Correlation Analysis of SNP and Haplotypes of SCD Gene with Growth Traits in Qinghai Plateau Yak (Bos grunniens)
QI Zeng-Yuan1, GAO Zhan-Hong2, ZHOU Jian-Qiang1, HAN Yin-Cang2, LIU Xiu1*, SUN Yong-Gang2*
1 Gansu Key Laboratory of Herbivore Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
2 Qinghai Academy of Animal Science and Veterinary Medicine, Xining 810016, China
Abstract Stearyl-CoA desaturase (SCD) is the key enzyme of monounsaturated fatty acid biosynthesis, which plays an important role in the lipid synthesis and oxidation dynamic balance. To explore the qinghai plateau yak SCD gene polymorphism and its correlation with growth traits, DNA sequencing method was used for gene polymorphism analysis,linkage disequilibrium analysis and the method of general linear model were used for correlation analysis. The results showed that there were 2 SNPs in SCD gene (g. 6614C>A and g.6660C>T), there were 2 genotypes in g.6614C>A and 3 genotypes in g.6660C>T. χ2 test showed that the g.6614C>A balanced in the Hardy Weinberg lattice state, g.6660C>T was in a state of imbalance. g.6614C> A was low polymorphic (PIC<0.25), and g.6660C>T was moderately polymorphic (0.50>PIC>0.25). And growth character correlation analysis found that the body weight, body height, body oblique length and tube circumference of CA genotype at g.6614C>A locus were significantly higher than those of CC genotype (P<0.05), but there was no significant difference in chest circumference between CA genotype and CC genotype. g. 6660C>T site of TT genotype individuals had no significant difference with CT and CC genotype, individuals weight, body height and chest circumference of TT genotype were significantly higher than CC and CT genotype (P<0.05), while TT genotype tube circumference was extremely significantly higher than CC genotype (P<0.01). Haplotype and linkage disequilibrium analysis showed that there were 4 haplotypes in the 2 loci, and there was no strong linkage between the 2 loci (r2=0.027). The combined haplotype analysis showed that H1H3 haploid type was the optimal combination. In conclusion, SCD gene polymorphism was related to some growth traits of Qinghai plateau yak, which can be used as candidate genes for marker-assisted selection in yaks. This study provides reference for improving yak breeding.
QI Zeng-Yuan,GAO Zhan-Hong,ZHOU Jian-Qiang, et al. Correlation Analysis of SNP and Haplotypes of SCD Gene with Growth Traits in Qinghai Plateau Yak (Bos grunniens)[J]. 农业生物技术学报, 2022, 30(7): 1314-1320.
[1] 蔡原, 赵生国, 唐红杰, 等 . 2015. 早胜牛及其杂交群体 SCD1 基因外显子 5 多态性研究[J]. 中国兽医医药杂志, 34(06): 11-15.
(Cai Y, Zhao S G, Tang H J.et al.2015. Polymorphism of exon 5 of SCD1 gene in Zaosheng cat‐ tle and its hybrid population[J]. Journal of Chinese Veterinary Medicine, 34(06): 11-15.)
[2] 陈忠琦 .2010. 奶山羊SCD 基因的克隆、多态性检测及其与经济性状的关联分析[D]. 硕士学位论文, 西北农林科技大学 , 导师 : 陈宏 . pp. 44-45.
(Chen Z Q.2010. Clone, polymorphism detection and association analysis with economic traits of SCD gene in dairy goat[D]. The‐ sis for M. S., Northwest A&F University, Supervisor: Chen H. pp. 44-45.)
[3] 董俊杰, 曾宇翔, 季芝娟, 等 . 2021. 273 份水稻种质资源的遗传多样性、群体结构与连锁不平衡分析[J]. 中国水稻科学 , 35(02): 130-140.
(Dong J J, Zeng Y X, Ji Z J.et al.2021. Analysis on genetic diversity, population structure, and linkage disequilibrium of 273 rice germ‐ plasms[J]. Chinese Journal of Rice Science, 35(02): 130-140.)
[4] 蓝贤勇 .2004. 西农萨能奶山羊经济性状的 DNA 分子标记及 5 个山羊品种 DNA 多态性研究[D]. 硕士学位论文, 西北农林科技大学, 导师: 陈宏 . pp. 41-42.
(Lan X Y.2004. Research on DNA molecular marker for econom‐ ic traits in Xinong Saanen dairy goat and polymorph Ci DNA of five goat breeds[D]. Thesis for M.S., Northwest A&F University, Supervisor: Chen H. pp. 41-42.)
[5] 李涛, 段小花, 荣华, 等 . 2019. 武定鸡与大围山微型鸡脂肪酸含量及 SCD 基因表达差异研究[J]. 中国家禽 , 41(01): 9-12.
(Li T, Duan X H, Rong H.et al.2019. Study on differences of fatty acid content and SCD gene ex‐ pression in Wuding chicken and daweishan mini chicken[J]. China Poultry, 41(01): 9-12.)
[6] 刘军 .2011. 青海高原型牦牛种质资源调查与分析[J]. 养殖与饲料 , 1(12): 65-67.
(Liu J.2011. Investigation and analysis of germplasm resources of Qinghai plateau yak[J]. Breeding and Feed, 1(12): 65-67.)
[7] 朴政玉, 夏广军, 严昌国, 等 . 2019. 延边黄牛 SCD1 基因多态性及其与经济性状的关联分析[J]. 中国畜牧兽医, 46(09): 2642-2650.
