Application of mathematical expectation (ME) strategy for detecting low frequency mutations: An example for evaluating 14-bp insertion/deletion (indel) within the bovine PRNP gene

Figures & data

FIGURE 1. The flow diagram of ME strategy's utilization in this experiment.

FIGURE 2. Electrophoresis pattern of 14-bp indel in 3′ UTR within bovine PRNP gene (genotyped by 3.5% agarose gel) (II demontrated 142-bp length band; ID demonstrated 142-bp and 128-bp length bands; DD demonstrated 128-bp length band).

TABLE 1. Genotypic and allelic frequencies and population indexes for 14-bp indel in the bovine PRNP gene.

		Genotypic frequencies			Allelic frequencies			Population parameters
Breeds/Loci	SizesN	II	ID	DD	I	D	HWEP values	Ho	He	Ne	PIC	References
Qinchuan	160	0.925	0.075	0	0.962	0.038	P > 0.05	0.928	0.072	1.078	0.160	In this study
Nanyang	197	0.975	0.025	0	0.987	0.013	P > 0.05	0.975	0.025	1.026	0.025
Jiaxian	199	0.994	0.006	0	0.997	0.003	P > 0.05	0.992	0.008	1.008	0.008
Xianan	214	0.949	0.037	0.014	0.967	0.033	P < 0.05	0.937	0.063	1.067	0.061
Ji'an	235	1.000	0	0	1.000	0	P > 0.05	1.000	0	1.000	0
Healthy^a	48	0.900	0.100	0	0.950	0.050	P > 0.05	0.901	0.099	1.110	0.094	Seabury et al. (2004)
Affected	43	0.860	0.120	0.020	0.920	0.080	P > 0.05	0.853	0.147	1.173	0.136
U.S. sires	132	0.890	0.110	0	0.940	0.060	P > 0.05	0.887	0.113	1.127	0.106
Cows	234	0.987	0.013	0	0.994	0.006	P > 0.05	0.988	0.012	1.012	0.011	Czarnik et al. (2006)
AI sires	47	1.000	0	0	1.000	0	P < 0.05	1.000	0	1.000	0
Vietnam native	100	0.680	0.280	0.040	0.820	0.180	P > 0.05	0.705	0.295	1.419	0.252	Shimogiri et al. (2010)
Laos native	72	0.597	0.375	0.028	0.780	0.220	P > 0.05	0.657	0.343	1.523	0.284
Myanmar native	110	0.682	0.282	0.036	0.820	0.180	P > 0.05	0.705	0.295	1.419	0.252
Mongolia native	44	0.614	0.318	0.068	0.770	0.230	P > 0.05	0.646	0.354	1.548	0.291
Japanese Holsen	65	0.614	0.383	0.030	0.790	0.210	P > 0.05	0.,668	0.322	1.497	0.277	Sander et al. (2004)
Japanese Short horn	1	1.000	0	0	1.000	0	P < 0.05	1.000	0	1.000	0
Kuchinoshima	52	1.000	0	0	1.000	0	P < 0.05	1.000	0	1.000	0
Japanese Brown	64	0.438	0.281	0.281	0.580	0.420	P < 0.01	0.513	0.487	1.950	0.369
BSE affected cattle	43	0.880	0.110	0.010	0.930	0.070	P > 0.05	0.870	0.130	1.150	0.122
Mishima	2	0.500	0	0.500	0.500	0.500	P > 0.05	0.500	0.500	2.000	0.375

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

TABLE 2. All reaction times of different group in 5 cattle breeds.

Breeds	Qinchuan	Xianan	Nanyang	Jiaxian	Ji'an
Sizes	160	214	197	199	235
Minor allelic frequencies (MAF)	0.038	0.033	0.013	0.003	0.000
Number of individuals in one reaction time (NR1)	1	1	1	1	1
Reaction times (RT1)	160	214	197	199	235
Number of individuals in one mixed group (NG3)	3	3	3	3	3
Predicting reaction times by the formulate (pTT3)	71	92	73	68	79
Reaction times (RT3)	90	100	81	70	79
Reduction rate (RR)	21.0%	8.0%	9.8%	2.9%	0
The opitical number of individuals in one mixed group (NGn)	5	6	8	16	—
Predicting reaction times by the formulate (pRTn)	93	90	52	29	—
Reaction times (RTn)	60	75	44	22	—
Reduction rate (RR)	35.5%	16.7%	15.4%	24.1%	—

Note: MAF, minor allelic frequencies; NG, the optimal number of one mixed group; RT, reaction times; pRT, predicting treaction times by the formulate; RR, reduction rate.

TABLE 3. Relationship between the 14-bp indel of PRNP gene and growth traits in Xianan and Qinchuan cattle breeds (LSM^a±SE) (P < 0.05).

		Genotypes
Breeds	Growth traits	II	ID	DD	P values
Xianan	CC (cm)	^a216.77±1.51	^c 202.29±2.84	^c 201.33±2.40	0.004
	BW (kg)	^a549.81±4.07	^a557.11±10.17	^b469.67±26.14	0.040
Qinchuan	BL (cm)	^b140.76±14.60	^a146.79±5.77	–	0.046

Note: CC, chest circumference; BW, body weight; BL, body length. The values with different letters (a and b; a and c) within the same row differ significantly at P < 0.05 and P < 0.01, respectively.

FIGURE 3. Reaction times about different sizes of one mixed group (different mutation frequency(1%–9%) when N = 1000 and N = 2000).