吐鲁番黑羊体重和体尺性状全基因组关联分析

doi:10.11843/j.issn.0366-6964.2025.09.016

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (9): 4315-4327.doi: 10.11843/j.issn.0366-6964.2025.09.016

吐鲁番黑羊体重和体尺性状全基因组关联分析

白锋¹, 玛尔孜娅·亚森¹, 阿米妮古丽·阿不来孜¹, 滕文³, 罗春彦¹, 纳扎开提·艾尼万尔², 张耘韬², 纪新民², 张艳花^1*

1. 新疆畜牧科学院畜牧研究所, 农业农村部畜禽资源(羊)评价利用重点实验室, 新疆绒毛用羊遗传育种与繁殖重点实验室, 乌鲁木齐 830026;
2. 新疆农业大学动物科学学院, 乌鲁木齐 830052;
3. 托克逊县风城国营牧业有限公司, 吐鲁番 838100

收稿日期:2025-02-12 发布日期:2025-09-30
通讯作者: 张艳花，主要从事绵羊遗传育种研究，E-mail：181103221@qq.com
作者简介:白锋(1996-),男，苗族，重庆酉阳人，硕士，主要从事动物遗传育种与繁殖研究，E-mail：BF95114@outlook.com.
基金资助:
中央引导地方科技发展专项资金：羊遗传资源评价与利用实验平台建设(ZYYD2023B10)；新疆自治区产业技术体系(XJARS-09-05)；吐鲁番市重点研发专项：吐鲁番黑羊核心群选育体系建立及优质肉产品开发(202316)；新疆牧区地方肉羊选育改良计划(XJMQ-1)

Genome-Wide Association Study of Body Weight and Body Size Traits In Turpan Black Sheep

BAI Feng¹, MAERZIYA·Yasen¹, AMINIGULI·Abulaizi¹, TENG Wen³, LUO Chunyan¹, NAZHAKAITI·Ainiwaner², ZHANG Yuntao², JI Xinmin², ZHANG Yanhua^1*

1. Xinjiang Key Laboratory of Genetic Breeding and Reproduction of Fleece Sheep, Key Laboratory of Evaluation and Utilization of Livestock and Poultry Resources (Sheep) of Ministry of Agriculture and Rural Affairs, Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry Sciences, Urumqi 830026, China;
2. College of Animal Science and Technology, Xinjiang Agricultural University, Urumqi 830052, China;
3. Toksun County Fengcheng State-run Herding Co., LTD., Turpan 838100, China

Received:2025-02-12 Published:2025-09-30

摘要/Abstract

摘要： 旨在利用全基因组关联分析(genome-wide association study, GWAS)挖掘与鉴定吐鲁番黑羊体重和体尺性状的相关候选基因及分子标记，为吐鲁番黑羊的选育提高及资源开发利用提供科学依据。本研究选取129只年龄在1~3岁、饲养环境一致的健康吐鲁番黑羊公羊，测定体重、体高、体斜长、胸围、管围、胸宽、胸深、尾宽、尾长共9项体重体尺性状表型数据；随后使用的一次性采血管(添加EDTA-K2抗凝剂)采集5 mL颈静脉外周血提取DNA。对合格的DNA样本进行简化基因组测序(genotyping-by-sequencing, GBS)，运用samtools、bcftools等软件对原始测序数据进行检测、过滤及功能注释；然后利用GCTA、TreeBeST、GEMMA等软件分别完成群体遗传结构分析、群体分层评估及全基因组关联分析。本研究测序得到160.88 G的Raw data，质控后Clean data为157.87 G，获得460 766个SNPs位点。全基因关联分析在9个性状中共筛选到74个显著SNPs位点(P＜10^-5)，进一步注释得到到39个候选基因。单倍型分析发现候选基因的多个显著位点均位于单倍型block区域内。本研究鉴定了与吐鲁番黑羊体重体尺性状显著关联的SNP位点及候选基因，为深入解析这些性状的遗传机制提供了重要依据，同时也为吐鲁番黑羊分子标记辅助育种提供了基础数据。