(Piao Z Y, Xia G J, Yan C G.et al.2019. Association analysis between the polymorphism of SCD1 gene and economic traits in Yanbian yellow cat‐ tles[J]. China Animal Husbandry & Veterinary Medi‐ cine, 46(09): 2642-2650.)
[8] 施雪奎 .2011. 肉牛CAPN1、CAST、GHR、SCD1 基因多态性及与胴体 、肉质性状的相关性研究[D]. 硕士学位论文, 扬州大学 , 导师 : 杨章平 . pp. 18-21.
(Shi X K.2011. Polymophisms of CAPN1, CAST, GHR and SCD1 genes in beeef cattle and their correlations with carcass and meat quality traits[D]. Thesis for M. S., Yangzhou University, Supervisor: Yang Z P. pp. 18-21.)
[9] 唐慧, 王巍, 方东辉, 等 . 2018. 不同品种牛 SCD1 基因表达与肌肉脂肪酸组成的关系研究[J]. 黑龙江畜牧兽医, 1:1-4.
(Tang H, Wang W, Fang D H, et al.2018. Study on the relationship between SCD1 gene expression level and muscle fatty acid composition in different breeds of cattle[J]. Heilongjiang Animal Science and Veterinary Medicine, 1: 1-4.)
[10] 唐红杰 .2014. 陇东肉牛A-FABP 和 SCD1 基因多态性及其与肉质性状的相关性研究[D]. 硕士学位论文, 甘肃农业大学, 导师: 吴建平 . pp. 41-42.
(Tang H J.2014. Poly‐ morphisms of A-FABP and SCD1 genes in Longdong beef cattle and its relationship with meat quality trait [D]. Thesis for M.S., Gansu Agricultural University, Su‐ pervisor: Wu J P. pp. 18-21.)
[11] 王冰冰, 耿爽, 耿春银, 等 . 2017. 膨化全脂大豆对延边黄牛 SCD 基因表达及肌肉脂肪酸含量的影响[J]. 饲料工业, 38(11): 21-24.
(Wang B B, Geng S, Geng C Y.et al.2017. Effect of puffing fullfat soybean on Yanbian cattle SCD gene expression and fatty acid content in muscle[J]. Feed Industry, 38(11): 21-24.)
[12] 王桂芝, 王金凤, 秦孜娟, 等 . 2013. 崂山奶山羊硬脂酰-CoA去饱和酶基因(SCD)多态性及其与泌乳性状的相关分析[J]. 畜牧兽医学报 , 44(07): 1131-1139.
(Wang G Z, Wang J F, Qin Z J.et al.2013. Association between polymorphism of stearoyl-CoA desaturase gene (SCD) and milk production traits in Laoshan dairy goat[J]. Acta Veterinaria et Zootechnica Sinica, 44(07): 1131-1139.)
[13] 王小龙, 常玲玲, 陈莹, 等 . 2014. 中国荷斯坦牛 SCD1 外显子5 基因多态性及其对乳中脂肪酸组成的影响[J]. 中国农业科学, 47(09): 1858-1864.
(Wang X L, Chang L L, Chen Y.et al.2014. Genetic polymorphism of the SCD1 gene and its associations with milking traits in Chinese Holstein[J]. Scientia Agricultura Sinica, 47(09): 1858-1864.)
[14] 张静静, 宋玉芹, 李桢, 等 . 2013. 中国西门塔尔牛 SCD1 基因多态性与肉质性状的相关分析[J]. 华北农学报 , 28(01): 54-57.
(Zhang J J, Song Y Q, Li Z, et al.2013. Polymorphisms of SCD1 gene and its association with meat quality traits in Chinese Simmental[J]. Acta Agriculturae Boreali Sinica, 28(01): 54-57)
[15] Campbell E M G, Gallagher D S, Davis S K, et al.2001. Rap‐ id communication: Mapping of the bovine stearoy-CoA desaturase (SCD) gene to BTA26[J]. American Society of Animal Science, 79: 1945-1955.
[16] Enoch H G, Strittmatter P.1978. Role of tyrosyl and arginyl residues in rat liver microsomal stearyl coenzymeA desaturase[J]. Biochemistry, 17(23): 4927-4932.
[17] Jun R.2003. lsolation and molecular characterization of the stearoyl-CoA desaturase (SCD) gene affecting fat deposition in pigs[D]. Germany: Degree of Doctor of Agricul‐ tural Sciences of the Faculty of Agricultural Sciences Georg-August-University Gttingen,105(9) :432-478.
[18] Medrano J F, Johnson A, DePeters E J.et al.1999. Genetic modification of the composition of milk fat: Identification of polymorphisms with the bovine stearoyl-Co-Ade‐saturase gene[J]. Journal of Dairy Science, 82: 71.
[19] Orru L, Cifuni G F, Piasentier E, et al.2011. Association analyses of single nucleotide polymorphisms in the LEP and SCD1 genes on the fatty acid profile of muscle fatin immental bulls[J]. Meat Science, 87: 344-348.
[20] Thiede M A, Ozols J, Strittmatter P.1986. Construction and sequence of cDNA for rat liver stearyl coenzyme A de‐ saturase[J]. The Journal of Biological Chemistry, 261(28): 13230-13235.
[21] Wang H, Zhong J, Zhang C, et al.2020. The whole-transcrip‐tome landscape of muscle and adipose tissues reveals the ceRNA regulation network related to intramuscular fat deposition in yak[J]. BMC Genomics, 21(1): 347.
[22] Xiong X R, Li J, Fu M.et al.2013. Oocyte extract improves epigenetic reprogramming of yak fibroblast cells and cloned embryo development[J]. Therognology, 79(3):462-469.
