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Table 7 Penstemon SNP marker name, GenBank dbSNP accession ID, polymorphism type, KASPar™ primer sequences (A1, A2 and common allele specific reverse) for all 75 functional SNP assays

From: Developing molecular tools and insights into the Penstemon genome using genomic reduction and next-generation sequencing

Name

Contig Source1

SNP Allele GenBank Accession #2

SNP Type

Allele Specific A1 Forward (5′→3′) 3

Common Allele Specific Reverse 5′→3′)

P. davidsonii

P. cyananthus

P. dissectus

P. fruticosus

P. pachyphyllus

P. cyananthus + P. davidsonii

P. dissectus + P. davidsonii

Allele Specific A2 Forward (5′→3′) 3

PenSNP00001

00336CD

JX649978

A/G

AAGATTGCATGGAGAGGAAATGGATT

CGATCCAAATGGCAGATCCGAGAAA

X4

Y

X

 

X

Y

Y

AGATTGCATGGAGAGGAAATGGATC

PenSNP00002

00405CD

JX649979

C/T

ACGCGAGTAATAAGTTGGTTTTCTTC

CCAACACTTCCGCAGAAGCTCTTAA

Y

X

Y

X

Y

H

H

GACGCGAGTAATAAGTTGGTTTTCTTT

PenSNP00003

02625CD

JX649980

A/T

AAAAGCTCCCAAACATGACTATGAACT

AATTCTTCGACACTTGAAGAGAGCGTAA

Y

X

Y

 

Y

H

H

 

AAAAGCTCCCAAACATGACTATGAACA

 

PenSNP00004

02857CD

JX649981

A/C

ATCAAATGAACTTGTCTCATGAGCCT

GCAACAAGGTGCAAAAAATTGTAGCGTAA

X

Y

X

 

X

H

H

 

CAAATGAACTTGTCTCATGAGCCG

 

PenSNP00005

03943CD

JX649982

A/G

ACTACCAAAACTACCCTTCCCTTA

GGGGTACAGAGTTGAGAAGAAGGAA

X

Y

X

 

X

H

H

 

ACTACCAAAACTACCCTTCCCTTG

 

PenSNP00006

04420CD

JX649983

A/C

TGTCTCTAAATCGATATGATGAGGCT

GTGGTTCTTCCCCTTTAGAGGACTT

Y

X

Y

X

Y

H

H

 

GTCTCTAAATCGATATGATGAGGCG

 

PenSNP00007

08446CD

JX649984

A/T

GGCAACATCCTCAGCAGAGACA

CCGACTCCCTTAGCAATCTTAGCAT

Y

X

X

 

X

H

X

 

GGCAACATCCTCAGCAGAGACT

 

PenSNP00008

11303CD

JX649985

C/G

GGGTGGTATTGGTTACTTTTATGGG

CGGTATAAGAGCAACTAAGCTAAATGACTT

Y

X

Y

 

Y

H

H

 

GGGTGGTATTGGTTACTTTTATGGC

 

PenSNP00009

11357CD

JX649986

C/T

ACAATATTTGATAATTCATTCTCAAGTGCG

AAGCATGCAGTGAGACAAAAGCTAAGAT

X

Y

X

Y

X

H

H

 

CACAATATTTGATAATTCATTCTCAAGTGCA

 

PenSNP00010

11935CD

JX649987

A/C

AGCCTGATTATCCCTTAAACCCAATT

GAATCACGGCGGGGGAGCAAAT

X

Y

X

 

X

Y

 
 

GCCTGATTATCCCTTAAACCCAATG

 

PenSNP00011

12047CD

JX649988

C/T

TTTGGCACTGCAGTGACCATC

TGCTCCAGTCCGAAGGAAGTTGAAT

X

Y

Y

 

X

Y

Y

 

CTTTTGGCACTGCAGTGACCATT

 

PenSNP00012

12119CD

JX649989

A/G

AAGATAGACGTGGTATTTCTTCAGCA

GCAATTAGTCACAGACCATAGTGG

X

Y

X

 

X

H

H

 

AGATAGACGTGGTATTTCTTCAGCG

 

PenSNP00013

12398CD

JX649990

A/T

TATTTTCCTTTCTGCAATCTCAACATTGA

GTTGAGTGTGATTTTAGAGTGCATTTAGTT

X

Y

X

 

X

Y

Y

 

ATTTTCCTTTCTGCAATCTCAACATTGT

 

PenSNP00014

13398CD

JX649991

A/C

AGGCCTGTGGCTGACTTGTCA

GGCATATCTTTGCCCGTTTCCACAA

X

Y

X

X

X

H

H

 

