Identification of Grain Size-Related QTLs in Korean japonica Rice Using Genome Resequencing and High-Throughput Image Analysis

Grain size is a key factor influencing the grain yield in rice. To identify the as-yet-unknown genes regulating grain size in Korean japonica rice, we developed a recombinant inbred line population (n = 162) from a cross between Odae (large-grain) and Joun (small-grain), and measured six traits including the thousand-grain weights of unhulled and hulled seeds, grain area, grain length, grain width and grain length-to-width ratio using high-throughput image analysis at the F8 and F9 generations. A genetic map was constructed using 248 kompetitive allele-specific PCR (KASP) markers that were polymorphic between the parental genotypes, and 29 QTLs affecting the six traits were identified, of which 15 were stable in both F8 and F9 generations. Notably, three QTL clusters affecting multiple traits were detected on chromosomes 6, 7 and 11. We analyzed whole-genome resequencing data of Odae and Joun, and selected candidate genes for the stable QTLs in the identified clusters that have high- or moderate-impact variations between Odae and Joun and encode proteins the families of which have been reported to be related to grain size regulation. These results will facilitate the identification of genes underlying the QTLs and promote molecular breeding of high-yielding Korean japonica rice varieties.

The Khoekhoegowab Personality Inventory: The Comparative Validity of a Locally Derived Measure of Traits

Objective: This study explores a personality inventory derived from the results of an indigenous lexical study of personality. From the 272 most commonly used personality descriptors in Khoekhoegowab, the most-spoken of extant Khoesan click languages of southern Africa, an 11-factor model of personality-trait structure was identified. Here, the Khoekhoegowab Personality Inventory (KPI) was created based on those results. Its psychometric properties, the convergent and divergent validity of its scales, and its incremental validity over Big Five and Six traits for predicting physical and mental health, religious practice and attitudes, and income are reported.Methods: Two to five key terms were selected for each of 10 KPI scales: Temperance, Prosocial Diligence, Gossip, Honesty/Morality, Temper, Implacability, Humility, Vanity, Resiliency vs. Agitation, and Courage vs. Fear. These 38 total items were administered to a large sample of adult speakers of Khoekhoegowab in Namibia (N = 632), together with five imported inventories translated into Khoekhoegowab: the 30-item Questionnaire Big Six (QB6), General Self-Reported Health, the Cascades Mental Health Assessment, the Satisfaction with Life Scale, the Duke Religion Index. The properties and intercorrelations of KPI subscales are explored, and their predictive ability for the other variables is compared to that of the QB6.Results: Due to the small number of items on each scale, poor internal consistency was anticipated, but the KPI scales' properties were somewhat better than those of the QB6. R-square change by the inventories as a whole, after accounting for age and gender, indicted that the KPI scales explained more variance than the QB6 scales in almost all criterion variables. Replication of established associations for Big Six traits was mixed: associations were largely as expected for Resiliency, Conscientiousness, and Honesty, but less so for Agreeableness and Extraversion.Conclusions: The KPI had some advantages over the QB6 in predicting physical and mental health. In particular, the four items of Resiliency vs. Agitation predicted lower scores on all physical and mental problem scales. Given psychological-care needs in Namibia, this might be used as a non-intrusive screener. Measurement challenges common to both surveys are discussed, possible solutions, and the utility of higher-order structures are discussed.

Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep

Background Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). Results Our dataset comprised 7135 individuals with phenotype data, among which 1217 had high-density (HD) genotype data (n = 372,534). The genotypes of 707 of these animals were imputed from the Illumina Ovine single nucleotide polymorphism (SNP) 54 BeadChip to the HD Array. The heritability of these traits ranged from 0.05 (CVFD) to 0.36 (MFD), and between-trait genetic correlations ranged from − 0.44 (CN vs. LW) to 0.77 (GFW vs. LW). By integrating the GWAS signals with RNA-seq data from 500 samples (representing 87 tissue types from 16 animals), we detected tissues that were relevant to each of the six traits, e.g. liver, muscle and the gastrointestinal (GI) tract were the most relevant tissues for LW, and leukocytes and macrophages were the most relevant cells for CN. For the six traits, 54 quantitative trait loci (QTL) were identified covering 81 candidate genes on 21 ovine autosomes. Multiple candidate genes showed strong tissue-specific expression, e.g. BNC1 (associated with MFD) and CHRNB1 (LW) were specifically expressed in skin and muscle, respectively. By conducting phenome-wide association studies (PheWAS) in humans, we found that orthologues of several of these candidate genes were significantly (FDR < 0.05) associated with similar traits in humans, e.g. BNC1 was significantly associated with MFD in sheep and with hair colour in humans, and CHRNB1 was significantly associated with LW in sheep and with body mass index in humans. Conclusions Our findings provide novel insights into the biological and genetic mechanisms underlying wool and growth traits, and thus will contribute to the genetic improvement and gene mapping of complex traits in sheep.

