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Barley 2n = 2x = 14 ~ 5,300 Mb Two-row vs. six-row The trait defines the two major germplasm groups in barley A reproductive fitness trait: 6-row 3X more yield than 2-row (?) Vrs1 locus (1916; 1997) High resolution mapping (2004) Map-based cloning • • • • • ~ 0.07 cM interval, 9.831 gametes 6 Bacterial Artificial Chromosomes (518 Kb) Three genes, 1 degenerate HvHox1 lies between flanking markers Wild type (2-row) ORF = 222 aa polypeptide • HD-ZIP motif Expression HD-ZIP I (HvHox1) stage- and tissue-specific in 2-row • Transcription levels of Vrs1 • Abundant early in spike development, then taper off • In situ hybridization localizes expression to lateral spikelet primordia, no expression in central spikelet primordia Mutant survey • 57 mutants (6-row) derived from 2-row and allelic at Vrs1 • Lesions in Vrs1 correlated with 6-row phenotype in 48/57mutants • 21 aa substitutions • 12 truncated protein due to premature stop codon • 3 SNPs at intron splice sites • 5 frameshifts • 7 complete deletion of the gene: Vrs1 is dispensable • 9 mutants no DNA change in coding region: • 7/9 no expression: regulatory mutations • 2 expression = 2-row: post-translational modification Inferring origin (Re-)Sequence Vrs1 • 15 2-rows, 16 6-rows • Haplotype analysis defines groups • Phylogenetic analysis: defines 2-row as ancestral Discussion 2-row ancestral; 6-row = loss of function = recessive • Vrs1 encodes HD-ZIP transcription factor • Sequence • Expression • No transformation • HD-ZIPs and plant developmental processes • Vrs1 encodes a repressor protein that binds to a gene (or genes) that regulate lateral spikelet fertility Discussion (At least) 3 independent processes gave rise to 6-row (but not necessarily origins) BUT there were likely multiple origins.. • Haplotypes could not be • achieved by intragenic recombination after hybridization • Explained by simple mutation • “Six-rowed barley originated independently at different times and in different regions….probably as a result of conscious selection by delighted farmers….” Discussion Domestication and dispersal • ~8000 years ago 2-row and 6-row • Then 6-row dominates • 2-row re-appears in Fertile Crescent 1,000 years ago • 2-row arrives in Europe 900 years ago • Detailed analysis of archaeological specimens required Discussion Long-term evolution • Continuous reduction – from panicle (e.g. rice) to 3 spikelets in barley to 1 spikelet from wheat to Next step Poaceae-wide assessment of variability of Vrs1 orthologs Domestication and dispersal Barley 6,000 years ago + today’s technology Mascher et al. 2016. Nature Genetics. 48: 1089-1093.