The trait defines the two major germplasm groups in barley

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The trait defines the two major germplasm groups in 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 (?)

High resolution mapping (2004) 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.