QTL mapping for grain yield and three yield components in a population derived from two high-yielding spring wheat cultivars

Key message Four genomic regions on chromosomes 4A, 6A, 7B, and 7D were discovered, each with multiple tightly linked QTL (QTL clusters) associated with two to three yield components. The 7D QTL cluster was associated with grain yield, fertile spikelet number per spike, thousand kernel weight, and heading date. It was located in the flanking region of FT-D1, a homolog gene of Arabidopsis FLOWERING LOCUS T, a major gene that regulates wheat flowering. Abstract Genetic manipulation of yield components is an important approach to increase grain yield in wheat (Triticum aestivum). The present study used a mapping population comprised of 181 doubled haploid lines derived from two high-yielding spring wheat cultivars, UI Platinum and LCS Star. The two cultivars and the derived population were assessed for six traits in eight field trials primarily in Idaho in the USA. The six traits were grain yield, fertile spikelet number per spike, productive tiller number per unit area, thousand kernel weight, heading date, and plant height. Quantitative Trait Locus (QTL) analysis of the six traits was conducted using 14,236 single-nucleotide polymorphism (SNP) markers generated from the wheat 90 K SNP and the exome and promoter capture arrays. Of the 19 QTL detected, 14 were clustered in four chromosomal regions on 4A, 6A, 7B and 7D. Each of the four QTL clusters was associated with multiple yield component traits, and these traits were often negatively correlated with one another. As a result, additional QTL dissection studies are needed to optimize trade-offs among yield component traits for specific production environments. Kompetitive allele-specific PCR markers for the four QTL clusters were developed and assessed in an elite spring wheat panel of 170 lines, and eight of the 14 QTL were validated. The two parents contain complementary alleles for the four QTL clusters, suggesting the possibility of improving grain yield via genetic recombination of yield component loci.

Test-Retest Reliability of the HEXACO-PI-R

Despite the widespread use of the HEXACO as a descriptive taxonomy of human personality, there remains very limited information on the test-retest reliability of commonly used tools to measure the six traits. We report 12-day test-retest of the 100-item HEXACO-PI-R (HEXACO-100) at the level of domains, facets and items. We compare test-retest estimates to internal consistency for domains and facets, and to cross-rater agreement for all levels of measurement. Median rTTs were r = .65, .81, and .88 (n = 416) for items, facets, and domains, respectively. Facets’ rCAs were highly correlated with rTTs but not s. We conclude that the HEXACO-100 demonstrates rTT similar to other contemporary measures, and that rTT data should be routinely collected for scales.

Identification of Additive–Epistatic QTLs Conferring Seed Traits in Soybean Using Recombinant Inbred Lines

Seed weight and shape are important agronomic traits that affect soybean quality and yield. In the present study, we used image analysis software to evaluate 100-seed weight and seed shape traits (length, width, perimeter, projection area, length/width, and weight/projection area) of 155 novel recombinant inbred soybean lines (NJRISX) generated by crossing “Su88-M21” and “XYXHD”. We examined quantitative trait loci (QTLs) associated with the six traits (except seed weight per projection area), and identified 42 additive QTLs (5–8 QTLs per trait) accounting for 24.9–37.5% of the phenotypic variation (PV). Meanwhile, 2–4 epistatic QTL pairs per trait out of a total of 18 accounted for 2.5–7.2% of the PV; and unmapped minor QTLs accounted for the remaining 35.0–56.7% of the PV. A total of 28 additive and 11 epistatic QTL pairs were concentrated in nine joint QTL segments (JQSs), indicating that QTLs associated with seed weight and shape are closely related and interacted. An interaction was also detected between additive and epistatic QTL pairs and environment, which made significant contributions of 1.4–9.5% and 0.4–0.8% to the PV, respectively. We annotated 18 candidate genes in the nine JQSs, which were important for interpreting the close relationships among the six traits. These findings indicate that examining the interactions between closely related traits rather than only analyzing individual trait provides more useful insight into the genetic system of the interrelated traits for which there has been limited QTL information.

