NIAB - National Institute of Agricultural Botany

Assay information: HvVRS1_GINS681

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Narrative

Three independent loss-of-function mutations (vrs1.a1, vrs1.a2, vrs1.a3) within the HvHOX1 gene underlying the VRS1 genetic locus result in the conversion of the dominant wild-type 2-row phenotype to the recesive 6-row phenotype. This marker assays for insertion/deletion of a single 'G' nucleotide underlying the vrs1.a1 allele: insertion = wild-type 2-row allele (SNP call 'G'); deletion = 6-row allele vrs1.a1 (SNP call 'C').

Note: see position 1352bp in reference sequence alignment.

Note: Genotypes for all three mutations need to considered together for identification of all instances of the 6-row phenotype. KASPar marker HvVRS1_C349G assays for the SNP underlying the vrs1.a3 allele. The assay for the 'T' insertion/deletion characeristic of 6-row allele vrs1.a2 (PMID: 17220272) failed to convert to the KASPar platform.

References

PMID: 17220272

Map AGOUEB ver1
Chromosome 2H
cM position 85.92
Assay ID 9720126
Assay Name HvVRS1_GINS681
Reference Allele Sequences
Sequence ID Allele Phenotype
gi|224487836|gb|AB489127 D 6-row (cv Morex, allele Vrs1.a3)
gi|224487838|gb|AB489123 G 2-row (cv Pamella Blue, allele Vrs1.b2)
gi|224487834|gb|AB489121 G 2-row (cv Bonus, allele Vrs1.b3)
Polymorphism sequence ACTGGGAGCGACTGA[G/]CAGGAGGTGCGGCGCC
Reference allele sequence alignment
Jalview displaying file: HvVRS1_GINS681_reference.aln
Validation plot
Genotype data
Accession Name Other Ref Genotype call (with filter) Reference sample of known genotype
Maris_Otter AFP 2/232 G
Golden_Promise AFP 2/235 G
Triumph AFP 2/278 G
Golf AFP 2/421 G
Klaxon AFP 2/456 G
Halycon AFP 2/514 G
Pipkin AFP 2/578 G
Dandy AFP 2/674 G
Blnheim AFP 2/688 G
Tyne AFP 2/750 G
Puffin AFP 2/806 G
Pastoral AFP 2/816 G
Posaune AFP 2/820 G
Gypsy AFP 2/884 G
Clarine AFP 2/899 G
Alexis AFP 2/904 G
Fighter AFP 2/947 G
Manitou AFP 2/951 G
Sprite AFP 2/954 G
Bronze AFP 2/994 G
Blanche AFP 2/1002 G
Derkado AFP 2/1011 G
Dallas AFP 2/1022 G
Graphic AFP 2/1029 G
Chariot AFP 2/1031 G
Willow AFP 2/1055 G
Swift AFP 2/1058 G
Intro AFP 2/1071 G
Felicie AFP 2/1091 G
Linnet AFP 2/1127 G
Delibes AFP 2/1133 G
Cooper AFP 2/1146 G
Brewster AFP 2/1147 G
Melanie AFP 2/1160 G
Sunrise AFP 2/1162 G
Rhythm AFP 2/1169 G
Tempo AFP 2/1170 G
Fanfare AFP 2/1171 G
Vivaldi AFP 2/1173 G
Emeraude AFP 2/1183 G
Hanna AFP 2/1184 G
Cork AFP 2/1187 G
Optic AFP 2/1188 G
Brahms AFP 2/1191 G
Canasta AFP 2/1194 G
