Study of polymorphism in the VRTN gene and its association with production traits in (Duroc×Saba)♂×[Yorkshire×(Landrace×Saba)]♀

doi:10.3969/j.issn.1004-1524.20230760

Acta Agriculturae Zhejiangensis ›› 2024, Vol. 36 ›› Issue (7): 1502-1510.DOI: 10.3969/j.issn.1004-1524.20230760

• Animal Science • Previous Articles Next Articles

Study of polymorphism in the VRTN gene and its association with production traits in (Duroc×Saba)♂×[Yorkshire×(Landrace×Saba)]♀

MA Li¹(), LAN Yi², XIE Bingxin², ZHOU Chunlu², LUO Shuyuan², XU Wenkun³, DONG Xinxing²^,^*(), YAN Dawei²^,⁴^,^*()

1. Department of Animal Husbandry and Veterinary Medicine, Yunnan Vocational College of Agriculture, Kunming 650212, China
2. College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
3. Yunnan Province Animal Husbandry Station, Kunming 650224, China
4. Yunnan Key Laboratory of Animal Nutrition and Feed of Yunnan Province, Kunming 650201, China

Received:2023-06-12 Online:2024-07-25 Published:2024-08-05

Abstract

Abstract:

To investigate the polymorphism of the vertnin (VRTN) gene in (Duroc×Saba, DS)♂×[Yorkshire×(Landrace×Saba), YLS]♀ (hereafter DS×YLS) and its effects on fattening, carcass and meat quality, the single nucleotide polymorphisms (SNPs) in promoter region and its 4 exons regions of VRTN gene were detected by PCR product directed sequencing in populations of DS×YLS, Duro, Landrace, Yorkshire, and the genotype frequency and gene frequency were calculated. Fattening, carcass and muscle quality were determined in 321 DS×YLS pigs. The association between different genotypes at each SNPs locus and fattening, carcass and meat quality were analyzed by least squares model. A total of two mutation loci, VRTN g.97615896_97615897ins291 and VRTN g.97622607G>A were detected to be polymorphic in four pig populations. g.97615896_97615897ins291 showed Q/Q, Q/Wt, and Wt/Wt genotypes in all four pig populations. All four populations were moderately polymorphic and in Hardy-Weinberg equilibrium state. In the VRTN g.97615896_97615897ins291 locus of DS×YLS pigs, the backfat thickness of Q/Q genotype was 0.36 mm less than that of Wt/Wt (P<0.05), the rib number of Q/Q genotype was 0.63 pairs more than that of Wt/Wt genotype (P<0.01), the carcass oblique length of Q/Wt genotype was 1.56 cm longer than Wt/Wt (P<0.05), the area of longissimus dorsi of Q/Q genotype and Q/Wt genotype were 4.38 cm², 4.34 cm² bigger than that of Wt/Wt genotype (P<0.05) respectively, the lean meat percentage of Q/Q genotype was 3.23 percentage points higher than that of Wt/Wt genotype (P<0.05), the fat percentage of Q/Q genotype was 4.1 percentage points lower than that of Wt/Wt genotype (P<0.05) at VRTN g.97615896_97615897ins291 loci in the population of DS×YLS. VRTN g.97622607G>A belonged to the low polymorphism site (PIC=0.079 9)in DS×YLS,and was in Hardy-Weinberg equilibrium state. In the VRTN g.97622607G>A locus of DS×YLS pigs, the average daily gain (ADG) between 30 kg and 100 kg of GG genotype was 61.43 g·d^-1 higher than that of GA genotype (P<0.01), the lean meat percentage of GG genotype was 2.53 percentage points higher than that of GA genotype (P<0.05) at VRTN g. 97622607G>A locus in the population of DS×YLS. The results showed that the insertion of the Q allele at VRTN g.97615896_97615897ins291 could increase the number of ribs, carcass oblique length, area of longissimus dorsi and lean meat percentage, and decrease the backfat and fat percentage. VRTN g.97622607G>A locus GG genotype could increase the ADG and lean meat rate of DS×YLS. This study provided a basis for molecular marker-assisted selection with the VRTN gene to improve the performance of Saba pigs.

