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

Table 5 Significant SNPs per Sus scrofa chromosome (SSC) associated with variation in 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, the Bayes Factor (BF) as an indication for significance (only SNP with BF ≤ 30 are reported) and overview of previously reported QTL for reproduction traits in pigs (based on PigQTLdb; February, 2015)

SSC	Most sign. SNP	Position (Mb)	MAF	Allele subs. effect^a	BF	Gen. var. expl. by SNP (%)	Overview of QTL reported within region
2	ALGA0106652	27.17	0.44	0.011	36.6	0.11
3	MARC0056802	28.40	0.27	0.016	46.4	0.20	corpus luteum number [44] plasma concentration of FSH [44]
7	INRA0025193	43.76	0.48	0.023	167.2	0.50	corpus luteum number [84] birth weight [46, 85–87]
7	ASGA0031511	17.47	0.20	0.010	36.6	0.06	corpus luteum number [84] female age at puberty [44]
10	H3GA0055101	0.05	0.47	0.011	44.2	0.12	number of stillborn [43]
10	MARC0015344	0.06	0.47	0.012	41.0	0.15	number of stillborn [43]
13	DRGA0013310	194.39	0.32	0.011	38.8	0.10	corpus luteum number [84]
15	MARC0077161	35.59	0.39	0.010	50.9	0.10	corpus luteum number [84]
16	DRGA0016314	73.39	0.31	0.009	37.7	0.07	birth weight [46]

^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]. The estimated allele substitution effects refer to the log-variance

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