Origin and evolution of qingke barley in Tibet

Detection of closely linked QTLs and candidate genes controlling germination indices in response to drought and salinity stresses in barley

The aim of current study was to identify closely linked QTLs and candidate genes related to germination indices under control, salinity and drought conditions in barley. A total of nine (a major), 28 (eight major) and 34 (five major) closely linked QTLs were mapped on the seven chromosomes in response to control, drought and salinity conditions using genome-wide composite interval mapping, respectively. The major QTLs can be used in marker-assisted selection (MAS) projects to increase tolerance to drought and salinity stresses during the germination. Overall, 422 unique candidate genes were associated with most major QTLs. Moreover, gene ontology analysis showed that candidate genes mostly involved in biological process related to signal transduction and response to stimulus in the pathway of resistance to drought and salinity stresses. Also, the protein-protein interaction network was identified 10 genes. Furthermore, 10 genes were associated with receptor-like kinase family. In addition, 16 transcription factors were detected. Three transcription factors including B3, bHLH, and FAR1 had the most encoding genes. Totally, 60 microRNAs were traced to regulate the target genes. Finally, the key genes are a suitable and reliable source for future studies to improve resistance to abiotic stress during the germination of barley.

Combined transcriptomic and metabolomic analysis revealed that pH changes affected the expression of carbohydrate and ribosome biogenesis-related genes in Aspergillus niger SICU-33

The process of carbohydrate metabolism and genetic information transfer is an important part of the study on the effects of the external environment on microbial growth and development. As one of the most significant environmental parameters, pH has an important effect on mycelial growth. In this study, the effects of environmental pH on the growth and nutrient composition of Aspergillus niger (A. niger) filaments were determined. The pH values of the medium were 5, 7, and 9, respectively, and the molecular mechanism was further investigated by transcriptomics and metabolomics methods. The results showed that pH 5 and 9 significantly inhibited filament growth and polysaccharide accumulation of A. niger. Further, the mycelium biomass of A. niger and the crude polysaccharide content was higher when the medium's pH was 7. The DEGs related to ribosome biogenesis were the most abundant, and the downregulated expression of genes encoding XRN1, RRM, and RIO1 affected protein translation, modification, and carbohydrate metabolism in fungi. The dynamic changes of pargyline and choline were in response to the oxidative metabolism of A. niger SICU-33. The ribophorin_I enzymes and DL-lactate may be important substances related to pH changes during carbohydrate metabolism of A.niger SICU-33. The results of this study provide useful transcriptomic and metabolomic information for further analyzing the bioinformatic characteristics of A. niger and improving the application in ecological agricultural fermentation.

Characterization of Fusarium species causing head blight of highland barley (qingke) in Tibet, China

Most of the research on the characterization of Fusarium species focused on wheat, barley, rice, and maize in China. However, there has been limited research in highland barley (qingke). Recently, Fusarium head blight (FHB) of qingke was recently observed in Tibet, China, especially around the Brahmaputra River. To gain a better understanding of the pathogens involver, 201 Fusarium isolates were obtained from qingke samples in 2020. Among these isolates, the most abundant species was F. avenaceum (45.3 %), followed by F. equiseti (27.8 %), F. verticillioides (13.9 %), F. acuminatum (9.0 %), F. flocciferum (3.5 %), and F. proliferatum (0.5 %). The distribution of Fusarium species varied along the Brahmaputra River, with F. avenaceum being predominant in the midstream and downstream regions, while F. equiseti was more common in the upstream region. Chemical analyses of all the isolates revealed the production of different mycotoxins by various Fusarium species. It was found that enniatins were produced by F. acuminatum, F. avenaceum, and F. flocciferum, beauvericin (BEA) and fumonisins were produced F. proliferatum and F. verticillioides, and zearalenone (ZEN) and nivalenol (NIV) were produced by F. equiseti. Pathogenicity test showed that F. avenaceum was more aggressive in causing FHB compared to F. acuminatum, F. equiseti, and F. flocciferum. The disease severity, measured by the area under the disease progress curve (AUDPC), was significantly positively (P < 0.01) correlated with the concentration of total toxins produced by each species. Furthermore, all the Fusarium strains which were used for pathogenicity test were susceptible to carbendazim, and the 50 % effective concentration (EC50) ranged from 0.406 μg/mL to 0.673 μg/mL with an average EC50 of 0.551 ± 0.012 μg/mL.

Most Tibetan weedy barleys originated via recombination between Btr1 and Btr2 in domesticated barley

Tibetan weedy barleys reside at the edges of qingke (hulless barley) fields in Tibet (Xizang). The spikes of these weedy barleys contain or lack a brittle rachis, with either two- or six-rowed spikes and either hulled or hulless grains at maturity. Although the brittle rachis trait of Tibetan weedy barleys is similar to that of wild barley (Hordeum vulgare ssp. spontaneum Thell.), these plants share genetic similarity with domesticated barley. The origin of Tibetan weedy barleys continues to be debated. Here, we show that most Tibetan weedy barleys originated from cross-pollinated hybridization of domesticated barleys, followed by hybrid self-pollination and recombination between Non-brittle rachis 1 (btr1) and 2 (btr2). We discovered the specific genetic ancestry of these weedy barleys in South Asian accessions. Tibetan weedy barleys exhibit lower genetic diversity than wild and Chinese landraces/cultivars and share a close relationship with qingke, genetically differing from typical eastern and western barley populations. We classified Tibetan weedy barleys into two groups, brittle rachis (BR) and non-brittle rachis (NBR); these traits align with the haplotypes of the btr1 and btr2 genes. Whereas wild barleys carry haplotype combinations of Btr1 and Btr2, each showing lower proportions in a population, the recombinant haplotype BTR2H8+BTR1H24 is predominant in the BR group. Haplotype block analysis based on whole-genome sequencing revealed two recombination breakpoints, which are present in 80.6% and 16.8% of BR accessions according to marker-assisted analysis. Hybridization events between wild and domesticated barley were rarely detected. These findings support the notion that Tibetan weedy barleys originated via recombination between Btr1 and Btr2 in domesticated barley.

Genomic variation, environmental adaptation, and feralization in ramie, an ancient fiber crop

Feralization is an important evolutionary process, but the mechanisms behind it remain poorly understood. Here, we use the ancient fiber crop ramie (Boehmeria nivea (L.) Gaudich.) as a model to investigate genomic changes associated with both domestication and feralization. We first produced a chromosome-scale de novo genome assembly of feral ramie and investigated structural variations between feral and domesticated ramie genomes. Next, we gathered 915 accessions from 23 countries, comprising cultivars, major landraces, feral populations, and the wild progenitor. Based on whole-genome resequencing of these accessions, we constructed the most comprehensive ramie genomic variation map to date. Phylogenetic, demographic, and admixture signal detection analyses indicated that feral ramie is of exoferal or exo-endo origin, i.e., descended from hybridization between domesticated ramie and the wild progenitor or ancient landraces. Feral ramie has higher genetic diversity than wild or domesticated ramie, and genomic regions affected by natural selection during feralization differ from those under selection during domestication. Ecological analyses showed that feral and domesticated ramie have similar ecological niches that differ substantially from the niche of the wild progenitor, and three environmental variables are associated with habitat-specific adaptation in feral ramie. These findings advance our understanding of feralization, providing a scientific basis for the excavation of new crop germplasm resources and offering novel insights into the evolution of feralization in nature.

Ethnobotanical studies on rice landraces under on-farm conservation in Xishuangbanna of Yunnan Province, China

BACKGROUND

A complex interaction and mutual influence exists among landscapes, cultures, and landraces, with rice culture being a typical embodiment of this relationship. The conservation of landraces operates alongside preserving traditional practices. The Xishuangbanna region stands out as a hub for the genetic diversity of landraces, boasting rich genetic resources. Despite the diverse rice resources in this region, a comprehensive and systematic study has not been undertaken.

