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Table 2 Summary of 14 SNP markers associated with reproduction traits

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

SNP marker

GGA

Position

Nearest gene

consequence type

SNP

Traits

Chicken populations

Reference

NC_006127.4: g24021190 G > A

Z

24,021,190

HMGCR

intron variant

G/A

EN at 300 days (P < 0.01)

F5 generation of Qing-Jiao-Ma breeding chickens

[20]

rs16349546

4

1,874,976

BMP15

synonymous variant

C/T

AFE, EWFE, EW at 43 weeks, EP at 43 weeks, EP at 46 weeks and EP at 48 weeks (P < 0.05)

LaiWu Black chickens

[21]

NC_006096.4: g22545152 G > C

9

22,545,152

RARRES1

nonsynonymous variant

G/C

EPR from 169 day to 280 day of age(P < 0.01)

F2 resource population crossed by White Leghorn males and Rhode Island Red females

[9]

rs16486559

5

30,579,826

GREM1

synonymous variant

G/A

EP at 43, 57, 66 weeks (P < 0.05)

Chinese Dagu chickens

[27]

rs317328077

3

36,305,243

GREM2

synonymous variant

T/C

EP at 30, 57, 66 weeks (P < 0.05)

Chinese Dagu chickens

[27]

rs14714701

7

20,960,237

KCNH7

intergenic variant

A/G

FEW (P < 0.01)

Jinghai Yellow Chicken

[19]

rs14085822

3

12,329,322

CDC42BPA

intron variant

A/G

EW at 300 days(P < 0.01)

Jinghai Yellow Chicken

[19]

rs13905010

1

92,440,932

GJA5

intron variant

T/C

EN between the age of 300 and 462 days (P < 0.01)

Jinghai Yellow Chicken

[19]

rs15602813

11

2,417,179

CBFB

intron variant

T/C

EN between the age of 300 and 462 days (P < 0.01)

Jinghai Yellow Chicken

[19]

rs14491030

4

76,458,342

NCAPG

missense variant

A/G

EN between the age of 26 and 28 weeks (P < 0.01), EN between the age of 42 and 46 weeks (P < 0.01)

six generations of a purebred brown egg layer line

[30]

rs14699480

4

76,411,761

LCORL

intron variant

T/G

EN between the age of 26 and 28 weeks (P < 0.01)

six generations of a purebred brown egg layer line

[30]

rs14652932

8

23,991,868

FAF1

intron variant

A/C

EN between the age of 26 and 28 weeks (P < 0.01)

six generations of a purebred brown egg layer line

[30]

rs315420959

5

41,036,029

21 kb U SEL1L

intergenic variant

A/G

EN between the age of 21 and 40 weeks (P < 0.01)

F2 resource population made up of reciprocal crosses between White Leghorn and Dongxiang Blue-shelled chicken

[32]

rs313187645

5

40,875,680

GTF2A1

intron variant

G/A

EN between 21 and 40 weeks of age(P < 0.01)

F2 resource population made up of reciprocal crosses between White Leghorn and Dongxiang Blue-shelled chicken

[32]