关键词: 吐鲁番黑羊, 体尺性状, 全基因组关联分析, 单倍型分析

Abstract: This study aimed to identify candidate genes and molecular markers associated with body weight and body size traits in Turpan black sheep using genome-wide association study (GWAS), thereby providing a scientific basis for genetic breeding and resource development of Turpan black sheep. In this study, 129 healthy male Turpan black sheep aged 1 to 3 years, raised under the uniform conditions, were selected. Phenotypic data for 9 traits were measured: body weight, body height, body length, chest circumference, tube circumference, chest width, chest depth, tail width, and tail length. Peripheral blood samples (5 mL) were collected from the jugular vein using EDTA-K₂ anticoagulant vacuum tubes for DNA extraction. Qualified DNA samples underwent genotyping-by-sequencing (GBS). Raw sequencing data were processed, filtered, and annotated using software such as samtools and bcftools.Subsequently, population genetic structure analysis, population stratification assessment, and GWAS were performed using GCTA, TreeBeST, and GEMMA softwares, respectively. Sequencing yielded 160.88 G of raw data. After quality control, 157.87 G of clean data were obtained, identifying 460 766 SNP loci. GWAS detected 74 significant SNPs (P<10^-5) associated with the 9 traits. Annotation revealed 39 candidate genes. Haplotype analysis showed that multiple significant SNPs were located within haplotype blocks. This study identified important genetic loci and candidate genes associated with body weight and body size traits of Turpan black sheep.The findings provide crucial insights for elucidating the genetic mechanisms underlying these traits and lay the foundation for molecular marker-assisted breeding in Turpan black sheep.

Key words: Turpan black sheep, body size traits, genome-wide association study, haplotype analysis

中图分类号:

S826.2

白锋, 玛尔孜娅·亚森, 阿米妮古丽·阿不来孜, 滕文, 罗春彦, 纳扎开提·艾尼万尔, 张耘韬, 纪新民, 张艳花. 吐鲁番黑羊体重和体尺性状全基因组关联分析[J]. 畜牧兽医学报, 2025, 56(9): 4315-4327.

BAI Feng, MAERZIYA·Yasen, AMINIGULI·Abulaizi, TENG Wen, LUO Chunyan, NAZHAKAITI·Ainiwaner, ZHANG Yuntao, JI Xinmin, ZHANG Yanhua. Genome-Wide Association Study of Body Weight and Body Size Traits In Turpan Black Sheep[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(9): 4315-4327.