METHODS

From October to November 2023, we collected rice landraces under the on-farm conservation in 18 townships including Menghai, Mengla and Jinghong in Xishuangbanna. Employing semi-structured interviews and various methods, we investigated factors influencing the preservation and loss of rice landraces in the region. Statistical analysis was applied to the agronomic traits of collected local rice, encompassing indica or japonica, glutinous or non-glutinous, grain shape, and hull color as second category traits. The second category included quantitative traits like thousand grain weight and grain length. Rice diversity among different regions, traits, and ethnic groups was assessed using the Shannon-Wiener index. Additionally, clustering analysis via the UPGMA method depicted the distribution characteristics of the resources.

RESULTS

A total of 70 rice landraces were collected in the Xishuangbanna region, each exhibiting distinct characteristics. Differences were observed across regions, trait, naming, and ethnic groups. Diversity analysis revealed that Mengla had the highest diversity, followed by Menghai, while Jinghong exhibited the lowest diversity. The second category of traits displayed broader diversity than the first, with the Dai people's glutinous rice showcasing greater diversity than other ethnic groups. Cluster analysis categorized the 70 samples into seven groups at a genetic distance of 1.15. Ethnobotanical interviews emphasized the rapid loss of rice landraces resources in Xishuangbanna, with indigenous ethnic cultures playing a vital role in the conservation of rice landraces. Dai traditions, in particular, played a crucial role in protecting glutinous rice resources, showcasing a mutual dependence between Dai culture and glutinous rice.

CONCLUSIONS

The rich natural environment and diverse ethnic cultures in Xishuangbanna have given rise to various rice landraces. The Dai, primary cultivators of glutinous rice with higher diversity, intertwine their traditional ethnic culture with the conservation of glutinous rice resources. At the same time, the preserving glutinous rice resources promotes the inheritance of Dai ethnic culture. However, rice landraces are facing the risk of loss. Hence, collecting and documenting rice landraces is crucial. Encourage local communities to sustain and expand their cultivation, promoting on-farm conservation. These measures contribute valuable germplasm and genes for rice breeding and serve as a means of cultural preservation.

Acyl-CoA-binding protein (ACBP) genes involvement in response to abiotic stress and exogenous hormone application in barley (Hordeum vulgare L.)

BACKGROUND

Acyl-CoA-Binding proteins (ACBPs) function as coenzyme A transporters and play important roles in regulating plant growth and development in response to abiotic stress and phytohormones, as well as in membrane repair. To date, the ACBP family has not been a comprehensively characterized in barley (Hordeum vulgare L.).

RESULTS

Eight ACBP genes were identified in the barley genome and named as HvACBP1-8. The analysis of the proteins structure and promoter elements of HvACBP suggested its potential functions in plant growth, development, and stress response. These HvACBPs are expressed in specific tissues and organs following induction by abiotic stressors such as drought, salinity, UV-B exposure, temperature extremes, and exposure to exogenous phytohormones. The HvACBP7 and HvACBP8 amino acid sequences were conserved during the domestication of Tibetan Qingke barley.

CONCLUSIONS

Acyl-CoA-binding proteins may play important roles in barley growth and environmental adaptation. This study provides foundation for further analyses of the biological functions of HvACBPs in the barley stress response.

Genomic evidence for climate-linked diversity loss and increased vulnerability of wild barley spanning 28 years of climate warming

The information on how plant populations respond genetically to climate warming is scarce. Here, landscape genomic and machine learning approaches were integrated to assess genetic response of 10 wild barley (Hordeum vulgare ssp. spontaneum; WB) populations in the past and future, using whole genomic sequencing (WGS) data. The WB populations were sampled in 1980 and again in 2008. Phylogeny of accessions was roughly in conformity with sampling sites, which accompanied by admixture/introgressions. The 28-y climate warming resulted in decreased genetic diversity, increased selection pressure, and an increase in deleterious single nucleotide polymorphism (dSNP) numbers, heterozygous deleterious and total deleterious burdens for WB. Genome-environment associations identified some candidate genes belonging to peroxidase family (HORVU2Hr1G057450, HORVU4Hr1G052060 and HORVU4Hr1G057210) and heat shock protein 70 family (HORVU2Hr1G112630). The gene HORVU2Hr1G120170 identified by selective sweep analysis was under strong selection during the climate warming of the 28-y, and its derived haplotypes were fixed by WB when faced with the 28-y increasingly severe environment. Temperature variables were found to be more important than precipitation variables in influencing genomic variation, with an eco-physiological index gdd5 (growing degree-days at the baseline threshold temperature of 5 °C) being the most important determinant. Gradient forest modelling revealed higher predicted genomic vulnerability in Sede Boqer under future climate scenarios at 2041-2070 and 2071-2100. Additionally, estimates of effective population size (Ne) tracing back to 250 years indicated a forward decline in all populations over time. Our assessment about past genetic response and future vulnerability of WB under climate warming is crucial for informing conservation efforts for wild cereals and rational use strategies.

The Quality Evaluation of Highland Barley and Its Suitability for Chinese Traditional Tsampa Processing

The physicochemical traits of highland barley prominently affect the quality of Tsampa. To find out the relevance between the physicochemical properties of raw material and the texture parameters of processed products, twenty-five physicochemical traits and ten quality parameters for seventy-six varieties of highland barley were measured and analyzed. The results showed that there was a significant difference between the physicochemical indexes for highland barleys of various colors. The dark highland barley generally has more fat, protein, total dietary fiber, phenolic, Mg, K, Ca, and Zn and less amylose, Fe, Cu, and Mo than light colored barley. Then, these highland barleys were made into Tsampa. A comprehensive quality evaluation model based on the color and texture parameters of Tsampa was established through principal component analysis. Then, cluster analysis was used to classify the tested samples into three edible quality grades predicated on the above evaluation model. At last, the regression analysis was applied to establish a Tsampa quality predictive model according to the physicochemical traits of the raw material. The results showed that amylose, protein, β-Glucan, and a* and b* could be used to predict the comprehensive quality of Tsampa. The predicted results indicated that 11 of 14 validated samples were consistent with the actual quality, and the accuracy was above 78.57%. Our study built the approach of the appropriate processing varieties evaluation. It may provide reference for processing specific highland barley.

Effect of mashing temperature on fermentation and antioxidant capacity of Qingke wort

Background and Objectives

Mashing temperature is important during beer brewing processes. Qingke malt was a new material whose application in the beer industry holds significant importance for the beer industry and agriculture development in the Qinghai–Tibet Plateau. The objective of this study was to investigate the effects of mashing temperature on the physicochemical parameters, fermentation capacity, and antioxidant capacity of Qingke wort.

Findings

Ethanol production and the real degree of fermentation decreased with increasing the temperature—S, while the real extract increased with increasing the temperature—S. A lower temperature—S proved to be more advantageous for the fermentation capacity of Qingke wort. In addition, a positive correlation between reducing power and the temperature—P and a negative correlation between the 2,2′‐azinobis‐(3‐ethylbenzothiazoline‐6‐sulfonate) free radical scavenging activity and the temperature—S were found.

Conclusion

The fermentation capacity of Qingke wort was obtained the best when the temperature—P was 50°C and the temperature—S was 60°C. The antioxidant capacity of Qingke wort was satisfactory; the best was obtained when the temperature—P was 45°C and the temperature—S was 60°C.

Significance and Novelty

This is the first study to investigate the mashing characteristics of Qingke wort under different mashing temperatures. The results show that β‐glucan content was abundant in Qingke wort and was positively correlative with the temperature—S.

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.

