Demographic, Clinical and Immunogenetic Profiles of a Greek Cohort of COVID-19 Patients

The present cross-sectional study consists of a comprehensive analysis of epidemiological, laboratory, and clinical characteristics of COVID-19 patients in relation to their immunogenetic profiles. We studied 125 COVID-19 patients comprising different stages of disease severity; non-hospitalized (mild n = 69) and hospitalized (n = 56). Analysis of disease characteristics revealed no major differences between males and females of each group of patients while hospitalized patients were older and presented with comorbidities. A positive allele association was observed for HLA-DRB1*01 in total COVID-19 patients versus healthy controls. Subgrouping of COVID-19 patients in mild and hospitalized further identified a statistically significant increase in HLA-DRB1*01 in mild COVID-19 patients versus controls. The frequency of A*11, A*23, and DRB1*09 alleles was higher, while the frequency of C*12 was lower, in hospitalized patients versus healthy controls albeit with uncorrected statistical significance. The identification of specific allele associations may provide useful future markers for disease susceptibility in order to allow successful clinical management of COVID-19 patients.

Diversity and Adaptation of Currently Grown Wheat Landraces and Modern Germplasm in Afghanistan, Iran, and Turkey

Collection of wheat landraces (WLR) was conducted in Afghanistan, Iran, and Turkey in 2010–2014. A representative subset of this collection was used in the current study and included 45 bread wheat landraces from Turkey, 19 from Iran, and 20 from Afghanistan. This material was supplemented by 73 modern cultivars and breeding lines adapted to semiarid conditions and irrigated conditions. Overall, 157 genotypes were tested in Turkey in 2018 and 2019 and in Afghanistan and Iran in 2019 under rainfed conditions to compare performance of WLR and modern material. The germplasm was genotyped using a high density Illumina Infinium 25K wheat SNP array and KASP markers for agronomic traits. The average grain yield ranged between 2.2 and 4.0 t/ha depending on the site and year. Three groups of landraces demonstrated similar average grain yield, though Afghanistan material was slightly higher yielding not only in Afghanistan but also in Turkey. Modern material outyielded the landraces in two environments out of four. The highest yielding landraces were competitive with the best modern germplasm. Frequency of gene Sus2-2B affecting 1000 kernel weight was 64% in WLR and only 3% in modern material. Presence of positive allele of Sus2-2B increased 1000 kernel weight by nearly 4%. Breeding strategy to improved landraces and modern cultivars is discussed.

The wheat Seven in Absentia gene is associated with increases in biomass and yield in hot climates

Wheat (Triticum aestivum L.) productivity is severely reduced by high temperatures. Breeding of heat tolerant cultivars can be achieved by identifying genes controlling physiological and agronomical traits when high temperatures occur and using these to select superior genotypes, but no gene underlying genetic variation for heat tolerance has previously been described. We advanced the positional cloning of qYDH.3BL, a quantitative trait locus (QTL) on bread wheat chromosome 3B associated with increased yield in hot and dry climates. The delimited genomic region contained 12 putative genes and a sequence variant in the promoter region of one gene, Seven in absentia, TaSINA. This was associated with the QTL’s effects on early vigour, root growth, plant biomass and yield components in two distinct wheat populations grown under various growth conditions. Near isogenic lines carrying the positive allele at qYDH.3BL under-expressed TaSINA and had increased vigour and water use efficiency early in development, as well as increased biomass, grain number and grain weight following heat stress. A survey of worldwide distribution indicated that the positive allele became widespread from the 1950s through the CIMMYT wheat breeding programme but, to date, has been selected only in breeding programmes in Mexico and Australia.

