BARN_BARley yield associated Network

• Applicants: Professor Dr. Gary J. Muehlbauer; Professor Dr. Nils Stein; Professor Dr. Robbie Waugh
• Subject Area: Plant Breeding and Plant Pathology ; Plant Genetics and Genomics
• Term: from 2018 to 2022
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 355397120

• Final Report Year: 2022

Final Report Abstract

Improving varieties requires a thorough understanding of the genetic architecture of morphological and physiological traits, as well as of the interaction and regulation of genes affecting these traits. In the ERA-CAPS-funded ‘BARN’ project, we generated several resources to facilitate studies of the European two-rowed spring barley germplasm over the past 100 years. Using the new reference transcriptome BaRTv2.0 for accurate transcript-level gene expression quantification, we developed an expression dataset of six tissues and developmental stages from seedling to grain filling in a panel of 209 two-rowed spring barley cultivars representing the European breeding germplasm of the last century, complemented with a high-density SNP dataset of 1.5M SNPs derived from RNAseq of these tissues and WGS sequencing. After removing low expressed genes, the dataset includes expression data of more than 20,000 genes per tissue. The panel was phenotyped for 29 traits, mainly earliness, grain and spike traits, in field trials in Gatersleben (Germany), Dundee (Scotland) and St. Paul, Minnesota (USA) in 2019 and 2020. Genome-wide association studies (GWAS) identified significant marker-trait associations for most traits, most notably for plant height related traits on chromosome 3H and fertility and grain size traits on chromosome 2H. One association identified with GWAS for awn length was a known locus on chromosome 5H, validating our approach. Using a combination of GWAS, eQTL (expression association with genotype) and TWAS (expression association with phenotype) highlighted potential candidate genes linked to one region on chromosome 3H correlating to height traits. The extensive dataset can be used to mine previously identified genomic events more into detail. An inversion on chromosome 7H which has been described in the first barley pangenome paper was associated with changes in gene expression. In a principal component analysis using the genotypic information the population shows a moderate separation into two clusters, one predominantly consisting of older cultivars released before the 1990s and one predominantly containing newer cultivars released after the 1980s. FST values above 0.8 identified a 250 Mbp region on chromosome 5H that is almost completely fixed for different alleles in the two clusters. A subset of 45 genes in this region showed no or low expression in the older group of cultivars and moderate to high expression in the newer group but was not associated with any of the 29 traits we studied. While the oldest cultivar carrying the new haplotype (haplotype 2) was released in 1954, only one of the 58 lines released after 2000 possessed the old haplotype (haplotype 1), indicating that there has been a strong direct or indirect selection pressure on the new haplotype. The region is further characterized by flanking structural rearrangements between Golden Promise (older cluster) and Barke (newer cluster) at 70 and 320 Mbp. Together, we developed a state-of-the-art, high-quality multi-omics dataset, a high-accuracy reference transcriptome and a phenotypic dataset of unprecedented comprehensiveness that will be directly applicable not only to research on European two-rowed spring barley but to barley research in general as well as comparative genomics and transcriptomics on cereals and other crops.

Publications

• 3D RNA-seq: a powerful and flexible tool for rapid and accurate differential expression and alternative splicing analysis of RNA-seq data for biologists. RNA Biology, 18(11), 1574-1587.
  Guo, Wenbin; Tzioutziou, Nikoleta A.; Stephen, Gordon; Milne, Iain; Calixto, Cristiane PG; Waugh, Robbie; Brown, John W. S. & Zhang, Runxuan
  
• Identification of yield-related genes in barley using a multilayered genomics and transcriptomics approach, poster abstract at Plant & Animal Genome conference 2020, San Diego, USA
  Ronja Wonneberger & Allison Haaning
  
• Identification of yield-related genes in barley using a multilayered genomics and transcriptomics approach, poster abstract at Monogram 2021
  Miriam Schreiber & Ronja Wonneberger
  
• BaRTv2 : a highly resolved barley reference transcriptome for accurate transcript‐specific RNA ‐seq quantification. The Plant Journal, 111(4), 1183-1202.
  Coulter, Max; Entizne, Juan Carlos; Guo, Wenbin; Bayer, Micha; Wonneberger, Ronja; Milne, Linda; Schreiber, Miriam; Haaning, Allison; Muehlbauer, Gary J.; McCallum, Nicola; Fuller, John; Simpson, Craig; Stein, Nils; Brown, John W. S.; Waugh, Robbie & Zhang, Runxuan
  
• Comprehensive multi-omics dataset for studies and characterization of European two-rowed spring barleys, conference talk at IBGS 2022, Riga, Latvia
  Ronja Wonneberger
  
• GridScore: a tool for accurate, cross-platform phenotypic data collection and visualization. BMC Bioinformatics, 23(1).
  Raubach, Sebastian; Schreiber, Miriam & Shaw, Paul D.
  
• The value of genotype-specific reference for transcriptome analyses in barley. Life Science Alliance, 5(8), e202101255.
  Guo, Wenbin; Coulter, Max; Waugh, Robbie & Zhang, Runxuan