Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau.

Understanding the local adaptation of crops has long been a concern of evolutionary biologists and molecular ecologists. Identifying the adaptive genetic variability in the genome is crucial not only to provide insights into the genetic mechanism of local adaptation but also to explore the adaptation potential of crops. This study aimed to identify the climatic drivers of naked barley landraces and putative adaptive loci driving local adaptation on the Qinghai-Tibetan Plateau (QTP). To this end, a total of 157 diverse naked barley accessions were genotyped using the genotyping-by-sequencing approach, which yielded 3123 high-quality SNPs for population structure analysis and partial redundancy analysis, and 37,636 SNPs for outlier analysis. The population structure analysis indicated that naked barley landraces could be divided into four groups. We found that the genomic diversity of naked barley landraces could be partly traced back to the geographical and environmental diversity of the landscape. In total, 136 signatures associated with temperature, precipitation, and ultraviolet radiation were identified, of which 13 had pleiotropic effects. We mapped 447 genes, including a known gene HvSs1. Some genes involved in cold stress and regulation of flowering time were detected near eight signatures. Taken together, these results highlight the existence of putative adaptive loci in naked barley on QTP and thus improve our current understanding of the genetic basis of local adaptation.

Corrigendum: Effects of different fertilization conditions and different geographical locations on the diversity and composition of the rhizosphere microbiota of Qingke (Hordeum vulgare L.) plants in different growth stages.

[This corrects the article DOI: 10.3389/fmicb.2023.1094034.].

Effects of different fertilization conditions and different geographical locations on the diversity and composition of the rhizosphere microbiota of Qingke (Hordeum vulgare L.) plants in different growth stages.

Introduction: The excessive use of chemical fertilizer causes increasing environmental and food security crisis. Organic fertilizer improves physical and biological activities of soil. Rhizosphere microbiota, which consist of highly diverse microorganisms, play an important role in soil quality. However, there is limited information about the effects of different fertilization conditions on the growth of Qingke plants and composition of the rhizosphere microbiota of the plants. Methods: In this study, we characterized the rhizosphere microbiota of Qingke plants grown in three main Qingke-producing areas (Tibet, Qinghai, and Gansu). In each of the three areas, seven different fertilization conditions (m1-m7, m1: Unfertilized; m2: Farmer Practice; m3: 75% Farmer Practice; m4: 75% Farmer Practice +25% Organic manure; m5: 50% Farmer Practice; m6: 50% Farmer Practice +50% Organic manure; m7: 100% Organic manure) were applied. The growth and yields of the Qingke plants were also compared under the seven fertilization conditions. Results: There were significant differences in alpha diversity indices among the three areas. In each area, differences in fertilization conditions and differences in the growth stages of Qingke plants resulted in differences in the beta diversity of the rhizosphere microbiota. Meanwhile, in each area, fertilization conditions, soil depths, and the growth stages of Qingke plants significantly affected the relative abundance of the top 10 phyla and the top 20 bacterial genera. For most of microbial pairs established through network analysis, the significance of their correlations in each of the microbial co-occurrence networks of the three experimental sites was different. Moreover, in each of the three networks, there were significant differences in relative abundance and genera among most nodes (i.e., the genera Pseudonocardia, Skermanella, Pseudonocardia, Skermanella, Aridibacter, and Illumatobacter). The soil chemical properties (i.e., TN, TP, SOM, AN, AK, CEC, Ca, and K) were positively or negatively correlated with the relative abundance of the top 30 genera derived from the three main Qingke-producing areas (p < 0.05). Fertilization conditions markedly influenced the height of a Qingke plant, the number of spikes in a Qingke plant, the number of kernels in a spike, and the fresh weight of a Qingke plant. Considering the yield, the most effective fertilization conditions for Qingke is combining application 50% chemical fertilizer and 50% organic manure. Conclusion: The results of the present study can provide theoretical basis for practice of reducing the use of chemical fertilizer in agriculture.

Population structure analysis and genome-wide association study of a hexaploid oat landrace and cultivar collection.

