Stem lodging resistance in hulless barley: Transcriptome and metabolome analysis of lignin biosynthesis pathways in contrasting genotypes.

Hulless barley is an important economic and food crop for local population in the Qinghai-Tibet plateau. However, due to extreme weather conditions, its production suffers from stem lodging stress, inflicting significant yield losses. Herein, we selected five lodging resistant and five non-resistant genotypes to investigate changes in concentration of lignin related metabolites and expression levels of related genes in node samples. The lodging resistant genotypes displayed high content of lignin intermediate metabolites. 57% of the expressed genes were differentially expressed (DEG) between the two groups. 31 DEGs participate in the lignin pathways and we found that 65% of these DEGs were strongly up-regulated in the lodging resistant group, indicating a mechanism towards high lignin synthesis within said group. The candidate structural genes as well as the co-expressed TFs identified in this study represent important molecular tools for functional characterization and exploitation in molecular breeding programmes.

An improved high-quality genome assembly and annotation of Tibetan hulless barley.

Hulless barley (Hordeum vulgare L. var. nudum) is a barley variety that has loose husk cover of the caryopses. Because of the ease in processing and edibility, hulless barley has been locally cultivated and used as human food. For example, in Tibetan Plateau, hulless barley is the staple food for human and essential livestock feed. Although the draft genome of hulless barley has been sequenced, the assembly remains fragmented. Here, we reported an improved high-quality assembly and annotation of the Tibetan hulless barley genome using more than 67X PacBio long-reads. The N50 contig length of the new assembly is at least more than 19 times larger than other available barley assemblies. The new genome assembly also showed high gene completeness and high collinearity of genome synteny with the previously reported barley genome. The new genome assembly and annotation will not only remove major hurdles in genetic analysis and breeding of hulless barley, but will also serve as a key resource for studying barley genomics and genetics.

Genome-wide Dissection of Co-selected UV-B Responsive Pathways in the UV-B Adaptation of Qingke.

Qingke (Tibetan hulless barley) has long been cultivated and exposed to long-term and strong UV-B radiation on the Tibetan Plateau, which renders it an ideal species for elucidating novel UV-B responsive mechanisms in plants. Here we report a comprehensive metabolite profiling and metabolite-based genome-wide association study (mGWAS) using 196 diverse qingke and barley accessions. Our results demonstrated both constitutive and induced accumulation, and common genetic regulation, of metabolites from different branches of the phenylpropanoid pathway that are involved in UV-B protection. A total of 90 significant mGWAS loci for these metabolites were identified in barley-qingke differentiation regions, and a number of high-level metabolite trait alleles were found to be significantly enriched in qingke, suggesting co-selection of various phenylpropanoids. Upon dissecting the entire phenylpropanoid pathway, we identified some key determinants controlling natural variation of phenylpropanoid content, including three novel proteins, a flavone C-pentosyltransferase, a tyramine hydroxycinnamoyl acyltransferase, and a MYB transcription factor. Our study, furthermore, demonstrated co-selection of both constitutive and induced phenylpropanoids for UV-B protection in qingke.