NIAB - National Institute of Agricultural Botany

Assay information: HvVRNH1_Hap2_InDel

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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).

The HvVRNH1_Hap2_InDel KASPar assay is a pseudo-SNP, assaying for the presence of the 0.7kb intron 1 Insertion found in VRN-H1 haplotype 2. When the insertion is absent (scored in the genotype data below as '0'), the assay returns a SNP call of 'G'. All other calls represent instances when the insertion is present (score '1' below).

Note: when no DNA is present in a well, a call of '?' will be made. Thus, final genotype call for a given accession using this assay should be based on more than one repetition of the assay.

References

PMID: 21115826

PMID: 17713756

Map AGOUEB ver1
Chromosome 5H
cM position 134.60
Assay ID 9720132
Assay Name HvVRNH1_Hap2_InDel
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 CTCGCTGTTTCCTTC[Ins/-]GGATTCTGCCGTCGC
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 0
Golden_Promise AFP 2/235 0
Triumph AFP 2/278 0
Golf AFP 2/421 0
Klaxon AFP 2/456 0
Halycon AFP 2/514 0
Pipkin AFP 2/578 0
Dandy AFP 2/674 0
Blenheim AFP 2/688 0
Tyne AFP 2/750 0
Puffin AFP 2/806 0
Pastoral AFP 2/816 0
Posaune AFP 2/820 0
Gypsy AFP 2/884 0
Clarine AFP 2/899 0
Alexis AFP 2/904 0
Fighter AFP 2/947 0
Manitou AFP 2/951 0
Sprite AFP 2/954 0
Bronze AFP 2/994 0
Blanche AFP 2/1002 0
Derkado AFP 2/1011 0
Dallas AFP 2/1022 0
Graphic AFP 2/1029 0
Chariot AFP 2/1031 0
Willow AFP 2/1055 0
Swift AFP 2/1058 0
Intro AFP 2/1071 0
Felicie AFP 2/1091 0
Linnet AFP 2/1127 0
Delibes AFP 2/1133 0
Cooper AFP 2/1146 0
Brewster AFP 2/1147 0
Melanie AFP 2/1160 0
Sunrise AFP 2/1162 1
Rhythm AFP 2/1169 0
Tempo AFP 2/1170 0
Fanfare AFP 2/1171 0
Vivaldi AFP 2/1173 0
Emeraude AFP 2/1183 0
Hanna AFP 2/1184 0
Cork AFP 2/1187 0
Optic AFP 2/1188 0
Brahms AFP 2/1191 0
Canasta AFP 2/1194 0
Reggae AFP 2/1196 1
Riviera AFP 2/1203 0
Tokyo AFP 2/1210 0
Arctic AFP 2/1211 0
Muscat AFP 2/1214 0
Mystique AFP 2/1219 0
Prelude AFP 2/1221 0
Crown AFP 2/1230 0
Tankard AFP 2/1238 0
Wren AFP 2/1242 0
Ragtime AFP 2/1244 0
Clarity AFP 2/1246 0
Trinidad AFP 2/1256 0
Volley AFP 2/1262 0
Rifle AFP 2/1263 0
Cobalt AFP 2/1264 0
Tiffany AFP 2/1266 0
Antigua AFP 2/1276 0
Emilia AFP 2/1281 0
Spice AFP 2/1285 0
Quartet AFP 2/1291 0
Landlord AFP 2/1293 0
Rainbow AFP 2/1301 0
Charm AFP 2/1303 0
Torup AFP 2/1311 0
Pearl AFP 2/1318 0
Jewel AFP 2/1320 0
Baton AFP 2/1326 0
Spirit AFP 2/1334 0
Candy AFP 2/1345 1
Ricarda AFP 2/1350 0
Bistro AFP 2/1392 0
Angela AFP 2/1397 0
Heligan AFP 2/1402 0
Tabetha AFP 2/1404 1
Acorn AFP 2/1409 0
Century AFP 2/1410 0
Decanter AFP 2/1411 0
Linden AFP 2/1415 0
Acapella AFP 2/1419 0
Horizon AFP 2/1423 0
Static AFP 2/1427 0
Pongo AFP 2/1431 0
Opal AFP 2/1435 0
Wizard AFP 2/1442 0
Steeple AFP 2/1443 0
Arrow AFP 2/1445 1
Rounder AFP 2/1457 0
Siberia AFP 2/1463 0
Halifax AFP 2/1466 0
Artist AFP 2/1468 0
Leonie AFP 2/1471 0
Berwick AFP 2/1474 0
Otira AFP 2/1485 0
Potter AFP 2/1492 0
Saloon AFP 2/1501 0
Anvil AFP 2/1511 0
Haka AFP 2/1528 0
Sarah AFP 2/1534 0
Carola AFP 2/1535 0
Violet AFP 2/1540 0
Akita AFP 2/1555 0
Prestige AFP 2/1566 1
Prot AFP 2/1567 0
County AFP 2/1572 0
Pewter AFP 2/1575 0
Brise AFP 2/1576 0
Viskosa AFP 2/1579 0
Neruda AFP 2/1580 0
Agenda AFP 2/1589 0
Azure AFP 2/1591 0
Alabama AFP 2/1597 0
Pippa AFP 2/1599 0
Diamond AFP 2/1604 0
Carat AFP 2/1606 0
Tucker AFP 2/1608 1
Pict AFP 2/1626 0
Scylla AFP 2/1628 0
Spire AFP 2/1668 0
Spike AFP 2/1669 0
Sunbeam AFP 2/1697 0
Cannock AFP 2/1700 0
Kestrel AFP 2/1705 0
Sequel AFP 2/1717 0
Outlook AFP 2/1726 0
Mead AFP 2/1728 0
Rakaia AFP 2/1741 0
Pelican AFP 2/1745 0
Catalina AFP 2/1746 0
Cocktail AFP 2/1769 0
Brazil AFP 2/1780 0
Camion AFP 2/1825 0
Mandolin AFP 2/1841 1
Carafe AFP 2/1862 0
Toby AFP 2/1864 0
Doyen AFP 2/1865 0
Drum AFP 2/1867 0
Rebecca AFP 2/1871 0
Saffron AFP 2/1880 0
Amarena AFP 2/1886 0
Faraday AFP 2/1892 0
Balasun AFP 2/1902 0
Thalia AFP 2/1919 0
Concept AFP 2/1923 0
Westminster AFP 2/1939 0
Oxford AFP 2/1940 0
SW Macsena AFP 2/1951 0
Waggon AFP 2/1963 0
NFC Tipple AFP 2/1966 0
Timori AFP 2/1974 0
Colibri AFP 2/2003 0
Corsica AFP 2/2025 0
Rummy AFP 2/2034 0
Silicon AFP 2/2040 1
Tuscon AFP 2/2050 0
Centurion AFP 2/2054 0
Paramount AFP 2/2055 0
Accent AFP 2/2073 0
Pelican AFP 2/2077 0
Acrobat AFP 2/2102 0
Calico AFP 2/2104 0
Quench AFP 2/2121 0
Azalea AFP 2/2180 1
Tamise AFP 2/2188 0