参考文献

[1] 关鸣轩,种丽伟,魏佩玲,等.吐鲁番黑羊肉品质分析[J].草食家畜,2024(5):11-17.
GUAN M X,CHONG L W,WEI P L. Analysis on mutton quality of Turpan Black sheep[J]. Grass-Feeding Livestock, 2024(5):11-17. (in Chinese)
[2] 施海娜,刘雨田,李世恩,等.杜泊羊体质量与体尺指标的相关及回归分析[J].饲料研究, 2021, 44(13):5.
SHI H N,LIU Y T,LI S E. Correlation and regression analyses of the body weight and body sizes in Dorper sheep[J]. Feed Research, 2021, 44(13):5. (in Chinese)
[3] 海萨·艾也力汗,张钰,杨博文,等.基于简化基因组测序筛选白斑狗鱼耐热性状关联的InDel标记[J].水产学报, 2024, 48(3):039105.
YELHAN HAISA, ZHANG Y, YANG B W, et al. Screening of InDel markers associated with heat tolerance traits in Esox lucius based on simplified genome sequencing[J]. Journal of Fisheries of China, 2024, 48(3):039105.(in Chinese)
[4] HAN M, WANG X, DU H, et al. Genome-wide association study identifies candidate genes affecting body conformation traits of Zhongwei goat[J].BMC Genomics,2025,26(1):37.
[5] XIANG X, PENG C, CAO D, et al. Whole genome sequencing reveals that five genes are related to BW trait in sheep[J]. Animal,2024,18(9):101282.
[6] LI Y, YANG H, GUO J, et al. Uncovering the candidate genes related to sheep body weight using multi-trait genome-wide association analysis[J]. Front Vet Sci, 2023,10:1206383.
[7] ZHANG F, LIU Q, GONG P, et al. Genome-wide association study provided insights into the polled phenotype and polled intersex syndrome (PIS) in goats[J].BMC Genomics, 2024,25(1):661.
[8] SELIONOVA M, AIBAZOV M, MAMONTOVA T,et al.Genome-wide association study of live body weight and body conformation traits in young Karachai goats[J]. Small Rumin Res, 2022,216:106836.
[9] 樊琛,艾克拜尔·艾合麦提,赵茜,等.己酮可可碱对吐鲁番黑羊新鲜精液生理活性的影响[J].中国畜牧杂志,2024,60(9):1-11.
FAN C, AKBAR AIHMET, ZHAO Q, et al. Effect of pentoxifylline on the physiological activity of fresh semen from Turpan Black Sheep[J]. Chinese Journal of Animal Science,2024, 60(9):1-11. (in Chinese)
[10] 艾克拜尔·艾合麦提,樊琛,英提扎尔·阿不力孜,等.原花青素对吐鲁番黑羊精液低温保存效果的影响[J].中国畜牧杂志,2024,60 (01): 244-248.
AKBAR AIHMET, FAN C, INTIZAR ABLIZ, et al. Effect of proanthocyanidins on cryopreservation efficiency of Turpan Black sheep semen at low temperature[J]. Chinese Journal of Animal Science,2024,60(9):244-248. (in Chinese)
[11] 阿尔曼·海热,艾克拜尔·艾合麦提,古丽沙热·吾甫尔,等.不同季节吐鲁番黑羊血清中生殖激素的变化规律研究[J].中国畜牧杂志, 2024,60 (1): 255-259.
ARMAN HAIRE, AKBAR AIHMET, GULSHAHERP WUPUR, et al. Study on the variation patterns of reproductive hormones in serum of Turpan Black Sheep in different seasons[J]. Chinese Journal of Animal Science, 2024,60 (1): 255-259. (in Chinese)
[12] HAIRE A, BAI J, ZHAO X, et al. Identifying the heat resistant genes by multi-tissue transcriptome sequencing analysis in Turpan Black sheep[J]. Theriogenology,2022,179:78-86.
[13] 王琼,曹行,张小洪,等. 新疆两个地方绵羊品种策勒黑羊、吐鲁番黑羊的基因组选择信号分析[J].草食家畜, 2021,(4): 1-7.
WANG Q, CAO H, ZHANG X H, et al. Signal analysis of genome-wide selection of two local sheep breeds in Xinjiang: Cele Black Sheep and Turpan Black Sheep[J]. Grass-Feeding Livestock, 2021,(4): 1-7. (in Chinese)
[14] MA L. 301 Methods of genome-wide association studies and their applications in dairy cattle[J] J Anim Sci, 2020,98(Supplement_4):31.
