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Table 3 Results of the genome-wide association study: significantly associated SNP markers with the studied traits (plant IVOMD, plant IVNDFD, stem IVNDFD, STA, ADFom, stem KL, stem length, and ear proportion) and candidate genes in proximity of the significant SNP markers

From: Genome-wide association study for in vitro digestibility and related traits in triticale forage

QTL

SNP marker

Candidate region

P

R²p

Median BLUP value per genotypic class (0/1/2)

Candidate gene

Annotation

(biological process)

Plant IVOMD (%)

PIVOMD_1

10517787_19_C/T

1R:38,333,322–39,433,322

6.04

0.14

67.9/62.6/64.6

SECCE1Rv1G0007100

Transporter activity, ATP binding, ATP hydrolysis activity

      

SECCE1Rv1G0007120

Peroxidase activity

PIVOMD_2

22077643_9_T/G

NA

8.20

0.16

NA/62.1/67.7

NA

NA

PIVOMD_3

3042285_21_A/C

NA

6.34

0.11

66.8/65.8/68.3

NA

NA

Plant IVNDFD (%)

PIVNDFD_1

4211801_19_C/T

1A:474,187,796–474,687,796

6.96

0.05

55.1/50.4/50.5

TraesCS1A02G278200

Carbohydrate binding, starch binding

      

TraesCS1A02G279000

Hydrolase activity, hydrolyzing O-glycosyl compounds

(carbohydrate metabolic process)

PIVNDFD_2

54358850_11_G/A

2A:24,803,946–25,923,946

10.33

0.07

55.6/54.0/53.1

TraesCS2A02G059800

Transmembrane transporter activity

(transmembrane transport)

PIVNDFD_3

54354903_15_A/G

2B:18,789,842–20,039,842

6.21

0.13

54.8/51.1/54.6

TraesCS2B02G041200

Methyltransferase activity, O-methyltransferase activity, protein dimerization activity

      

TraesCS2B02G041400

TraesCS2B02G041700

TraesCS2B02G042100

UDP-glycosyltransferase activity

      

TraesCS2B02G041600

ATPase-coupled transmembrane transporter activity, ABC-type transporter activity

(transmembrane transport)

      

TraesCS2B02G041800

TraesCS2B02G042000

TraesCS2B02G042200

UDP-glycosyltransferase activity, hexosyltransferase activity

      

TraesCS2B02G042300

TraesCS2B02G042400

TraesCS2B02G042900

TraesCS2B02G043000

TraesCS2B02G043100

TraesCS2B02G043200

(exocytosis, protein transport)

PIVNDFD_4

4370557_20_A/G

5A:704,492,970–705,452,970

7.32

0.02

55.4/54.3/54.8

NA

NA

PIVNDFD_5

3623312_68_T/C

NA

5.85

0.01

54.2/52.8/55.9

NA

NA

PIVNDFD_6

4567261_61_T/C

7A:284,227,044–284,827,044

8.24

0.10

NA/54.8/54.1

NA

NA

PIVNDFD_7

14469989_24_A/G

NA

6.91

0.11

54.9/NA/49.2

NA

NA

PIVNDFD_8

15998020_11_A/C

NA

11.95

0.27

NA/57.3/54.1

NA

NA

PIVNDFD_9

22077643_9_T/G

NA

10.80

0.18

NA/49.5/54.9

NA

NA

PIVNDFD_10

3046586_39_G/A

5R:609,761,318–610,861,318

10.30

0.20

55.6/50.5/53.7

NA

NA

Stem IVNDFD (%)

SIVNDFD_1

4211801_19_C/T

1A:474,187,796–474,687,796

16.12

0.14

38.0/32.1/33.3

See QTL PIVNDFD_1

See QTL PIVNDFD_1

SIVNDFD_2

54345599_25_T/G

2A:62,591,738–63,711,738

6.04

0.10

37.4/37.6/NA

TraesCS2A02G112200

Acyltransferase activity

(GPI anchor biosynthetic process)

