target of social welfare would be the same in meaning of people\u27s living issues. This note argues that “Living Theory” should be a basic subject of the social work education

Telomere-to-telomere genome assembly of an allotetraploid pernicious weed, Echinochloa phyllopogon

タイヌビエのゲノムを高精度解読 --除草剤に抵抗性を持つ水田の雑草タイヌビエの高精度ゲノム解読に成功--. 京都大学プレスリリース. 2023-11-07.Echinochloa phyllopogon is an allotetraploid pernicious weed species found in rice fields worldwide that often exhibit resistance to multiple herbicides. An accurate genome sequence is essential to comprehensively understand the genetic basis underlying the traits of this species. Here, the telomere-to-telomere genome sequence of E. phyllopogon was presented. Eighteen chromosome sequences spanning 1.0 Gb were constructed using the PacBio highly fidelity long technology. Of the 18 chromosomes, 12 sequences were entirely assembled into telomere-to-telomere and gap-free contigs, whereas the remaining six sequences were constructed at the chromosomal level with only eight gaps. The sequences were assigned to the A and B genome with total lengths of 453 and 520 Mb, respectively. Repetitive sequences occupied 42.93% of the A genome and 48.47% of the B genome, although 32, 337, and 30, 889 high-confidence genes were predicted in the A and B genomes, respectively. This suggested that genome extensions and gene disruptions caused by repeated sequence accumulation often occur in the B genome before polyploidization to establish a tetraploid genome. The highly accurate and comprehensive genome sequence could be a milestone in understanding the molecular mechanisms of the pernicious traits and in developing effective weed control strategies to avoid yield loss in rice production

Construction of a consensus linkage map for red clover (Trifolium pratense L.)

<p>Abstract</p> <p>Background</p> <p>Red clover (<it>Trifolium pratense </it>L.) is a major forage legume that has a strong self-incompatibility system and exhibits high genetic diversity within populations. For several crop species, integrated consensus linkage maps that combine information from multiple mapping populations have been developed. For red clover, three genetic linkage maps have been published, but the information in these existing maps has not been integrated.</p> <p>Results</p> <p>A consensus linkage map was constructed using six mapping populations originating from eight parental accessions. Three of the six mapping populations were established for this study. The integrated red clover map was composed of 1804 loci, including 1414 microsatellite loci, 181 amplified fragment length polymorphism (AFLP) loci and 204 restriction fragment length polymorphism (RFLP) loci, in seven linkage groups. The average distance between loci and the total length of the consensus map were 0.46 cM and 836.6 cM, respectively. The locus order on the consensus map correlated highly with that of accession-specific maps. Segregation distortion was observed across linkage groups. We investigated genome-wide allele frequency in 1144 red clover individuals using 462 microsatellite loci randomly chosen from the consensus map. The average number of alleles and polymorphism information content (PIC) were 9.17 and 0.69, respectively.</p> <p>Conclusion</p> <p>A consensus genetic linkage map for red clover was constructed for the first time based on six mapping populations. The locus order on the consensus map was highly conserved among linkage maps and was sufficiently reliable for use as a reference for genetic analysis of random red clover germplasms.</p

Chromosome-scale genome assembly of the transformation-amenable common wheat cultivar ‘Fielder’

We have established a high-quality, chromosome-level genome assembly for the hexaploid common wheat cultivar ‘Fielder’, an American, soft, white, pastry-type wheat released in 1974 and known for its amenability to Agrobacterium tumefaciens-mediated transformation and genome editing. Accurate, long-read sequences were obtained using PacBio circular consensus sequencing with the HiFi approach. Sequence reads from 16 SMRT cells assembled using the hifiasm assembler produced assemblies with N50 greater than 20 Mb. We used the Omni-C chromosome conformation capture technique to order contigs into chromosome-level assemblies, resulting in 21 pseudomolecules with a cumulative size of 14.7 and 0.3 Gb of unanchored contigs. Mapping of published short reads from a transgenic wheat plant with an edited seed-dormancy gene, TaQsd1, identified four positions of transgene insertion into wheat chromosomes. Detection of guide RNA sequences in pseudomolecules provided candidates for off-target mutation induction. These results demonstrate the efficiency of chromosome-scale assembly using PacBio HiFi reads and their application in wheat genome-editing studies

Mapping candidate QTLs related to plant persistency in red clover

Red clover (Trifolium pratense L.) is a diploid (2n = 14), self-incompatible legume that is widely cultivated as a forage legume in cold geographical regions. Because it is a short-lived perennial species, improvement of plant persistency is the most important objective for red clover breeding. To develop a marker-assisted selection (MAS) approach for red clover, we identified candidate QTLs related to plant persistency. Two full-sib mapping populations, 272 × WF1680 and HR × R130, were used for QTL identification. Resistance to Sclerotinia trifoliorum and Fusarium species, as well as to winter hardiness, was investigated in the laboratory and in field experiments in Moscow region (Russia), and Sapporo (Japan). With the genotype data derived from microsatellite and other DNA markers, candidate QTLs were identified by simple interval mapping (SIM), Kruskal–Wallis analysis (KW analysis) and genotype matrix mapping (GMM). A total of 10 and 23 candidate QTL regions for plant persistency were identified in the 272 × WF1680 and the HR × R130 mapping populations, respectively. The QTLs identified by multiple mapping approaches were mapped on linkage group (LG) 3 and LG6. The significant QTL interactions identified by GMM explained the higher phenotypic variation than single effect QTLs. Identification of haplotypes having positive effect QTLs in each parent were first demonstrated in this study for pseudo-testcross mapping populations in plant species using experimental data. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00122-009-1253-5) contains supplementary material, which is available to authorized users

Pengaruh Penyuluhan Obat Terhadap Peningkatan Perilaku Pengobatan Sendiri Di Kabupaten Banyumas

Self-medication is the mostly effort to coped health complaint, therefore to drug consume decrease unsuitable, it needed safety socialization to self-medication. The study was take to analyze the effect of drug counseling to self-medication increase in Banyumas regency. In addition to analyze the method effectiveness used in drug counseling to self-medication act. The instrument research used questionnaires in this study and purposive sampling used to took the sample. The respondents were 192 residents whom live in Banyumas regency. The type of research quasi-experimental with non-equivalent control group pretest and posttest research design. The data then analyzed by dependent-sampel t-test to find the effect of counseling to self-medication behavior in α = 0.05. While to find the effectiveness of between discussion group and lecture method by leaflet used independen-sampel t-test in α = 0.05. The results showed there significant different between before and after drug counseling by discussion goup and lecture method used leaflet media, able to self-medication attitude improved such as knowledge and attitude about self-medication (P= 0.000), also it can to know both of methods as effective as to self-medication attitude which showed P=0.05. It\u27s mean both of drug counseling methods used as effective as to self-medication attitude improvement. Key words: self medication attitude, counseling methods, housewife, Banyumas