[15] REN J, GAO Z, LU Y, et al. Application of GWAS and mGWAS in livestock and poultry breeding[J]. Animals, 2024,14(16):2382.
[16] SATZ-JACOBOWITZ B, HUBMACHER D. The quest for substrates and binding partners: A critical barrier for understanding the role of ADAMTS proteases in musculoskeletal development and disease[J]. Dev Dyn,2021,250(1):8-26.
[17] MOHAMEDI Y, FONTANIL T, CAL S, et al. ADAMTS-12: Functions and challenges for a complex metalloprotease[J]. Front Mol Biosci,2021,8:686763.
[18] HOEFT K, KOCH L, ZIEGLER S, et al. ADAMTS12 promotes fibrosis by restructuring extracellular matrix to enable activation of injury-responsive fibroblasts[J]. J Clin Invest, 2024,134(18):e170246.
[19] JAIN B P, PANDEY S.WD40 repeat proteins: signalling scaffold with diverse functions[J]. Protein J,2018,37(5):391-406.
[20] XU C, MIN J. Structure and function of WD40 domain proteins[J]. Protein Cell,2011,2(3):202-214.
[21] ZHAO X, NIE C, ZHANG J, et al. Identification of candidate genomic regions for chicken egg number traits based on genome-wide association study[J]. BMC Genomics,2021,22(1):610.
[22] SHIN S, HAN J Y, LEE K. Cloning of avian Delta-like 1 homolog gene: the biallelic expression of Delta-like 1 homolog in avian species[J]. Poult Sci,2010, 89(5):948-955.
[23] DEL CID J S, REED N I, MOLNAR K, et al. A disease-associated mutation in fibrillin-1 differentially regulates integrin-mediated cell adhesion[J]. J Biol Chem,2019, 294(48):18232-18243.
[24] LI L, HUANG J, LIU Y. The extracellular matrix glycoprotein fibrillin-1 in health and disease[J]. Front Cell Dev Biol,2024,11:1302285.
[25] MUTHU M L, REINHARDT D P. Fibrillin-1 and fibrillin-1-derived asprosin in adipose tissue function and metabolic disorders[J]. J Cell Commun Signal,2020, 14(2):159-173.
[26] MUTHU M L, TIEDEMANN K, FRADETTE J, et al. Fibrillin-1 regulates white adipose tissue development, homeostasis, and function[J]. Matrix Biol,2022, 110:106-128.
[27] SEDES L, WONDIMU E, CROCKETT B, et al. Fibrillin-1 deficiency in the outer perichondrium causes longitudinal bone overgrowth in mice with Marfan syndrome[J]. Hum Mol Genet,2022, 31(19):3281-3289.
[28] VANSCHOUWEN B, SELVARATNAM R, GIRI R, et al. Mechanism of camp partial agonism in protein kinase g (PKG)[J]. J Biol Chem,2015, 290(48):28631-28641.
[29] TAWA P, ZHANG L, METWALLY E, et al. Mechanistic insights on novel small molecule allosteric activators of cGMP-dependent protein kinase PKG1α[J]. J Biol Chem,2022, 298(9):102284.
[30] REN Y, CHEN X, ZHENG X, et al. Diverse WGBS profiles of longissimus dorsi muscle in Hainan black goats and hybrid goats[J]. BMC Genom Data,2023,24(1):77.
[31] SCHALL N, GARCIA J J, KALYANARAMAN H, et al. Protein kinase G1 regulates bone regeneration and rescues diabetic fracture healing[J]. JCI Insight,2020,5(9):e135355.
[32] JAFARI A, SIERSBAEK M S, CHEN L, et al. Pharmacological inhibition of protein kinase g1 enhances bone formation by human skeletal stem cells through activation of rhoa-akt signaling[J].Stem Cells,2015,33(7):2219-2231.
[33] 庄兆辉,仲永,陈月婵,等.Krüppel样因子在肌肉组织中的功能研究进展[J].遗传, 2018, 40(9):16.
