A Large-Scale Genome-Wide Association Analyses of Ethiopian Sorghum Landrace Collection Reveal Loci Associated With Important Traits

The eastern Africa region, Ethiopia and its surroundings, is considered as the center of origin and diversity for sorghum, and has contributed to global sorghum genetic improvement. The germplasm from this region harbors enormous genetic variation for various traits but little is known regarding the genetic architecture of most traits. Here, 1425 Ethiopian landrace accessions were phenotyped under field conditions for presence or absence of awns, panicle compactness and shape, panicle exsertion, pericarp color, glume cover, plant height and smut resistance under diverse environmental conditions in Ethiopia. In addition, F1 hybrids obtained from a subset of 1341 accessions crossed to an A1 cytoplasmic male sterile line, ATx623, were scored for fertility/sterility reactions. Subsequently, genotyping-by-sequencing generated a total of 879,407 SNPs from which 72,190 robust SNP markers were selected after stringent quality control (QC). Pairwise distance-based hierarchical clustering identified 11 distinct groups. Of the genotypes assigned to either one of the 11 sub-populations, 65% had high ancestry membership coefficient with the likelihood of more than 0.60 and the remaining 35% represented highly admixed accessions. A genome-wide association study (GWAS) identified loci and SNPs associated with aforementioned traits. GWAS based on compressed mixed linear model (CMLM) identified SNPs with significant association (FDR ≤ 0.05) to the different traits studied. The percentage of total phenotypic variation explained with significant SNPs across traits ranged from 2 to 43%. Candidate genes showing significant association with different traits were identified. The sorghum bHLH transcription factor, ABORTED MICROSPORES was identified as a strong candidate gene conditioning male fertility. Notably, sorghum CLAVATA1 receptor like kinase, known for regulation of plant growth, and the ETHYLENE RESPONSIVE TRANSCRIPTION FACTOR gene RAP2-7, known to suppress transition to flowering, were significantly associated with plant height. In addition, the YELLOW SEED1 like MYB transcription factor and TANNIN1 showed strong association with pericarp color validating previous observations. Overall, the genetic architecture of natural variation representing the complex Ethiopian sorghum germplasm was established. The study contributes to the characterization of genes and alleles controlling agronomic traits, and will serve as a source of markers for molecular breeding

Heterotic Trait Locus (HTL) Mapping Identifies Intra-Locus Interactions That Underlie Reproductive Hybrid Vigor in Sorghum bicolor

Identifying intra-locus interactions underlying heterotic variation among whole-genome hybrids is a key to understanding mechanisms of heterosis and exploiting it for crop and livestock improvement. In this study, we present the development and first use of the heterotic trait locus (HTL) mapping approach to associate specific intra-locus interactions with an overdominant heterotic mode of inheritance in a diallel population using Sorghum bicolor as the model. This method combines the advantages of ample genetic diversity and the possibility of studying non-additive inheritance. Furthermore, this design enables dissecting the latter to identify specific intra-locus interactions. We identified three HTLs (3.5% of loci tested) with synergistic intra-locus effects on overdominant grain yield heterosis in 2 years of field trials. These loci account for 19.0% of the heterotic variation, including a significant interaction found between two of them. Moreover, analysis of one of these loci (hDPW4.1) in a consecutive F2 population confirmed a significant 21% increase in grain yield of heterozygous vs. homozygous plants in this locus. Notably, two of the three HTLs for grain yield are in synteny with previously reported overdominant quantitative trait loci for grain yield in maize. A mechanism for the reproductive heterosis found in this study is suggested, in which grain yield increase is achieved by releasing the compensatory tradeoffs between biomass and reproductive output, and between seed number and weight. These results highlight the power of analyzing a diverse set of inbreds and their hybrids for unraveling hitherto unknown allelic interactions mediating heterosis