Reggae AFP 2/1196 G
Riviera AFP 2/1203 G
Tokyo AFP 2/1210 G
Arctic AFP 2/1211 G
Muscat AFP 2/1214 G
Mystique AFP 2/1219 G
Prelude AFP 2/1221 G
Crown AFP 2/1230 G
Tankard AFP 2/1238 G
Wren AFP 2/1242 ?
Ragtime AFP 2/1244 G
Clarity AFP 2/1246 G
Trinidad AFP 2/1256 G
Volley AFP 2/1262 G
Rifle AFP 2/1263 G
Cobalt AFP 2/1264 G
Tiffany AFP 2/1266 G
Antigua AFP 2/1276 G
Emilia AFP 2/1281 G
Spice AFP 2/1285 G
Quartet AFP 2/1291 G
Landlord AFP 2/1293 G
Rainbow AFP 2/1301 G
Charm AFP 2/1303 G
Torup AFP 2/1311 G
Pearl AFP 2/1318 G
Jewel AFP 2/1320 G
Baton AFP 2/1326 G
Spirit AFP 2/1334 G
Candy AFP 2/1345 G
Ricarda AFP 2/1350 G
Bistro AFP 2/1392 G
Angela AFP 2/1397 G
Heligan AFP 2/1402 G
Tabetha AFP 2/1404 G
Acorn AFP 2/1409 G
Century AFP 2/1410 G
Decanter AFP 2/1411 G
Linden AFP 2/1415 G
Acapella AFP 2/1419 G
Horizon AFP 2/1423 G
Static AFP 2/1427 G
Pongo AFP 2/1431 G
Opal AFP 2/1435 G
Wizard AFP 2/1442 G
Steeple AFP 2/1443 G
Arrow AFP 2/1445 G
Rounder AFP 2/1457 G
Siberia AFP 2/1463 G
Halifax AFP 2/1466 G
Artist AFP 2/1468 G
Leonie AFP 2/1471 G
Berwick AFP 2/1474 G
Otira AFP 2/1485 G
Potter AFP 2/1492 G
Saloon AFP 2/1501 G
Anvil AFP 2/1511 G
Haka AFP 2/1528 G
Sarah AFP 2/1534 G
Carola AFP 2/1535 G
Violet AFP 2/1540 G
Akita AFP 2/1555 G
Prestige AFP 2/1566 G
Prot AFP 2/1567 G
County AFP 2/1572 G
Pewter AFP 2/1575 G
Brise AFP 2/1576 G
Viskosa AFP 2/1579 G
Neruda AFP 2/1580 G
Agenda AFP 2/1589 G
Azure AFP 2/1591 G
Alabama AFP 2/1597 G
Pippa AFP 2/1599 G
Diamond AFP 2/1604 G
Carat AFP 2/1606 G
Tucker AFP 2/1608 G
Pict AFP 2/1626 G
Scylla AFP 2/1628 G
Spire AFP 2/1668 G
Spike AFP 2/1669 G
Sunbeam AFP 2/1697 G
Cannock AFP 2/1700 G
Kestrel AFP 2/1705 G
Sequel AFP 2/1717 G
Outlook AFP 2/1726 G
Mead AFP 2/1728 G
Rakaia AFP 2/1741 G
Pelican AFP 2/1745 G
Catalina AFP 2/1746 G
Cocktail AFP 2/1769 G
Brazil AFP 2/1780 G
Camion AFP 2/1825 G
Mandolin AFP 2/1841 G
Carafe AFP 2/1862 G
Toby AFP 2/1864 G
Doyen AFP 2/1865 G
Drum AFP 2/1867 G
Rebecca AFP 2/1871 -
Saffron AFP 2/1880 G
Amarena AFP 2/1886 G
Faraday AFP 2/1892 G
Balasun AFP 2/1902 G
Thalia AFP 2/1919 G
Concept AFP 2/1923 G
Westminster AFP 2/1939 G
Oxford AFP 2/1940 G
SW Macsena AFP 2/1951 G
Waggon AFP 2/1963 G
NFC Tipple AFP 2/1966 G
Timori AFP 2/1974 G
Colibri AFP 2/2003 G
Corsica AFP 2/2025 G
Rummy AFP 2/2034 G
Silicon AFP 2/2040 G
Tuscon AFP 2/2050 G
Centurion AFP 2/2054 G
Paramount AFP 2/2055 G
Accent AFP 2/2073 G
Pelican AFP 2/2077 G
Acrobat AFP 2/2102 G
Calico AFP 2/2104 G
Quench AFP 2/2121 G
Azalea AFP 2/2180 G
Tamise AFP 2/2188 G