| Narrative |
Numerous dominant spring or recessive winter alleles at the vernalization locus VRN-H1 have been previously described. Within the European context, these were systematically investigated (PMID 17713756), identifying seven spring and two winter alleles. Spring Vrn-H1 alleles are differentiated from winter alleles, predominantly due to the presence of deletions within intron 1. Combined haplotypes from KASPar markers HvVRNH1_SNP2 and HvVRNH1_0P5_InDel can be used to identify all but one of the known VRN-H1 alleles (allele 1B, PMID 17713756, see reference allele sequence table below for haplotype combinations from these two KASPar markers. Note: allele 1B is relatively rare in European barley). |
| References |
PMID: 21115826; 17713756 |
| Map |
AGOUEB ver1 |
| Chromosome |
5H |
| cM position |
134.60 |
| Assay ID |
9720117 |
| Assay Name |
HvVRNH1_SNP2 |
| Reference Allele Sequences |
| Sequence ID |
Allele |
Phenotype |
| gi|156616792|gb|EF591644 |
A/Del |
winter (cv Panda, haplotype 1A) |
| gi|156616792|gb|EF591649 |
A/Del |
spring (cv Etu, haplotype 1B) |
| gi|156616792|gb|EF591650 |
G/Del |
spring (cv Varunda, haplotype 2) |
| gi|156616792|gb|EF591636 |
G/Del |
spring (cv Dandy, haplotype 3) |
| gi|156616792|gb|EF591639 |
G/Del |
spring (cv Optic, haplotype 4A) |
| gi|156616792|gb|EF591641 |
G/Del |
spring (cv Prisma, haplotype 4B) |
| gi|156616792|gb|EF591637 |
G/Del |
spring (cv Golden Promise, haplotype 5A) |
| gi|156616792|gb|EF591646 |
G/Del |
spring (cv Oriol, haplotype 5B) |
| gi|156616792|gb|EF591647 |
G/Ins |
winter (cv Express, haplotype 5C) |
|
| Polymorphism sequence |
AAAACTGTGCATCTA[A/G]CAGTATATTTTTTTT |
| Reference allele sequence alignment |
|
| Validation plot |
|
| Genotype data |
| Accession Name |
Other Ref |
Genotype call (with filter) |
Reference sample of known genotype |
| Maris_Otter |
AFP 2/232 |
A |
|
| 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 |
A |
|
| Pipkin |
AFP 2/578 |
A |
|
| Dandy |
AFP 2/674 |
G |
|
| Blenheim |
AFP 2/688 |
G |
|
| Tyne |
AFP 2/750 |
G |
|
| Puffin |
AFP 2/806 |
A |
|
| Pastoral |
AFP 2/816 |
A |
|
| Posaune |
AFP 2/820 |
A |
|
| Gypsy |
AFP 2/884 |
A |
|
| Clarine |
AFP 2/899 |
A |
|
| Alexis |
AFP 2/904 |
G |
|
| Fighter |
AFP 2/947 |
G |
|
| Manitou |
AFP 2/951 |
A |
|
| Sprite |
AFP 2/954 |
A |
|
| Bronze |
AFP 2/994 |
A |
|
| 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 |
A |
|
| Swift |
AFP 2/1058 |
G |
|
| Intro |
AFP 2/1071 |
A |
|
| Felicie |
AFP 2/1091 |
G |
|
| Linnet |
AFP 2/1127 |
A |
|
| Delibes |
AFP 2/1133 |
G |
|
| Cooper |
AFP 2/1146 |
G |
|
| Brewster |
AFP 2/1147 |
G |
|
| Melanie |
AFP 2/1160 |
