Table 2 Protein-changing variants with contrasting frequencies in wild and cultivated barley
From: Episodes of gene flow and selection during the evolutionary history of domesticated barley
Location (Morex V1) | Gene (Morex V1) | Gene (Morex V2) | Variant type | Variant in wild barley (frequency) | Variant in domesticated barley (frequency) | Variant in the 6ky barley | Groups where the position falls under a hard sweep | Significant BLASTP hit (species; query coverage; percent identity) |
|---|---|---|---|---|---|---|---|---|
chr1H: 106920539 | HORVU1 Hr1G024040 | – | NS SNP | Ala (0.902) | Val (0.987) | Domesticated | I, II, III, V, VI, supersample | – |
chr1H: 165877256 | HORVU1 Hr1G029720 | – | Indel | Wild-type transcripts .18 and .19 have premature stop codon (0.902) | transcripts .18 and 19 are 10 codons and 35 codons longer (0.981) | Missing data | I, III, V, VI, supersample | – |
chr1H: 527209977 | HORVU1 Hr1G081150 | – | NS SNP | Ala (0.938) | Thr (0.986) | Wild-type | I, II, IV, supersample | – |
chr1H: 545254976 | HORVU1 Hr1G090080 | HORVU.MOREX.r2.1 HG0074340 | NS SNP | Arg (0.955) | Trp (0.995) | Domesticated | II, III, IV, V, VI, supersample | SPA2 (supressor of phyA-105) (Arabidopsis; 81%; 47.21%) |
chr3H: 135052223 | HORVU3 Hr1G029370 | HORVU.MOREX.r2.3 HG0204760 | NS SNP | Glu (0.951) | Asp (0.987) | Domesticated | IV | MRH1/MDIS2 (Arabidopsis; 97%; 44.93%) |
chr5H: 592511492 | HORVU5 Hr1G093710 | – | NS SNP | Pro (0.906) | Leu (0.992) | Domesticated | I, V, VI | – |
chr5H: 593178296 | HORVU5 Hr1G093850 | HORVU.MOREX.r2.5 HG0422940 | NS SNP | Leu (0.911) | Val (0.982) | Domesticated | I, V, VI | Phototrophic-responsive NPH3 family protein (Arabidopsis; 97%; 44.99%) |
chr7H: 540527349 | HORVU7 Hr1G089090 | – | NS SNP | Val (0.928) | Ala (0.995) | Domesticated | II, III | – |
chr7H: 552413998 | HORVU7 Hr1G090560 | HORVU.MOREX.r2.7 HG0597530 | Indel | wild-type C-terminus (0.996) | 3-codon difference at the C-terminus (0.979) | Domesticated | II, III, V, VI | Cinnamyl alcohol dehydrogenase (Triticum aestivum; 98%; 92.37%) |
chr7H: 552532125 | HORVU7 Hr1G090580 | HORVU.MOREX.r2.7 HG0597570 | NS SNP | Leu (0.902) | Ile (0.990) | Domesticated | II, III, V, VI | – |