Key words: DS×YLS, VRTN gene, production trait, genetic diversity, association analysis

CLC Number:

S828

MA Li, LAN Yi, XIE Bingxin, ZHOU Chunlu, LUO Shuyuan, XU Wenkun, DONG Xinxing, YAN Dawei. Study of polymorphism in the VRTN gene and its association with production traits in (Duroc×Saba)♂×[Yorkshire×(Landrace×Saba)]♀[J]. Acta Agriculturae Zhejiangensis, 2024, 36(7): 1502-1510.

Figures/Tables 9

References 26

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引物名 Name of primer	引物序列 Sequence of primer(5'→3')	退火引物 Annealing temperature/℃	产物长度 Length of PCR product/bp	位置 Site
VRTN-1F	GGCAGGGAAGGTGTTTGTTA^[21]	60.0	120/411	启动子Promoter
VRTN-1R	GACTGGCCTCTGTCCCTTG
VRTN-2F	GCCTGGCTTCAGACTCTCTT	61.2	593	外显子1 Exon1
VRTN-2R	TCGTTTGGGTCACTCCTTG
VRTN-3F	AACAGAGGAACCAGAAGCAT	62.0	1 412	外显子2-1 Exon2-1
VRTN-3R	TCCAGGCATAATAGGTAGAGC
VRTN-4F	CCAATGTGTGGCACTTGT	61.2	1 537	外显子2-2 Exon2-2
VRTN-4R	TGTAGTAGGTAGAGCGAGCAGT
VRTN-5F	AGGAGGTGGAGGAGAAACAG	62.0	1 407	外显子2-3 Exon2-3
VRTN-5R	AGAAATGGTCACAGTCAGTCC

引物名 Name of primer	引物序列 Sequence of primer(5'→3')	退火引物 Annealing temperature/℃	产物长度 Length of PCR product/bp	位置 Site
VRTN-1F	GGCAGGGAAGGTGTTTGTTA^[21]	60.0	120/411	启动子Promoter
VRTN-1R	GACTGGCCTCTGTCCCTTG
VRTN-2F	GCCTGGCTTCAGACTCTCTT	61.2	593	外显子1 Exon1
VRTN-2R	TCGTTTGGGTCACTCCTTG
VRTN-3F	AACAGAGGAACCAGAAGCAT	62.0	1 412	外显子2-1 Exon2-1
VRTN-3R	TCCAGGCATAATAGGTAGAGC
VRTN-4F	CCAATGTGTGGCACTTGT	61.2	1 537	外显子2-2 Exon2-2
VRTN-4R	TGTAGTAGGTAGAGCGAGCAGT
VRTN-5F	AGGAGGTGGAGGAGAAACAG	62.0	1 407	外显子2-3 Exon2-3
VRTN-5R	AGAAATGGTCACAGTCAGTCC

指标Index	样本量	平均数±标准差	最小值	最大值
30~100 kg日增重Average daily gain of 30-100 kg/(g·d^-1)	321	520.69±10.39	490.74	551.18
100 kg活体背膘厚Backfat thickness of 100 kg body weight/mm	321	29.46±0.14	29.10	29.80
屠宰率Dressing ratio/%	321	75.56±0.26	74.80	76.32
肋骨数/对Rib numbers/pair	321	14.03±0.17	13.00	15.00
胴体直长Carcass straight length/cm	321	97.93±0.90	95.50	100.00
胴体斜长Carcass oblique length/cm	321	84.88±0.91	82.50	87.00
平均背膘厚Average backfat/mm	321	33.61±0.81	31.19	36.39
6~7肋膘厚6-7 intercostal fat thickness/mm	321	36.24±1.01	33.30	39.20
皮厚Skin thickness/mm	321	3.67±0.23	30.00	43.40
眼肌面积Area of longissimus dorsi/cm²	321	34.51±2.14	28.19	40.92
瘦肉率Lean meat percentage/%	321	54.35±0.82	51.90	56.74
脂率Fat percentage/%	321	26.74±0.94	23.92	29.46
皮率Skin percentage/%	321	8.84±0.22	8.18	9.47
骨率Bone percentage/%	321	9.85±0.23	9.17	10.54
pH	321	6.15±0.04	6.03	6.27
肉色/分Meat colour	321	3.27±0.05	3.00	3.50
大理石纹/分Marbling score	321	2.92±0.05	2.50	3.50
失水率Water loss ratio/%	321	16.09±0.35	15.05	17.12
熟肉率Cooked meat percentage/%	321	60.57±0.44	59.25	61.89
滴水损失Drop loss/%	321	2.17±0.09	1.90	2.43

