The association of very low-density lipoprotein receptor (VLDLR) haplotypes with egg production indicates VLDLR is a candidate gene for modulating egg production

Wang, ZhePeng; Meng, GuoHua; Li, Na; Yu, MingFen; Liang, XiaoWei; Min, YuNa; Liu, FuZhu; Gao, YuPeng

doi:10.1590/1678-4685-GMB-2015-0206

ZhePeng Wang

College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China

GuoHua Meng

College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China

Na Li

College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China

MingFen Yu

College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China

XiaoWei Liang

College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China

YuNa Min

College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China

FuZhu Liu

College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China

YuPeng Gao Send correspondence to Yupeng Gao. College of Animal Science and Technology, Northwest A&F University, Xinong Road No. 22, Yangling, 712100, Shaanxi, China. E-mail: gaoyupeng112@sina.com

College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China

Send correspondence to Yupeng Gao. College of Animal Science and Technology, Northwest A&F University, Xinong Road No. 22, Yangling, 712100, Shaanxi, China. E-mail: gaoyupeng112@sina.com

Description^a a SNP positions on chromosome Z are based on the chicken genome galGal4 assembly.	dbSNP accession number^b b Accession number in the dbSNP database (http://www.ncbi.nlm.nih.gov/snp)	Position in VLDLR	Primer sequences	Restriction enzymes
g.26 419 086 G > A	rs312633123	Intron 1	F: 5'-AAAGCCTGGATAAGAGCG-3'	HaeIII
			R: 5'-TTCCAAATGAAGGGAAGC-3'
g.26,420,908T > G	novel SNP	Intron 2	F: 5'-TAACAGCAGGAAGTGGAT-3'	HinfI
			R: 5'-GCATACTAATGGCAACAA-3'
g.26,423,124A > G	novel SNP	Intron 4	F: 5'-TCAGGGTTTCTTAACAGC-3'	SnaBI
			R: 5'-ACACCTCAGGCAACTCAT-3'
g.26,424,657G > A	rs317219970	Exon 6 (synonymous mutation)	F: 5'-GATGAAATCAACTGCCGTAA-3'	XbaI
			R: 5'-CAGGTCCAGAACACTGAATAAC-3'
g.26426398T > C	rs317314828	Intron 10	F: 5'- GCCAAATCTGTATCAACC-3'	MfeI
			R: 5'- ACGGGTATCAATAGAGGC-3'
g.26,427,922AG	rs314567990	Intron 14	F: 5'-CGTGTATTCTGGATTGACGGAG-3'	HinfI
			R: 5'-CAGCAGGGGTGCTAGGCT-3'
g.26,429,604A > C	rs14777635	Intron 15	F: 5'-ATGAAATGCCAAGAGTGC-3'	ApoI
			R: 5'-AAGTAGTGAGGCTGCTTA-3'
g.26,431,186C > T	rs314284862	3' UTR	F: 5'-ACGGGTTACTATGATTGC-3'	BseRI
			R: 5'-TCCAGCCAGACTCTTACA-3'

Groups	Models	AIC	MSE	R²	MME
NC	Segmented polynomial	−6491.4	0.0219	0.968	−0.00124
	Yang	−6493.9	0.0219	0.967	0.0393
	Persistency	−6489.6	0.0219	0.968	−0.0116
LY	Segmented polynomial	−22892.2	0.0748	0.663	−0.119
	Yang	−22906.5	0.0747	0.663	−0.110
	Persistency	−22893.2	0.0748	0.663	−0.127
ATAATA(A/C)T	Segmented polynomial	−2674.7	0.0646	0.758	−0.114
	Yang	−2678.9	0.0644	0.759	−0.0965
	Persistency	−2672.4	0.0647	0.758	−0.116
GGAACACT	Segmented polynomial	−5356.7	0.0735	0.684	−0.104
	Yang	−5356.7	0.0734	0.684	−0.0716
	Persistency	−5354.7	0.0734	0.684	−0.100
GGGGCGCC	Segmented polynomial	−6283.3	0.0747	0.649	−0.115
	Yang	−6285.9	0.0746	0.649	−0.101
	Persistency	−6281.3	0.0746	0.649	−0.123
GTA(A/G)TACT	Segmented polynomial	−4361.6	0.0761	0.629	−0.102
	Yang	−4366.9	0.0759	0.629	−0.0958
	Persistency	−4359.6	0.0761	0.628	−0.101

