Tibet as a potential domestication center of cultivated barley of China

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.

Transcriptome and Metabolite Insights into Domestication Process of Cultivated Barley in China

The domestication process of cultivated barley in China remains under debate because of the controversial origins of barley. Here, we analyzed transcriptomic and non-targeted metabolic data from 29 accessions together with public resequencing data from 124 accessions to explore the domestication process of cultivated barley in China (Cb-C). These analyses revealed that both Cb-C and Tibetan wild barley (Wb-T) were the descendants of wild barley from the Near East Fertile Crescent (Wb-NE), yielding little support for a local origin of Wb-T. Wb-T was more likely an intermediate in the domestication process from Wb-NE to Cb-C. Wb-T contributed more genetically to Cb-C than Wb-NE, and was domesticated into Cb-C about 3300 years ago. These results together seem to support that Wb-T may be a feralized or hybrid form of cultivated barley from the Near East Fertile Crescent or central Asia. Additionally, the metabolite analysis revealed divergent metabolites of alkaloids and phenylpropanoids and these metabolites were specifically targeted for selection in the evolutionary stages from Wb-NE to Wb-T and from Wb-T to Cb-C. The key missense SNPs in the genes HORVU6Hr1G027650 and HORVU4Hr1G072150 might be responsible for the divergence of metabolites of alkaloids and phenylpropanoids during domestication. Our findings allow for a better understanding of the domestication process of cultivated barley in China.

Food and Grain Consumption Per Capita in the Qinghai-Tibet Plateau and Implications for Conservation

Background: Grain security is crucial for social stability and ecosystem conservation regionally and globally, and it is particularly concerned widely in the Qinghai-Tibet Plateau (QTP) due to its high altitude and harsh climate for agriculture. Method: In this paper, we calculated and analyzed per capita food and grain consumption, including direct grain consumption, grain for fodder, industry consumption, seeds consumption, and wastage consumption and its changes in the QTP during 1995–2019. Results: The results showed that (1) in 2019, the average food consumption per capita was 333.35 kg, was stable since 1995. The dietary structure of residents was composed of direct grain consumption (44.15%), meat (10.72%), and milk (6.94%). The consumption of meat and milk was higher than the national average. (2) The average daily intake of energy and protein, animal protein, and the ratio of high-quality protein and fat energy were 2156.21 kcal·d⁻¹, 73.53 g·d⁻¹, 23.06 g·d⁻¹, 38.32%, and 27.77% in 2019. Their changes were −342.98 kcal·d⁻¹, −8.91 g·d⁻¹, 11.16 g·d⁻¹, 18.37%, and 11.08%, respectively. (3) The corresponding grain consumption per capita was 284.90 kg·a⁻¹ in 1995, 262.19 kg·a⁻¹ in 2010, and then remained stable until 2019. Conclusion: The study suggested that food consumption per capital was guaranteed at the well-off level since 2010, and food and dietary structure of residents were corresponding to physical geographic and climatic environment in the QTP. The conflict between food security and the ecosystem conservation can be managed without scarifying nature as the total grain consumption was stable since 2010, and the yield per unit area and total grain yield were both increasing since 2003 for agricultural condition improved in the QTP.

Domestication and crop evolution of wheat and barley: Genes, genomics, and future directions

Wheat and barley are two of the founder crops of the agricultural revolution that took place 10,000 years ago in the Fertile Crescent and both crops remain among the world's most important crops. Domestication of these crops from their wild ancestors required the evolution of traits useful to humans, rather than survival in their natural environment. Of these traits, grain retention and threshability, yield improvement, changes to photoperiod sensitivity and nutritional value are most pronounced between wild and domesticated forms. Knowledge about the geographical origins of these crops and the genes responsible for domestication traits largely pre-dates the era of next-generation sequencing, although sequencing will lead to new insights. Molecular markers were initially used to calculate distance (relatedness), genetic diversity and to generate genetic maps which were useful in cloning major domestication genes. Both crops are characterized by large, complex genomes which were long thought to be beyond the scope of whole-genome sequencing. However, advances in sequencing technologies have improved the state of genomic resources for both wheat and barley. The availability of reference genomes for wheat and some of its progenitors, as well as for barley, sets the stage for answering unresolved questions in domestication genomics of wheat and barley.

