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Table 1 Summary of 14 SNP markers associated with growth traits or carcass traits

From: Genotype frequency distributions of 28 SNP markers in two commercial lines and five Chinese native chicken populations

SNP marker

GGAa

Positionb

Nearest genec

consequence typed

SNPd

Traitse

Chicken populationsf

Reference

rs13687128

1

92,866,047

POU1F1

synonymous variant

T/C

BW at 21, 35 days and SD at 63 days (P < 0.05), BW at 28 days and ADG from 0 to 4 weeks of age (P < 0.01)

F2 resource population made up of reciprocal cross between White Recessive Rock and Xinghua chickens

[25]

rs317360945

7

23,386,524

IGFBP2

synonymous variant

C/T

BW at 7, 14, 21, 28, 35, 42, 49, 56, 90 days, and CW, EW, BMW at 90 days (P < 0.01), LMW at 90 days (P < 0.05)

F2 resource population made up of reciprocal cross between White Recessive Rock and Xinghua chickens

[23]

rs14734533

4

70,143,452

TBC1D1

3 prime UTR variant

G/A

BW, CW, EW, SEW and LMW at 90 days (P < 0.05)

Erlang Mountainous chickens

[28]

rs314127605

5

15,760,767

ATGL

missense variant

C/T

BW at 14, 21, 35, 63, 70, 77 days, CFW and AFW (P < 0.05), BW at 42, 49, and 56 days (P < 0.01)

F2 resource population made up of reciprocal cross between White Recessive Rock and Chinese Xinghua chickens

[26]

NC_006092.4: g.25657391 T > A

5

25,657,391

CAPN3

intron variant

T/A

BW, EP, BMP at 90 days (P < 0.05)

five commercial pure lines (S01, S02, S03, S05, and D99) and 4 Chinese native breeds (Huiyang Huxu chicken, Qingyuan Ma chicken, Caoke chicken and Mountainous black-bone chicken)

[33]

NT_464126.1: g. 66916G > A

30

66,916

SLC27A1

missense variant

G/A

LW, CW, SEW, EW and BMWP at 91 days (P < 0.05)

eight meat-type quality chicken populations including S01, S02, S03, S05, S06, D99, S05 × S01, and S06 × S01 of Dahen chicken

[29]

rs314901473

1

14,235,966

PBEF1

synonymous variant

G/A

BW at 4, 6 weeks, and SL, BWLR and BFD at 4 weeks (P < 0.05), and BBL at 4 weeks (P < 0.01)

F2 resource population made up of reciprocal cross between Gushi chicken and Anka broilers

[22]

rs316142388

1

169,208,798

SETDB2

intron variant

T/C

BW at 12, 14, 16 weeks (P < 0.05)

Jinghai yellow chickens

[17]

rs314403820

3

67,466,233

FOXO3

intron variant

G/A

CW, SEW, EW and BMW at 49 days (P < 0.05)

White Recessive Rock and Xinghua chickens

[18]

rs14202565

2

69,322,385

MC4R

missense variant

G/C

BW, CW, SHL at 7 weeks (P < 0.05)

F6 generation of Arbor Acres grandsire line

[24]

rs16438236

4

77,857,657

87 kb U BOD1Lg

intergenic variant

C/T

BW at 10, 11, 12 weeks and ADG from 6 weeks to 12 weeks of age (P < 0.01)

F2 resource population made up of reciprocal crosses of Silky Fowl and White Plymouth Rock

[31]

rs13939265

1

130,801,788

OCA2

intron variant

C/T

BW at 11 weeks and 12 weeks (P < 0.01)

F2 resource population made up of reciprocal crosses of Silky Fowl and White Plymouth Rock

[31]

rs15620544

4

77,233,676

FBXL5

intron variant

C/T

BW at 10 weeks (P < 0.01)

F2 resource population made up of reciprocal crosses of Silky Fowl and White Plymouth Rock

[31]

rs16434462

4

73,027,691

—h

intergenic variant

T/C

BW at 11, 12 weeks and ADG from 6 weeks to 12 weeks of age (P < 0.01)

F2 resource population made up of reciprocal crosses of Silky Fowl and White Plymouth Rock

[31]

  1. a‘GGA’ refers to chromosome of Gallus gallus
  2. bPosition was based on chicken genome version of Gallus_gallus-5.0
  3. cThe nearest genes were obtained from the NCBI database or the reference in the rightmost column
  4. dThe consequence types and SNP were obtained from Ensemble database or the reference in the rightmost column
  5. eThe traits were obtained from the reference in the rightmost column and showed strong association with SNP marker in the leftmost column
  6. fThe chicken populations refer to the experimental material of the reference
  7. g‘U’ indicates that the SNP is upstream of the gene
  8. h‘—’ indicates that there was no nearest gene of rs16434462