Egg production parameters	LueYang chicken	Nick Chick	Δpar^a a Δpar – difference between parameters of Nick chickens (NKpar) and ones of chickens (LYpar). The Δpar were estimated with the indicated models by reparameterizing NKpar as LYpar + Δpar.	95% Confidence interval of Δpar^b b Approximate 95% confidence intervals of Δpar were used to assess whether parameters varied between the Nick (NC) and Lueyang (LY) groups. A confidence interval of Δpar excluded zero (0) indicated that the parameter had a significant difference between LY and NC (SAS Institute Inc., 2008).	F value, P value^c c F and P values were obtained by the sum of squares reduction test that indicated any significant difference between the egg-production curves for LY and NC (SAS Institute Inc., 2008).	Model
n	381	91	–
Record N	8829	3094	–
P	0.53 ± 0.006 (0.52, 0.54)^d d Numbers in parenthesis indicate approximate 95% confidence limits of parameters.	0.89 ± 0.008 (0.88, 0.91)	0.37 ± 0.015	0.34, 0.39	1008.25, < 0.000001	Segmented polynomial
S	0.008 ± 0.0005 (0.007, 0.009)	0.002 ± 0.0005 (0.001, 0.003)	−0.006 ± 0.0010	−0.008, −0.004
Tp	25.1 ± 0.15 (24.8, 25.4)	23.3 ± 0.17 (23.0, 23.6)	−1.8 ± 0.33	−2.44, −1.15
tip	4.6 ± 0.28 (4.1, 5.2)	6.9 ± 0.31 (6.3, 7.5)	2.2 ± 0.60	1.0, 3.4
a	0.85 ± 0.035 (0.78, 0.92)	0.96 ± 0.022 (0.92, 1.00)	0.11 ± 0.050	0.01, 0.21	1009.71, < 0.000001	Yang model
c	1.50 ± 0.11 (1.28, 1.71)	1.00 ± 0.0552 (0.89, 1.10)	−0.49 ± 0.140	−0.77, −0.22
x	0.018 ± 0.0011 (0.016, 0.021)	0.003 ± 0.0006 (0.002, 0.004)	−0.016 ± 0.0015	−0.019, −0.013
d	22.8 ± 0.058 (22.8, 23.0)	19.9 ± 0.065 (19.8, 20.1)	−3.0 ± 0.13	−3.2, −2.7
yp	0.53 ± 0.006 (0.52, 0.54)	0.88 ± 0.009 (0.86 0.89)	0.34 ± 0.010	0.32, 0.36	809.168, < 0.000001	Persistency model
t1	21.4 ± 0.13 (21.2, 21.7)	17.5 ± 0.12 (17.3, 17.8)	−3.9 ± 0.25	−4.4, −3.4
t2	24.3 ± 0.13 (24.0, 24.6)	22.2 ± 0.13 (21.9, 22.4)	−2.1 ± 0.26	−2.6, −1.6
Persistancy	0	18.5 ± 1.98 (14.6, 22.3)	18.5 ± 3.47	11.7, 25.3
b4	−0.008 ± 0.0005 (−0.009, −0.007)	−0.008 ± 0.0025 (−0.013, −0.003)	0.000 ± 0.0043	−0.008 0.008

Name	Haplotype	Lueyang (n=381)	Nick Chick (n=91)	Lohmann (n=50)
LYhap1	GGGGCGCC	0.283	–	–
LYhap2	GGAACACT	0.228	–	–
LYhap3	GTAGTACT	0.108	–	–
LYhap4	GTAATACT	0.089	–	–
LYhap5	ATAATAAT ^a a The haplotypes in bold letters were the two LY haplotypes that showed the highest similarity to two NC haplotypes.	0.079	–	–
LYhap6	GGGACGCC	0.042	–	–
LYhap7	GGGGCACT	0.024	–	–
LYhap8	ATAATACT	0.032	–	–
LYhap9	GGGGCGCT	0.018	–	–
LYhap10	GGGACGCT	0.021	–	–
LYhap11	GTAGTAAT	0.018	–	–
LYhap12	GTAGTACC	0.018	–	–
LYhap13	GGAGCGCC	0.018	–	–
LYhap14	GGAACGCC	0.021	–	–
NChap1	ATAATAAC	–	0.66	–
NChap2	ATAACAAC	–	0.34	0.925
Lohhap1	ATAACACC	–	–	0.05
Lohhap2	ATGACACC	–	–	0.025