GGCCTGTGGCTGACTTGTCC

 

PenSNP00015

13752CD

JX649992

A/C

AAATGCTCCCTCATTTTGACCATATGA

GTCAACGGATTTGTGGAAGTCGGTA

Y

X

Y

 

Y

H

H

 

ATGCTCCCTCATTTTGACCATATGC

 

PenSNP00016

14394CD

JX649993

C/G

TGAAAATTTCAGATTTAATGAACAAACAGTC

AGACTTGTAACAAATTCCTTGGGTCCAAA

X

Y

X

  

Y

H

 

GAAAATTTCAGATTTAATGAACAAACAGTG

 

PenSNP00017

14661CD

JX649994

A/G

TGACCAAGGAATCTGTTCAAGAACTT

CTTCTACTGTGGCTGTTTCACCTCTA

Y

X

Y

  

H

H

 

GACCAAGGAATCTGTTCAAGAACTC

 

PenSNP00018

15226CD

JX649995

G/T

TACCTCCAATTGTGATGCAACATTAG

CTAAGTGAGAAGCACAAGGA

X

Y

X

 

X

H

H

 

CTTACCTCCAATTGTGATGCAACATTAT

 

PenSNP00019

17421CD

JX649996

G/T

ATCCTCCTCCTTTGCATCAAAGC

GAGCCAACCTCGACTGCTTCTATTT

Y

X

Y

 

Y

X

H

 

CATCCTCCTCCTTTGCATCAAAGA

 

PenSNP00020

17816CD

JX649997

A/G

AAGGACTGAGTACCAAGACAGATCT

GCCAGGGTACTGAACCTGTCTTTTA

X

Y

X

 

X

H

H

 

GGACTGAGTACCAAGACAGATCC

 

PenSNP00021

18745CD

JX649998

C/T

AGCATATTGAAAAGATCAGTCGCATAG

CAGCTGCTCCTATCCAATCTTCGAA

Y

X

Y

 

Y

H

H

 

AAAGCATATTGAAAAGATCAGTCGCATAA

 

PenSNP00022

19267CD

JX649999

A/G

AAATACCTGAGCTTCTGCCTCTTGT

GATGCTCGTCATCTTGCTCAACGAT

X

Y

X

Y

X

H

H

 

ACCTGAGCTTCTGCCTCTTGC

 

PenSNP00023

21409CD

JX650000

C/G

ACCATTCAGGTAATATTTCCAAAGGC

AGCGGTTCTAGAACCGTCAATGCTT

Y

X

Y

Y

Y

X

H

 

ACCATTCAGGTAATATTTCCAAAGGG

 

PenSNP00024

22934CD

JX650001

A/G

GTACAATTGTCAAGTGTGTATTTTCTTACATA

GCACTGCACCATTCATGCCCTAAAA

Y

X

Y

 

Y

H

H

 

ACAATTGTCAAGTGTGTATTTTCTTACATG

 

PenSNP00025

22942CD

JX650002

A/T

ATCCGATTCTTCGTCTACTATGCCA

AGAAAAGCACAAGCTGAAATCAGGGAA

X

Y

X

 

Y

H

H

 

ATCCGATTCTTCGTCTACTATGCCT

 

PenSNP00026

27992CD

JX650003

A/G

TCCTCCTCGTCTCTTCCTCTT

CTTGGACCGTCCAAAGAAGGAAAGAA

Y

X

Y

 

Y

H

H

 

CCTCCTCGTCTCTTCCTCTC

 

PenSNP00027

01179DD

JX650004

A/G

TCGACCCCAACCTGTCACA

CTTGCTTGGTTTCGGAAAGAG

Y

X

Y

 

Y

H

H

 

CTTCGACCCCAACCTGTCACG

 

PenSNP00028

01235DD

JX650005

C/T

TGTGATCTTTGGTTTGAACTTTGTC

CTACCAAACTCACTCTAACATCCGGAT

X

Y

X

 

X

H

H

 

CACTTGTGATCTTTGGTTTGAACTTTGTT

 

PenSNP00029

01600DD

JX650006

A/G

TGGTCTTGTTCTTTACCATTACGCAT

GAAGTAGCTGCCATGGAAAAGGAAGTT

X

X

Y

X

X

X

H

 

GGTCTTGTTCTTTACCATTACGCAC

 

PenSNP00030

04630DD

JX650007

A/G

AGTAGTACAGAATACTTAAAACTATCACCA

GTTGGGGGAGTTGCCTTCTTGAAAT

X

X

Y

 

X

X

H

 

GTAGTACAGAATACTTAAAACTATCACCG

 