CoreSNP: an efficient pipeline for core marker profile selection from genome-wide SNP datasets in crops

BACKGROUND

DNA marker profiles play a crucial role in the identification and registration of germplasm, as well as in the distinctness, uniformity, and stability (DUS) testing of new plant variety protection. However, selecting minimal marker sets from large-scale SNP dataset can be challenging to distinguish a maximum number of samples.

RESULTS

Here, we developed the CoreSNP pipeline using a "divide and conquer" strategy and a "greedy" algorithm. The pipeline offers adjustable parameters to guarantee the distinction of each sample pair with at least two markers. Additionally, it allows datasets with missing loci as input. The pipeline was tested in barley, soybean, wheat, rice and maize. A few dozen of core SNPs were efficiently selected in different crops with SNP array, GBS, and WGS dataset, which can differentiate thousands of individual samples. The core SNPs were distributed across all chromosomes, exhibiting lower pairwise linkage disequilibrium (LD) and higher polymorphism information content (PIC) and minor allele frequencies (MAF). It was shown that both the genetic diversity of the population and the characteristics of the original dataset can significantly influence the number of core markers. In addition, the core SNPs capture a certain level of the original population structure.

CONCLUSIONS

CoreSNP is an efficiency way of core marker sets selection based on Genome-wide SNP datasets of crops. Combined with low-density SNP chip or genotyping technologies, it can be a cost-effective way to simplify and expedite the evaluation of genetic resources and differentiate different crop varieties. This tool is expected to have great application prospects in the rapid comparison of germplasm and intellectual property protection of new varieties.

Loss of ADP-glucose transporter in barley sex1 mutant caused shrunken endosperm but with elevated protein and β-glucan content in whole meal

Grain shape and plumpness affect barley yield. Despite numerous studies on shrunken endosperm mutants in barley, their molecular mechanism and application potential in the food industry are largely unknown. Here, map-based cloning, co-segregation analyses, and allelic variant validation revealed that the loss of HORVU6Hr1G037950 encoding an ADP-glucose transporter caused the shrunken endosperm in sex1. Haplotype analysis suggested that hap4 in the promoter sequence was positively related to the hundred-grain weight showing a breeding potential. A pair of near-isogenic lines targeting HORVU6Hr1G037950 was produced and characterized to investigate molecular mechanisms that SEX1 regulates endosperm development. Results presented that the absence of the SEX1 gene led to the decrease of starch content and A-type granules size, the increase of β-glucan, protein, gelatinization temperature, soluble sugar content, amylopectin A chains, and B1 chains. Enzymatic activity, transcriptome and metabolome analyses revealed the loss of SEX1 results in an impaired ADP-glucose-to-starch conversion process, consequently leading to higher soluble sugar contents and lower starch accumulation, thereby inducing a shrunken-endosperm phenotype in sex1. Taken together, this study provides new insights into barley grain development, and the elevated protein and β-glucan contents of the whole meal in sex1 imply its promising application in the food industry.

Genetic and cultural adaptations underlie the establishment of dairy pastoralism in the Tibetan Plateau

BACKGROUND

Domestication and introduction of dairy animals facilitated the permanent human occupation of the Tibetan Plateau. Yet the history of dairy pastoralism in the Tibetan Plateau remains poorly understood. Little is known how Tibetans adapted to milk and dairy products.

RESULTS

We integrated archeological evidence and genetic analysis to show the picture that the dairy ruminants, together with dogs, were introduced from West Eurasia into the Tibetan Plateau since ~ 3600 years ago. The genetic admixture between the exotic and indigenous dogs enriched the candidate lactase persistence (LP) allele 10974A > G of West Eurasian origin in Tibetan dogs. In vitro experiments demonstrate that - 13838G > A functions as a LP allele in Tibetans. Unlike multiple LP alleles presenting selective signatures in West Eurasians and South Asians, the de novo origin of Tibetan-specific LP allele - 13838G > A with low frequency (~ 6-7%) and absence of selection corresponds - 13910C > T in pastoralists across eastern Eurasia steppe.

CONCLUSIONS

Results depict a novel scenario of genetic and cultural adaptations to diet and expand current understanding of the establishment of dairy pastoralism in the Tibetan Plateau.

Response of salt stress resistance in highland barley (Hordeum vulgare L. var. nudum) through phenylpropane metabolic pathway

Highland barley (Hordeum vulgare L. var. nudum) is a grain crop that grows on the plateau under poor and high salt conditions. Therefore, to cultivate high-quality highland barley varieties, it is necessary to study the molecular mechanism of strong resistance in highland barley, which has not been clearly explained. In this study, a high concentration of NaCl (240 mmol/L), simulating the unfavorable environment, was used to spray the treated highland barley seeds. Transcriptomic analysis revealed that the expression of more than 8,000 genes in highland barley seed cells was significantly altered, suggesting that the metabolic landscape of the cells was deeply changed under salt stress. Through the KEGG analysis, the phenylpropane metabolic pathway was significantly up-regulated under salt stress, resulting in the accumulation of polyphenols, flavonoids, and lignin, the metabolites for improving the stress resistance of highland barley seed cells, being increased 2.71, 1.22, and 1.17 times, respectively. This study discovered that the phenylpropane metabolic pathway was a significant step forward in understanding the stress resistance of highland barley, and provided new insights into the roles of molecular mechanisms in plant defense.

Plant genome resequencing and population genomics: Current status and future prospects

Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.

Triticeae crop genome biology: an endless frontier

Triticeae, the wheatgrass tribe, includes several major cereal crops and their wild relatives. Major crops within the Triticeae are wheat, barley, rye, and oat, which are important for human consumption, animal feed, and rangeland protection. Species within this tribe are known for their large genomes and complex genetic histories. Powered by recent advances in sequencing technology, researchers worldwide have made progress in elucidating the genomes of Triticeae crops. In addition to assemblies of high-quality reference genomes, pan-genome studies have just started to capture the genomic diversities of these species, shedding light on our understanding of the genetic basis of domestication and environmental adaptation of Triticeae crops. In this review, we focus on recent signs of progress in genome sequencing, pan-genome analyses, and resequencing analysis of Triticeae crops. We also propose future research avenues in Triticeae crop genomes, including identifying genome structure variations, the association of genomic regions with desired traits, mining functions of the non-coding area, introgression of high-quality genes from wild Triticeae resources, genome editing, and integration of genomic resources.

Genome resequencing and transcriptome profiling reveal molecular evidence of tolerance to water deficit in barley

INTRODUCTION

Frequent climate change-induced drought events are detrimental environmental stresses affecting global crop production and ecosystem health. Several efforts have facilitated crop breeding for resilient varieties to counteract stress. However, progress is hampered due to the complexity of drought tolerance; a greater variety of novel genes are required across varying environments. Tibetan annual wild barley is a unique and precious germplasm that is well adapted to abiotic stress and can provide elite genes for crop improvement in drought tolerance.

OBJECTIVES

To identify the genetic basis and unique mechanisms for drought tolerance in Tibetan wild barley.

METHODS

Whole genome resequencing and comparative RNA-seq approaches were performed to identify candidate genes associated with drought tolerance via investigating the genetic diversity and transcriptional variation between cultivated and Tibetan wild barley. Bioinformatics, population genetics, and gene silencing were conducted to obtain insights into ecological adaptation in barley and functions of key genes.

RESULTS

Over 20 million genetic variants and a total of 15,361 significantly affected genes were identified in our dataset. Combined genomic, transcriptomic, evolutionary, and experimental analyses revealed 26 water deficit resilience-associated genes in the drought-tolerant wild barley XZ5 with unique genetic variants and expression patterns. Functional prediction revealed Tibetan wild barley employs effective regulators to activate various responsive pathways with novel genes, such as Zinc-Induced Facilitator-Like 2 (HvZIFL2) and Peroxidase 11 (HvPOD11), to adapt to water deficit conditions. Gene silencing and drought tolerance evaluation in a natural barley population demonstrated that HvZIFL2 and HvPOD11 positively regulate drought tolerance in barley.