Genetic Mapping and Evolutionary Analyses of the Black Grain Trait in Barley

Barley occupies the widest ecological area among the major cereal crops, thereby generating a high potential for adaptive genetic diversity against various environmental factors. Colored barley such as black grain barley has been suggested to result from environmental adaptation to biotic and abiotic stresses. Using one double haploid population (433 lines), plus three F5 recombinant inbred line (RIL) populations (1,009 lines), the black lemma and pericarp (Blp) gene was mapped between two Insertion/deletion (Indel) markers MC_1570156 and MC_162350 with a physical distance of 0.807 Mb, containing 21 annotated genes in the mapped interval. Whole-genome re-sequencing was performed on two Tibetan wild barley lines (X1 and W1) with black grain phenotype. The probable candidate genes for Blp were discussed based on gene functional annotation and gene sequence variation analyses. Thirteen polymorphic Indel markers covering the target genetic region were used to analyze 178 barley accessions including 49 black husk entries. Genotype-based clustering analyses showed that the black landraces of different geographical background may have evolved from a single origin. Our study represents a significant improvement on the genetic mapping of Blp and would facilitate future study on the characterization of the genetic basis underlying this interesting agronomic trait.

Origin and evolution of qingke barley in Tibet

Tibetan barley (Hordeum vulgare L., qingke) is the principal cereal cultivated on the Tibetan Plateau for at least 3,500 years, but its origin and domestication remain unclear. Here, based on deep-coverage whole-genome and published exome-capture resequencing data for a total of 437 accessions, we show that contemporary qingke is derived from eastern domesticated barley and it is introduced to southern Tibet most likely via north Pakistan, India, and Nepal between 4,500 and 3,500 years ago. The low genetic diversity of qingke suggests Tibet can be excluded as a center of origin or domestication for barley. The rapid decrease in genetic diversity from eastern domesticated barley to qingke can be explained by a founder effect from 4,500 to 2,000 years ago. The haplotypes of the five key domestication genes of barley support a feral or hybridization origin for Tibetan weedy barley and reject the hypothesis of native Tibetan wild barley.

Barley heads east: Genetic analyses reveal routes of spread through diverse Eurasian landscapes

One of the world’s most important crops, barley, was domesticated in the Near East around 11,000 years ago. Barley is a highly resilient crop, able to grown in varied and marginal environments, such as in regions of high altitude and latitude. Archaeobotanical evidence shows that barley had spread throughout Eurasia by 2,000 BC. To further elucidate the routes by which barley cultivation was spread through Eurasia, simple sequence repeat (SSR) analysis was used to determine genetic diversity and population structure in three extant barley taxa: domesticated barley (Hordeum vulgare L. subsp. vulgare), wild barley (H. vulgare subsp. spontaneum) and a six-rowed brittle rachis form (H. vulgare subsp. vulgare f. agriocrithon (Åberg) Bowd.). Analysis of data using the Bayesian clustering algorithm InStruct suggests a model with three ancestral genepools, which captures a major split in the data, with substantial additional resolution provided under a model with eight genepools. Our results indicate that H. vulgare subsp. vulgare f. agriocrithon accessions and Tibetan Plateau H. vulgare subsp. spontaneum are closely related to the H. vulgare subsp. vulgare in their vicinity, and are therefore likely to be feral derivatives of H. vulgare subsp. vulgare. Under the eight genepool model, cultivated barley is split into six ancestral genepools, each of which has a distinct distribution through Eurasia, along with distinct morphological features and flowering time phenotypes. The distribution of these genepools and their phenotypic characteristics is discussed together with archaeological evidence for the spread of barley eastwards across Eurasia.

Patterns of Evolutionary Trajectories and Domestication History within the Genus Hordeum Assessed by REMAP Markers

The patterns of genetic diversity related to the taxonomy and domestication history of 85 accessions representing the main four species of the genus Hordeum were examined by retrotransposon-microsatellite amplified polymorphism (REMAP) markers based on the retrotransposon BARE-1. A substantial level of genetic polymorphisms at among- and within-species level was observed showing that this retrotransposon family and its adjacent genomic regions has been a target for genome dynamics during the evolution and domestication of barley. The obtained data are consistent with the current taxonomic status within the genus Hordeum. Similar level of genetic diversity was observed between the wild and the domesticated barley accessions suggesting that transposable elements` activity and accumulation may counteract the decrease of genome-wide diversity following domestication. In addition, eco-geographical sub-genome pools of the cultivated barley were identified in support to the theory of multiple origins of domestication within the genus Hordeum. We also provide conclusions about the relationship between accessions of different species and the putative routes of barley domestication. In conclusion, the retrotransposon BARE-1 stands as a reliable and perspective DNA marker for the assessment of the phylogenetic and domestication history in the genus Hordeum and other crop species.