指标Index	样本量	平均数±标准差	最小值	最大值
30~100 kg日增重Average daily gain of 30-100 kg/(g·d^-1)	321	520.69±10.39	490.74	551.18
100 kg活体背膘厚Backfat thickness of 100 kg body weight/mm	321	29.46±0.14	29.10	29.80
屠宰率Dressing ratio/%	321	75.56±0.26	74.80	76.32
肋骨数/对Rib numbers/pair	321	14.03±0.17	13.00	15.00
胴体直长Carcass straight length/cm	321	97.93±0.90	95.50	100.00
胴体斜长Carcass oblique length/cm	321	84.88±0.91	82.50	87.00
平均背膘厚Average backfat/mm	321	33.61±0.81	31.19	36.39
6~7肋膘厚6-7 intercostal fat thickness/mm	321	36.24±1.01	33.30	39.20
皮厚Skin thickness/mm	321	3.67±0.23	30.00	43.40
眼肌面积Area of longissimus dorsi/cm²	321	34.51±2.14	28.19	40.92
瘦肉率Lean meat percentage/%	321	54.35±0.82	51.90	56.74
脂率Fat percentage/%	321	26.74±0.94	23.92	29.46
皮率Skin percentage/%	321	8.84±0.22	8.18	9.47
骨率Bone percentage/%	321	9.85±0.23	9.17	10.54
pH	321	6.15±0.04	6.03	6.27
肉色/分Meat colour	321	3.27±0.05	3.00	3.50
大理石纹/分Marbling score	321	2.92±0.05	2.50	3.50
失水率Water loss ratio/%	321	16.09±0.35	15.05	17.12
熟肉率Cooked meat percentage/%	321	60.57±0.44	59.25	61.89
滴水损失Drop loss/%	321	2.17±0.09	1.90	2.43

品种(组合) Breed (Combination)	基因型 Genotype	基因型频率(个体数) Genotypic frequency (Numbers)	等位基因 Allele	等位基因频率 Allelic frequency	杂合度 H	多态信息含量 PIC
杜撒×大长撒DS×YLS	Q/Q	0.040 5(13)	Q	0.386 3	0.474 1	0.361 7
	Q/Wt	0.691 6(222)
	Wt/Wt	0.267 9(86)	Wt	0.613 7
杜洛克Duroc	Q/Q	0.220 6(15)	Q	0.558 8	0.493 1	0.371 5
	Q/Wt	0.676 5(46)
	Wt/Wt	0.102 9(7)	Wt	0.441 2
长白Landrace	Q/Q	0.134 6(14)	Q	0.432 7	0.490 9	0.370 4
	Q/Wt	0.596 2(62)
	Wt/Wt	0.269 2(28)	Wt	0.567 3
大白Large White	Q/Q	0.442 5(50)	Q	0.663 7	0.446 4	0.346 8
	Q/Wt	0.442 5(50)
	Wt/Wt	0.115 0(13)	Wt	0.336 3

Study of polymorphism in the VRTN gene and its association with production traits in (Duroc×Saba)♂×[Yorkshire×(Landrace×Saba)]♀

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品种(组合) Breed (Combination)	基因型 Genotype	基因型频率(个体数) Genotypic frequency (Numbers)	等位基因 Allele	等位基因频率 Allelic frequency	杂合度 H	多态信息含量 PIC
杜撒×大长撒DS×YLS	GG	0.912 8(293)	G	0.956 4	0.083 4	0.079 9
	GA	0.087 2(28)
	AA	0(0)	A	0.043 6
杜洛克Duroc	GG	1.000 0(68)	G	1.000 0	0	0
	GA	0(0)
	AA	0(0)	A	0
长白Landrace	GG	1.000 0(104)	G	1.000 0	0	0
	GA	0(0)
	AA	0(0)	A	0
大白Large White	GG	1.000 0(113)	G	1.000 0	0	0
	GA	0(0)
	AA	0(0)	A	0