CONCLUSION

Our findings reveal functional genes that have been selected across barley's complex history of domestication to thrive in water deficit environments. This will be useful for molecular breeding and provide new insights into drought-tolerance mechanisms in wild relatives of major cereal crops.

Transcriptome Screening of Long Noncoding RNAs and Their Target Protein-Coding Genes Unmasks a Dynamic Portrait of Seed Coat Coloration Associated with Anthocyanins in Tibetan Hulless Barley

Many plants have the capability to accumulate anthocyanins for coloration, and anthocyanins are advantageous to human health. In the case of hulless barley (Hordeum vulgare L. var. nudum), investigation into the mechanism of anthocyanin formation is limited to the level of protein-coding genes (PCGs). Here, we conducted a comprehensive bioinformatics analysis to identify a total of 9414 long noncoding RNAs (lncRNAs) in the seed coats of purple and white hulless barley along a developmental gradient. Transcriptome-wide profiles of lncRNAs documented several properties, including GC content fluctuation, uneven length, a diverse range of exon numbers, and a wide variety of transcript classifications. We found that certain lncRNAs in hulless barley possess detectable sequence conservation with Hordeum vulgare and other monocots. Furthermore, both differentially expressed lncRNAs (DElncRNAs) and PCGs (DEPCGs) were concentrated in the later seed development stages. On the one hand, DElncRNAs could potentially cis-regulate DEPCGs associated with multiple metabolic pathways, including flavonoid and anthocyanin biosynthesis in the late milk and soft dough stages. On the other hand, there was an opportunity for trans-regulated lncRNAs in the color-forming module to affect seed coat color by upregulating PCGs in the anthocyanin pathway. In addition, the interweaving of hulless barley lncRNAs and diverse TFs may function in seed coat coloration. Notably, we depicted a dynamic portrait of the anthocyanin synthesis pathway containing hulless barley lncRNAs. Therefore, this work provides valuable gene resources and more insights into the molecular mechanisms underlying anthocyanin accumulation in hulless barley from the perspective of lncRNAs, which facilitate the development of molecular design breeding in crops.

Occurrence of Fusarium mycotoxins in freshly harvested highland barley (qingke) grains from Tibet, China

Highland barley, also called "qingke" in Tibetan, is mainly cultivated in the Tibetan Plateau of China and has been used as a major staple food for Tibetans. Recently, Fusarium head blight (FHB) of qingke was frequently observed around the Brahmaputra River in Tibet. Considering the importance of qingke for Tibetans, the assessment of Fusarium mycotoxin contamination is essential for food safety. In this study, a total of 150 freshly harvested qingke grain samples were obtained from three regions around the Brahmaputra River in Tibet (China) in 2020. The samples were investigated for the occurrence of 20 Fusarium mycotoxins using high-performance liquid chromatography-tandem mass spectrometry (HPLC‒MS/MS). The most frequently occurring mycotoxin was enniatin B (ENB) (46%), followed by enniatin B₁ (ENB₁) (14.7%), zearalenone (ZEN) (6.0%), enniatin A₁ (ENA₁) (3.3%), enniatin A (ENA) (1.3%), beauvericin (BEA) (0.7%), and nivalenol (NIV) (0.7%). Due to the increase in altitude, the cumulative precipitation level and average temperature decreased from the downstream to the upstream of the Brahmaputra River; this directly correlated to the contamination level of ENB in qingke, which gradually decreased from downstream to upstream. In addition, the level of ENB in qingke obtained from qingke-rape rotation was significantly lower than that from qingke-wheat and qingke-qingke rotations (p < 0.05). These results disseminated the occurrence of Fusarium mycotoxins and provided further understanding of the effect of environmental factors and crop rotation on Fusarium mycotoxins.

Study on the Changes in Volatile Flavor Compounds in Whole Highland Barley Flour during Accelerated Storage after Different Processing Methods

The effect of heat processing on the flavor characteristics of highland barley flour (HBF) in storage was revealed by analyzing differences in volatile compounds associated with flavor deterioration in HBF using GC-MS identification and relative odor activity values (ROAVs). Hydrocarbons were the most abundant in untreated and extrusion puffed HBFs, while heterocycles were found to be the most abundant in explosion puffed, baked, and fried HBFs. The major contributors to the deterioration of flavor in different HBFs were hexanal, hexanoic acid, 2-pentylfuran, 1-pentanol, pentanal, 1-octen-3-ol, octanal, 2-butyl-2-octanal, and (E,E)-2,4-decadienal. Amino acid and fatty acid metabolism was ascribed to the main formation pathways of these compounds. Baking slowed down the flavor deterioration in HBF, while extrusion puffing accelerated the flavor deterioration in HBF. The screened key compounds could predict the quality of HBF. This study provides a theoretical basis for the regulation of the flavor quality of barley and its products.

Genome diversity and highland-adaptative variation in Tibet barley landrace population of China

Barley landraces accumulated variation in adapting to extreme highland environments during long-term domestication in Tibet, but little is known about their population structure and genomic selection traces. In this study, tGBS (tunable genotyping by sequencing) sequencing, molecular marker and phenotypic analyses were conducted on 1,308 highland and 58 inland barley landraces in China. The accessions were divided into six sub-populations and clearly distinguished most six-rowed, naked barley accessions (Qingke in Tibet) from inland barley. Genome-wide differentiation was observed in all five sub-populations of Qingke and inland barley accessions. High genetic differentiation in the pericentric regions of chromosomes 2H and 3H contributed to formation of five types of Qingke. Ten haplotypes of the pericentric regions of 2H, 3H, 6H and 7H were further identified as associated with ecological diversification of these sub-populations. There was genetic exchange between eastern and western Qingke but they shared the same progenitor. The identification of 20 inland barley types indicated multiple origins of Qingke in Tibet. The distribution of the five types of Qingke corresponded to specific environments. Two predominant highland-adaptative variations were identified for low temperature tolerance and grain color. Our results provide new insights into the origin, genome differentiation, population structure and highland adaptation in highland barley which will benefit both germplasm enhancement and breeding of naked barley.

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.

Genome-wide analysis of pathogenesis-related protein-1 (PR-1) genes from Qingke (Hordeum vulgare L. var. nudum) reveals their roles in stress responses

Proteins that are pathogenesis-related 1 (PR-1) can accumulate to high levels when plants employ defenses, being major participants in processes critical for stress responses as well as development of many species. Yet we still lack information concerning PR-1 family members in Qingke plants (Hordeum vulgare L. var. nudum). In this work, we distinguished 20 PR-1s from the Qingke genome whose encoded proteins often featured at the N-terminus a signal peptide; all 20 PR-1s were predicted to localize either periplasmically or extracellularly. The CAP domain was confirmed as being highly conserved in all these PR-1s. Phylogeny-based inference revealed that PR-1 proteins clustered into four major clades, with the majority of Qingke PR-1s distributed in clade I (17 out 20), and the other 3 distributed in clade II. Gene structure analysis showed that 16 PR-1s did not contain any introns, whereas the other four had 1-4 introns. We identified a variety of motifs that are cis-acting in the promoter regions of PR-1s; these included those potentially involved in Qingke's light response, hormonal and stress responses, circadian control and regulation of development and growth, in addition to sites where transcription factors bind to. Expression analysis uncovered several members of PR-1 genes that were strongly and rapidly induced by powdery mildew infection, phytohormones, and cold stimulus. Altogether, our study's findings enhance what is known about genetic features of PR-1 family members in H. vulgare plants, especially Qingke, and could thereby facilitate further exploration aiming to elucidate the functioning of these proteins.

BarleyExpDB: an integrative gene expression database for barley

BACKGROUND

RNA-sequencing (RNA-seq) has been widely used to study the dynamic expression patterns of transcribed genes, which can lead to new biological insights. However, processing and analyzing these huge amounts of histological data remains a great challenge for wet labs and field researchers who lack bioinformatics experience and computational resources.