Haplotypes	ATAATA(A/C)T^a a ATAATA(A/C)T were defined as NC-like haplotypes based on their high similarity to the NC haplotypes ATAA(T/C)AAC.	GGAACACT	Δpar (95% CI)^b b Δpar represents difference between parameters of the three haplotype groups (Parcont) and ones of the ATAATA(A/C)T group (Parcase), and was estimated using the models indicated in the Table by reparameterizing Parcont as Parcase + Δpar. The numbers in parentheses indicate the approximate 95% confidence interval (CI) of parameters. The CIs of Δpar that exclude zero (0) indicate that the parameters have significant between two haplotype groups (SAS Institute Inc., 2008).	GGGGCGCC	Δpar (95% CI)	GTA(A/G)TACT^a a ATAATA(A/C)T were defined as NC-like haplotypes based on their high similarity to the NC haplotypes ATAA(T/C)AAC.	Δpar (95% CI)	F value	Model
N	42	87		108		75		P value^c c F and P values were determined by the sum of squares reduction test which indicated whether there was a significant difference in the egg-production curves fitted for the different haplotype groups (SAS Institute Inc., 2008).
Record N	978	2053		2423		1695
p	0.61 ± 0.016	0.55 ± 0.012	−0.06 ± 0.021	0.51 ± 0.011	−0.10 ± 0.020	0.48 ± 0.013	−0.13 ± 0.022	7.16525	Segmented polynomial
	(0.59, 0.65)	(0.53, 0.57)	(−0.10, −0.00) ^d d Numbers in bold indicate the 95% CI of Δpar that excluded zero (0), indicating that the corresponding parameters were significantly different between ATAATA(A/C)T and the other haplotype groups.	(0.49, 0.53)	(−0.14, −0.06)	(0.46, 0.51)	(−0.17, −0.09)	< 0.000001	Segmented polynomial
s	0.009 ± 0.0013	0.008 ± 0.0010	−0.001 ± 0.0020	0.008 ± 0.0010	−0.001 ± 0.0017	0.006 ± 0.0011	−0.003 ± 0.0020
	(0.006, 0.011)	(0.006, 0.010)	(−0.004, 0.003)	(0.006, 0.010)	(−0.004, 0.002)	(0.004, 0.008)	(−0.006, 0.000)
Tp	25.1 ± 0.38	25.1 ± 0.30	0.0 ± 0.50	25.2 ± 0.30	0.1 ± 0.50	25.0 ± 0.38	−0.1 ± 0.55
	(24.4, 25.8)	(24.5, 25.7)	(−1.0, 1.0)	(24.7, 25.8)	(−0.86, 1.10)	(24.3, 25.8)	(−1.2, 1.0)
tip	4.9 ± 0.69	4.3 ± 0.55	−0.6 ± 0.92	4.8 ± 0.54	−0.1 ± 0.91	4.9 ± 0.70	−0.0 ± 1.01
	(3.6, 6.3)	(3.2, 5.4)	(−2.4, 1.2)	(3.7, 5.9)	(−1.9, 1.7)	(3.5, 6.3)	(−2.0, 1.9)
a	1.00 ± 0.105	0.88 ± 0.071	−0.11 ± 0.13	0.83 ± 0.067	−0.17 ± 0.12	0.75 ± 0.074	−0.25 ± 0.128	7.12442	Yang
	(0.79, 1.20)	(0.74, 1.02)	(−0.36, 0.13)	(0.69, 0.96)	(−0.415, 0.072)	(0.60, 0.89)	(−0.50, 0.003)	< 0.000001
c	1.29 ± 0.223	1.59 ± 0.238	0.30 ± 0.327	1.46 ± 0.201	0.17 ± 0.301	1.34 ± 0.223	0.045 ± 0.316
	(0.85, 1.73)	(1.12, 2.06)	(−0.34, 0.94)	(1.06, 1.85)	(−0.42, 0.76)	(0.90, 1.78)	(−0.57, 0.67)
x	0.019 ± 0.003	0.018 ± 0.0023	−0.000 ± 0.0038	0.018 ± 0.002	−0.000 ± 0.0038	0.017 ± 0.0029	−0.002 ± 0.0042
	(0.013, 0.024)	(0.014, 0.023)	(−0.008, 0.007)	(0.014, 0.023)	(−0.008, 0.007)	(0.011, 0.022)	(−0.010, 0.006)
d	22.7 ± 0.16	23.0 ± 0.11	0.3 ± 0.20	22.9 ± 0.11	0.1 ± 0.20	22.7 ± 0.15	−0.1 ± 0.22
	(22.4, 23.1)	(22.8, 23.2)	(−0.1, 0.7)	(22.7, 23.1)	(−0.2, 0.5)	(22.4, 23.0)	(−0.5, 0.4)
yp	0.62 ± 0.018	0.56 ± 0.013	−0.06 ± 0.022	0.52 ± 0.011	−0.1 ± 0.021	0.49 ± 0.014	−0.13 ± 0.023	7.08413	Persistency
(0.58, 0.65)	(0.53, 0.58)	(−0.11, −0.02)	(0.50, 0.54)	(−0.14, −0.06)	(0.46, 0.51)	(−0.18, −0.09)	< 0.000001
t1	21.0 ± 0.33	21.5 ± 0.25	0.5 ± 0.42	21.4 ± 0.24	0.4 ± 0.41	20.9 ± 0.31	0.2 ± 0.52
	(20.4, 21.7)	(1.1, 2.0)	(−0.3, 1.3)	(0.9, 1.9)	(−0.4, 1.2)	(20.3, 21.5)	(−0.8, 1.2)
t2	24.3 ± 0.34	24.4 ± 0.26	0.1 ± 0.43	24.3 ± 0.25	0.0 ± 0.42	24.3 ± 0.33	0.1 ± 0.53
	(23.6, 25.0)	(23.9, 24.9)	(−0.7, 1.0)	(23.8, 24.8)	(−0.8, 0.9)	(23.6, 24.9)	(−0.9, 1.2)
Persistency	0	0	–	0	–	0	–
b4	−0.009 ± 0.0014	−0.008 ± 0.0010	0.001 ± 0.0017	−0.008 ± 0.0009	0.001 ± 0.0017	−0.006 ± 0.0011	−0.002 ± 0.0021
	(−0.012, −0.006)	(−0.010, −0.006)	(−0.003, 0.004)	(−0.010, −0.006)	(−0.002, 0.004)	(−0.008, 0.004)	(−0.006, 0.002)