Molecular evidence of RNA polymerase II gene reveals the origin of worldwide cultivated barley

The origin and domestication of cultivated barley have long been under debate. A population-based resequencing and phylogenetic analysis of the single copy of RPB2 gene was used to address barley domestication, to explore genetic differentiation of barley populations on the worldwide scale, and to understand gene-pool exchanges during the spread and subsequent development of barley cultivation. Our results revealed significant genetic differentiation among three geographically distinct wild barley populations. Differences in haplotype composition among populations from different geographical regions revealed that modern cultivated barley originated from two major wild barley populations: one from the Near East Fertile Crescent and the other from the Tibetan Plateau, supporting polyphyletic origin of cultivated barley. The results of haplotype frequencies supported multiple domestications coupled with widespread introgression events that generated genetic admixture between divergent barley gene pools. Our results not only provide important insight into the domestication and evolution of cultivated barley, but also enhance our understanding of introgression and distinct selection pressures in different environments on shaping the genetic diversity of worldwide barley populations, thus further facilitating the effective use of the wild barley germplasm.

Coevolution between Cancer Activities and Food Structure of Human Being from Southwest China

Yunnan and Tibet are the lowest cancer mortality and the largest producer for anticancer crops (brown rice, barley, buckwheat, tea, walnut, mushrooms, and so forth). Shanghai and Jiangsu province in China have the highest mortality of cancers, which are associated with the sharp decline of barley.

Genetic divergence in domesticated and non-domesticated gene regions of barley chromosomes

Little is known about the genetic divergence in the chromosomal regions with domesticated and non-domesticated genes. The objective of our study is to examine the effect of natural selection on shaping genetic diversity of chromosome region with domesticated and non-domesticated genes in barley using 110 SSR markers. Comparison of the genetic diversity loss between wild and cultivated barley for each chromosome showed that chromosome 5H had the highest divergence of 35.29%, followed by 3H, 7H, 4H, 2H, 6H. Diversity ratio was calculated as (diversity of wild type – diversity of cultivated type)/diversity of wild type×100%. It was found that diversity ratios of the domesticated regions on 5H, 1H and 7H were higher than those of non-domesticated regions. Diversity ratio of the domesticated region on 2H and 4H is similar to that of non-domesticated region. However, diversity ratio of the domesticated region on 3H is lower than that of non-domesticated region. Averaged diversity among six chromosomes in domesticated region was 33.73% difference between wild and cultivated barley, and was 27.56% difference in the non-domesticated region. The outcome of this study advances our understanding of the evolution of crop chromosomes.

Origin of worldwide cultivated barley revealed by NAM-1 gene and grain protein content

The origin, evolution, and distribution of cultivated barley provides powerful insights into the historic origin and early spread of agrarian culture. Here, population-based genetic diversity and phylogenetic analyses were performed to determine the evolution and origin of barley and how domestication and subsequent introgression have affected the genetic diversity and changes in cultivated barley on a worldwide scale. A set of worldwide cultivated and wild barleys from Asia and Tibet of China were analyzed using the sequences for NAM-1 gene and gene-associated traits-grain protein content (GPC). Our results showed Tibetan wild barley distinctly diverged from Near Eastern barley, and confirmed that Tibet is one of the origin and domestication centers for cultivated barley, and in turn supported a polyphyletic origin of domesticated barley. Comparison of haplotype composition among geographic regions revealed gene flow between Eastern and Western barley populations, suggesting that the Silk Road might have played a crucial role in the spread of genes. The GPC in the 118 cultivated and 93 wild barley accessions ranged from 6.73 to 12.35% with a mean of 9.43%. Overall, wild barley had higher averaged GPC (10.44%) than cultivated barley. Two unique haplotypes (Hap2 and Hap7) caused by a base mutations (at position 544) in the coding region of the NAM-1 gene might have a significant impact on the GPC. Single nucleotide polymorphisms and haplotypes of NAM-1 associated with GPC in barley could provide a useful method for screening GPC in barley germplasm. The Tibetan wild accessions with lower GPC could be useful for malt barley breeding.