RESULTS

We present BarleyExpDB, an easy-to-operate, free, and web-accessible database that integrates transcriptional profiles of barley at different growth and developmental stages, tissues, and stress conditions, as well as differential expression of mutants and populations to build a platform for barley expression and visualization. The expression of a gene of interest can be easily queried by searching by known gene ID or sequence similarity. Expression data can be displayed as a heat map, along with functional descriptions as well as Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Proteins Families Database, and Simple Modular Architecture Research Tool annotations.

CONCLUSIONS

BarleyExpDB will serve as a valuable resource for the barley research community to leverage the vast publicly available RNA-seq datasets for functional genomics research and crop molecular breeding.

Virulence and Genetic Types of Blumeria graminis f. sp. hordei in Tibet and Surrounding Areas

Barley (Hordeum vulgare L.) is the most important cereal crop in the Qinghai-Tibet Plateau, and the yield has been seriously threatened by Blumeria graminis f. sp. hordei (Bgh) in recent years. To understand the virulence and genetic traits of different Bgh populations, 229 isolates of Bgh were collected from Tibet, Sichuan, Gansu and Yunnan provinces of China during 2020 and 2021, and their pathogenicity to 21 barley lines of different genotypes was assessed. A total of 132 virulent types were identified. The Bgh isolates from Yunnan showed the highest diversity in terms of virulence complexity (Rci) and genetic diversity (KWm), followed by those from Sichuan, Gansu, and Tibet, in that order. Single nucleotide polymorphism (SNP) in genes coding for alternative oxidase (AOX), protein kinase A (PKA), and protein phosphatase type 2A (PPA) were detected at seven polymorphic sites. Nine haplotypes (H1–H9) with an average haplotype diversity (Hd) and nucleotide diversity π of 0.564 and 0.00034, respectively, were observed. Of these, haplotypes H1 and H4 accounted for 88.8% of the isolates, and H4 was predominant in Tibet. Genetic diversity analysis using the STRUCTURE (K = 2) and AMOVE indicated that the inter-group variation accounted for 54.68%, and inter- and intra-population genotypic heterogeneity accounted for 23.90% and 21.42%, respectively. The results revealed the recent expansion of the Bgh population in Tibet, accompanied by an increase in virulence and a loss of genetic diversity.

Mixed organic and inorganic amendments enhance soil microbial interactions and environmental stress resistance of Tibetan barley on plateau farmland

Sufficient crop yield while maintaining soil health and sustainable agricultural development is a global objective, serving a special challenge to certain climate-sensitive plateau areas. Despite conducting trails on a variety of soil amendments in plateau areas, systematic research is lacking regarding the influences of organic and inorganic amendments on soil quality, particularly soil microbiome. To our knowledge, this was the first study that compared the effects of inorganic, organic, and mixed amendments on typical plateau crop hulless barley (Hordeum vulgare L. var. Nudum, also known as "Qingke" in Chinese) over the course of tillering, jointing, and ripening. Microbial communities and their responses to amendments, soil properties and Tibetan hulless barley growth, yield were investigated. Results indicated that mixed organic and inorganic amendments promoted the abundance of rhizosphere microorganisms, enhancing the rhizosphere root-microbes interactions and resistance to pathogenic bacteria and environmental stresses. The rhizosphere abundant and significantly different genera Arthrobacter, Rhodanobacter, Sphingomona, Nocardioides and so on demonstrated their unique adaptation to the plateau environment based on the results of metagenomic binning. The abundance of 23 genes about plant growth and environmental adaptations in the mixed amendment soil were significantly higher than other treatments. Findings from this study suggest that the mixed organic/inorganic amendments can help establish a healthy microbiome and increase soil quality while achieving sufficient hulless barley yields in Tibet and presumably other similar geographic areas of high altitude.

Population genomics unravels the Holocene history of bread wheat and its relatives

Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accessions, we found that bread wheat originated from the southwest coast of the Caspian Sea and underwent a slow speciation process, lasting ~3,300 yr owing to persistent gene flow from its relatives. Soon after, bread wheat spread across Eurasia and reached Europe, South Asia and East Asia ~7,000 to ~5,000 yr ago, shaping a diversified but occasionally convergent adaptive landscape in novel environments. By contrast, the cultivated relatives of bread wheat experienced a population decline by ~82% over the past ~2,000 yr due to the food choice shift of humans. Further biogeographical modelling predicted a continued population shrinking of many bread wheat relatives in the coming decades because of their vulnerability to the changing climate. These findings will guide future efforts in protecting and utilizing wheat biodiversity to enhance global wheat production.

Agricultural weeds: the contribution of domesticated species to the origin and evolution of feral weeds

Agricultural weeds descended from domesticated ancestors, directly from crops (endoferality) and/or from crop-wild hybridization (exoferality), may have evolutionary advantages by rapidly acquiring traits pre-adapted to agricultural habitats. Understanding the role of crops on the origin and evolution of agricultural weeds is essential to develop more effective weed management programs, minimize crop losses due to weeds, and accurately assess the risks of cultivated genes escaping. In this review, we first describe relevant traits of weediness: shattering, seed dormancy, branching, early flowering and rapid growth, and their role in the feralization process. Furthermore, we discuss how the design of "super-crops" can affect weed evolution. We then searched for literature documenting cases of agricultural weeds descended from well-domesticated crops, and describe six case studies of feral weeds evolved from major crops: maize, radish, rapeseed, rice, sorghum, and sunflower. Further studies on the origin and evolution of feral weeds can improve our understanding of the physiological and genetic mechanisms underpinning the adaptation to agricultural habitats and may help to develop more effective weed-control practices and breeding better crops. © 2022 Society of Chemical Industry.

Polyphenol Profile and In Vitro Antioxidant and Enzyme Inhibitory Activities of Different Solvent Extracts of Highland Barley Bran

Five different solvent extracts of highland barley bran were analyzed and compared for their polyphenol profile, antioxidant activity, and α-glucosidase and α-amylase inhibitory activities. The highland barley bran acetone extract had the highest total phenolic content, total flavonoid content, and antioxidant capacity. It was followed by the methanol and ethanol extracts, while n-butanol and ethyl acetate extracts exhibited lower measured values. Diosmetin, luteolin, protocatechuic acid, vanillic acid, ferulic acid, phlorogucinol, diosmin, isoquercitrin, catechin, and isovitexin were among the most abundant phenolic compounds identified in different solvent extracts, and their concentrations varied according to the solvent used. The highest α-glucosidase and α-amylase inhibitory activity were observed in the ethyl acetate extract of highland barley bran, followed by the acetone and methanol extracts. In contrast, n-butanol and ethanol extracts exhibited lower measured values. The different solvent extracts were effective inhibitors for α-glucosidase and α-amylase with activity reaching to 34.45-94.32% and 22.08-35.92% of that of positive control acarbose, respectively. There were obvious correlations between the phenolic content and composition of different solvent extracts and their in vitro antioxidant activity, α-glucosidase inhibition activity and α-amylase inhibition activity. Black barley bran is an excellent natural raw material for developing polyphenol-rich functional foods and shows good antioxidant and hypoglycemic potential to benefit human health.