ZHUANG Z H, ZHONG Y, CHEN Y C, et al. Research progress on the roles of Krü ppel-like factors in muscle tissues[J]. Hereditas, 2018, 40(9):16.(in Chinese)
[34] ZAKERI S, AMINIAN H, SADEGHI S, et al. Krüppel-like factors in bone biology[J]. Cell Signal,2022,93:110308.
[35] YANG J, LIU Z, LIU B, et al. Silencing of circCYP51A1 represses cell progression and glycolysis by regulating miR-490-3p/KLF12 axis in osteosarcoma under hypoxia[J]. J Bone Oncol,2022,37:100455.
[36] DU Y, WANG Y, LI Y, et al.miR-214-5p Regulating differentiation of intramuscular pre-adipocytes in goats via targeting KLF12[J]. Front Genet,2021,12:748629.
[37] ZAKI-DIZAJI M, ABAZARI M F, RAZZAGHI H, et al. GRM7 deficiency, from excitotoxicity and neuroinflammation to neurodegeneration: Systematic review of GRM7 deficient patients[J]. Brain Behavior Immun Health,2024,39:100808.
[38] EDMOND M A, HINOJO-PEREZ A, EFREM M, et al. Lipophilic compounds restore function to neurodevelopmental-associated KCNQ3 mutations[J]. Commun Biol,2024,7(1):1181.
[39] SHSNG T, CHEN X, XUE H, et al. The PKHD1 gene inhibits tumor proliferation and invasion in intrahepatic cholangiocarcinoma by activating the Notch pathway[J]. Int J Med Sci, 2024,21(14):2655-2663.
[40] LIU K, CHEN R, WANG X, et al. Biallelic ANKS6 null variants cause notable extrarenal phenotypes in a nephronophthisis patient and lead to hepatobiliary abnormalities by YAP1 deficiency[J]. Clin Genet,2023,104(6):625-636.
[41] ANDO K, TONG L, PENG D, et al. KCNJ8/ABCC9-containing K-ATP channel modulates brain vascular smooth muscle development and neurovascular coupling[J]. Dev Cell,2022,57(11):1383-1399.e7.
[42] SAMPER N, HAREARDÓTTIR L, DEPIERREUX D M, et al. Kir6.1, a component of an ATP-sensitive potassium channel, regulates natural killer cell development[J]. Front Immunol,2024,15:1490250.
[43] 朱兰,江炎庭,欧阳依娜,等.云上黑山羊11号染色体单倍型构建及与产羔性状的关联性分析[J].中国畜牧杂志,2024,60(2):202-207+214.
ZHU L, JIANG Y T, OUYANG Y N, et al. Construction of haplotype on chromosome 11 and association analysis with litter size traits in Yunshang Black Goat[J]. Chinese Journal of Animal Science, 2024,60(2):202-207+214.(in Chinese)
[44] 骆娜,安炳星,魏立民,等.全基因关联分析筛选文昌鸡体尺性状相关分子标记[J].中国农业科学, 2024, 57(10):2046-2060.
LUO N,AN B X,WEI L M,et al. Identification of molecular markers associated with body size traits through genome-wide association analysis in Wenchang Chickens[J]. Scientia Agricultura Sinica, 2024, 57(10):2046-2060.(in Chinese)
[45] ARATA M, SUGIMURA K, UEMURA T. Difference in dachsous levels between migrating cells coordinates the direction of collective cell migration[J]. Dev Cell,2017;42(5):479-497.e10.
[46] LE A P, RUPPRRECHT J F, MōGE R M, et al. Adhesion-mediated heterogeneous actin organization governs apoptotic cell extrusion[J]. Nat Commun,2021,12(1):397.
[47] HAYES A J, MELROSE J. Hs, an ancient molecular recognition and information storage glycosaminoglycan, equips hs-proteoglycans with diverse matrix and cell-interactive properties operative in tissue development and tissue function in health and disease[J]. Int J Mol Sci,2023,24(2):1148.