指标 Index	基因型Genotype
指标 Index	Wt/Wt	Q/Wt	Q/Q
样本量Number	86	222	13
30~100 kg日增重Average daily gain of 30-100 kg/(g·d^-1)	513.56±10.49	523.80±6.54	514.70±26.98
100 kg活体背膘厚Backfat thickness of 100 kg body weight/mm	29.64±0.10 a	29.40±0.06 ab	29.28±0.26 b
屠宰率Dressing ratio/%	75.69±0.27	75.53±0.17	75.12±0.70
肋骨数/对Rib numbers/pair	13.78±0.06 B	14.11±0.04 A	14.41±0.15 A
胴体直长Carcass straight length/cm	97.18±0.80	98.30±0.50	96.63±2.07
胴体斜长Carcass oblique length/cm	83.78±0.66 b	85.34±0.41 a	84.22±1.70 ab
平均背膘厚Average backfat/mm	34.10±0.80	33.50±0.50	32.20±2.10
6~7肋膘厚6-7 intercostal fat thickness/mm	37.30±0.90	35.90±0.50	35.00±2.20
皮厚Skin thickness/mm	3.60±0.20	3.70±0.20	3.60±0.60
眼肌面积Area of longissimus dorsi/cm²	31.33±1.66 b	35.67±0.40 a	35.71±0.65 a
瘦肉率Lean meat percentage/%	54.18±0.59 b	54.24±0.39 b	57.41±1.52 a
脂率Fat percentage/%	27.39±0.61 a	26.69±0.38 a	23.29±1.56 b
皮率Skin percentage/%	8.64±0.20	8.91±0.13	8.94±0.52
骨率Bone percentage/%	9.68±0.22	9.88±0.13	10.34±0.56
pH	6.19±0.03	6.14±0.02	6.09±0.08
肉色/分Meat colour	3.29±0.05	3.25±0.03	3.38±0.13
大理石纹/分Marbling score	2.91±0.06	2.92±0.04	2.87±0.15
失水率Water loss ratio/%	16.28±0.36	15.99±0.22	16.46±0.92
熟肉率Cooked meat percentage/%	60.22±0.36	60.76±0.23	59.67±0.94
滴水损失Drop loss/%	2.09±0.09	2.19±0.06	2.26±0.23

指标 Trait	基因型Genotype
指标 Trait	GG	GA
样本量Number	293	28
30~100 kg日增重Average daily gain of 30-100 kg/(g·d^-1)	576.74±18.08 A	515.31±5.60 B
100 kg活体背膘厚Backfat thickness of 100 kg body weight/mm	29.47±0.05	29.43±0.18
屠宰率Dressing ratio/%	75.63±0.15	74.69±0.48
肋骨数/对Rib numbers/pair	14.05±0.03	13.84±0.11
胴体直长Carcass straight length/cm	97.85±0.44	98.72±1.42
胴体斜长Carcass oblique length/cm	84.72±0.36	86.55±1.16
平均背膘厚Average backfat/mm	33.70±0.40	32.60±1.40
6-7肋膘厚6-7 intercostal fat thickness/mm	36.40±0.50	35.10±1.50
皮厚Skin thickness/mm	3.60±0.10	3.90±0.40
眼肌面积Area of longissimus dorsi/cm²	35.66±0.35	33.98±1.14
瘦肉率Lean meat percentage/%	54.58±0.32 a	52.05±1.04 b
脂率Fat percentage/%	26.67±0.33	27.41±1.08
皮率Skin percentage/%	8.83±0.11	8.94±0.36
骨率Bone percentage/%	9.88±0.12	9.54±0.38
pH	6.14±0.02	6.28±0.06
肉色/分Meat colour	3.26±0.03	3.37±0.09
大理石纹/分Marbling score	2.90±0.03	3.02±0.10
失水率Water loss ratio/%	16.07±0.19	16.31±0.63
熟肉率Cooked meat percentage/%	60.58±0.20	60.52±0.64
滴水损失Drop loss/%	2.17±0.05	2.20±0.17

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