Study of whole genome linkage disequilibrium in Nellore cattle

Espigolan, Rafael; Baldi, Fernando; Boligon, Arione A; Souza, Fabio RP; Gordo, Daniel GM; Tonussi, Rafael L; Cardoso, Diércles F; Oliveira, Henrique N; Tonhati, Humberto; Sargolzaei, Mehdi; Schenkel, Flavio S; Carvalheiro, Roberto; Ferro, Jesus A; Albuquerque, Lucia G

doi:10.1186/1471-2164-14-305

BMC Genomics

Table 1 Summary of the SNP markers analyzed and average linkage disequilibrium (r²and |D'|) between synthetic adjacent markers obtained for each autosome (BTA)¹

From: Study of whole genome linkage disequilibrium in Nellore cattle

BTA	Size (Mb)	SNP (n)	Mean distance ±SD (kb)	Mean r²±SD	Median r²	Mean \|D'\| ±SD	Median \|D'\|	Mean MAF ±SD
1	158.5	28,569	5.0±2.9	0.12±0.22	0.015	0.38±0.34	0.26	0.25±0.13
2	136.8	23,866	5.1±2.9	0.19±0.25	0.077	0.57±0.32	0.60	0.25±0.13
3	121.4	22,592	5.1±2.9	0.19±0.25	0.081	0.57±0.32	0.60	0.25±0.13
4	120.6	20,907	5.1±2.9	0.18±0.24	0.071	0.56±0.32	0.59	0.25±0.13
5	121.1	20,092	5.1±2.9	0.20±0.25	0.086	0.58±0.32	0.62	0.26±0.13
6	119.4	23,500	5.1±2.9	0.19±0.25	0086	0.57±0.32	0.62	0.27±0.13
7	112.6	20,181	5.1±2.9	0.20±0.25	0.082	0.56±0.32	0.60	0.25±0.13
8	113.3	21,667	5.2±2.8	0.20±0.25	0.097	0.59±0.32	0.64	0.26±0.13
9	105.6	20,593	5.1±2.9	0.19±0.25	0.078	0.56±0.32	0.59	0.26±0.13
10	104.2	17,213	5.0±2.9	0.18±0.25	0.064	0.57±0.32	0.55	0.25±0.13
11	107.2	18,477	5.0±2.9	0.19±0.25	0.070	0.56±0.32	0.59	0.24±0.13
12	91.1	15,556	5.1±2.9	0.18±0.24	0.070	0.55±0.32	0.57	0.24±0.13
13	84.2	14,145	5.1±2.9	0.21±0.26	0.094	0.59±0.32	0.65	0.25±0.13
14	83.9	16,909	5.2±2.8	0.18±0.24	0.079	0.56±0.32	0.59	0.26±0.13
15	85.2	14,669	5.0±2.9	0.18±0.24	0.067	0.54±0.32	0.56	0.24±0.13
16	81.7	14,715	5.0±2.9	0.18±0.24	0.072	0.56±0.32	0.59	0.25±0.13
17	75.1	14,108	5.1±2.9	0.19±0.26	0.068	0.55±0.32	0.58	0.24±0.13
18	65.9	11,461	5.0±2.9	0.15±0.22	0.051	0.52±0.31	0.52	0.24±0.13
19	63.9	9,889	5.0±2.9	0.20±0.26	0.088	0.59±0.32	0.63	0.24±0.13
20	71.9	12,734	5.0±2.9	0.18±0.24	0.067	0.54±0.32	0.55	0.25±0.13
21	71.6	12,882	5.1±2.9	0.17±0.24	0.064	0.55±0.32	0.57	0.24±0.13
22	61.3	10,442	5.0±2.9	0.16±0.23	0.061	0.54±0.32	0.55	0.25±0.13
23	52.5	9,369	5.1±2.9	0.17±0.24	0.063	0.55±0.32	0.58	0.25±0.13
24	62.3	11,300	5.1±2.9	0.17±0.23	0.063	0.54±0.32	0.56	0.25±0.13
25	42.8	7,537	5.1±2.9	0.16±0.22	0.058	0.55±0.32	0.56	0.23±0.13
26	51.6	9,503	5.0±2.9	0.17±0.23	0.062	0.54±0.31	0.56	0.24±0.13
27	45.4	7,963	5.0±2.9	0.09±0.18	0.020	0.42±0.31	0.36	0.25±0.13
28	46.2	7,858	4.9±2.9	0.02±0.07	0.003	0.25±0.25	0.16	0.25±0.13
29	51.1	8,289	4.9±2.9	0.003±0.01	0.001	0.12±0.14	0.07	0.24±0.13

SNP: single-nucleotide polymorphism; MAF: minor allele frequency; SD: Standard deviation. ¹Data in the table is based on the UMD 3.1 assembly.

Back to article page

ISSN: 1471-2164

Contact us

Submission enquiries: bmcgenomics@biomedcentral.com
General enquiries: ORSupport@springernature.com