NIAB - National Institute of Agricultural Botany

Assay information: HvANT2_C4289T

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The presence (to varying degrees of intensity) or absence of anthocyanin pigmentation within plant tissues (awn, auricle, lemma nerve) is controlled by the genetic locus ANTHOCYANINLESS 2 (ANT2), thought to be encoded by HvbHLH1. A 16bp exonic deletion within HvbHLH1 results in a truncated predicted protein that is diagnostic for the recessive ant2 allele that results in the absence of anthocyanin in all tissues. This assay tests for a SNP found to be in perfect linkage disequilibrium with the 16bp deletion in all UK barley varieties assayed to date. SNP T = anthocyanin non-expresser (diagnostic for haplotype 1), SNP C = anthocyanin expresser. Note: see position 4289bp in reference sequence alignment.

Note: a marker designed to directly assay the 16bp HvbHLH1 InDel failed to convert to the KASPar platform. However, a PCR/agarose-gel based marker for the 16bp InDel is published (PMID: 21115826).



Map AGOUEB ver1
Chromosome 2H
cM position 96.82
Assay ID 9720085
Assay Name HvANT2_C4289T
Reference Allele Sequences
Sequence ID Allele Phenotype
gi||gb|HM370325 C anthocyanin expresser (cv Swift, haplotype 2)
gi||gb|HM370331 C anthocyanin expresser (cv Acrobat, haplotype 3)
gi||gb|HM370379 C anthocyanin expresser (cv Token, haplotype 4)
gi||gb|HM370298 G anthocyanin non-expresser (cv Duet, haplotype 1)
Reference allele sequence alignment
Jalview displaying file: HvANT2_C4289T_reference.aln
Validation plot
Genotype data
Accession Name Other Ref Genotype call (with filter) Reference sample of known genotype
Maris_Otter AFP 2/232 T
Golden_Promise AFP 2/235 C
Triumph AFP 2/278 C
Golf AFP 2/421 C
Klaxon AFP 2/456 C
Halycon AFP 2/514 C
Pipkin AFP 2/578 C
Dandy AFP 2/674 C
Blenheim AFP 2/688 C
Tyne AFP 2/750 C
Puffin AFP 2/806 C
Pastoral AFP 2/816 T
Posaune AFP 2/820 C
Gypsy AFP 2/884 C
Clarine AFP 2/899 T
Alexis AFP 2/904 C
Fighter AFP 2/947 T
Manitou AFP 2/951 C
Sprite AFP 2/954 C
Bronze AFP 2/994 C
Blanche AFP 2/1002 T
Derkado AFP 2/1011 C
Dallas AFP 2/1022 C
Graphic AFP 2/1029 C
Chariot AFP 2/1031 C
Willow AFP 2/1055 C
Swift AFP 2/1058 C
Intro AFP 2/1071 T
Felicie AFP 2/1091 C
Linnet AFP 2/1127 C
Delibes AFP 2/1133 C
Cooper AFP 2/1146 C
Brewster AFP 2/1147 C
Melanie AFP 2/1160 C
Sunrise AFP 2/1162 T
Rhythm AFP 2/1169 C
Tempo AFP 2/1170 T
Fanfare AFP 2/1171 C
Vivaldi AFP 2/1173 C
Emeraude AFP 2/1183 C
Hanna AFP 2/1184 C
Cork AFP 2/1187 C
Optic AFP 2/1188 C
Brahms AFP 2/1191 C