A |
|
| Sunrise |
AFP 2/1162 |
A |
|
| Rhythm |
AFP 2/1169 |
A |
|
| Tempo |
AFP 2/1170 |
A |
|
| Fanfare |
AFP 2/1171 |
A |
|
| Vivaldi |
AFP 2/1173 |
A |
|
| Emeraude |
AFP 2/1183 |
A |
|
| Hanna |
AFP 2/1184 |
A |
|
| 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 |
A |
|
| Mystique |
AFP 2/1219 |
A |
|
| Prelude |
AFP 2/1221 |
A |
|
| Crown |
AFP 2/1230 |
G |
|
| Tankard |
AFP 2/1238 |
G |
|
| Wren |
AFP 2/1242 |
G |
|
| Ragtime |
AFP 2/1244 |
G |
|
| Clarity |
AFP 2/1246 |
G |
|
| Trinidad |
AFP 2/1256 |
G |
|
| Volley |
AFP 2/1262 |
A |
|
| Rifle |
AFP 2/1263 |
A |
|
| Cobalt |
AFP 2/1264 |
A |
|
| Tiffany |
AFP 2/1266 |
A |
|
| Antigua |
AFP 2/1276 |
A |
|
| Emilia |
AFP 2/1281 |
G |
|
| Spice |
AFP 2/1285 |
A |
|
| Quartet |
AFP 2/1291 |
G |
|
| Landlord |
AFP 2/1293 |
G |
|
| Rainbow |
AFP 2/1301 |
G |
|
| Charm |
AFP 2/1303 |
G |
|
| Torup |
AFP 2/1311 |
A |
|
| Pearl |
AFP 2/1318 |
A |
|
| Jewel |
AFP 2/1320 |
A |
|
| Baton |
AFP 2/1326 |
A |
|
| Spirit |
AFP 2/1334 |
A |
|
| Candy |
AFP 2/1345 |
G |
|
| Ricarda |
AFP 2/1350 |
G |
|
| Bistro |
AFP 2/1392 |
A |
|
| Angela |
AFP 2/1397 |
G |
|
| Heligan |
AFP 2/1402 |
A |
|
| Tabetha |
AFP 2/1404 |
U |
|
| 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 |
A |
|
| Wizard |
AFP 2/1442 |
A |
|
| Steeple |
AFP 2/1443 |
A |
|
| Arrow |
AFP 2/1445 |
A |
|
| Rounder |
AFP 2/1457 |
A |
|
| Siberia |
AFP 2/1463 |
G |
|
| Halifax |
AFP 2/1466 |
A |
|
| Artist |
AFP 2/1468 |
A |
|
| Leonie |
AFP 2/1471 |
A |
|
| Berwick |
AFP 2/1474 |
G |
|
| Otira |
AFP 2/1485 |
G |
|
| Potter |
AFP 2/1492 |
G |
|
| Saloon |
AFP 2/1501 |
G |
|
| Anvil |
AFP 2/1511 |
A |
|
| Haka |
AFP 2/1528 |
A |
|
| Sarah |
AFP 2/1534 |
A |
|
| Carola |
AFP 2/1535 |
A |
|
| 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 |
A |
|
| Diamond |
AFP 2/1604 |
A |
|
| Carat |
AFP 2/1606 |
A |
|
| Tucker |
AFP 2/1608 |
A |
|
| Pict |
AFP 2/1626 |
A |
|
| Scylla |
AFP 2/1628 |
A |
|
| Spire |
AFP 2/1668 |
G |
|
| Spike |
AFP 2/1669 |
G |
|
| Sunbeam |
AFP 2/1697 |
A |
|
| Cannock |
AFP 2/1700 |
A |
|
| Kestrel |
AFP 2/1705 |
A |
|
| Sequel |
AFP 2/1717 |
G |
|
| Outlook |
AFP 2/1726 |
A |
|
| Mead |
AFP 2/1728 |
A |
|
| 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 |
A |
|
| 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 |
G |
|
| Saffron |
AFP 2/1880 |
A |
|
| Amarena |
AFP 2/1886 |
A |
|
| Faraday |
AFP 2/1892 |
A |
|
| Balasun |
AFP 2/1902 |
A |
|
| Thalia |
AFP 2/1919 |
A |
|
| Concept |
AFP 2/1923 |
A |
|
| 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 |
A |
|
| Pelican |
AFP 2/2077 |
A |
|
| 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 |
|
|
