Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

Table 2 Genetic diversity parameters using Porcine SNP60 Beadchip (SNP) and Next generation sequence data (NGS)

Continent	Category	Population	SNP			NGS
Continent	Category	Population	Ho	He	F	Het
Europe	Local	BS	0.28	0.29	0.13	2.16E-03
Europe	Local	CA	0.27	0.24	0.17	1.62E-03
Europe	Local	CM	0.26	0.28	0.17	1.87E-03
Europe	Local	CS	0.19	0.2	0.41	1.14E-03
Europe	Local	CT	0.26	0.27	0.21	1.27E-03
Europe	Local	GO	0.21	0.21	0.34	1.45E-03
Europe	Local	IB	0.21	0.23	0.33	1.34E-03
Europe	Local	LB	0.25	0.25	0.23	1.86E-03
Europe	Local	MA	0.15	0.19	0.55	7.58E-04
Europe	Local	MW	0.27	0.27	0.16	1.81E-03
Europe	Local	TA	0.2	0.2	0.38	1.45E-03
Europe	Commercial	DU	0.26	0.27	0.29	1.63E-03
Europe	Commercial	LR	0.31	0.32	0.16	2.07E-03
Europe	Commercial	LW	0.3	0.31	0.19	1.82E-03
Europe	Commercial	PI	0.31	0.3	0.16	2.09E-03
Europe	Wild	WB_NL	0.17	0.19	0.55	1.01E-03
Asia	Wild	WB_NCH	0.17	0.18	0.53	2.96E-03
Asia	Wild	WB_SCH	0.21	0.22	0.45	3.49E-03
Asia	Local	MS	0.17	0.17	0.53	2.54E-03

Ho: Observed heterozygosity; He: expected heterozygosity; F: inbreeding coefficient; Het: Heterozygosity estimated using NGS data [15].

ISSN: 1471-2164