PenSNP00031

05304DD

JX650008

C/T

AGTTTTCCTTTTGTCCTTATGTGCAG

AAGGCTTAGCTTGGATGATATCCTACAA

Y

Y

X

 

Y

Y

Y

 

CAGTTTTCCTTTTGTCCTTATGTGCAA

 

PenSNP00032

05884DD

JX650009

A/T

GTCACCGCCTCCGATTGAGATT

CGGCTTTTGACGCCGCCGTAAA

X

Y

X

 

X

H

H

 

GTCACCGCCTCCGATTGAGATA

 

PenSNP00033

06956DD

JX650010

G/T

GTTGATTCTACAGATCTTAATTCTTGATTG

TACTACAAAGGGTAAAAAGTGCAATTCATA

X

Y

X

 

X

H

H

 

AGTTGATTCTACAGATCTTAATTCTTGATTT

 

PenSNP00034

08307DD

JX650011

C/G

ACATTAAGGGTCCACCAAAAATCCG

GCGCAATTAAAATCTCTTAAATCACCTGGT

Y

Y

X

  

Y

H

 

ACATTAAGGGTCCACCAAAAATCCC

 

PenSNP00035

08352DD

JX650012

A/T

AGTACAAGGAAAAACCTTTTATTAGTAAGTATA

CTGACACAAACCCATTCTAATATGACCAA

X

Y

X

 

X

H

H

 

AGTACAAGGAAAAACCTTTTATTAGTAAGTATT

 

PenSNP00036

08488DD

JX650013

A/T

GTGTTGGAGAGCCAGGTGCGA

GTATTGAGGATCATTCTGACAAAAAACATA

Y

X

Y

 

Y

H

H

 

GTGTTGGAGAGCCAGGTGCGT

 

PenSNP00037

08608DD

JX650014

C/T

GTAGATAAGTTGATTGCGAGAGGC

CCAAACAAATGCACCACATTCTCCTT

X

Y

X

Y

X

Y

H

 

GGTAGATAAGTTGATTGCGAGAGGT

 

PenSNP00038

08831DD

JX650015

A/T

TTTGAACTGCCATGTAAAGTTGTTTTAGA

ATTTTGAACCAAGGAGCTATCAGAGG

X

Y

X

 

X

Y

H

 

TTGAACTGCCATGTAAAGTTGTTTTAGT

 

PenSNP00039

08947DD

JX650016

A/T

GGGATCGTAAAACTCAGGAAAAATGA

TCAGATACTCGTGGGGTCTTCGATT

X

Y

X

H

X

Y

H

 

GGGATCGTAAAACTCAGGAAAAATGT

 

PenSNP00040

08959DD

JX650017

A/G

AGAGAATGAAGAAGGAGAAGGAAGAAA

CTCCTACGGTTGCATTATCGGTAGTA

Y

X

Y

 

Y

Y

Y

 

GAGAATGAAGAAGGAGAAGGAAGAAG

 

PenSNP00041

09272DD

JX650018

A/T

TTCTACAAAACAATCAGCAGTCATCATT

TCGACACCTTTTGCCTTATCTTGAA

X

Y

X

 

X

Y

H

 

TCTACAAAACAATCAGCAGTCATCATA

 

PenSNP00042

09369DD

JX650019

C/T

GTTTTTATACGCATCCATATACATAATAATAG

GGTTCACTCTCCAGAAATAAAATCTTATAT

Y

X

Y

 

Y

H

X

 

GTTTTTATACGCATCCATATACATAATAATAA

 

PenSNP00043

09764DD

JX650020

A/G

AATTCAACGTCAAATTGCAAGGTTGCA

TTCACTATACCGGCTGAGTTGGCAT

Y

X

Y

 

Y

H

H

 

CAACGTCAAATTGCAAGGTTGCG

 

PenSNP00044

10765DD

JX650021

A/G

TTTTTTAATAAATATCCTGGTGGATAATTTAT

AAATTGAGTGGATGGCTAGGAAGACTAA

X

Y

X

Y

X

H

H

 

TTTTTAATAAATATCCTGGTGGATAATTTAC

 

PenSNP00045

10870DD

JX650022

A/T

AGATCTGGAGACTAAAT

CGAAGAGTTTGGGTGGGCGGAT

X

Y

X

 

X

Y

Y

 

AGATCTGGAGACTAAAA

 

PenSNP00046

11107DD

JX650023

C/T

GTCCGACGTGACAATGCAGC

CGCCGTCAAAGAGACTTTGTTGGAT

Y

X

Y

 

Y

H

H

 

CTGTCCGACGTGACAATGCAGT

 