吐鲁番黑羊体重和体尺性状全基因组关联分析

Genome-Wide Association Study of Body Weight and Body Size Traits In Turpan Black Sheep

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 15

编辑推荐

Metrics

本文评价

[1]	李聪, 苏江天, 李一丹, 王朝飞, 于杰, 雷初朝, 党瑞华. 德州驴体尺性状的全基因组关联分析[J]. 畜牧兽医学报, 2025, 56(4): 1744-1754.
[2]	黄雅妮, 唐熹, 李井泉, 魏嘉诚, 吴珍芳, 李新云, 肖石军, 张志燕. 大规模群体解析猪日增重及达百千克体重日龄的潜在因果基因[J]. 畜牧兽医学报, 2025, 56(3): 1100-1109.
[3]	杨苗苗, 谢莉, 简宝怡, 罗超维, 谢卓君, 朱飘, 周天日, 李华, 向海. 利用机器学习构建和优化早期体尺性状对成年母鸡腹脂沉积的预测模型[J]. 畜牧兽医学报, 2025, 56(2): 548-558.
[4]	黄红艳, 张力允, 黄智荣, 伍仲平, 张续勐, 欧阳宏佳, 陈俊鹏, 林桢平, 田允波, 李秀金, 黄运茂. 狮头鹅群体遗传多样性和体重体尺全基因组关联分析[J]. 畜牧兽医学报, 2024, 55(9): 3914-3924.
[5]	张瑞琪, 厐彦芹, 李再山, 尚秀国, 兰干球, 郭金彪, 赵云翔. 基于智能饲喂开展哺乳母猪采食量基因组遗传评估研究[J]. 畜牧兽医学报, 2024, 55(7): 2890-2900.
[6]	康佳威, 黄宣凯, 王志鹏, 张爱珍, 孟芳荣, 盖鹏, 包军付, 孙可心, 宋少康, 孙攀, 陈一川, 张蕾, 高圣玥, 常铭航. 大白猪生长、繁殖和体尺性状遗传参数估计[J]. 畜牧兽医学报, 2024, 55(5): 1936-1944.
[7]	崔晟頔, 王凯, 赵真坚, 陈栋, 申琦, 余杨, 王俊戈, 陈子旸, 禹世欣, 陈佳苗, 王翔枫, 唐国庆. 利用GWAS和DNA甲基化共定位鉴定猪肉质性状的候选基因[J]. 畜牧兽医学报, 2024, 55(5): 1945-1957.
[8]	钟欣, 张晖, 张充, 刘小红. 母猪繁殖力基因遗传育种研究进展[J]. 畜牧兽医学报, 2024, 55(2): 438-450.
[9]	林晓坤, 都萌萌, 周李生, 黄振刚, 王頔, 周东辉, 曹欣欣, 贺建宁, 赵金山, 李和刚. 敖汉细毛羊羊毛经济性状的全基因组关联分析[J]. 畜牧兽医学报, 2024, 55(10): 4346-4359.
[10]	唐鑫鑫, 郑炬梅, 骆娜, 营凡, 朱丹, 李森, 刘大伟, 安炳星, 文杰, 赵桂苹, 李和刚. 基于全基因组关联分析揭示肉鸡腿病发生的遗传机制[J]. 畜牧兽医学报, 2024, 55(1): 99-109.
[11]	李柯安宁, 杜丽丽, 安炳星, 邓天宇, 梁忙, 曹晟, 杜悦莹, 徐凌洋, 高雪, 张路培, 李俊雅, 高会江. 华西牛胴体及原始分割肉块重量性状遗传参数估计与全基因组关联分析[J]. 畜牧兽医学报, 2023, 54(9): 3664-3676.
[12]	张笑科, 廖伟莉, 陈信佑, 李婷婷, 袁晓龙, 李加琪, 黄翔, 张豪. 杜洛克猪生长性状全基因组关联分析及候选基因鉴定[J]. 畜牧兽医学报, 2023, 54(5): 1868-1876.
[13]	吴骏, 蔡晓钿, 林清, 钟展明, 叶浩强, 魏趁, 徐志婷, 吴细波, 司景磊, 张哲, 李加琪. 大白猪眼肌面积、估计瘦肉率和背膘厚的加权一步法全基因组关联分析[J]. 畜牧兽医学报, 2023, 54(4): 1403-1414.
[14]	张高猛, 丁纪强, 刘昱宏, 郑麦青, 文杰, 赵桂苹, 李庆贺. 全基因组关联分析揭示白羽肉鸡孵化性状的遗传基础[J]. 畜牧兽医学报, 2023, 54(2): 534-544.
[15]	范晨宇, 单艳菊, 章明, 姬改革, 巨晓军, 屠云洁, 贺喜, 束婧婷, 刘一帆, 张海涵. 立华麻黄鸡体重和肉品质性状全基因组关联分析[J]. 畜牧兽医学报, 2023, 54(12): 4982-4992.