Genome-wide analysis of zygotic linkage disequilibrium and its components in crossbred cattle

BMC Genomic Data

Table 1 Means and standard deviations (SD) of gametic LD ( ${φ_{GLD}^{2}}^{a}$ ), composite LD ( $φ_{CLD}^{2}$ ) and zygotic LD ( ${φ_{ZLD}^{2}}^{a}$ ) between syntenic SNP pairs for different ranges of distance (≤ 5 Mb) in the Kinsella composite beef population

Distance range (Mb)	Pairs (n)	$φ_{GLD}^{2}$ ±SD	$φ_{CLD}^{2}$ ± SD	$φ_{ZLD}^{2}$ ± SD	$φ_{GLD}^{2}$ ≥0.25 (%)	$φ_{CLD}^{2}$ ≥0.25 (%)	$φ_{ZLD}^{2}$ ≥0.25 (%)
<0.025	5692	0.2853±0.3071	0.2857±0.3070	0.1812±0.3011	38.3	38.5	22.9
0.025-0.05	20032	0.2175±0.2638	0.2178±0.2638	0.1230±0.2425	29.5	29.4	15.8
0.05-0.075	18041	0.1615±0.2191	0.1619±0.2192	0.0799±0.1884	20.8	20.9	10.0
0.075-0.1	17838	0.1277±0.1832	0.1278±0.1832	0.0561±0.1479	15.6	15.5	6.7
0.1-0.2	69905	0.0912±0.1420	0.0914±0.1422	0.0340±0.1059	9.4	9.5	3.6
0.2-0.5	205321	0.0569±0.0885	0.0571±0.0887	0.0159±0.0559	3.7	3.7	1.0
0.5-1.5	665397	0.0394±0.0580	0.0395±0.0581	0.0091±0.0300	1.3	1.3	0.3
1.5-3	968768	0.0286±0.0424	0.0286±0.0424	0.0062±0.0195	0.5	0.5	0.1
3-5	1252994	0.0214±0.0315	0.0214±0.0316	0.0045±0.0131	0.1	0.1	0.0

Percentages of SNP pairs with LD values of ≥0.25 are also presented. ^a The Generalized measures of gametic and zygotic LD ( $φ_{GLD}^{2}$ and $φ_{ZLD}^{2}$ ) are based on an exact 2 × 2 contingency table and thus they are simply the squared correlations, i.e., $φ_{GLD}^{2} = r_{GLD}^{2}$ and $φ_{ZLD}^{2} = r_{ZLD}^{2}$ .

ISSN: 2730-6844