First insights in the genetics of caseous lymphadenitis in goats

Figures & data

Table 1. Distribution of minor allele frequency, successful genotypes per marker, sample heterozygosity and mean heterozygosity.

Minor allele frequency distribution
		x< =0.01	0.01 < x< =0.05	0.05 < x< =0.1	0.1 < x< =0.2	x > 0.2
Before QC	n°	1507	1083	2172	7662	40923
	proportion	0.028	0.02	0.041	0.144	0.767
After QC	n°	0	424	2030	7338	39333
	proportion	0	0.009	0.041	0.149	0.801
Cumulative distribution of successful genotypedSNP per sample
		x< =0.9	0.9 < x< =0.95	0.95 < x< =0.98	0.98 < x< =0.99	x > 0.99
Before QC	n°	1	0	22	47	0
	proportion	0.014	0	0.314	0.672	0
After QC	n°	0	0	1	1	67
	proportion	0	0	0.014	0.014	1
Distribution of successful genotypes per marker
		x< =0.9	0.9 < x< =0.95	0.95 < x< =0.98	0.98 < x< =0.99	x > 0.99
Before QC	n°	1631	1420	2759	11732	35805
	proportion	0.031	0.027	0.051	0.22	0.671
After QC	n°	0	0	1765	3614	43746
	proportion	0	0	0.036	0.073	0.891
Mean hereozygosity for a SNP	Mean	SD
Before QC	0.38	0.12
After QC	0.40	0.10
Mean hereozygosity per sample	Mean	SD
Before QC	0.39	0.03
After QC	0.39	0.03

QC: Quality check.

Figure 1. Manhattan plot displaying the results (−log10 of p-value) of the genome-wide scan using the GRAMMAR-GC method with respect to their genomic position.

Table 2. List of SNP associated with CLA identified by Genome Wide Association study in goat.

SNP Name	CHR	Position	Coding A1	N	p-value
rs268245496	7	3,60,3410	C	69	9.21 e-06
rs268256983	8	18,050,225	C	69	1.28 e-05
rs268256651	11	39,878,893	T	69	5.35 e-05
rs268259057	5	105,527,370	G	69	6.12 e-05

SNP name: SNP name; CHR: goat chromosome; Position: position on the goat genome in base pairs; p-value: p-values adjusted for Genomic Control; N: number of animals tested; Coding A1: coding of the minor allele.

Reference sequence is CHIR_1.0, whole genome shotgun sequence (Capra hircus, breed Yunnan black goat).

Table 3. Distribution of samples per genotype and Minor allele frequencies per group.

SNP Name	CHR	Group	N	MAF	A1/A1	A1/A2	A2/A2
snp12701-scaffold1488-1176933	7	total	69	0.33	29	34	6
		cases	25	0.12	19	6	0
		controls	44	0.45	10	28	6
snp24586-scaffold25-1074498	8	total	69	0.3	34	28	7
		cases	25	0.52	5	14	6
		controls	44	0.18	29	14	1
snp24249-scaffold247-2525760	11	total	69	0.23	40	25	4
		cases	25	0.44	5	18	2
		controls	44	0.12	35	7	2
snp26709-scaffold2806-516071	5	total	68	0.31	32	29	7
		cases	25	0.52	4	16	5
		controls	43	0.19	28	13	2

SNP name: SNP name as in the goat 50K SNP Chip data; CHR: goat chromosome; Group: definition of cases, controls and total samples; MAF: minor allele frequency; A1/A1: number of samples showing homozygous for allele A1; A1/A2: number of heterozygous samples; A2/A2: number of samples homozygous for allele A2.