Table 2 Functional relevance of 22 trait-associated genomic loci (gene-associated targets) identified by integrating GWAS, QTL mapping and differential expression profiling.

From: A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea

SNP IDs*a

Desi and kabuli chromosomes/ scaffolds

SNPs physical positions (bp)

SNPs (major/minor alleles)

Minor allele frequency (MAF)

Genes/gene-associated targets b

Structural annotation

Association analysis

Genetic/QTL mapping c

P

R2 (%)

Associated traits

LGs/chromosomes

QTLs identity

QTL intervals with genetic positions (cM)

LOD

R2(%)

CaSNP190

Desi-Sc-289

150550

(G/T)

0.29

Ca11846b (AP-1 complex subunit sigma-1)

Intergenic

2.5 × 10−6-3.4 × 10−6

26 & 38

PN & SN

CaLG(Chr5)

qPN5.2 & qSN5.2

38.8-40.6

7.2

18.6

CaSNP52

Desi-Sc-330

3079

(G/T)

0.30

Ca12072b (Leucine-rich repeat receptor-like protein kinase)

Intergenic

2.4 × 10−6-8.2 × 10−6

28 & 37

PN & SN

–

–

–

–

–

CaSNP192

Desi-Sc-994

225780

(A/T)

0.30

Ca09657b (Unknown expressed protein)

Intron

2.1 × 10−6-8.5 × 10−6

35 & 26

PN & SN

CaLG(Chr5)

qPN5.2 & qSN5.2

38.8-40.6

7.2

18.6

CaSNP24

Desi-Sc-2103

15896

(A/G)

0.29

—

Intergenic

3.2 × 10−6-1.1 × 10−5

34 & 23

PN & SN

CaLG(Chr1)

qPN1.1

46.1-50.2

8.4

23.6

CaSNP7

Desi-Sc-2103

15914

(T/G)

0.29

—

Intergenic

2.6 × 10−6-1.3 × 10−5

28 & 31

PN & SN

—

—

—

—

—

CaSNP70

Desi-Sc-4437

15942

(C/T)

0.30

—

Intergenic

4.7 × 10−5

26

PN

—

—

—

—

—

CaSNP182

Desi-Sc-8364

45741

(A/G)

0.29

Ca20029b (Ca_Desi_CesA10)d

URR

1.1 × 10−7-2.2 × 10−7

42 & 40

PN & SN

—

—

—

—

—

CaSNP37

Desi-Chr2

595853

(C/A)

0.24

Ca01065b (AP2/ERF transcription factor)

Intron

4.5 × 10−5-7.6 × 10−5

29

PN

CaLG(Chr2)

qPN2.1 & qSN2.1

2.9-9.8

7.4

21.7

CaSNP191

Kabuli-Sc-193

186515

(T/G)

0.30

Ca25161b (Unknown expressed protein)

Intergenic

6.8 × 10−5

24

PN

CaLG(Chr5)

qPN5.2 & qSN5.2

38.8-40.6

7.2

18.6

CaSNP26

Kabuli-Sc-193

186523

(T/C)

0.30

Ca25161 (Unknown expressed protein)

Intergenic

6.2 × 10−5

26

PN

CaLG(Chr1)

qPN1.1

46.1-50.2

8.4

23.6

CaSNP28

Kabuli-Sc-1504

189681

(C/T)

0.30

Ca24092b (Unknown expressed protein)

Intergenic

2.5 × 10−6- 9.3 × 10−6

31 & 36

PN & SN

CaLG(Chr1)

qPN1.1

46.1-50.2

8.4

23.6

CaSNP183

Kabuli-Chr5

16766270

(A/G)

0.35

Ca17942b (Ca_Kabuli_CesA3)d

URR

1.1 × 10−7- 1.3 × 10−7

45 & 47

PN & SN

CaLG(Chr5)

qPN5.1 & qSN5.1

6.8-18.9

9.7

28.7

CaSNP207

Kabuli-Chr6

27310325

(G/T)

0.25

Ca14618b (AP2/ERF transcription factor)

Intron

7.7 × 10−5

25

PN

CaLG(Chr6)

qPN6.1

37.7-40.1

8.0

18.2

CaSNP212

Kabuli-Chr6

41708309

(G/A)

0.28

—

Intergenic

3.6 × 10−5

27

PN

CaLG(Chr6)

qPN6.2

63.2-68.7

7.4

19.0

CaSNP292

Kabuli-Chr8

16102414

(G/T)

0.30

Ca15527b(Domain of unknown function DUF292

Intergenic

2.9 × 10−6-9.8 × 10−6

31 & 35

PN & SN

CaLG(Chr8)

qPN8.1

59.4-62.3

7.4

17.9

CaSNP181

Kabuli-De novo

309293

(C/G)

0.30

—

—

2.4 × 10−6-9.0 × 10−6

30 & 33

PN & SN

CaLG(Chr5)

qPN5.1 & qSN5.1

6.8-18.9

9.7

28.7

CaSNP184

Kabuli-De novo

316184

(G/C)

0.30

—

—

5.5 × 10−5

25

PN

CaLG(Chr5)

qPN5.1 & qSN5.1

6.8-18.9

9.7

28.7

CaSNP157

Kabuli-Chr4

38343633

(A/T)

0.32

Ca13120b (Calcium dependent protein kinase)

Intergenic

5.5 × 10−5

28

SN

CaLG(Chr4)

qSN4.1

105.1-108.7

7.8

21.8

CaSNP198

Kabuli-Chr6

16113521

(G/T)

0.21

Ca19678b (Haloacid dehydrogenase)

CDS (Syn)

2.8 × 10−5

38

SW

CaLG(Chr6)

qSW6.1

12.5-19.7

8.2

19.5

CaSNP199

Kabuli-Chr6

16113522

(A/T)

0.24

Ca19678 (Haloacid dehydrogenase)

CDS (NSyn)

2.7 × 10−5

39

SW

CaLG(Chr6)

qSW6.1

12.5-19.7

8.2

19.5

CaSNP200

Kabuli-Chr6

16113523

(T/C)

0.23

Ca19678 (Haloacid dehydrogenase)

CDS (NSyn)

2.7 × 10−5

37

SW

CaLG(Chr6)

qSW6.1

12.5-19.7

8.2

19.5

CaSNP186

Kabuli-De novo

63305

(T/G)

0.30

—

—

1.2 × 10−5

35

SW

CaLG(Chr5)

qSW5.1

24.7-25.7

6.5

18.7

  1. *CaSNP (Cicer arietinum SNP).
  2. aDetails regarding markers are provided in the Table S2.
  3. bValidated through differential expression profiling.
  4. cDetails regarding QTLs are mentioned in the Table S5.
  5. dDetails provided in the Table S6 and Figure S7.
  6. CDS (coding sequences), Nsyn (non-synonymous), Syn (synonymous) and URR (upstream regulatory region). AP2/ERF transcription factor classified following Magnani et al. (2004) Plant Cell 16:2265 and Nakano et al. (2006) Plant Physiology 140:411.
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