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Table 4 Description of some expected MTAs using imputed SNPs for agronomic traits of Iranian wheat accessions in rain-fed 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

rs65348

TGCAGTTTTCCGATCGGATATGTCAGCGGCGTCGAGGACCATGCATGGATCGTTTAAAGGTGAT

SH

1 A

44,512

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

-

-

protein binding

2

rs64529

TGCAGTTGTCTATCTCCAGAGAGGCCAGAGACCGTAAACCTCGCAAACAAGTACCCAGCTGCTC

TKW

1B

47,847

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

-

-

ADP binding

3

rs51900

TGCAGGGTGGGGGCGGAGAAAAAGGAGGAGGGGCGGCCGAGATCGGAAGAGCGGGATCACCGAC

TKW

2D

28,183

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

vesicle-mediated transport

plasma membrane, integral component of membrane

protein binding

4

rs56561

TGCAGTACTGGTACCCGCCGCCGCCGTACCAACCGCACCTGTGCCACCTCGCCGAGGAGGACCC

PH

2D

82,753

pGWAS

metal ion transport

 

metal ion binding

5

rs64448

TGCAGTTGTAATCTTCCATGGAATCCCAACAAGTTTAGAGCGTGTCGATTCGTGGTAGATGGAT

SW

3B

56,892

pGWAS

-

membrane, integral component of membrane

monooxygenase activity, iron ion binding, oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, heme binding

6

rs16023

TGCAGCAGAGGTGGTTTGGAGGTTTGGTGGCGGCAGGATTCCCCTCCCGCGGGCGGCTCGGCTC

GY

3B

56,892

pGWAS

auxin-activated signaling pathway, transmembrane transport, intracellular auxin transport

membrane, integral component of membrane

-

7

rs51991

TGCAGGGTTCGCTCGTCGACGTCAACCCTTTGGAAGCGCAGCTCGAGCGCGGCATCCTTCTGGA

GY

4 A

129,369

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

  

ATP binding, ATPase

8

rs38090

TGCAGCTCTGGTTACAGTAGAACGACGAACAAACCTGAACCTGCATCCACACCACCCAGCATTC

TKW

3B

7980

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

fatty acid biosynthetic process

membrane, integral component of membrane

acyltransferase activity, acyltransferase activity, transferring groups other than amino-acyl groups

9

rs5942

TGCAGAGCATGGTCAGCTTCAGCAGTTCGACAAGCACACGCACCATAGGAGAAAGGTTGCACAT

SA

4B

93,598

pGWAS, eGWAS(BRR)

-

-

methyltransferase activity, protein dimerization activity

10

rs60493

TGCAGTGCAGACGGTATACTTACTCTAGAGTGCAAGCAAAGGAGAAACCGAGGGGAGGAGGAGG

SA

5 A

5684

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

proteolysis

-

serine-type endopeptidase activity, peptidase activit, serine-type peptidase activity, hydrolase activity

11

rs32859

TGCAGCGGTAGTTCGCTGGCATTGGCATTAGCCAAGGAGCGATGAGCATGGACCCGAGATCGGA

SA

5 A

38,892

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

-

integral component of membrane

-

12

rs40738

TGCAGCTTCATAGGTCGTACTAGATACTGCAAATACTTTGAAAGCTTAGTTACATGGTTTGTGG

SA

6B

94,461

pGWAS, eGWAS(BRR,gBLUP)

-

integral component of membrane

-

13

rs3733

TGCAGACCAGCACGCCCGCCGCGGCCGCCGTGGTAACGGCGCCGAGATCGGAAGAGCGGGATCA

FS

7B

51,193

pGWAS, eGWAS(BRR,gBLUP,rrBLUP)

microtubule-based movement

-

microtubule motor activity, ATP binding, microtubule binding, ATP-dependent microtubule motor activity

14

rs50966

TGCAGGGGAGGGGCGAGGAAAAGCCTAGCCGCCGAAGCCGTAGAGGGTGCGGCCCTGGCGCTTG

GY

1 A

50,198

eGWAS(rrBLUP)

nucleosome assembly, response to water deprivation

nucleosome, nucleus, chromosome, nucleolus, vacuolar membrane, cytosol, plasma membrane, plasmodesma, chloroplast,thylakoid

DNA binding, protein heterodimerization activity

15

rs60665

TGCAGTGCATTCCTAGCAAGTACTAGGTTAGTTTACTCGTTCAAATACCAAAAGGCAATCTAAG

FS

1 A

66,684

eGWAS(BRR,gBLUP,rrBLUP)