Canasta AFP 2/1194 C
Reggae AFP 2/1196 C
Riviera AFP 2/1203 C
Tokyo AFP 2/1210 C
Arctic AFP 2/1211 T
Muscat AFP 2/1214 C
Mystique AFP 2/1219 C
Prelude AFP 2/1221 C
Crown AFP 2/1230 T
Tankard AFP 2/1238 C
Wren AFP 2/1242 C
Ragtime AFP 2/1244 C
Clarity AFP 2/1246 C
Trinidad AFP 2/1256 C
Volley AFP 2/1262 T
Rifle AFP 2/1263 C
Cobalt AFP 2/1264 C
Tiffany AFP 2/1266 T
Antigua AFP 2/1276 C
Emilia AFP 2/1281 C
Spice AFP 2/1285 T
Quartet AFP 2/1291 C
Landlord AFP 2/1293 C
Rainbow AFP 2/1301 C
Charm AFP 2/1303 C
Torup AFP 2/1311 C
Pearl AFP 2/1318 C
Jewel AFP 2/1320 T
Baton AFP 2/1326 C
Spirit AFP 2/1334 T
Candy AFP 2/1345 C
Ricarda AFP 2/1350 C
Bistro AFP 2/1392 C
Angela AFP 2/1397 T
Heligan AFP 2/1402 T
Tabetha AFP 2/1404 T
Acorn AFP 2/1409 C
Century AFP 2/1410 C
Decanter AFP 2/1411 C
Linden AFP 2/1415 C
Acapella AFP 2/1419 C
Horizon AFP 2/1423 C
Static AFP 2/1427 C
Pongo AFP 2/1431 C
Opal AFP 2/1435 C
Wizard AFP 2/1442 T
Steeple AFP 2/1443 C
Arrow AFP 2/1445 T
Rounder AFP 2/1457 C
Siberia AFP 2/1463 C
Halifax AFP 2/1466 T
Artist AFP 2/1468 C
Leonie AFP 2/1471 T
Berwick AFP 2/1474 C
Otira AFP 2/1485 C
Potter AFP 2/1492 C
Saloon AFP 2/1501 C
Anvil AFP 2/1511 C
Haka AFP 2/1528 C
Sarah AFP 2/1534 T
Carola AFP 2/1535 T
Violet AFP 2/1540 T
Akita AFP 2/1555 C
Prestige AFP 2/1566 C
Prot AFP 2/1567 C
County AFP 2/1572 C
Pewter AFP 2/1575 C
Brise AFP 2/1576 C
Viskosa AFP 2/1579 C
Neruda AFP 2/1580 C
Agenda AFP 2/1589 C
Azure AFP 2/1591 C
Alabama AFP 2/1597 C
Pippa AFP 2/1599 C
Diamond AFP 2/1604 T
Carat AFP 2/1606 T
Tucker AFP 2/1608 T
Pict AFP 2/1626 C
Scylla AFP 2/1628 C
Spire AFP 2/1668 C
Spike AFP 2/1669 C
Sunbeam AFP 2/1697 T
Cannock AFP 2/1700 C
Kestrel AFP 2/1705 C
Sequel AFP 2/1717 C
Outlook AFP 2/1726 T
Mead AFP 2/1728 T
Rakaia AFP 2/1741 C
Pelican AFP 2/1745 C
Catalina AFP 2/1746 C
Cocktail AFP 2/1769 C
Brazil AFP 2/1780 C
Camion AFP 2/1825 C
Mandolin AFP 2/1841 C
Carafe AFP 2/1862 C
Toby AFP 2/1864 C
Doyen AFP 2/1865 C
Drum AFP 2/1867 C
Rebecca AFP 2/1871 C
Saffron AFP 2/1880 T
Amarena AFP 2/1886 T
Faraday AFP 2/1892 T
Balasun AFP 2/1902 T
Thalia AFP 2/1919 T
Concept AFP 2/1923 C
Westminster AFP 2/1939 C
Oxford AFP 2/1940 C
SW Macsena AFP 2/1951 C
Waggon AFP 2/1963 C
NFC Tipple AFP 2/1966 C
Timori AFP 2/1974 C
Colibri AFP 2/2003 C
Corsica AFP 2/2025 C
Rummy AFP 2/2034 C
Silicon AFP 2/2040 C
Tuscon AFP 2/2050 C
Centurion AFP 2/2054 C
Paramount AFP 2/2055 C
Accent AFP 2/2073 C
Pelican AFP 2/2077 T
Acrobat AFP 2/2102 C
Calico AFP 2/2104 C
Quench AFP 2/2121 C
Azalea AFP 2/2180 C
Tamise AFP 2/2188 C