PenSNP00047

11531DD

JX650024

C/T

AGAAGATTCTTCGGCTGGGAGC

TCTTCACATGATTACGACAATGGCTGAAT

X

Y

X

 

X

H

H

 

AAGAAGATTCTTCGGCTGGGAGT

 

PenSNP00048

11655DD

JX650025

A/G

ACGTCCATGGAGGACCATAAA

GCTGTCTTCCTGCAAGGAACTTCTT

X

Y

X

 

X

H

H

 

CTACGTCCATGGAGGACCATAAG

 

PenSNP00049

11974DD

JX650026

G/T

AAAATGCATGTAGTTTGGTTTACG

CACACCCCCAAAGGAAGAATAGCAT

Y

X

Y

 

Y

H

H

 

AAAATGCATGTAGTTTGGTTTACT

 

PenSNP00050

13159DD

JX650027

C/T

TGAATGTACTTTTCATTGATAGAGAACG

AACAATAGTACAACACAACTAAAGCAGAGA

Y

Y

X

 

Y

Y

H

 

GTTGAATGTACTTTTCATTGATAGAGAACA

 

PenSNP00051

13463DD

JX650028

G/T

GCCTTTGACGGCGAAGGATTTC

GCAAGCACGGCACTAAGCCCTT

X

Y

X

 

X

H

H

 

CGCCTTTGACGGCGAAGGATTTA

 

PenSNP00052

14334DD

JX650029

A/G

AGAAACAACAAATACGAATAAATCACCCA

TTCGAAAATTGTGCTTGAATCACGCAGT

X

X

Y

H

X

X

Y

 

GAAACAACAAATACGAATAAATCACCCG

 

PenSNP00053

00290DD03373CD

JX650030

C/T

TGCCTTTGCGTCGCCACAATC

AGCTAAGAGATGGGCAGACTTTACAAAAT

Y

X

Y

 

Y

H

H

 

CTTGCCTTTGCGTCGCCACAATT

 

PenSNP00054

00354DD04637CD

JX650031

A/G

GCAAAAGGGAACCCTCATTTCGTT

TACTTGTCTGGGACTTTTCCTTTCTCTTT

X

X

Y

 

X

X

H

 

CAAAAGGGAACCCTCATTTCGTC

 

PenSNP00055

01161DD11697CD

JX650032

A/G

ACTGGTAAATACACTACGTTCACAGT

GAAACACAGCAGCCCAACGACATAT

Y

Y

X

X

Y

Y

H

 

CTGGTAAATACACTACGTTCACAGC

 

PenSNP00056

01323DD15501CD

JX650033

A/G

ACCTGAAGAATTTGTTCACTACTTCGT

GGATCGGGTGGAACGATTTGTGTT

X

Y

X

 

X

H

H

 

CCTGAAGAATTTGTTCACTACTTCGC

 

PenSNP00057

01541DD02481CD

JX650034

A/G

AATTAGAACCACATCCACTGATTCCAA

GGAGCCCAAACCTTTTACATTCTTTTCTA

Y

X

Y

 

Y

H

H

 

AGAACCACATCCACTGATTCCAG

 

PenSNP00058

02019DD03127CD

JX650035

A/G

GTGATTGTTAAATCTGAATATATAATTTCTTTT

GTACGAGGCTTCGAAAAAGACCAGAT

X

Y

X

 

X

H

H

 

GTGATTGTTAAATCTGAATATATAATTTCTTTC

 

PenSNP00059

02851DD17191CD

JX650036

A/G

AAGAGGTTGATCCTAAGTTATCGAGA

GAAGAAAATCATTGTCCACATCTCGTGTA

X

Y

X

 

X

Y

H

 

AGAGGTTGATCCTAAGTTATCGAGG

 

PenSNP00060

03089DD14703CD

JX650037

C/T

TTTCAGAGTCACTAATGTTCTCACG

GCATTTCTTGTCCATCTCTTCAAGATGTA

X

X

Y

Y

X

X

H

 

GTTTTCAGAGTCACTAATGTTCTCACA

 

PenSNP00061

03423DD25897CD

JX650038

A/C

AATTCTTCTACGTCCATTTGATCGGAT

TATTCTTAGACATGGACATGGAAATTGAGA

Y

X

Y

 

Y

H

H

 

CTTCTACGTCCATTTGATCGGAG

 

PenSNP00062

04632DD19186CD

JX650039

A/T

AAATGGGTCAGCTGAAATTTCCGCA

CTCTTCTTTACTCTGTTTTTTCTTCTTTTT

Y

Y

X

  

Y

H

 

AAATGGGTCAGCTGAAATTTCCGCT

 

