The evaluation of 23-bp and 12-bp insertion/deletion within the PRNP gene and their effects on growth traits in healthy Chinese native cattle breeds

Figures & data

Figure 1. The structure of bovine PRNP gene, the different genotypes of two indel loci and their associations with growth traits.

Note: P: promoter region; F1: 23-bp-indel-promoter-foward; R1: 23-bp-indel-promoter-reverse; F2: 12-bp-indel-intron 1-forward; R2: 12-bp-indel-intron 1-reverse.

Table 1. Genotypic and allelic frequencies and population indexes of 23-bp indel for bovine PRNP.

Breeds/loci	Sample sizes	Genotypic frequencies			Allelic frequencies		HWE	Population parameters				Reference
23-bp indel	N	II	ID	DD	I	D	P values	Ho	He	Ne	PIC
XN	195	0.144	0.549	0.307	0.418	0.582	>.05	0.514	0.486	1.948	0.368	In this study
QC	217	0.359	0.415	0.226	0.567	0.433	<.05	0.509	0.491	1.965	0.370
NY	252	0.575	0.313	0.111	0.732	0.268	<.05	0.608	0.392	1.645	0.315
JX	409	0.374	0.477	0.149	0.612	0.388	>.05	0.525	0.475	1.904	0.362
JA	235	0.096	0.416	0.488	0.304	0.696	>.05	0.577	0.423	1.734	0.334
PN	250	0.203	0.510	0.387	0.458	0.542	>.05	0.503	0.496	1.986	0.373
Healthy^a	48	0.210	0.440	0.350	0.430	0.570	>.05	0.510	0.490	1.962	0.370	Seabury et al. (2004)
Affected	43	0.050	0.440	0.510	0.270	0.730	>.05	0.606	0.394	1.651	0.317
US sires	132	0.140	0.320	0.540	0.300	0.700	<.05	0.580	0.420	1.724	0.332
Cows	234	0.116	0.504	0.380	0.368	0.632	>.05	0.536	0.464	1.865	0.356	Walawski and Czarnik (2003) &
AI sires	47	0.128	0.489	0.382	0.372	0.628	>.05	0.532	0.468	1.879	0.358
Vietnam native	100	0.090	0.500	0.410	0.340	0.660	>.05	0.551	0.449	1.814	0.348	Shimogiri et al. (2010)
Laos native	71	0.099	0.549	0.352	0.373	0.627	>.05	0.532	0.468	1.879	0.358
Myanmar native	110	0.045	0.300	0.655	0.195	0.805	>.05	0.685	0.315	1.459	0.265
Mongolia native	44	0.045	0.500	0.455	0.295	0.705	>.05	0.584	0.416	1.713	0.330
Japanese Holsen	65	0.415	0.338	0.246	0.585	0.415	<.05	0.514	0.486	1.944	0.368	Sander et al. (2004)
Japanese Short horn	1	0	1.000	0	0.500	0.500	<.05	0.500	0.500	2.000	0.375
Japanese Brown	58	0.155	0.345	0.500	0.328	0.672	>.05	0.559	0.441	1.787	0.344
Mishima	2	0.500	0	0.500	0.500	0.500	>.05	0.500	0.500	2.000	0.375
Kuchinoshima	52	0	0	1.000	0	1.000	<.05	1.000	0.000	1.000	0.000
BSE affected cattle	43	0.163	0.512	0.326	0.419	0.581	>.05	0.513	0.487	1.948	0.368

Note: HWE: Hardy–Weinberg equilibrium; Ho: homozygosity; He: heterozygosity; Ne: effective allele numbers; PIC: polymorphism information content.

Table 2. Genotypic and allelic frequencies and population indexes of 12-bp indel for bovine PRNP.

