Genome-wide association study reveals novel loci for litter size and its variability in a Large White pig population

Table 4 Significant SNPs per Sus scrofa chromosome (SSC) associated with litter size and detected in boars and sows from a Large White pig population. Description of significant regions includes: minor allele frequency (MAF), allele substitution effect and the Bayes Factor (BF) as an indication for significance (only SNP with BF ≥ 30 are reported)

SSC	Significant SNP	Position (Mb)	MAF	Allele subs. effect^a	BF	Gen. var. expl. by SNP (%)
1	ALGA0001244	17.28	0.30	0.052	85.4	0.10
1	ASGA0005117	182.38	0.48	0.039	36.6	0.07
1	ALGA0006771	182.42	0.48	0.034	30.1	0.05
5	ASGA0023713	1.38	0.35	0.034	36.6	0.04
8	ASGA0097249	42.52	0.42	0.021	59.9	0.02
11	ASGA0050328	23.81	0.26	0.105	295.5	0.36
11	MARC0020561	23.87	0.45	0.030	30.1	0.04
13	ASGA0059543	192.72	0.25	0.042	38.8	0.06
18	ALGA0098906	58.86	0.29	0.038	35.5	0.05
18	INRA0056201	58.88	0.29	0.036	42.1	0.04

^aAllele substitution effects were estimated as \( \alpha =\sqrt{\sigma_a^2{(2pq)}^{-1}} \) , where σ ²_a is the genetic variance explained by the SNP, and p and q are the frequencies of the two alleles [83].

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