PenSNP00063

05160DD08243CD

JX650040

C/G

TCGATCGTTGAAATGATAATTGATACAAG

GATCCCATAGACTTCTTTTAAGGATTCTAA

Y

X

Y

Y

Y

H

H

 

CGATCGTTGAAATGATAATTGATACAAC

 

PenSNP00064

06332DD03627CD

JX650041

A/C

ATCAAATGCCATAGATCCTGCAGATTT

ACATTTCCTACACCAACTTCTTCCACTA

X

X

Y

 

X

X

H

 

CAAATGCCATAGATCCTGCAGATTG

 

PenSNP00065

08748DD13630CD

JX650042

C/G

AGCTGTTCAGGAGGTTCATGAATG

CACCATGTGAACCAACACTATTGTCATTT

X

Y

X

 

X

H

H

 

AGCTGTTCAGGAGGTTCATGAATC

 

PenSNP00066

09773DD14323CD

JX650043

A/G

TCATGCCCATTCCCCA

CCTGGTATGAACATGGGGAGGTTAT

Y

Y

X

 

Y

Y

 
 

CATGCCCATTCCCCG

 

PenSNP00067

10248DD06150CD

JX650044

C/G

TGTGTCATTGAAATCAATCCGC

GTTTCATATCTCCCTTTGAGCTTCTTGAA

Y

Y

X

Y

Y

Y

H

 

GCTTGTGTCATTGAAATCAATCCGG

 

PenSNP00068

10624DD11358CD

JX650045

A/G

GTGGCAGTGTGAAACTGCATCA

GTTTTTCCCTGGGTGCTAAGGTTCAT

Y

X

Y

 

Y

H

H

 

GTGGCAGTGTGAAACTGCATCG

 

PenSNP00069

11267DD06273CD

JX650046

A/C

ACCAAATACTTATTAGCTCCAGTCGAA

GACTGAAGGATGTTGCGAGAGGC

Y

Y

X

 

Y

Y

H

 

CCAAATACTTATTAGCTCCAGTCGAC

 

PenSNP00070

11564DD17128CD

JX650047

C/T

TGGACTTGGCATTGAAACAAAAGATC

ATATGAAACTCCCCACAAGAAA

Y

X

Y

 

X

H

H

 

AATTGGACTTGGCATTGAAACAAAAGATT

 

PenSNP00071

11647DD17264CD

JX650048

C/G

GCACGAGCCAAAATCCTGAGC

ATTGGCATGTGTATCCTGTGTGGGA

X

Y

X

Y

X

H

H

 

GCACGAGCCAAAATCCTGAGG

 

PenSNP00072

11671DD17144CD

JX650049

C/T

GTGCAGCAACCCCTATTCATGAC

CCTGTCCAAAACATATGATCTTCATTGGAA

X

Y

X

  

H

H

 

ATGTGCAGCAACCCCTATTCATGAT

 

PenSNP00073

12915DD17470CD

JX650050

A/G

AAGAAAAGGGTGGACAAATTAAACCGT

CAGAACAACATCATACTTGATAAATCTCTT

X

X

Y

 

X

X

H

 

GAAAAGGGTGGACAAATTAAACCGC

 

PenSNP00074

13828DD14937CD

JX650051

C/T

GTAAGATATGCTGCCAGATGG

CTCTGAAGAAGTTTTTGTCCTTGATAGCTA

Y

Y

X

 

Y

Y

H

 

GTAAGATATGCTGCCAGATGA

 

PenSNP00075

14286DD18608CD

JX650052

G/T

GTATTGAGAGCCACTACCGG

CCACTTGAATTGTTTGAAGAGTTTGGGAA

Y

X

Y

 

Y

X

H

 

CTGTATTGAGAGCCACTACCGT

 
  1. 1These contigs have been deposited at DDBJ/EMBL/GenBank as a Whole Genome Shotgun project under the accessions AKKG00000000 (P. cyananthus), AKKH00000000 (P. dissectus), AKKI00000000 (P. davidsonii), and AKKJ00000000 (P. fruticosus). The version described in this paper is the first version for each accession, XXXX01000000.
  2. 2The GenBank accession identification for the full sequence for each allele with the specific SNP bp identified.
  3. 3KASPar™ primers: A1 and A2 primers are SNP allele specific. All A1 Forward primers had the follow universal primer GAAGGTGACCAAGTTCATGCT added to the 5′ end of the allele specific sequence. All A2 Forward primers had the follow universal primer GAAGGTCGGAGTCAACGGATT added to end of the 5′ allele specific sequence.
  4. 4H = heterozygous compared to either homozygous condition for either “X” or “Y”.
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