The 2-/6-row phenotype is predominantly controlled by the VRS1 locus on chromosome 2H, with the wild type Vrs1.b alleles conferring the wild-type 2-row phenotype, and mutant VRS1.a alleles conferring the 6-row phenotype. However, mutation studies have shown that the phenotypic effect of the wild-type 2-row Vrs1.b allele can be modified by mutations at a second locus, INT-C, located on chromosome 4H. Wild-type Int-C.b alleles are associated with Vrs1.b alleles, conferring the standard 2-row phenotype, in which the sterile spikelets are sterile. However, when Int-c.a alleles are combined with Vrs1.b alleles, this results in enlarged partially sterile lateral spikelets. Similarly, when Int-C.b alleles are combined with Vrs1.a alleles, smaller lateral lateral spikelets are formed.

While the underlying causative mutation underlying the naturally occuring Int-C.a allele is unknown, haplotypes at two SNPs predict allelic state at INT-C, termed here HvINTC_C124G and HvINTC_C498T. Haplotypes CT and CC are diagnostic for the Int-C.b allele. Haplotype GC is diagnostic fot the Int-C.a allele.

PMID: 21217754

GDC ******** GeneDoc Multiple Sequence Alignment Editor ********
GDC 01065b0190000affffffffffff000000000000000000808080c0c0c0ffff
GDC ff000000000000f43f000000000000f43f000000000000f03f0000000000
GDC 00f03f00A000300000190000cA54696d6573204e657720526f6d616e00B0
GDC 064000d000000000000000000000028496e742d432e612c0d0a496e742d4
GDC 32e62312c0d0a496e742d432e6232293b0d0a00CBAADAAA0000002a000a0
GDC 0020001B20AAA000a203a2000203a2000000000000000594000000000000
GDC 00000000c5058000000ffff000047580000ff00ff000041475358000000f
GDC fffff0056434147444e535450580000ff00ffff00484b525800ff0000000
GDC 0ff4544580000ff000000ff484b5245445800ffffff0000ff48524551444
GDC e425a5800ff000000ff005957484b524551444e5354425a580000000000f
GDC f00494c56415800ff00008080804659574858000000ff808080494c56434
GDC 1474d4659574854505800ffffff0000000c505800ffffff0000004758004
GDC 141b9000000414347535800ffffff3d0100564147444e535450580000000
GDC 0ffffff484b5258003e01004141b945445800000000ffffff484b5245445
GDC 8004747b900000048524551444e425a5800ffffff400100435957484b524
GDC 551444e5354425a5800000000ffffff494c564158004101004747b946595
GDC 7485800ffffff000000494c564341474d46595748545058004343b900000
GDC 00300ffffff00000000ffffff80808000000000c0c0c00000ABBBBBBBBBB
GDC BBBB00ff00A0003000100010001A0018AA000000000000000000000003A0
GDC 0ff00A000000000080564000000000008051400000000000004940000002
GDC 0000000000001440A0000000098b20c41000000001025064100000000189
GDC 806410000000078b10b4100AAABB00005374616e646172640046464c4c53
GDC 53535359592a2a43432a574c4c4c4c505050504848515152525252494949
GDC 4d545454544e4e4b4b535352525656565641414141444445454747474700
GDC 2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d
GDC 2d2d2d2d2d4d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d2d
GDC 2d2d2d2d00BBBBB00000000000000030000000000000003000000000000B
GDC BAB0003000000020117B0000000000005940000000000000544000000000
GDC 00004e4000DAAB000000ffffff03020141470000ff00ff00000243545500
GDC ff000000ff00020147430000ff00ff00000241545500ff000000ff000501
GDC 4100000000ff000002430000000000ff00035455000000000000ff044700
GDC 000000ffff00054e5800ffffff0000000000000000Affffff80808000A
 ALIGNMENT_FINAL.msf  MSF: 1165  Type: N  July 2, 2012  12:36  Check: 4459 ..

 Name: Int-C.a          Len:  1165  Check: 6145  Weight:   1.00
 Name: Int-C.b1         Len:  1165  Check: 3800  Weight:   1.00
 Name: Int-C.b2         Len:  1165  Check: 4514  Weight:   1.00

//

          1                                                   50 
 Int-C.a  ATGTTTCCTT TCTATGATTC CCCAAGCCCC ATGGACTTAC CCCTTTACCA 
Int-C.b1  ATGTTTCCTT TCTATGATTC CCCAAGCCCC ATGGACTTAC CCCTTTACCA 
Int-C.b2  ATGTTTCCTT TCTATGATTC CCCAAGCCCC ATGGACTTAC CCCTTTACCA 

          51                                                 100 
 Int-C.a  GCAGCTGCAG CTCAGCCCTC CCTCCCCAAA GGCGCCGGAT CACCAATCCT 
Int-C.b1  GCAGCTGCAG CTCAGCCCTC CCTCCCCAAA GGCGCCGGAT CACCAATCCT 
Int-C.b2  GCAGCTGCAG CTCAGCCCTC CCTCCCCAAA GGCGCCGGAT CACCAATCCT 

