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Table 3 Description of some expected MTAs using imputed SNPs for agronomic traits of Iranian wheat accessions in well-watered environment

From: Genome-wide association mapping and genomic prediction of agronomical traits and breeding values in Iranian wheat under rain-fed and well-watered conditions

No

SNP

Sequence

Trait- Index

Chromosome

Position (bp)

Analysis method

Biological process

Cellular component

Molecular process

1

rs15519

TGCAGCACTCTGCAAGAAAAACGTCAAAGTAAGAACCACCTACCCACATCTGCTCCAATTCAAA

TKW

1D

47,767

pGWAS

lipid biosynthetic process

integral component of membrane

iron ion binding, oxidoreductase activity

2

rs23792

TGCAGCCCCTGGTCCTCCTGGTGGGAGAGCGTGTGGAACTCAAGGTAGCTGCCGTCCGTCACAA

SA

2 A

11,390

pGWAS

protein binding

-

-

3

rs59777

TGCAGTCTTTCAGAAGTGCAGATGTAAACGTATTGCTATATCAGTGGTTTGAACTACATGGTAA

TKW

2D

58,883

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

protein ubiquitination, positive regulation of protein catabolic process

Protein binding

-

4

rs61092

TGCAGTGCTGCTAGCGATCAGCTTGGTAGTCTGACAGGAAGGAGAGGCGTATCTACCTATTTAT

GY

3D

54,810

pGWAS

carbohydrate binding

-

-

5

rs23471

TGCAGCCCCATGGCTGGCCACTGCCCCGCCGACGCCACCTGCGGGTTTGGAGACGCCACCACGC

GY

5 A

58,225

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

RNA binding

-

 

6

rs31132

TGCAGCGCTCTCGGCGGTGACTCGTCGTCGCTCGGTGGCATCACCATCAACAAGACACGCGCGC

TKW

5 A

58,225

pGWAS

lipid transport

lipid binding

-

7

rs55428

TGCAGGTTTCAATTACGGAGGGAAAAACTCCAAGAAACTTATTGTTAGCAAGACGAAGTGACTG

GY

5 A

109,694

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

protein binding

-

-

8

rs31181

TGCAGCGCTGCATCTCTGGATTGTAGCGACAAGGAACTAAGCATGGATTGGAGGTATTATGTAA

PH

5B

26,242

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

-

-

-

9

rs63031

TGCAGTTCATCAAATTCGAAGGCCTCTCGTGCTAGCATAGCCATCACTTAGTTTGGGAACTGAA

GN

5B

45,594

pGWAS, eGWAS (BRR,gBLUP)

nucleoside metabolic process, UMP salvage, CTP salvage

uridine kinase activity, ATP binding, kinase activity

-

10

rs11075

TGCAGCAAATCGTCACTGCCTTCTAGCACGCCCGCCGTCTCTTAGTTGCAGCACCTAGCCGCCG

SH

6 A

46,797

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

-

-

-

11

rs44444

TGCAGGAGCTGAGCAACGAGGCCACAGCCGCCGCAGAAAAGGAGTCCCTGAACGGCACACTGGC

TKW

6B

92,187

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

ubiquitin-dependent protein catabolic process, protein deubiquitination

intracellular anatomical structure

thiol-dependent deubiquitinase

12

rs34582

TGCAGCTACCGCGTGACAAGCTACGTTACGCACGGGGTGCCGCCTCTGGCCGTGGCGGCATGGC

PH

6B

58,062

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

protein binding

-

-

14

rs44962

TGCAGGAGTCGCCACAGGATGTCTCATTTCTTGCCTTTGCTGGAAGCGTGAATTTCTGCCGATT

SA

1B

45,574

eGWAS(rrBLUP)

DNA topological change

chromosome

DNA binding, DNA topoisomerase activity, DNA topoisomerase type I (single strand cut, ATP-independent) activity

15

rs2390

TGCAGAAGTTCGACCTTTCAACATCTGTCCTGGCAATGCCAGCCATATGAAAAACTTCACATGG

GN

1B

45,574

eGWAS(gBLUP,rrBLUP)

-

anaphase-promoting complex

 

16

rs64529

TGCAGTTGTCTATCTCCAGAGAGGCCAGAGACCGTAAACCTCGCAAACAAGTACCCAGCTGCTC

SH

1B

47,847

eGWAS(BRR)