Genomic footprints of Kam Sweet Rice domestication indicate possible migration routes of the Dong people in China and provide resources for future rice breeding

The Dong people are one of China's 55 recognized ethnic minorities, but there has been a long-standing debate about their origins. In this study, we performed whole-genome resequencing of Kam Sweet Rice (KSR), a valuable, rare, and ancient rice landrace unique to the Dong people. Through comparative genomic analyses of KSR and other rice landraces from south of the Yangtze River Basin in China, we provide evidence that the ancestors of the Dong people likely originated from the southeast coast of China at least 1000 years ago. Alien introgression and admixture in KSR demonstrated multiple migration events in the history of the Dong people. Genomic footprints of domestication demonstrated characteristics of KSR that arose from artificial selection and geographical adaptation by the Dong people. The key genes GS3, Hd1, and DPS1 (related to agronomic traits) and LTG1 and MYBS3 (related to cold tolerance) were identified as domestication targets, reflecting crop improvement and changes in the geographical environment of the Dong people during migration. A genome-wide association study revealed a candidate yield-associated gene, Os01g0923300, a specific haplotype in KSR that is important for regulating grain number per panicle. RNA-sequencing and quantitative reverse transcription-PCR results showed that this gene was more highly expressed in KSR than in ancestral populations, indicating that it may have great value in increasing yield potential in other rice accessions. In summary, our work develops a novel approach for studying human civilization and migration patterns and provides valuable genomic datasets and resources for future breeding of high-yield and climate-resilient rice varieties.

Different Photosynthetic Response to High Light in Four Triticeae Crops

Photosynthetic capacity is usually affected by light intensity in the field. In this study, photosynthetic characteristics of four different Triticeae crops (wheat, triticale, barley, and highland barley) were investigated based on chlorophyll fluorescence and the level of photosynthetic proteins under high light. Compared with wheat, three cereals (triticale, barley, and highland barley) presented higher photochemical efficiency and heat dissipation under normal light and high light for 3 h, especially highland barley. In contrast, lower photoinhibition was observed in barley and highland barley relative to wheat and triticale. In addition, barley and highland barley showed a lower decline in D1 and higher increase in Lhcb6 than wheat and triticale under high light. Furthermore, compared with the control, the results obtained from PSII protein phosphorylation showed that the phosphorylation level of PSII reaction center proteins (D1 and D2) was higher in barley and highland barley than that of wheat and triticale. Therefore, we speculated that highland barley can effectively alleviate photodamages to photosynthetic apparatus by high photoprotective dissipation, strong phosphorylation of PSII reaction center proteins, and rapid PSII repair cycle under high light.

Genetic diversity and population structure of barley landraces from Southern Ethiopia's Gumer district: Utilization for breeding and conservation

Barley is the fifth most important food crop in Ethiopia. The genetic relationship and population structure studies of barley are limited to gene bank collections. Therefore, this study fills a gap by investigating the selection, consumption, economic value, genetic diversity, and population structure of farm-collected barley from the Gumer district of the Gurage Zone, which has received little attention. The information on the use of barley in the study area was collected using semi-structured interviews and questionnaires. 124 households of 11 kebeles, the smallest community unit, were interviewed. Barley landraces collected were compared with those collected from Japan, the United States (USA), and other Ethiopian locations. Illumina iSelect (50K genotyping platform) was used to identify single nucleotide polymorphisms (SNP) (20,367). Thirty landraces were found in Gumer. Burdaenadenber had the highest on-farm Shannon index estimate (2.0), followed by Aselecha (1.97) and Enjefo (1.95). Aselecha and Fetazer had the highest (44%) and the lowest (29%) richness values, respectively. High and low Simpson index values were found in Aselecha (84%) and Wulbaragenateretero (79%), respectively. The neighbor-joining tree revealed that Gumer landraces formed a separate subcluster with a common ancestral node; a sister subcluster contained barley landraces from Japan. According to the population structure analysis, barley landraces from Gumer differed from Japan and the United States. The principal component analysis revealed that US barley was the most distant group from Gumer barley. The markers' allele frequencies ranged from 0.10 to 0.50, with an average value of 0.28. The mean values of Nei's gene diversity (0.38) and the polymorphic information content (0.30) indicated the presence of high genetic diversity in the samples. The clustering of accessions was not based on geographic origin. Significant genetic diversity calls for additional research and analysis of local barley diversity because the selection and use of barley in Ethiopia would have been affected by the preference of ethnic groups.

Exchanges of economic plants along the land silk road

BACKGROUD

The greatest contribution of the Silk Road is to communicate among different countries and nationalities, and promote two-way cultural exchanges between the East and the West. We now have clearer understanding about how material civilization and religious culture of Central Asia and West Asia spread eastward along the Land Silk Road. However, there is controversial about how crops migrate along the Land Silk Road.

RESULTS

We summarize archaeology, genetics, and genomics data to explore crop migration patterns. Of the 207 crops that were domesticated along the Land Silk Road, 19 for which genomic evidence was available were selected for discussion.

CONCLUSIONS

There were conflicting lines of evidence for the domestication of Tibetan barley, mustard, lettuce, buckwheat, and chickpea. The main reasons for the conflicting results may include incomplete early knowledge, record differences in different period, sample sizes, and data analysis techniques. There was strong evidence that Tibetan barley, barley, wheat, and jujube were introduced into China before the existence of the Land Silk Road; and mustard, lettuce, buckwheat, chickpea, alfalfa, walnut, cauliflower, grape, spinach, apple, cucumber, mulberry, and pea spread to China via trade and human migration along the Land Silk Road.

Inferring regulatory element landscapes and gene regulatory networks from integrated analysis in eight hulless barley varieties under abiotic stress

BACKGROUND

The cis-regulatory element became increasingly important for resistance breeding. There were many DNA variations identified by resequencing. To investigate the links between the DNA variations and cis-regulatory element was the fundamental work. DNA variations in cis-regulatory elements caused phenotype variations in general.

RESULTS

We used WGBS, ChIP-seq and RNA-seq technology to decipher the regulatory element landscape from eight hulless barley varieties under four kinds of abiotic stresses. We discovered 231,440 lowly methylated regions (LMRs) from the methylome data of eight varieties. The LMRs mainly distributed in the intergenic regions. A total of 97,909 enhancer-gene pairs were identified from the correlation analysis between methylation degree and expression level. A lot of enriched motifs were recognized from the tolerant-specific LMRs. The key transcription factors were screened out and the transcription factor regulatory network was inferred from the enhancer-gene pairs data for drought stress. The NAC transcription factor was predicted to target to TCP, bHLH, bZIP transcription factor genes. We concluded that the H3K27me3 modification regions overlapped with the LMRs more than the H3K4me3. The variation of single nucleotide polymorphism was more abundant in LMRs than the remain regions of the genome.

CONCLUSIONS

Epigenetic regulation is an important mechanism for organisms to adapt to complex environments. Through the study of DNA methylation and histone modification, we found that many changes had taken place in enhancers and transcription factors in the abiotic stress of hulless barley. For example, transcription factors including NAC may play an important role. This enriched the molecular basis of highland barley stress response.

Genetic architecture of inducible and constitutive metabolic profile related to drought resistance in qingke (Tibetan hulless barley)

Qingke (Tibetan hulless barley, Hordeum vulgare L. var. nudum) is the primary food crop on the Tibet Plateau, the long-term drought and other harsh environments makes qingke an important resource for the study of abiotic resistance. Here, we evaluated the drought sensitivity of 246 qingke varieties. Genome-wide association studies (GWAS) found that root-specific expressed gene CYP84 may be involved in the regulation of drought resistance. Based on widely targeted metabolic profiling, we identified 2,769 metabolites in qingke leaves, of which 302 were significantly changed in response to drought stress, including 4-aminobutyric acid (GABA), proline, sucrose and raffinose. Unexpectedly, these drought-induced metabolites changed more violently in drought-sensitive qingkes, while the constitutive metabolites that had little response to drought stress, such as C-glycosylflavonoids and some amino acids, accumulated excessively in drought-resistant qingkes. Combined with metabolite-based genome-wide association study (mGWAS), a total of 1,006 metabolites under optimal condition and 1,031 metabolites under mild drought stress had significant associated loci. As a marker metabolite induced by drought stress, raffinose was significantly associated with two conservatively adjacent α-galactosidase genes, qRT-PCR suggests that these two genes may jointly regulate the raffinose content in qingke. Besides, as constituent metabolites with stable differences between drought-sensitive and drought-resistant qingkes, a class of C-glycosylflavonoids are simultaneously regulated by a UDP-glucosyltransferase gene. Overall, we performed GWAS for sensitivity and widely targeted metabolites during drought stress in qingke for the first time, which provides new insights into the response mechanism of plant drought stress and drought resistance breeding.

Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars

Genome resequencing uncovers genome-wide DNA polymorphisms that are useful for the development of high-density InDel markers between two barley cultivars. Discovering genomic variations and developing genetic markers are crucial for genetics studies and molecular breeding in cereal crops. Although InDels (insertions and deletions) have become popular because of their abundance and ease of detection, discovery of genome-wide DNA polymorphisms and development of InDel markers in barley have lagged behind other cereal crops such as rice, maize and wheat. In this study, we re-sequenced two barley cultivars, Golden Promise (GP, a classic British spring barley variety) and Hua30 (a Chinese spring barley variety), and mapped clean reads to the reference Morex genome, and identified in total 13,933,145 single nucleotide polymorphisms (SNPs) and 1,240,456 InDels for GP with Morex, 11,297,100 SNPs and 781,687 InDels for Hua30 with Morex, and 13,742,399 SNPs and 1,191,597 InDels for GP with Hua30. We further characterized distinct types, chromosomal distribution patterns, genome location, functional effect, and other features of these DNA polymorphisms. Additionally, we revealed the functional relevance of these identified SNPs/InDels regarding different flowering times between Hua30 and GP within 17 flowering time genes. Furthermore, we developed a series of InDel markers and validated them experimentally in 43 barley core accessions, respectively. Finally, we rebuilt population structure and phylogenetic tree of these 43 barley core accessions. Collectively, all of these genetic resources will facilitate not only the basic research but also applied research in barley.

Compared analysis with a high-quality genome of weedy rice reveals the evolutionary game of de-domestication

The weedy rice (Oryza sativa f. spontanea) harbors large numbers of excellent traits and genetic diversities, which serves as a valuable germplasm resource and has been considered as a typical material for research about de-domestication. However, there are relatively few reference genomes on weedy rice that severely limit exploiting these genetic resources and revealing more details about de-domestication events. In this study, a high-quality genome (~376.4 Mb) of weedy rice A02 was assembled based on Nanopore ultra-long platform with a coverage depth of about 79.3× and 35,423 genes were predicted. Compared to Nipponbare genome, 5,574 structural variations (SVs) were found in A02. Based on super pan-genome graph, population SVs of 238 weedy rice and cultivated rice accessions were identified using public resequencing data. Furthermore, the de-domestication sites of weedy rice and domestication sites of wild rice were analyzed and compared based on SVs and single-nucleotide polymorphisms (SNPs). Interestingly, an average of 2,198 genes about de-domestication could only be found by F _ST analysis based on SVs (SV-F _ST) while not by F _ST analysis based on SNPs (SNP-F _ST) in divergent region. Additionally, there was a low overlap between domestication and de-domestication intervals, which demonstrated that two different mechanisms existed in these events. Our finding could facilitate pinpointing of the evolutionary events that had shaped the genomic architecture of wild, cultivated, and weedy rice, and provide a good foundation for cloning of the superior alleles for breeding.

Genome-Wide Identification, Evolution and Expressional Analysis of OSCA Gene Family in Barley (Hordeum vulgare L.)

The hyperosmolality-gated calcium-permeable channel gene family (OSCA) is one kind of conserved osmosensors, playing a crucial role in maintaining ion and water homeostasis and protecting cellular stability from the damage of hypertonic stress. Although it has been systematically characterized in diverse plants, it is necessary to explore the role of the OSCA family in barley, especially its importance in regulating abiotic stress response. In this study, a total of 13 OSCA genes (HvOSCAs) were identified in barley through an in silico genome search method, which were clustered into 4 clades based on phylogenetic relationships with members in the same clade showing similar protein structures and conserved motif compositions. These HvOSCAs had many cis-regulatory elements related to various abiotic stress, such as MBS and ARE, indicating their potential roles in abiotic stress regulation. Furthermore, their expression patterns were systematically detected under diverse stresses using RNA-seq data and qRT-PCR methods. All of these 13 HvOSCAs were significantly induced by drought, cold, salt and ABA treatment, demonstrating their functions in osmotic regulation. Finally, the genetic variations of the HvOSCAs were investigated using the re-sequencing data, and their nucleotide diversity in wild barley and landrace populations were 0.4966 × 10-3 and 0.391 × 10-3, respectively, indicating that a genetic bottleneck has occurred in the OSCA family during the barley evolution process. This study evaluated the genomic organization, evolutionary relationship and genetic expression of the OSCA family in barley, which not only provides potential candidates for further functional genomic study, but also contributes to genetically improving stress tolerance in barley and other crops.

Naked barley: taxonomy, breeding, and prospects of utilization

This review surveys the current state of taxonomy, origin, and utilization prospects for naked barley. The cultivated barley Hordeum vulgare L. incorporates the covered and naked barley groups. Naked barleys are divided into six-row naked barley (convar. сoeleste (L.) A. Trof.) and two-row naked barley (convar. nudum (L.) A. Trof.). The groups include botanical varieties differing in the structural features of spikes, awns, floret and spikelet glumes, and the color of kernels. The centers of morphogenesis for naked barley are scrutinized employing archeological and paleoethnobotanical data, and the diversity of its forms. Hypotheses on the centers of its origin are discussed using DNA marker data. The main areas of its cultivation are shown, along with possible reasons for such a predominating or exclusive distribution of naked barley in highland areas. Inheritance of nakedness and mechanisms of its manifestation are considered in the context of new data in genetics. The biochemical composition of barley grain in protein, some essential and nonessential amino acids, β-glucans, vitamins, and antioxidants is described. Naked barley is shown to be a valuable source of unique combinations of soluble and insoluble dietary fibers and polysaccharides. The parameters limiting wider distribution of naked barley over the world are emphasized, and breeding efforts that could mitigate them are proposed. Pathogen-resistant naked barley accessions are identified to serve as promising sources for increasing grain yield and quality. Main stages and trends of naked barley breeding are considered and the importance of the VIR global germplasm collection as the richest repository of genetic material for the development of breeding is shown.

Distribution of Core Root Microbiota of Tibetan Hulless Barley along an Altitudinal and Geographical Gradient in the Tibetan Plateau

The Tibetan Plateau is regarded as the third pole of the earth and is one of the least explored places on the planet. Tibetan hull-less barley (Hordeum vulgare L. var. nudum) is the only cereal crop grown widely in the Tibetan Plateau as a staple food. Extensive and long-term cropping of barley may influence the soil’s chemical and biological properties, including microbial communities. However, microbiota associated with hull-less barley is largely unexplored. This study aimed to reveal the composition and diversity of bacterial and fungal communities associated with the hull-less barley at different elevations in the Tibetan Plateau. The core bacterial and fungal taxa of Tibetan hull-less barley were identified, with Bacillaceae, Blastocatellaceae, Comamonadaceae, Gemmatimonadaceae, Planococcaceae, Pyrinomonadaceae, Sphingomonadaceae, and Nitrospiraceae being the most abundant bacterial taxa and Ceratobasidiaceae, Chaetomiaceae, Cladosporiaceae, Didymellaceae, Entolomataceae, Microascaceae, Mortierellaceae, and Nectriaceae being the most abundant fungal taxa (relative abundance > 1%). Both bacterial and fungal diversities of hull-less barley were affected by altitude and soil properties such as total carbon, total nitrogen, and available phosphorus and potassium. Both bacterial and fungal diversities showed a significant negative correlation with altitude, indicating that the lower elevations provide a conducive environment for the survival and maintenance of hull-less barley-associated microbiota. Our results also suggest that the high altitude-specific microbial taxa may play an important role in the adaptation of the hull-less barley to the earth’s third pole.

