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Table 3 Candidate causative SNPs in bak1 - 5 mob2

From: Mapping mutations in plant genomes with the user-friendly web application CandiSNP

Chr

Position

Ref/ Alt

AF (%)

AGI

Gene ID

AA change

Sanger F3

1

7446564

C/T

76.2

At1g21270

WAK2

P > L

Seg

1

11892984

C/T

100

At1g32830

Transposable element

n.a.

Homa,b

1

16513961

T/G

77.1

At1g43740

Transposable element

n.a.

Homa,b

1

17757465

C/T

76.0

At1g48090

Calcium-dependent lipid-binding protein

D > N

Seg

1

18192647

C/T

76.0

At1g49190

ARR19

R > W

Seg

1

22178447

C/T

82.6

At1g60140

TPS10

D > N

Hom

2

2568811

C/T

83.3

At2g06470

Transposable element

n.a.

Homa

2

5277241

T/G

100

At2g12850

Transposable element

n.a.

Not tested

4

2362567

C/A

100

At4g04655

Transposable element

n.a.

Sega

5

5569896

G/A

94.1

At5g16930

AAA-type ATPase family protein

W > stop

Seg

5

14285189

G/A

81.3

At5g36260

Eukaryotic aspartyl protease family protein

S > L

Absent

5

14579245

G/A

75.0

At5g36935

Transposable element

n.a.

Not tested

5

15751875

G/A

77.2

At5g39350

Tetratricopeptide repeat-like superfamily protein

R > K

Seg

5

17503318

G/A

82.7

At5g43560

TRAF-like superfamily protein

E > K

Seg

5

17597830

G/A

80.0

At5g43800

Transposable element

n.a.

Not tested

5

17820568

G/A

93.3

At5g44240

ALA2

A > T

Seg

5

18251689

G/A

83.3

At5g45140

Nuclear RNAP2

P > S

Seg

5

18261108

G/A

75.0

At5g45150

RTL3

D > N

Seg

5

18399206

G/A

80.9

At5g45400

RPA70C

V > M

Seg

5

21859555

G/A

90.0

At5g53840

F-box/RNI-like/FBD-like domains-containing protein

S > F

Seg

5

21939106

G/A

80.9

At5g54062

Unknown protein

E > K

Seg

5

22002355

G/A

88.9

At5g54203

Transposable element

n.a.

Absent

5

22066915

G/A

79.3

At5g54340

C2H2 and C2HC zinc-finger superfamily protein

V > I

Seg

5

22430866

G/A

90.0

At5g55310

TOP1β

A > V

Seg

5

22565056

G/A

76.5

At5g55750

Hydroxyproline-rich glycoprotein family protein

P > S

Seg

5

26458017

C/T

93.1

At5g66210

CPK28

W > stop

Homc

5

26560691

C/T

95.8

At5g66550

Maf-like protein

G > R

Hom

5

26626055

C/T

78.9

At5g66690

UGT72E2

P > S

Hom

5

26710709

C/T

75.0

At5g66880

SNRK2.3

P > S

Hom

5

26716839

C/T

80.9

At5g66900

CC-NB-LRR family protein

D > N

Hom

5

26935248

C/T

75.0

At5g67500

VDAC2

T > I

Hom

  1. Unique SNPs in annotated coding regions with allele frequencies (AF) over 75% identified by CandiSNP for bak1-5 mob2, listing the Chromosome number (Chr), position, reference base (Ref), sequenced alternate base (Alt), locus number (AGI), gene identification (Gene ID), amino acid change (AA change; ‘n.a.’ is not applicable). All SNPs were confirmed in at least three independent back-crossed lines (F3 generation) by Sanger sequencing compared to bak1-5. SNPs that were homozygous (Hom), segregating (Seg), not identified (Absent), or not tested are listed.
  2. aThese SNPs were also identified in bak1-5 by Sanger sequencing (however, not by Illumina sequencing) and are therefore not unique to bak1-5 mob2.
  3. bThese are single base deletion mutations.
  4. cThis SNP is the causative mutation for bak1-5 mob2[13].
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Plant Methods

ISSN: 1746-4811