A global experiment on motivating social distancing during the COVID-19 pandemic

Finding communication strategies that effectively motivate social distancing continues to be a global public health priority during the COVID-19 pandemic. This cross-country, preregistered experiment (n = 25,718 from 89 countries) tested hypotheses concerning generalizable positive and negative outcomes of social distancing messages that promoted personal agency and reflective choices (i.e., an autonomy-supportive message) or were restrictive and shaming (i.e., a controlling message) compared with no message at all. Results partially supported experimental hypotheses in that the controlling message increased controlled motivation (a poorly internalized form of motivation relying on shame, guilt, and fear of social consequences) relative to no message. On the other hand, the autonomy-supportive message lowered feelings of defiance compared with the controlling message, but the controlling message did not differ from receiving no message at all. Unexpectedly, messages did not influence autonomous motivation (a highly internalized form of motivation relying on one’s core values) or behavioral intentions. Results supported hypothesized associations between people’s existing autonomous and controlled motivations and self-reported behavioral intentions to engage in social distancing. Controlled motivation was associated with more defiance and less long-term behavioral intention to engage in social distancing, whereas autonomous motivation was associated with less defiance and more short- and long-term intentions to social distance. Overall, this work highlights the potential harm of using shaming and pressuring language in public health communication, with implications for the current and future global health challenges

Genetic Resistance to Fungal Pathogens in Sorghum [Sorghum Bicolor (L.) Moench]

Sorghum [Sorghum bicolor (L.) Moench] is the fifth most widely grown cereal crop in the world that serves as a staple food for millions of people. Grain mold of sorghum, caused by a consortium of fungal pathogens, is a leading constraint to sorghum production. A second sorghum disease with significant economic impact is anthracnose caused by the ascomycete fungus Colletotrichum sublineolum(Cs). Grain mold causes yield reduction and is highly detrimental to food quality due to contamination by toxigenic fungi and mycotoxins while anthracnose results in significant yield reduction in susceptible cultivars. Genetic resistance is considered the only effective and sustainable way to control both diseases, but the genetic control of these diseases are not well understood. In this project, we implemented genetic, genomic and molecular approaches to identify loci and/or genes underlying resistance to the two diseases. The results presented in Chapters 2 to 5 provide new insights to the genetic and genomic architecture of resistance to grain mold and anthracnose. Chapter 1 provides background information and review of the literature on the pathology of the two diseases, the contrasting and shared mechanisms of genetic resistance and approaches to QTL and gene identification. Chapter 2 and Chapter 3 describe genome wide association studies (GWAS) conducted on sorghum landrace accessions from Ethiopia. Results of both sets of GWAS were recently published (Nida et al., 2019, Journal of Cereal Science 85, 295- 304; Nida et al., 2021, Theoretical Applied Genetics, https://doi.org/10.1007/s00122-020-03762- 2). Chapter 4 describes global transcriptome profiles of early stage of the developing grain from resistant and susceptible sorghum genotypes which uncovered process that correlate with resistance or susceptibility to grain mold. Finally, Chapter 5 summarizes two anthracnose resistance genes identified through whole genome resequencing and genetic mapping. In Chapter 2, genomic regions associated with grain mold resistance were identified through GWAS conducted using sorghum landraces. A major grain mold resistance locus containing tightly linked and sequence related MYB transcription factor genes were identified based on association between SNPs and grain mold resistance scores of 1425 accessions. The locus contains YELLOW SEED1 (Y1, Sobic.001G398100), a likely non-functional pseudo gene (Y2, Sobic.001G398200), and YELLOW SEED3 (Y3, Sobic.001G397900). SNPs and other sequence polymorphisms that alter the Y1 and Y3 genes correlated with susceptibility to grain mold and provided a strong genetic evidence. Although Y1has long been known as a regulator of kernel color and the biosynthesis of 3-deoxyanthocynidin phytoalexins, it was not annotated in the sorghum genome. The data suggest that the MYB genes and their grain and glume specific expressions determine responses to molding fungi. Chapter 3 focuses on GWAS conducted on a subset of early to medium flowering accessions to identify grain mold resistance loci. In addition, because of the caveats associated with grain flavonoid mediated mold resistance, we specifically aimed to identify resistance loci independent of grain flavonoids. A multi-environment grain mold phenotypic data and 173,666 SNPs were used to conduct GWAS using 635 accessions and a subset of non-pigmented accessions, potentially producing no tannins and/or phenols