SIVNDFD_3

4206397_9_C/A

2R:844,945,966–846,045,966

6.49

0.10

37.2/39.0/39.6

SECCE2Rv1G0126200

UDP-glycosyltransferase activity

      

SECCE2Rv1G0126220

ATP binding, ABC-type transporter activity

      

SECCE2Rv1G0126260 SECCE2Rv1G0126280 SECCE2Rv1G0126290

SECCE2Rv1G0126300

SECCE2Rv1G0126310

SECCE2Rv1G0126320

Transmembrane transporter activity

(transmembrane transport)

      

SECCE2Rv1G0126340

Hydrolase activity, hydrolyzing O-glycosyl compounds,

xyloglucan:xyloglucosyl transferase activity

(carbohydrate metabolic process, cellular glucan metabolic process, xyloglucan metabolic process, cell wall biogenesis)

SIVNDFD_4

10514146_31_A/C

3B:763,613,048–764,533,048

7.13

0.11

37.2/35.8/37.8

NA

NA

SIVNDFD_5

3607057_38_A/G

NA

7.35

0.10

NA/41.9/36.6

NA

NA

SIVNDFD_6

54360481_5_G/T

NA

6.22

0.07

NA/35.9/39.7

NA

NA

SIVNDFD_7

15998020_11_A/C

NA

11.20

0.36

NA/43.2/37.0

NA

NA

SIVNDFD_8

8539528_31_A/G

NA

5.92

0.15

NA/35.1/37.9

NA

NA

STA (g/kg DM)

STA_1

11912016_38_T/C

3B:23,305,225–24,225,225

7.14

0.12

270/259/272

TraesCS3B02G046100

C-5 sterol desaturase activity

(sterol biosynthetic process)

      

TraesCS3B02G046700

Protein kinase activity

(protein phosphorylation)

      

TraesCS3B02G046900

TraesCS3B02G047000

Acetylglucosaminyltransferase activity, transferase activity, glycosyltransferase activity

      

TraesCS3B02G047300

Transmembrane transporter activity

(transmembrane transport)

      

TraesCS3B02G047600

ATP hydrolysis activity, ABC-type transporter activity

(transmembrane transport)

STA_2

36892899_23_G/A

4A:619,145,783–619,605,783

6.73

< 0.01

265/273/270

TraesCS4A02G336800

Protein kinase activity

(protein phosphorylation)

STA_3

10521380_21_A/G

4B:572,153,890–572,953,890

6.29

0.08

271/NA/256

NA

NA

STA_4

3606416_67_C/G

5B:488,820,374–489,660,374

11.95

0.35

279/244/260

TraesCS5B02G305100

Actin binding, actin filament binding

(actin cytoskeleton organisation, actin nucleation)

      

TraesCS5B02G305300

TraesCS5B02G305400

TraesCS5B02G305500

UDP-glycosyltransferase activity, hexosyltransferase activity

      

TraesCS5B02G305600

UDP-glycosyltransferase activity

STA_5

3045349_41_T/G

5B:688,784,316–689,624,316

11.50

0.12

275/260/271

NA

NA

STA_6

22077643_9_T/G

NA

8.15

0.11

NA/236/272

NA

NA

STA_7

3043904_26_C/T

NA

9.60

0.31

265/272/276

NA

NA

STA_8

4350778_5_C/G

NA

6.18

0.18

272/243/236

NA

NA

ADFom (g/kg DM)

ADFom_1

8536912_31_C/A

7A:704,030,351–704,630,351

7.10

0.03

260/235/250

TraesCS7A02G519800

Actin binding

(regulation of actin filament polymerization, Arp2/3 complex-mediated actin nucleation)

ADFom_2

3610345_15_G/C

NA

15.08

0.38

243/NA/258

NA

NA

ADFom_3

54358455_11_T/C

NA

6.68

0.15

255/248/237

NA

NA

Stem KL (g/kg aNDFom)

SKL_1

4366914_47_G/C

3A:685,868,646–687,208,646

8.25

0.13

129/129/126

TraesCS3A02G444500

TraesCS3A02G445900 TraesCS3A02G446800

TraesCS3A02G447300

Protein kinase activity, ATP binding

(protein phosphorylation)