y = {\begin{cases} p - 3 \times p \times {(\frac{t p - t}{t i p})}^{2} + 2 \times p \times {(\frac{t p - t}{t i p})}^{3}, t p - t i p \leq t \leq t p \\ p - s (t - t p), t p \leq t, \end{cases}

\begin{array}{l} y = 0.3 \times (\frac{y p}{t 2 - t 1}) \times [\ln (\frac{e^{\frac{t}{0.3}} + e^{\frac{t 1}{0.3}}}{1 + e^{\frac{t 1}{0.3}}}) - \ln (\frac{e^{\frac{t}{0.3}} + e^{\frac{t 2}{0.3}}}{1 + e^{\frac{t 2}{r 0.3}}})] + \\ 0.3 \times b 4 \times \ln (\frac{e^{\frac{t}{0.3}} + e^{\frac{(t 2 + p)}{0.3}}}{1 + e^{\frac{(t 2 + p)}{0.3}}}) \end{array}

[1] Send correspondence to Yupeng Gao. College of Animal Science and Technology, Northwest A&F University, Xinong Road No. 22, Yangling, 712100, Shaanxi, China. E-mail: gaoyupeng112@sina.com

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The association of very low-density lipoprotein receptor (VLDLR) haplotypes with egg production indicates VLDLR is a candidate gene for modulating egg production

Abstract