Controlled injection of compressed air in marine diesel engine intake for improved load acceptance

Background and Objectives: Injera (a fermented pancake-like product) is a traditional food in Ethiopia but is traditionally made from tef (Eragrostis tef). But sorghum also a traditional Ethiopian crop can be used although considered having a lower quality. A 139 sorghum (Sorghum bicolor) cultivars and their corresponding injera were tested for a range of chemical tests, namely total starch, amylose, and tannin contents, plus a newly developed image analysis program to provide objective measures of the injera.Findings: The results showed several sorghums were superior to tef in making injera, based on the chemical, image, and/or sensory analysis. Tannin content was highly positively correlated with color and negatively with taste, while high starch content was more related to softness and rollability. The imaging analysis also provided a rapid and more objective assessment of injera. Two sensory traits, color and eye evenness, were strongly positively correlated to the image data, through L*, a* and b*, and average pixel count per "eye," respectively. Conclusions: Quality testing involving human sensory panels within a breeding program is time consuming, costly and can be impractical for the selection of superior lines from large numbers of selection candidates to the next stage. Objective tests such as imaging analysis can be used at earlier stages in the breeding program which would allow breeding lines with suitable injera quality to be progressed. This would result in new sorghum varieties with fresh injera quality similar too or better than tef. Significance and novelty: A new image analysis program compliments chemical analysis for early screening of sorghums for injera, saving time and costs

The <i>hDPW4.1</i> grain yield heterotic trait locus (HTL).

<p><b>A.</b> Chromosomal location of the Dsenhabm39 SSR marker is indicated by star on the physical map of chromosome 4. Black and white coloring indicate pericentric-heterochromatic and telomeric-euchromatic chromosomal regions, respectively. Gray indicates markers within pericentric-heterochromatic chromosomal regions. <b>B.</b> Cumulative distribution function plot showing the ODH values of the significant hetero-genotypic (154/164) and homo-genotypic (H:H) groups for the same marker in the diallel (year 2011). <b>C.</b> Linkage analysis of the <i>hDPW4.1</i> locus with dry panicle weight (DPW) in the F2 population. Different letters above bars denote significant difference (<i>P</i><0.05; Hsu’s MCB test) between mean values.</p

Contribution of heterotic trait loci and their epistatic interactions to heterotic variation in a diallel population.

<p><b>A.</b> Heterosis least squared means plot. The x axis represents the genotypes of <i>hDPW1.1</i>. The lines represent different genotypes of <i>hDPW1.2.</i> N, neutral non-interacting genotypic allelic combinations; P, positive interacting combination. <b>B.</b> Accumulated variation explained by the model (<i>R²)</i> with each additional factor. <b>C.</b> The factors included in each of the models.</p

Genetic analysis of the diallel founder lines.

<p><b>A.</b> Clustering analysis of the 19 <i>Sorghum bicolor</i> inbreds based on unrooted neighbor joining tree. Color coding representing the four identified clusters. <b>B.</b> Model-based ancestry for each founder line with enforcement of the cluster number (K) to 4 (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038993#s2" target="_blank">Materials and Methods</a>). Distruct plot is shown with color coding representing the four clusters of the STRUCTURE analysis and the name of each founder line is depicted below.</p

The <i>Sorghum bicolor</i> lines used for heterosis mapping.

<p><b>A.</b> Origin of the wide collection of lines includes accessions collected worldwide (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0038993#pone.0038993.s006" target="_blank">Table S1</a> for details). <b>B.</b> Phylogenetic tree of the wide <i>Sorghum bicolor</i> ssp. bicolor collection. The external nodes and coding of founder lines (FLs) are indicated.</p

Overdominant heterosis (ODH) in the diallel.

<p>ODH distribution of vegetative (height, H; diameter, D; leaf weight, LW; stem weight, SW) and reproductive (dry panicle weight, DPW) traits. Different letters denote significant difference between ODH distributions (Kruskal-Wallis test, <i>P</i><0.0001). Quantile boxes show the range between the 25th and 75th percentiles, including the 50th percentile indicated in between. The bottom and upper outer lines depict the 10th and 90th percentiles, respectively.</p