Introduction: Oat (Avena sativa L.) is an important cereal crop grown worldwide for grain and forage, owing to its high adaptability to diverse environments. However, the genetic and genomics research of oat is lagging behind that of other staple cereal crops. Methods: In this study, a collection of 288 oat lines originating worldwide was evaluated using 2,213 single nucleotide polymorphism (SNP) markers obtained from an oat iSelect 6K-beadchip array to study its genetic diversity, population structure, and linkage disequilibrium (LD) as well as the genotype-phenotype association for hullessness and lemma color. Results: The average gene diversity and polymorphic information content (PIC) were 0.324 and 0.262, respectively. The first three principal components (PCs) accounted for 30.33% of the genetic variation, indicating that the population structure of this panel of oat lines was stronger than that reported in most previous studies. In addition, accessions could be classified into two subpopulations using a Bayesian clustering approach, and the clustering pattern of accessions was closely associated with their region of origin. Additionally, evaluation of LD decay using 2,143 mapped markers revealed that the intrachromosomal whole-genome LD decayed rapidly to a critical r2 value of 0.156 for marker pairs separated by a genetic distance of 1.41 cM. Genome-wide association study (GWAS) detected six significant associations with the hullessness trait. Four of these six markers were located on the Mrg21 linkage group between 194.0 and 205.7 cM, while the other two significant markers mapped to Mrg05 and Mrg09. Three significant SNPs, showing strong association with lemma color, were located on linkage groups Mrg17, Mrg18, and Mrg20. Discussion: Our results discerned relevant patterns of genetic diversity, population structure, and LD among members of a worldwide collection of oat landraces and cultivars proposed to be 'typical' of the Qinghai-Tibetan Plateau. These results have important implications for further studies on association mapping and practical breeding in high-altitude oat.

Cerebral venous sinus thrombosis caused by traumatic brain injury complicating thyroid storm: a case report and discussion.

INTRODUCTION: Cerebral venous sinus thrombosis (CVST) is an uncommon cerebrovascular disease with diverse predisposing factors. We report a case of CVST caused by a thyroid storm induced by traumatic brain injury. CASE PRESENTATION: A 29-year-old male patient with a history of Graves' disease with hyperthyroidism presented to our hospital with head trauma of cerebral contusion and laceration in both frontal lobes confirmed by admission CT scan. He received mannitol to lower intracranial pressure, haemostatic therapy, and antiepileptic treatment. Eight days later, he presented with signs of thyroid storms, such as tachycardia, hyperthermia, sweating and irritation, and his thyroid function tests revealed high levels of TPO-Ab, TR-Ab, TG-Ab, FT3 and FT4. Then, he entered a deep coma. His brain CT showed a thrombosis of multiple venous sinuses, along with the opening of peripheral collateral vessels, congestive infarction with haemorrhage and brain swelling. He regained consciousness after treatment with antithyroid drugs, anticoagulants, respiratory support and a regimen of sedation/analgesia. After a half-year follow-up, most of the patient's blocked cerebral venous sinuses had been recanalized, but there were still some sequelae, such as an impaired fine motor performance of the right hand and verbal expression defects. CONCLUSIONS: CVST can be induced by thyroid storms, and trauma-related thyroid storms can develop on the basis of hyperthyroidism. The purpose of this case report is to raise clinicians' awareness and improve their ability to diagnose CVST early in patients with traumatic brain injury complicating thyroid storms to improve the neurological prognosis among similar patients.

Evolutionary patterns of plastome resolve multiple origins of the Ns-containing polyploid species in Triticeae.

Tracing evolutionary history proves challenging for polyploid groups that have evolved rapidly, especially if an ancestor of a polyploid is extinct. The Ns-containing polyploids are recognized as the NsXm and StHNsXm genomic constitutions in Triticeae. The Ns originated from Psathyrostachys, while the Xm represented a genome of unknown origin. Here, we use genetic information in plastome to trace the complex lineage history of the Ns-containing polyploid species by sampling 26 polyploids and 90 diploid taxa representing 23 basic genomes in Triticeae. Phylogenetic reconstruction, cluster plot of genetic distance matrix, and migration event demonstrated that (1) the Ns plastome originated from different Psathyrostachys species, and the Xm plastome may originate from an ancestral lineage of Henrardia, Agropyron, and Eremopyrum; (2) the Ns, Xm, and St genome donors separately served as the maternal parents during the speciation of the Ns-containing polyploid species, resulting in a maternal haplotype polymorphism; (3) North AmericanLeymusspecies might originate from colonization during late Miocene via the Bering land bridge and were the paternal donor of the StHNsXm genome Pascopyrum species. Our results shed new light on our understanding of the rich diversity and ecological adaptation of the Ns-containing polyploid species.