-

-

tRNA binding,GTPase activity,GTP binding

16

rs52091

TGCAGGGTTTGACATTCTGCAAGTACCACCTCAACACCGAGATCGGAAGAGCGGGATCACCGAC

GN

1B

45,574

eGWAS(BRR,gBLUP,rrBLUP)

-

-

protein binding

17

rs14671

TGCAGCACCTTCACGGCAACCATGGAGCCGTCCCGCAGCGTGCCGCGGTACACGCGGCTGTAGC

PH

5 A

3411

eGWAS(BRR,gBLUP)

protein phosphorylation

-

protein kinase activity,ATP binding

18

rs17744

TGCAGCAGGAGCTTGCCGATAAGGTGGCTCTCGACCGAAACGTGGACGAGGCAGACCTCAACAA

PH

1D

9094

eGWAS(BRR)

-

-

monooxygenase activity, iron ion binding,oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen,heme binding

19

rs33741

TGCAGCGTGCCTGTGGCTATACGTACTGATCGTTTCCCCGTGTTCCTCCACACGGGCAGGTTCG

PH

2 A

59,228

eGWAS(BRR,gBLUP)

biosynthetic process

-

strictosidine synthase activity

20

rs61008

TGCAGTGCTACTCACACAGGGGAATCAGGCCTGACATTCGCCATCTTCTTCTGCTCAGCCAACC

SW

2B

59,184

eGWAS(BRR,gBLUP,rrBLUP)

-

integral component of membrane

 

21

rs21291

TGCAGCCACCTTCGAAATGTGCATCCCCTTTACCCGTATCGGGAGAACGAGGTGTAGCTCAGTT

SH

2B

67,141

eGWAS(BRR)

-

-

ADP binding

22

rs48315

TGCAGGCGGATCTGGTCCAGCAGACGGTCCGCCTCGCCCTCGGCGTCGGCGTCGGCGGCGTCGG

TKW

2D

27,046

eGWAS(BRR,gBLUP)

lipid metabolic process, signal transduction,lipid catabolic process,intracellular signal transduction

intracellular anatomical structure

phosphatidylinositol phospholipase C activity,phosphoric diester hydrolase activity

23

rs16199

TGCAGCAGCAACCACCACCATGGAAAGAGAGAGACAGAGACGGTGAGCTCCTCTGGACAGCGAG

TKW

2D

28,183

eGWAS(BRR,gBLUP,rrBLUP)

lipid metabolic process

-

oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water

24

rs25087

TGCAGCCGCAGAAACATGACCGCGCTGACACCGACCATCCTGCCCGCCGCGCCGTCGCCGACGA

FS

3 A

53,669

eGWAS(BRR,gBLUP)

-

-

protein binding

25

rs10286

TGCAGATTGGAATTTCTGAAAGGCCTCCACAAGATGAAGGAAGCAACGATCGATCCG

PH

5B

35,359

eGWAS(BRR,gBLUP)

-

-

hydrolase activity

26

rs19868

TGCAGCATGGAGTTTAAAAATATTCAATGGTAATTTACCAGACCGAAAGACAAATAAGCAATGC

PH

3B

18,217

eGWAS(rrBLUP)

-

-

nucleotide binding, nucleic acid binding, RNA helicase activity,helicase activity,ATP binding

27

rs27041

TGCAGCCTCTCTACCTTAGAGATCTTGGGGATGACCACCGTGTTCCTCTGGAGGCCCCACCGAG

SW

3B

22,764

eGWAS(rrBLUP)

-

-

oxidoreductase activity, aldose-6-phosphate reductase (NADPH) activity,D-threo-aldose 1-dehydrogenase activity

28

rs3365

TGCAGACACTAGTATCATTGGAAGCACAGGATGAGTCCGTTAGACAGTTGGGGGAGCTGAGGCA

TKW

4 A

61,015

eGWAS(rrBLUP)

-

-

ADP binding

29

rs31074

TGCAGCGCTATGGTAGCTTTGGTTGGTAGTTACTCTGAACCGAGATCGGAAGAGCGGGATCACC

PH

4 A

125,958

eGWAS(BRR,gBLUP)

-

integral component of membrane

-

30

rs17272

TGCAGCAGCGGCGGGAGCATAGGATCGTGGAGAGGGAGCAGGGACGGCGAGCTTACGGAGCGGG

PH

4 A

125,958

eGWAS(gBLUP)

transmembrane transport

integral component of membrane

oligopeptide transmembrane transporter activity

  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