      

TraesCS3A02G444600

Carbohydrate binding

      

TraesCS3A02G446600

TraesCS3A02G446700

Potassium ion transmembrane transporter activity

(potassium ion transmembrane transport)

SKL_2

4563722_14_A/G

7B:583,845,567–584,225,567

9.69

0.08

127/129/119

TraesCS7B02G328700

Transmembrane transporter activity

(transmembrane transport)

      

TraesCS7B02G328800

Protein kinase activity, ATP binding

(protein phosphorylation)

SKL_3

4551138_8_C/G

NA

9.27

0.02

131/127/125

NA

NA

SKL_4

4212151_44_G/A

NA

6.85

0.07

128/131/127

NA

NA

SKL_5

15998020_11_A/C

NA

7.21

0.40

NA/117/130

NA

NA

SKL_6

3046493_23_G/A

NA

6.29

0.11

124/NA/132

NA

NA

SKL_7

4567564_20_T/G

NA

11.63

0.10

126/135/132

NA

NA

Stem length (cm)

SL_1

8512008_13_G/C

NA

8.71

0.01

123/123/101

NA

NA

SL_2

4370804_7_T/G

1R:675,629,057–676,729,057

8.06

0.04

100/147/113

NA

NA

SL_3

4369682_17_C/G

NA

19.28

0.21

102/117/NA

NA

NA

SL_4

10519076_15_G/A

NA

8.34

0.10

NA/100/104

NA

NA

SL_5

15998020_11_A/C

NA

14.22

0.12

NA/91/107

NA

NA

SL_6

3621151_19_T/G

NA

10.45

0.07

107/105/93

NA

NA

SL_7

4208358_19_A/G

NA

19.58

0.21

100/127/144

NA

NA

SL_8

4348644_14_A/G

NA

6.19

0.02

102/104 /NA

NA

NA

SL_9

54357631_62_G/A

NA

20.33

0.15

150/NA/101

NA

NA

Ear prop (%)

EP_1

4211801_19_C/T

1A:474,187,796–474,687,796

12.90

0.23

59.1/52.1/53.7

See QTL PIVNDFD_1

See QTL PIVNDFD_1

EP_2

8530946_28_G/A

5B:645,663,357–646,503,357

6.17

0.10

58.9/50.8/51.5

NA

NA

EP_3

10514469_23_C/G

NA

6.95

0.13

58.2/55.2/59.5

NA

NA

EP_4

36892695_26_C/G

NA

8.00

0.16

60.8/56.1/58.2

NA

NA

EP_5

4209538_61_C/T

5R:610,604,285–611,704,285

11.36

0.27

59.9/56.6/56.7

NA

NA

  1. QTL: trait abbreviation followed by an ordinal number per trait; SNP marker: ID for the sequence in which the significant SNP marker occurs; Candidate region: chromosomal position of the significant SNP marker, expressed in basepairs (start and end position of the candidate region is defined by the LD decay distance around the significant SNP); P: - log10 of the P-value of the significant SNP marker; R²p: partial phenotypic variance explained by the significant SNP; Median BLUP value per genotypic class presented as 0/1/2 where 0: homozygous REF, 1: homozygous ALTERNATIVE, 2: heterozygous; Candidate gene: genes in the Wheat_ChineseSpring10 reference genome v1.0 (2018) and in the Secale cereale Lo7 v1 pseudomolecules (2021) reference genome in the candidate region defined by the LD decay distance of the different chromosomes around the significant SNP marker (retrieved from ‘The GrainGenes Genome Browsers’, https://wheat.pw.usda.gov/GG3/genome_browser); Annotation: function description retrieved from Ensembl Plants with the biological function in parenthesis (https://plants.ensembl.org/Triticum_aestivum/Info/Index, https://plants.ensembl.org/Secale_cereale/Info/Index). In italics: SNP markers with mapped positions to the rye reference genome after running a BLAST query (https://wheat.pw.usda.gov/blast/). NA: not available
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BMC Plant Biology

ISSN: 1471-2229

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