Combined RNA-seq and Phenotype Analysis Reveals a Potential Molecular Mechanism of the Difference in Grain Size of Naked Barley From the Qinghai-Tibetan Plateau.

To understand the molecular mechanism controlling the size of barley grains, a number of traits were analyzed and RNA-seq was conducted on grains of two barley materials with a significant difference in thousand-grain weight (TGW) after flowering. The trait dataset delineates the dynamic changes in grain size after flowering, and it provides an understanding of the source of the difference in TGW. By comparing the transcripts of barley grains at several stages after flowering, we identified the gene expression characteristics and significantly enriched pathways in each stage. At the early stage of grain development, genes involved in fatty acid metabolism, plant hormone signal transduction, and pathways involved in cytoskeleton formation were significantly upregulated. At the later stage of grain development, genes involved in starch synthesis, glucose metabolism, and other pathways were significantly upregulated. Further, we used weighted gene coexpression network analysis (WGCNA) and correlation analysis of trait datasets to identify the coexpressed gene modules significantly associated with traits, such as grain length (GL), grain width (GW), and dry weight (DW). After comparing the modules with the differentially expressed gene (DEG) set, 12 candidate genes were selected, and among these, four genes were homologous to genes that regulate grain size in rice and other plants. The combined analysis identified many potential key regulatory factors that may control barley grain size and yield potential, thus providing new insights into the molecular mechanism of barley grain size.

Characterization of the complete chloroplast genome of Avena chinensis (Poales: Poaceae).

Avena chinensis is recognized as one of the cereals with high nutritional value in the world. In this study, the complete chloroplast (cp) genome sequence of A. chinensis was reported. The complete cp genome of A. chinensis was 135,899 bp in length with a GC content of 38.51%, including a large single copy (LSC) region of 80,117 bp, a small single copy (SSC) region of 12,576 bp, and a pair of inverted repeated regions of 21,603 bp. The A. chinensis cp genome encoded 128 functional genes, including 82 protein-coding genes, 38 tRNAs, and eight rRNAs. The phylogenetic analysis showed that A. chinensis was closely related to Avena hybrid and Avena occidentalis.

The alternative splicing of EAM8 contributes to early flowering and short-season adaptation in a landrace barley from the Qinghai-Tibetan Plateau.

KEY MESSAGE: The early flowering of Lalu was determined to be due to a novel spontaneous eam8 mutation, which resulted in intron retention and the formation of a putative truncated protein. Barley is a staple crop grown over an extensive area in the Qinghai-Tibetan Plateau. Understanding the genetic mechanism for its success in a high altitude is important for crop improvement in marginal environments. Early flowering is a critical adaptive trait that strongly influences reproductive fitness in a short growing season. Loss-of-function mutations at the circadian clock gene EARLY MATURITY 8 (EAM8) promote rapid flowering. In this study, we identified a novel, spontaneous recessive eam8 mutant with an early flowering phenotype in a Tibetan barley landrace Lalu, which is natively grown at a high altitude of approximately 4000 m asl. The co-segregation analysis in a F2 population derived from the cross Lalu (early flowering) × Diqing 1 (late flowering) confirmed that early flowering of Lalu was determined to be due to an allele at EAM8. The eam8 allele from Lalu carries an A/G alternative splicing mutation at position 3257 in intron 3, designated eam8.l; this alternative splicing event leads to intron retention and a putative truncated protein. Of the 134 sequenced barley accessions, which are primarily native to the Qinghai-Tibet Plateau, three accessions carried this mutation. The eam8.l mutation was likely to have originated in wild barley due to the presence of the Lalu haplotype in H. spontaneum from Tibet. Overall, alternative splicing has contributed to the evolution of the barley circadian clock and in the short-season adaptation of local barley germplasm. The study has also identified a novel donor of early-flowering barley which will be useful for barley improvement.