          101                                                150 
 Int-C.a  TGCTCTACTA CCATTCCTCC CCTGCATTCG CCGCCGACCC TTTCCACCAC 
Int-C.b1  TGCTCTACTA CCATTCCTCC CCTCCATTCG CCGCCGACCC TTTCCACCAC 
Int-C.b2  TGCTCTACTA CCATTCCTCC CCTCCATTCG CCGCCGACCC TTTCCACCAC 

          151                                                200 
 Int-C.a  AACTACCTCT GTGCCGGTGC CGGTGCCGGT TCCGGTGCCG GTGAGGCCAC 
Int-C.b1  AACTACCTCT GTGCCGGTGC CGGTGCCGGT TCCGGTGC.. ....GGCCAC 
Int-C.b2  AACTACCTCT GTGCCGGTGC CGGTGCCGGT TCCGGTGC.. ....GGCCAC 

          201                                                250 
 Int-C.a  GCCGCCAGCA GCCGAGATCG ACGACCAGTC GCCGTCGGAG CTGCTTCTGA 
Int-C.b1  GCCGCCAGCA GCCGAGATCG ACGACCAGTC GCCGCCGGAG CTGCTTCTGA 
Int-C.b2  GCCGCCAGCA GCCGAGATCG ACGACCAGTC GCCGCCGGAG CTGCTTCTGA 

          251                                                300 
 Int-C.a  TGGATCAGGC GCCGGCGCCC AGGCCAGACG GGGCTGGAAA GGCACAAGGC 
Int-C.b1  TGGATCAGGC GCCGGCGCCC AGGCCAGACG GGGTTGGAAA GGCACAAGGC 
Int-C.b2  TGGATCAGGC GCCGGCGCCC AGGCCAGACG GGGTTGGAAA GGCACAAGGC 

          301                                                350 
 Int-C.a  CTGCACGGCG GTGGAGGCCT CGACAGCGCG GCCGCTAGGA AAGACCGTCA 
Int-C.b1  CTGCACGGCG GTGGAGGCCT CGACAGCGCG GCCGCTAGGA AAGACCGTCA 
Int-C.b2  CTGCACGGCG GTGGAGGCCT CGACAGCGCG GCCGCTAGGA AAGACCGTCA 

          351                                                400 
 Int-C.a  CAGCAAGATA TGCACCGCCG GCGGGATGAG GGACCGGCGG ATGCGGCTGT 
Int-C.b1  CAGCAAGATA TGCACCGCCG GCGGGATGAG GGACCGGCGG ATGCGGCTGT 
Int-C.b2  CAGCAAGATA TGCACCGCCG GCGGGATGAG GGACCGGCGG ATGCGGCTGT 

          401                                                450 
 Int-C.a  CCCTCGACGT CGCCCGCAAG TTCTTCGCGC TCCAGGACAT GCTCGGCTTC 
Int-C.b1  CCCTCGACGT CGCCCGCAAG TTCTTCGCGC TCCAGGACAT GCTCGGCTTC 
Int-C.b2  CCCTCGACGT CGCCCGCAAG TTCTTCGCGC TCCAGGACAT GCTCGGCTTC 

          451                                                500 
 Int-C.a  GACAAGGCCA GCAAGACGGT GCAATGGCTC CTCAATACGT CAAAGGGCGC 
Int-C.b1  GACAAGGCCA GCAAGACGGT GCAATGGCTC CTCAATACGT CAAAGGGCGC 
Int-C.b2  GACAAGGCCA GCAAGACGGT GCAATGGCTC CTCAATACGT CAAAGGGTGC 

          501                                                550 
 Int-C.a  CATCAAGGAG GTCATGACTG ACGAGGCGTC CTCCGACTGC GAGGAGGACG 
Int-C.b1  CATCAAGGAG GTCATGACTG ACGAGGCGTC CTCCGACTGC GAGGAGGACG 
Int-C.b2  CATCAAGGAG GTCATGACTG ACGAGGCGTC CTCCGACTGC GAGGAGGACG 

          551                                                600 
 Int-C.a  GCTCCAGCAG CCTCTCCGTC GCCGACGGCA AGCACAAGCA GCCAGGGACG 
Int-C.b1  GCTCCAGCAG CCTCTCCGTC GCCGACGGCA AGCACAAGCA GCCAGGGACG 
Int-C.b2  GCTCCAGCAG CCTCTCCGTC GCCGACGGCA AGCACAAGCA GCCAGGGACG 