-

 

ADP binding

17

rs9736

TGCAGATGTGCTTGGCCGTTCGATTGATGCTCTGTTCTTCTTTGCCAGATCCCCAACGGGTGCG

SA

1B

47,279

eGWAS(BRR,gBLUP,rrBLUP)

carbohydrate transport

integral component of membrane

 

18

rs28731

TGCAGCGAGCAAGAACATGGCCAAAACGCCGTCGCCGAGATCGGAAGAGCGGGATCACCGACTG

SW

2 A

92,517

eGWAS(rrBLUP)

-

-

electron transfer activity

19

rs3810

TGCAGACCCAAACAAACAGTGTTCAGCCCATGCAAAGCACGAACGTACGTACTAGTATATGCAA

PH

2B

59,184

eGWAS(BRR,gBLUP)

transmembrane transport

membrane, integral component of membrane

transmembrane transporter activity

20

rs49651

TGCAGGGACGGAGACGGAGGTAGGCGGAGGCGTGGTCGGCTTCTTCGCCCTCGTCCTTGGTGGC

SA

2B

71,688

eGWAS(BRR,gBLUP,rrBLUP)

-

-

protein binding

21

rs7932

TGCAGATATTTATCGCCCAAGAGCAAAGATGCTTGACCAGGATTTGGATTGCGGACCGAGATCG

SH

2B

86,479

eGWAS(rrBLUP)

transcription, DNA-templated

-

DNA binding, DNA-directed 5’-3’ RNA polymerase activity, ribonucleoside binding

22

rs41022

TGCAGCTTCTACAGGTCTCTCGTGCTCCATGCATCAAACATGTGGGGACTGGATTCTTGCAGGC

FS

7B

118,551

eGWAS(BRR,rrBLUP)

-

-

ADP binding

23

rs38543

TGCAGCTGCAACCAACACCCTGACGGCGGGCCAGTCGCTCGCCGTCGGCGGCAGCAAGCTCGTC

PH

2D

79,343

eGWAS(BRR)

protein phosphorylation, recognition of pollen

integral component of membrane

protein kinase activity, protein serine/threonine kinase activity, ATP binding

24

rs54935

TGCAGGTTCATTGAGAGAGCGCAGGCTCTGATTCATGGAGATCTCCATACTGGTTCCATCATGT

SH

2D

82,753

eGWAS(BRR,gBLUP)

methionine biosynthetic process, phosphorylation

-

S-methyl-5-thioribose kinase activity

25

rs46842

TGCAGGCCAGCCAAATTTATTGGCACGCGAACGGGAAAACGAACTGTTAAAATATCTGTAACTA

PH

3B

45,525

eGWAS(BRR,gBLUP)

-

-

oxidoreductase activity, oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor, metal ion binding

26

rs24758

TGCAGCCGACGGAGCTCGCGAGCCACATGAGCTCCCGCTGCCCTGCTCTCGAGGACTTGAAACT

PH

3B

121,341

eGWAS(rrBLUP)

-

-

protein binding

27

rs63419

TGCAGTTCGAGCGCCGATGGTGCCTCTTGTTGTGTTGTGTCCCCCCTCGCCATGTGTTGTCCAT

GY

4 A

61,015

eGWAS(rrBLUP)

cation transport, calcium ion transport, transmembrane transport

integral component of membrane

cation transmembrane transporter activity, calcium:proton antiporter activity

28

rs40457

TGCAGCTTAAACATACAAGCAAGCCATACATGCCACGGATGTGGCGCCATTGGTTTACCTTTTA

SH

4 A

146,426

eGWAS(BRR,gBLUP)

-

integral component of membrane

-

29

rs62498

TGCAGTTAATCATTTATTAGTACTAGTTATTAAAAGACCAAGATAGTGAAGACAGAATTCCCTG

SA

4 A

147,563

eGWAS(BRR)

protein phosphorylation

-

protein kinase activity, ATP binding

  1. Abbreviations: PH Plant height, GY Grain yield, GN Grain number per spike, TKW Thousand kernel weight, SW Spike weight, SA Spike area, SH Spike harvest index, SF Spike fertility
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BMC Genomics

ISSN: 1471-2164

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