Exploring a local genetic interaction network using evolutionary replay experiments

ABSTRACTUnderstanding how genes interact is a central challenge in biology. Experimental evolution provides a useful, but underutilized, tool for identifying genetic interactions, particularly those that involve non-loss-of-function mutations or mutations in essential genes. We previously identified a strong positive genetic interaction between specific mutations in KEL1 (P344T) and HSL7 (A695fs) that arose in an experimentally-evolved Saccharomyces cerevisiae population. Because this genetic interaction is not phenocopied by gene deletion, it was previously unknown. Using “evolutionary replay” experiments we identified additional mutations that have positive genetic interactions with the kel1-P344T mutation. We replayed the evolution of this population 672 times from six timepoints. We identified 30 populations where the kel1-P344T mutation reached high frequency. We performed whole-genome sequencing on these populations to identify genes in which mutations arose specifically in the kel1-P344T background. We reconstructed mutations in the ancestral and kel1-P344T backgrounds to validate positive genetic interactions. We identify several genetic interactors with KEL1, we validate these interactions by reconstruction experiments, and we show these interactions are not recapitulated by loss-of-function mutations. Our results demonstrate the power of experimental evolution to identify genetic interactions that are positive, allele specific, and not readily detected by other methods, and sheds light on a previously under-explored region of the yeast genetic interaction network.

The development and validation of new DNA markers linked to the thousand-grain weight QTL in bread wheat (Triticum aestivum L.)

Thousand-grain weight (TGW) is an important trait affecting wheat production. We previously identified a major quantitative trait loci (QTL) controlling the TGW on the 2D chromosome of wheat using a recombinant inbred line (RIL) population constructed by the cross between Tibetan semi-wild wheat Q1028 (Q1028) and Zhengmai 9023 (ZM9023). The positive allele at this QTL is from ZM9023. To further characterise this QTL, here, we try to develop and validate the high-resolution melting (HRM) and sequence-characterised amplified region (SCAR) markers. One HRM marker (0C98-411) and two SCAR markers (E301-700 and B0BB-10470) were developed and integrated into the genetic map. All of these three markers were validated in three populations with different genetic backgrounds. 0C98-411 is the most closely linked marker that could trace QTgw.sau-2D in molecular marker assisted breeding.

The wheat Seven in Absentia gene is associated with increases in biomass and yield in hot climates

Wheat productivity is severely reduced by high temperatures. Breeding of heat tolerant cultivars can be achieved by identifying genes controlling physiological and agronomical traits with high temperature and using these to select superior genotypes, but no gene underlying genetic variation for heat tolerance has previously been described. We completed the positional cloning of qYDH.3BL, a quantitative trait locus (QTL) on bread wheat chromosome 3B associated with increased yield in hot and dry climates. The delimited genomic region contained 12 putative genes and a sequence variant in the promoter region of one gene - seven in absentia, TaSINA. This was associated with the QTL’s effects on early vigour, plant biomass and yield components in two distinct wheat populations grown under various growth conditions. Near isogenic lines carrying the positive allele at qYDH.3BL under-expressed TaSINA and had increased vigour and water use efficiency early in development, as well as increased biomass, grain number and grain weight following heat stress. A survey of worldwide distribution indicated that the positive allele became widespread from the 1950s through the CIMMYT wheat breeding programme but, to date, has been selected only in breeding programmes in Mexico and Australia.Significance statementWheat is the world’s most widely grown crop and a staple of human diet. Even brief episodes of high temperature in the growing season cause severe yield reductions. Finding and deploying genes for heat stress tolerance in new varieties is a priority for food security with climate change. We narrowed a genetic locus to a small genomic region where genetic variation was present only in one gene that showed clear differences of expression and improved yield and physiology under stress in the populations. Using diagnostic markers to track the positive haplotype in nearly 750 accessions, we found many regions where the allele could be used in breeding programmes to increase wheat’s heat tolerance.