          601                                                650 
 Int-C.a  GAGGCTGGAG GTGGTGATCA CGCCGACGGG AAGAAGCCGG CGCCGAGGGC 
Int-C.b1  GAGGCTGGAG GTGGTGATCA CGCCGACGGG AAGAAGCCGG CGCCGAGGGC 
Int-C.b2  GAGGCTGGAG GTGGTGATCA CGCCGACGGG AAGAAGCCGG CGCCGAGGGC 

          651                                                700 
 Int-C.a  TTCCAAAAGG GCACCCGCCA ACCCCAAGCC GCAAAGGAAA TTGGCCAGTG 
Int-C.b1  TTCCAAAAGG GCACCCGCCA ACCCCAAGCC GCAAAGGAAA TTGGCCAGTG 
Int-C.b2  TTCCAAAAGG GCACCCGCCA ACCCCAAGCC GCAAAGGAAA TTGGCCAGTG 

          701                                                750 
 Int-C.a  CGCACCTGAT CCCCGACAAG GAGTCGAGGA CAAAGGCGAG GGAGAGGGCA 
Int-C.b1  CGCACCTGAT CCCCGACAAG GAGTCGAGGA CAAAGGCGAG GGAGAGGGCA 
Int-C.b2  CGCACCTGAT CCCCGACAAG GAGTCGAGGA CAAAGGCGAG GGAGAGGGCA 

          751                                                800 
 Int-C.a  AGGGAGCGGA CGAGGGAGAA GAACCGGATG CGATGGGTGA CGCTCGCGTC 
Int-C.b1  AGGGAGCGGA CGAGGGAGAA GAACCGGATG CGATGGGTGA CGCTCGCGTC 
Int-C.b2  AGGGAGCGGA CGAGGGAGAA GAACCGGATG CGATGGGTGA CGCTCGCGTC 

          801                                                850 
 Int-C.a  CACAATCAAC ATCGAGCCGG CAACCACCGG CATGGCGGCG GCGAGGCTGG 
Int-C.b1  CACAATCAAC ATCGAGCCGG CAACCACCGG CATGGCGGCG GCGAGGCTGG 
Int-C.b2  CACAATCAAC ATCGAGCCGG CAACCACCGG CATGGCGGCG GCGAGGCTGG 

          851                                                900 
 Int-C.a  ACGAGTTGGT CACCAGCCCC AACAATTTGA TCAATCGCTC CTCGTCCATG 
Int-C.b1  ACGAGTTGGT CACCAGCCCC AACAATTTGA TCAATCGCTC CTCGTCCATG 
Int-C.b2  ACGAGTTGGT CACCAGCCCC AACAATTTGA TCAATCGCTC CTCGTCCATG 

          901                                                950 
 Int-C.a  AACACGCCAG GCGCTGAATT GGAGGAGGGG TGCTCGTCGT CCATGCCGAG 
Int-C.b1  AACACGCCAG GCGCTGAATT GGAGGAGGGG TGCTCGTCGT CCATGCCGAG 
Int-C.b2  AACACGCCAG GCGCTGAATT GGAGGAGGGG TGCTCGTCGT CCATGCCGAG 

          951                                               1000 
 Int-C.a  CGAAGCGATC ATGGCTGGCT TCGGCAATGG AGGGTACGGC AGCATCGGCA 
Int-C.b1  CGAAGCGATC ATGGCTGGCT TCGGCAATGG AGGGTACGGC AGCATCGGCA 
Int-C.b2  CGAAGCGATC ATGGCTGGCT TCGGCAATGG AGGGTACGGC AGCATCGGCA 

          1001                                              1050 
 Int-C.a  ACTACTACCA GCACCAGCTG GAGCAGCAAT GGGAGCTCGG TGGAGTGGTG 
Int-C.b1  ACTACTACCA GCACCAGCTG GAGCAGCAAT GGGAGCTCGG TGGAGTGGTG 
Int-C.b2  ACTACTACCA GCACCAGCTG GAGCAGCAAT GGGAGCTCGG TGGAGTGGTG 

          1051                                              1100 
 Int-C.a  TTTGCCAACT CCCAGCACTA CTGAGAAGCG ACGACGTGCG TACACGGTAC 
Int-C.b1  TTTGCCAACT CCCAGCACTA CTGAGAAGCG ACGACGTGCG TACACGGTAC 
Int-C.b2  TTTGCCAACT CCCAGCACTA CTGAGAAGCG ACGACGTGCG TACACGGTAC 

          1101                                              1150 
 Int-C.a  AAGAACTACT TCCGCTGTCT CGCCTTGAAC GTGCACTTAA TTTATATATA 
Int-C.b1  AAGAACTACT TCCGCTGTCT CGCCTTGAAC GTGCACTTAA TTTATATATA 
Int-C.b2  AAGAACTACT TCCGCTGTCT CGCCTTGAAC GTGCACTTAA TTTATATATA 

          1151        1165 
 Int-C.a  TATATATATA TATCC    
Int-C.b1  TATATATATA TATCC    
Int-C.b2  TATATATATA TATCC