ddRAD sequencing-based identification of inter-genepool SNPs and association analysis in Brassica juncea

Background Narrow genetic base, complex allo-tetraploid genome and presence of repetitive elements have led the discovery of single nucleotide polymorphisms (SNPs) in Brassica juncea (AABB; 2n = 4x = 36) at a slower pace. Double digest RAD (ddRAD) - a genome complexity reduction technique followed by NGS was used to generate a total of 23 million paired-end reads from three genotypes each of Indian (Pusa Tarak, RSPR-01 and Urvashi) and Exotic (Donskaja IV, Zem 1 and EC287711) genepools. Results Sequence data analysis led to the identification of 10,399 SNPs in six genotypes at a read depth of 10x coverage among the genotypes of two genepools. A total of 44 hyper-variable regions (nucleotide variation hotspots) were also found in the genome, of which 93% were found to be a part of coding genes/regions. The functionality of the identified SNPs was estimated by genotyping a subset of SNPs on MassARRAY® platform among a diverse set of B. juncea genotypes. SNP genotyping-based genetic diversity and population studies placed the genotypes into two distinct clusters based mostly on the place of origin. The genotypes were also characterized for six morphological traits, analysis of which revealed a significant difference in the mean values between Indian and Exotic genepools for six traits. The association analysis for six traits identified a total of 45 significant marker-trait associations on 11 chromosomes of A- and B- group of progenitor genomes. Conclusions Despite narrow diversity, the ddRAD sequencing was able to identify large number of nucleotide polymorphisms between the two genepools. Association analysis led to the identification of common SNPs/genomic regions associated between flowering and maturity traits, thereby underscoring the possible role of common chromosomal regions-harboring genes controlling flowering and maturity in Brassica juncea.

Kompleks Narcyza: wzór — cechy — elementy. Stare metody i coraz bardziej aktualne problemy

Narcissus complex: Pattern and traits. Old concepts and problems that keep being validIn this paper I ponder on the dominance of the “narcistic culture,” or a culture in which narcissism disseminates as a basic behaviour type, with its characteristic values inspired by Ruth Bene­dict’s idea. I describe the “narcissism culture” typologically: I put it in an opposition towards the “culture of common good” and characterise it as a diffusive net of traits inspired by Alfred L. Kroe­ber’s idea, which actualises itself in concrete local conditions. “Narcissism culture” is based upon individualism, ambition, and care for keeping up the image, while distancing itself from the “culture of common good,” i.e. community oriented, honour, caring for keeping up the image and reputation. The conditions for the narcissism to spread were possible because or were created by industrialisa­tion, with its six traits indicated by Alvin Toffler: standardisation, specialisation, synchronisation, concentration, maximalisation, and centralisation, whereas due to the development of capitalism the narcistic behaviours were reinforced and gained social importance.

Casual Games Before Casual Games: Historicizing Paper Puzzle Games in an Era of Digital Play

This article examines “paper puzzle games”—crosswords, Sudoku, Kakuro, word searches, and so forth—in order to historicize and contextualize “casual games,” complicate our notions of “casual” play, and open up paper puzzle games to game studies consideration for the first time. The article begins by identifying the dearth of literature on paper puzzle games and offers an initial examination of these games through the lens of casual games, play, and players. It focuses on six traits in casual game design: appealing themes, ease of access, ease of learning, minimal required expertise, fast rewards, and temporal flexibility. It demonstrates that—from a perspective of mechanics, demographics, and contexts of play—paper puzzle games are excellent examples of casual games and therefore important to fully study. It also shows the complexity of paper puzzles as a topic in their own right, opening them up for future examination.

Preservice Teachers' Self-Reflection Practices When Integrating Educational Technology in the Classroom

As digital tools become common in the modern classroom, teachers must be equipped with understanding how to create lessons for modern learning. Reflective teaching practices are one such way to help preservice teachers learn quality skills for both creating and implementing digital tools. While working through the six traits of the reflective practitioner (Eby & Kujawa, 1998) over the course of one semester, 29 participants kept a reflective journal detailing their process of creating a lesson using technology. The creation process also included complete lesson plans and a video presentation of the lesson; the video presentation was submitted to an online education technology conference (www.c2lconference.com). Sources of data included reflective journals, lesson plans, self-reflection questionnaires, and conference evaluations. The emergent themes for both the reflective journals and the comments on the self-reflection were aligned to produce three main themes, which were then connected to the six traits.