Loci Controlling Adaptation to Heat Stress Occurring at the Reproductive Stage in Durum Wheat

Heat stress occurring during the reproductive stage of wheat has a detrimental effect on productivity. A durum wheat core set was exposed to simulated terminal heat stress by applying plastic tunnels at the time of flowering over two seasons. Mean grain yield was reduced by 54% compared to control conditions, and grain number was the most critical trait for tolerance to this stress. The combined use of tolerance indices and grain yield identified five top performing elite lines: Kunmiki, Berghouata1, Margherita2, IDON37-141, and Ourgh. The core set was also subjected to genome wide association study using 7652 polymorphic single nucleotide polymorphism (SNPs) markers. The most significant genomic regions were identified in association with spike fertility and tolerance indices on chromosomes 1A, 5B, and 6B. Haplotype analysis on a set of 208 elite lines confirmed that lines that carried the positive allele at all three quantitative trait loci (QTLs) had a yield advantage of 8% when field tested under daily temperatures above 31° C. Three of the QTLs were successfully validated into Kompetitive Allele Specific PCR (KASP) markers and explained >10% of the phenotypic variation for an independent elite germplasm set. These genomic regions can now be readily deployed via breeding to improve resilience to climate change and increase productivity in heat-stressed areas.

Loci Controlling Adaptation to Heat Stress Occurring at the Reproductive Stage in Durum Wheat

Heat stress occurring during the reproductive stage of wheat has a detrimental effect on productivity. A durum wheat core set was exposed to simulated terminal heat stress by applying plastic tunnels at the time of flowering over two seasons. Mean grain yield was reduced by 54% compared to control conditions, and grain number was the most critical trait for tolerance to this stress. The combined use of tolerance indices and grain yield identified five elites: Kunmiki, Berghouata1, Margherita2, IDON37-141, and Ourgh. The core set was also subjected to genome wide association study using 7,652 polymorphic SNPs markers. The most critical genomic regions were identified in association with spike fertility and tolerance indices on chromosome 1A, 5B and 6B. Haplotype analysis on a set of 208 elites confirmed that lines that carried the positive allele at all three QTLs resulted in a yield advantage of 8% when field tested under daily temperatures above 31° C. Two of the QTLs were successfully validated into KASP markers and explained >10% of the phenotypic variation for an independent elite germplasm set. These genomic regions can now be readily deployed via breeding to improve resilience to climate change and increase productivity in heat-stressed areas.

Holocene Selection for Variants Associated With General Cognitive Ability: Comparing Ancient and Modern Genomes

Human populations living during the Holocene underwent considerable microevolutionary change. It has been theorized that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene co-evolution that favored via directional selection genetic variants associated with higher general cognitive ability (GCA). To examine whether GCA might have risen during the Holocene, we compare a sample of 99 ancient Eurasian genomes (ranging from 4.56 to 1.21 kyr BP) with a sample of 503 modern European genomes (Fst= 0.013), using three different cognitive polygenic scores (130 SNP, 9 SNP and 11 SNP). Significant differences favoring the modern genomes were found for all three polygenic scores (odds ratios = 0.92,p= 001; .81,p= 037; and .81,p= .02 respectively). These polygenic scores also outperformed the majority of scores assembled from random SNPs generated via a Monte Carlo model (between 76.4% and 84.6%). Furthermore, an indication of increasing positive allele count over 3.25 kyr was found using a subsample of 66 ancient genomes (r= 0.22,pone-tailed= .04). These observations are consistent with the expectation that GCA rose during the Holocene.

Holocene selection for variants associated with cognitive ability: Comparing ancient and modern genomes

ABSTRACTHuman populations living in Eurasia during the Holocene experienced considerable microevolutionary change. It has been predicted that the transition of Holocene populations into agrarianism and urbanization brought about culture-gene coevolution that favoured via directional selection genetic variants associated with higher general cognitive ability (GCA). To examine whether GCA might have risen during the Holocene, we compare a sample of 99 ancient Eurasian genomes (ranging from 4.56 to 1.21 kyr BP) with a sample of 503 modern European genomes, using three different cognitive polygenic scores. Significant differences favouring the modern genomes were found for all three polygenic scores (Odds Ratios=0.92, p=0.037; 0.81, p=0.001 and 0.81, p=0.02). Furthermore, a significant increase in positive allele count over 3.25 kyr was found using a subsample of 66 ancient genomes (r=0.217, pone-taiied=0.04). These observations are consistent with the expectation that GCA rose during the Holocene.