Pathogenesis-related protein-4 (PR-4) gene family in Qingke (Hordeum vulgare L. var. nudum): genome-wide identification, structural analysis and expression profile under stresses

BACKGROUND

Pathogenesis-related (PR) proteins are active participants of plant defense against biotic and abiotic stresses. The PR-4 family features a Barwin domain at the C-terminus, which endows the host plant with disease resistance. However, comprehensive analysis of PR-4 genes is still lacking in Qingke (Hordeum vulgare L. var. nudum).

METHODS AND RESULTS

Herein, a total of four PR-4 genes were identified from the genome of Qingke through HMM profiling. Devoid of the chitin-binding domain, these 4 proteins were grouped as class II PR-4s. Phylogenic analysis revealed that 127 PR-4s from 47 species were clustered into 3 major groups, among which the four Qingke PR-4s were claded into group I. Analysis of gene structure demonstrated that no intron was found in 3 out of the 4 Qingke PR-4s, and HOVUSG0928500 was the only gene contained one intron. An array of cis-acting motifs were detected in promoters of Qingke PR-4 genes, including elements associated with hormone response, light response, stress response, growth and development processes and binding sites of transcription factors, implying their diverse role. Expression profiling confirmed that Qingke PR-4s were involved in defense response against drought, cold and powdery mildews infection, and transcription of HOVUSG1974300 and HOVUSG5705400 was differentially regulated by MeJA and SA.

CONCLUSION

Findings of the study provided insights into the genetic basis of the PR-4 family genes, and would promote further investigation on protein function and utilization.

Genome-wide analysis of the Thaumatin-like gene family in Qingke (Hordeum vulgare L. var. nudum) uncovers candidates involved in plant defense against biotic and abiotic stresses

Thaumatin-like proteins (TLPs) participate in the defense responses of plants as well as their growth and development processes, including seed germination. Yet the functioning of TLP family genes, in addition to key details of their encoded protein products, has not been thoroughly investigated for Qingke (Hordeum vulgare L. var. nudum). Here, a total of 36 TLP genes were identified in the genome of Qingke via HMM profiling. Of them, 25 TLPs contained a signal peptide at the N-terminus, with most proteins predicted to localize in the cytoplasm or outer membrane. Sequence alignment and motif analysis revealed that the five REDDD residues required for β-1,3-glucanase activity were conserved in 21 of the 36 Qingke TLPs. Phylogenetically, the TLPs in plants are clustered in 10 major groups. Our analysis of gene structure did not detect an intron in 15 Qingke TLPs whereas the other 21 did contain 1-7 introns. A diverse set of cis-acting motifs were found in the promoters of the 36 TLPs, including elements related to light, hormone, and stress responses, growth and development, circadian control, and binding sites of transcription factors, thus suggesting a multifaceted role of TLPs in Qingke. Expression analyses revealed the potential involvement of TLPs in plant defense against biotic and abiotic stresses. Taken together, the findings of this study deepen our understanding of the TLP family genes in Qingke, a staple food item in Tibet, which could strengthen future investigations of protein function in barley and its improved genetic engineering.

Accumulation and regulation of anthocyanins in white and purple Tibetan Hulless Barley (Hordeum vulgare L. var. nudum Hook. f.) revealed by combined de novo transcriptomics and metabolomics

BACKGROUND

Colored barley, which may have associated human health benefits, is more desirable than the standard white variety, but the metabolites and molecular mechanisms underlying seedcoat coloration remain unclear.

RESULTS

Here, the development of Tibetan hulless barley was monitored, and 18 biological samples at 3 seedcoat color developmental stages were analyzed by transcriptomic and metabolic assays in Nierumuzha (purple) and Kunlun10 (white). A total of 41 anthocyanin compounds and 4186 DEGs were identified. Then we constructed the proanthocyanin-anthocyanin biosynthesis pathway of Tibetan hulless barley, including 19 genes encoding structural enzymes in 12 classes (PAL, C4H, 4CL, CHS, CHI, F3H, F3'H, DFR, ANS, ANR, GT, and ACT). 11 DEGs other than ANR were significantly upregulated in Nierumuzha as compared to Kunlun10, leading to high levels of 15 anthocyanin compounds in this variety (more than 25 times greater than the contents in Kunlun10). ANR was significantly upregulated in Kunlun10 as compared to Nierumuzha, resulting in higher contents of three anthocyanins compounds (more than 5 times greater than the contents in Nierumuzha). In addition, 22 TFs, including MYBs, bHLHs, NACs, bZips, and WD40s, were significantly positively or negatively correlated with the expression patterns of the structural genes. Moreover, comparisons of homologous gene sequences between the two varieties identified 61 putative SNPs in 13 of 19 structural genes. A nonsense mutation was identified in the coding sequence of the ANS gene in Kunlun10. This mutation might encode a nonfunctional protein, further reducing anthocyanin accumulation in Kunlun10. Then we identified 3 modules were highly specific to the Nierumuzha (purple) using WGCNA. Moreover, 12 DEGs appeared both in the putative proanthocyanin-anthocyanin biosynthesis pathway and the protein co-expression network were obtained and verified.

CONCLUSION

Our study constructed the proanthocyanin-anthocyanin biosynthesis pathway of Tibetan hulless barley. A series of compounds, structural genes and TFs responsible for the differences between purple and white hulless barley were obtained in this pathway. Our study improves the understanding of the molecular mechanisms of anthocyanin accumulation and biosynthesis in barley seeds. It provides new targets for the genetic improvement of anthocyanin content and a framework for improving the nutritional quality of barley.

Six-rowed wild-growing barleys are hybrids of diverse origins

Crop-wild gene flow is common when domesticated plants and their wild relatives grow close to each other. The resultant hybrid forms appear as semi-domesticates and were sometimes considered as missing links between crops and their wild progenitors. Wild-growing barleys in Central and Eastern Asia, named Hordeum agriocrithon, show hallmark characters of both wild and domesticated forms. Their spikes disintegrate at maturity to disperse without human intervention, but bear lateral grains, which were favored by early farmers and are absent from other wild barleys. As an intermediate form, H. agriocrithon has been proposed several times as a progenitor of domesticated barley. Here, we used genome-wide marker data and whole-genome resequencing to show that all H. agriocrithon accessions of a major germplasm collection are hybrid forms that arose multiple times by admixture of diverse domesticated and wild populations. Although H. agriocrithon barleys have not played a special role in barley domestication, future analysis of the adaptative potential of bi-directional crop-wild gene flow in extant barleys may prove a fertile research field.

Evaluation of Nutritional Components, Phenolic Composition, and Antioxidant Capacity of Highland Barley with Different Grain Colors on the Qinghai Tibet Plateau

The nutritional composition, polyphenol and anthocyanin composition, and antioxidant capacity of 52 colored highland barley were evaluated. The results showed that the protein content of highland barley in the black group was the highest, the total starch and fat contents in the blue group were the highest, the amylose content in the purple group was quite high, the fiber content in the yellow group was quite high, and the β-glucan content of the dark highland barley (purple, blue and black) was quite high. The polyphenol content and its antioxidant capacity in the black group were the highest, while the anthocyanin content and its antioxidant capacity in the purple highland barley were the highest. Ten types of monomeric phenolic substances were the main contributors to DPPH, ABTS, and FRAP antioxidant capacity. All varieties could be divided into four categories according to nutrition or function. The grain color could not be used as an absolute index to evaluate the quality of highland barley, and the important influence of variety on the quality of highland barley also needed to be considered. In actual production, suitable raw materials must be selected according to the processing purpose and variety characteristics of highland barley.