Breeds/loci	Sample sizes	Genotypic frequencies			Allelic frequencies		HWE	Population parameters				Reference
12-bp indel	N	II	ID	DD	I	D	P values	Ho	He	Ne	PIC
XN	189	0.270	0.573	0.157	0.557	0.443	<.05	0.506	0.494	1.975	0.372	In this study
QC	124	0.387	0.427	0.185	0.601	0.399	>.05	0.520	0.480	1.922	0.365
NY	224	0.531	0.415	0.054	0.739	0.261	>.05	0.614	0.386	1.628	0.311
JX	333	0.526	0.417	0.057	0.734	0.266	>.05	0.610	0.390	1.640	0.314
JA	235	0.423	0.496	0.081	0.671	0.329	>.05	0.558	0.442	1.791	0.344
PN	250	0.235	0.765	0	0.618	0.382	<.05	0.528	0.472	1.895	0.361
Healthy^a	48	0.210	0.560	0.230	0.490	0.510	>.05	0.500	0.500	1.999	0.375	Seabury et al. (2004)
Affected	43	0.090	0.470	0.440	0.325	0.675	>.05	0.561	0.439	1.782	0.342
US sires	132	0.320	0.350	0.330	0.495	0.505	<.05	0.500	0.500	2.000	0.375
Cows	234	0.209	0.492	0.299	0.455	0.545	>.05	0.504	0.496	1.984	0.373	Walawski and Czarnik (2003)
AI sires	47	0.170	0.639	0.191	0.489	0.511	>.05	0.500	0.500	1.999	0.375
Vietnam native	100	0.870	0.120	0.010	0.930	0.070	>.05	0.870	0.130	1.150	0.122	Shimogiri et al. (2010)
Laos native	72	0.875	0.097	0.028	0.924	0.076	<.05	0.859	0.141	1.164	0.131
Myanmar native	110	0.673	0.282	0.045	0.814	0.186	>.05	0.697	0.303	1.435	0.257
Mongolia native	44	0.136	0.705	0.159	0.489	0.511	<.05	0.500	0.500	1.999	0.375
Japanese Holsen	65	0.185	0.523	0.292	0.446	0.554	>.05	0.506	0.494	1.977	0.372	Sander et al. (2004)
Japanese Short horn	2	0.500	0.000	0.500	0.500	0.500	>.05	0.500	0.500	2.000	0.375
Japanese Brown	58	0.121	0.345	0.534	0.293	0.707	>.05	0.586	0.414	1.708	0.329
Mishima	2	0	0	1.000	0	1.000	<.05	1.000	0.000	1.000	0.000
Kuchinoshima	52	0	0	1.000	0	1.000	<.05	1.000	0.000	1.000	0.000
BSE affected cattle	43	0.047	0.442	0.512	0.267	0.733	>.05	0.608	0.392	1.644	0.315

Note: HWE: Hardy–Weinberg equilibrium; Ho: homozygosity; He: heterozygosity; Ne: effective allele numbers; PIC: Polymorphism information content.

Table 3. Haplotype frequency within PRNP in cattle breeds.

Haplotypes	23-bp indel-12-bp indel	Haplotype frequency
		Xianan cattle	Nanyang cattle	Qinchuan cattle	Jiaxian cattle	Ji'an cattle	Pi'nan cattle
Hap1	DD	0.355	0.247	0.310	0.250	0.171	0.289
Hap2	DI	0.230	0.495	0.287	0.427	0.318	0.253
Hap3	ID	0.074	0.024	0.079	0.089	0.149	0.145
Hap4	II	0.340	0.235	0.324	0.234	0.079	0.313

Note: ‘Hap’ represented ‘haplotype’; Indel 23: 23-bp indel within the promoter region; Indel 12: 12-bp indel within the intron 1.

Table 4. D′ and r² values of pairwise LD of PRNP in cattle breeds.

Breeds	Loci	12-bp indel
		D′	r^2
Xia'nan	23-bp indel	0.583	.181
Nanyang	23-bp indel	0.662	.057
Qinchuan	23-bp indel	0.496	.106
Jiaxian	23-bp indel	0.188	.009
Ji'an	23-bp indel	0.057	.001
Pi'nan	23-bp indel	0.270	.047

Note: Pair-loci D′/r² value.

Table 5. Relationship between the two indel loci of PRNP and growth traits in three cattle breeds (LSM^a± SE) (P < .05).

Breeds	Locus	Age	Growth traits	Genotypes			P value
				II	ID	DD
Xia'nan	12-bp	Adult	BW	561.61^a ± 7.66	539.93^b ± 5.20	556.45 ± 11.72	.051
Nanyang	23-bp	6 Months	HW	17.81 ± 0.53	18.75 ± 0.24	18.23 ± 0.17	.094
		18 Months	BL	125.54^c ± 2.13	127.75^c ± 1.22	131.63^a ± 0.88	.004
			HG	152.73^b ± 3.27	153.39 ± 1.40	158.26^a ± 1.01	.012
	12-bp	6 Months	DGW	0.70 ± 0.02	0.75 ± 0.01	0.69 ± 0.03	.065
		12 Months	HW	20.67 ± 0.23	20.81 ± 0.26	22.83 ± 0.17	.078
			DGW	0.38^a ± 0.018	0.32^b ± 0.015	0.30 ± 0.11	.031
Ji'an	12-bp	Adult	CC	15.74^bc ± 0.24	14.87^c ± 0.22	16.20^a ± 0.38	.009
		Adult	RL	57.94^b ± 6.98	70.89^a ± 7.84	39.11^b ± 1.01	.029

Note: BW: body weight; BL: body length; HW: hucklebone width; DGW: daily gain weight; HG: heart girth; CC: cannon circumference; RL: rump length. The values with different letters (a and b; a and c) within the same row differ significantly at P < .05 and P < .01: respectively.

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