Population genetics and phylogenetic analysis of the vrs1 nucleotide sequence in wild and cultivated barley

Spike morphology is a key characteristic in the study of barley genetics, breeding, and domestication. Variation at the six-rowed spike 1 (vrs1) locus is sufficient to control the development and fertility of the lateral spikelet of barley. To study the genetic variation of vrs1 in wild barley (Hordeum vulgare subsp. spontaneum) and cultivated barley (Hordeum vulgare subsp. vulgare), nucleotide sequences of vrs1 were examined in 84 wild barleys (including 10 six-rowed) and 20 cultivated barleys (including 10 six-rowed) from four populations. The length of the vrs1 sequence amplified was 1536 bp. A total of 40 haplotypes were identified in the four populations. The highest nucleotide diversity, haplotype diversity, and per-site nucleotide diversity were observed in the Southwest Asian wild barley population. The nucleotide diversity, number of haplotypes, haplotype diversity, and per-site nucleotide diversity in two-rowed barley were higher than those in six-rowed barley. The phylogenetic analysis of the vrs1 sequences partially separated the six-rowed and the two-rowed barley. The six-rowed barleys were divided into four groups.

Development and characterization of polymorphic EST-SSR and genomic SSR markers for Tibetan annual wild barley

Tibetan annual wild barley is rich in genetic variation. This study was aimed at the exploitation of new SSRs for the genetic diversity and phylogenetic analysis of wild barley by data mining. We developed 49 novel EST-SSRs and confirmed 20 genomic SSRs for 80 Tibetan annual wild barley and 16 cultivated barley accessions. A total of 213 alleles were generated from 69 loci with an average of 3.14 alleles per locus. The trimeric repeats were the most abundant motifs (40.82%) among the EST-SSRs, while the majority of the genomic SSRs were di-nuleotide repeats. The polymorphic information content (PIC) ranged from 0.08 to 0.75 with a mean of 0.46. Besides this, the expected heterozygosity (He) ranged from 0.0854 to 0.7842 with an average of 0.5279. Overall, the polymorphism of genomic SSRs was higher than that of EST-SSRs. Furthermore, the number of alleles and the PIC of wild barley were both higher than that of cultivated barley, being 3.12 vs 2.59 and 0.44 vs 0.37. Indicating more polymorphism existed in the Tibetan wild barley than in cultivated barley. The 96 accessions were divided into eight subpopulations based on 69 SSR markers, and the cultivated genotypes can be clearly separated from wild barleys. A total of 47 SSR-containing EST unigenes showed significant similarities to the known genes. These EST-SSR markers have potential for application in germplasm appraisal, genetic diversity and population structure analysis, facilitating marker-assisted breeding and crop improvement in barley.

Genetic diversity and ecological niche modelling of wild barley: refugia, large-scale post-LGM range expansion and limited mid-future climate threats?

Describing genetic diversity in wild barley (Hordeum vulgare ssp. spontaneum) in geographic and environmental space in the context of current, past and potential future climates is important for conservation and for breeding the domesticated crop (Hordeum vulgare ssp. vulgare). Spatial genetic diversity in wild barley was revealed by both nuclear- (2,505 SNP, 24 nSSR) and chloroplast-derived (5 cpSSR) markers in 256 widely-sampled geo-referenced accessions. Results were compared with MaxEnt-modelled geographic distributions under current, past (Last Glacial Maximum, LGM) and mid-term future (anthropogenic scenario A2, the 2080s) climates. Comparisons suggest large-scale post-LGM range expansion in Central Asia and relatively small, but statistically significant, reductions in range-wide genetic diversity under future climate. Our analyses support the utility of ecological niche modelling for locating genetic diversity hotspots and determine priority geographic areas for wild barley conservation under anthropogenic climate change. Similar research on other cereal crop progenitors could play an important role in tailoring conservation and crop improvement strategies to support future human food security.