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Table 5 Most significant (in italics) and suggestive SNPs in identified vQTL for litter size variabilitya

From: Evaluation of the phenotypic and genomic background of variability based on litter size of Large White pigs

SSC

Name

Position (Mb)

MAF

SNP effect (with SE)

Genetic. variance explained

Phenotypic variance explained

− log(p-value)

SNP location

Candidate genes

Previously detected QTL

1

AX-116127462

129.07

0.01

− 0.083 (0.020)

0.013

0.002

4.57

Intron

GANC

None

AX-116127463

129.08

0.01

− 0.100 (0.021)

0.017

0.003

5.53

Intron

GANC

AX-116127466

129.09

0.01

− 0.097 (0.020)

0.018

0.003

6.02

Intron

GANC

AX-116702728

129.17

0.01

− 0.083 (0.018)

0.015

0.003

5.30

Intron

VPS39

AX-116127269

127.69

0.03

− 0.047 (0.012)

0.012

0.002

4.23

Non-coding

Nonea

7

AX-116317099

36.59

0.47

0.020 (0.005)

0.016

0.003

4.35

Non-coding

NCR2

Birthweight variability [66]; number mummified piglets [67]; age at puberty [68]

AX-116317159

36.80

0.49

0.019 (0.004)

0.015

0.003

4.78

Non-coding

NRN1

AX-116317552

38.26

0.36

0.018 (0.005)

0.013

0.002

4.03

Intron

CUL9

AX-116317553

38.26

0.36

0.018 (0.005)

0.013

0.002

4.07

Intron

CUL9

AX-116317740

38.97

0.36

− 0.019 (0.005)

0.015

0.003

4.43

Non-coding

Nonea

AX-116689108

41.80

0.01

0.106 (0.018)

0.020

0.003

8.50

Non-coding

ADGRF1; ADGRF5

18

AX-116596013

18.07

0.05

− 0.039 (0.009)

0.012

0.002

4.60

Intron

LMBR1

Litter weight [69]; litter size [69]; litter weight of piglets born alive [69]; birthweight [70]

AX-116596024

18.19

0.09

− 0.030 (0.007)

0.013

0.002

4.83

Non-coding

KLF14; TSGA13; COPG2

AX-116596140

18.88

0.04

0.045 (0.011)

0.01

0.002

4.08

Intron

UBE2H

AX-116596204

19.30

0.07

− 0.034 (0.008)

0.012

0.002

4.53

Intron

AHCYL2

AX-116596216

19.37

0.09

− 0.029 (0.007)

0.011

0.002

5.01

Intron

AHCYL2

AX-116596225

19.40

0.06

− 0.041 (0.009)

0.015

0.003

5.56

Intron

AHCYL2

AX-116596239

19.45

0.05

− 0.039 (0.009)

0.013

0.002

4.82

Intron

SMO

  1. SSC Sus scrofa chromosomes; SNPs on each SSC present confirmed candidate QTL region
  2. MAF minor allele frequency
  3. aObtained with a log-transformed variance of residuals
  4. bWithin ± 50 kb