草业学报 ›› 2022, Vol. 31 ›› Issue (9): 183-194.DOI: 10.11686/cyxb2021464
• 研究论文 • 上一篇
马士龙1,2(), 李小伟4, 李响1,2, 谢书琼2,3, 刘益丽1,2, 唐娇2,3, 江明锋1,2()
收稿日期:
2021-12-13
修回日期:
2022-03-14
出版日期:
2022-09-20
发布日期:
2022-08-12
通讯作者:
江明锋
作者简介:
Corresponding author. E-mail: mingfengjiang@vip.sina.com基金资助:
Shi-long MA1,2(), Xiao-wei LI4, Xiang LI1,2, Shu-qiong XIE2,3, Yi-li LIU1,2, Jiao TANG2,3, Ming-feng JIANG1,2()
Received:
2021-12-13
Revised:
2022-03-14
Online:
2022-09-20
Published:
2022-08-12
Contact:
Ming-feng JIANG
摘要:
麦洼牦牛是青藏高原地区优良的乳肉兼用型牦牛品种,本研究旨在探究四川省龙日种畜场麦洼牦牛保种群的遗传多样性和遗传结构,评价3个不同保种群的保种效果并挖掘重要种质特性基因。对麦洼牦牛3个保种群粉嘴群(n=140)、全黑群(n=211)、弗洛群(n=55)进行GBS简化基因组测序,基于检测到的126122个单核苷酸多态性(SNPs)标记计算遗传统计量,结果表明,整个牦牛群的平均观测杂合度(Ho)和平均期望杂合度(He)为0.3038和0.3036,麦洼牦牛的遗传多样性较丰富。全黑群、粉嘴群、弗洛群的观测杂合度Ho分别为0.3029、0.3042、0.3044,近交系数Fis分别为0.0144、0.0152、0.0209,弗洛群和粉嘴群受人工选择的强度大于全黑群,较低的近交水平说明3个群的保种效果较好。Structure分析中全黑、弗洛群部分个体血缘较纯正,而其他个体血缘关系非常混杂;粉嘴群和全黑群的遗传分化系数(Fst)和遗传距离(DR)最大为0.03513、0.0358,结合系统进化树表明两者亲缘关系最远,有遗传分化趋势。利用Fst和π法对3个保种群进行选择信号分析,发现有104个受选择基因广泛参与生殖机能、免疫系统、胚胎发育、脂质代谢等条目以及生殖激素、内/外分泌、信号传递等通路,其中部分基因提示麦洼牦牛的繁殖、肉质、毛色性状以及应激反应得到了人工选择,如PPP3CC、KCNMA1、ROCK2、GNAQ、MEF2C、KIT等。现有的麦洼牦牛保种策略是可行的,研究结果为未来麦洼牦牛的保种选育和遗传改良提供了参考依据。
马士龙, 李小伟, 李响, 谢书琼, 刘益丽, 唐娇, 江明锋. 基于GBS简化基因组测序评估3个麦洼牦牛保种群的遗传结构研究[J]. 草业学报, 2022, 31(9): 183-194.
Shi-long MA, Xiao-wei LI, Xiang LI, Shu-qiong XIE, Yi-li LIU, Jiao TANG, Ming-feng JIANG. Assessment of genetic structure of 3 Maiwa yak preserved populations based on genotyping-by-sequencing technology[J]. Acta Prataculturae Sinica, 2022, 31(9): 183-194.
群体 Population | 年龄 Age (year) | 样本量 Sample number | 公牛数 Bulls | 母牛数 Cows | 地理来源 Geographic origin | 海拔 Elevation (m) | 纬度 Latitude | 经度 Longitude |
---|---|---|---|---|---|---|---|---|
全黑群QH | 1~12 | 211 | 51 | 160 | 红原Hongyuan | 3566 | 32°33′ | 102°16′ |
弗洛群FL | 1~12 | 55 | 12 | 43 | 红原Hongyuan | 3572 | 32°35′ | 102°17′ |
粉嘴群FZ | 1~12 | 140 | 31 | 109 | 红原Hongyuan | 3598 | 32°37′ | 102°15′ |
共计Total | - | 406 | 94 | 312 | - | - | - | - |
表1 3个保种群的采集信息
Table 1 The sample information of 3 breeding populations
群体 Population | 年龄 Age (year) | 样本量 Sample number | 公牛数 Bulls | 母牛数 Cows | 地理来源 Geographic origin | 海拔 Elevation (m) | 纬度 Latitude | 经度 Longitude |
---|---|---|---|---|---|---|---|---|
全黑群QH | 1~12 | 211 | 51 | 160 | 红原Hongyuan | 3566 | 32°33′ | 102°16′ |
弗洛群FL | 1~12 | 55 | 12 | 43 | 红原Hongyuan | 3572 | 32°35′ | 102°17′ |
粉嘴群FZ | 1~12 | 140 | 31 | 109 | 红原Hongyuan | 3598 | 32°37′ | 102°15′ |
共计Total | - | 406 | 94 | 312 | - | - | - | - |
图1 部分样本血液基因组DNA电泳图M: BM5000 DNA指示剂BM5000 DNA marker; 1~15: 不同样本DNA DNA samples from different samples.
Fig.1 Genome DNA electrophoresis of some blood samples
类型 Type | 原始碱基数 Raw bases (Mb) | 有效碱基数 Clean bases (Mb) | 有效率 Effective rate (%) | 碱基检测错误率 Error rate (%) |
---|---|---|---|---|
麦洼牦牛Maiwa yak | 279.211~2456.350 | 279.210~2456.340 | 99.990~100.000 | 0.040~0.060 |
共计Toal | 327.517 | 327.512 | - | - |
平均Mean | 806.690 | 806.680 | 99.990 | 0.044 |
表2 麦洼牦牛测序数据统计
Table 2 Summary of sequencing data of Maiwa yak
类型 Type | 原始碱基数 Raw bases (Mb) | 有效碱基数 Clean bases (Mb) | 有效率 Effective rate (%) | 碱基检测错误率 Error rate (%) |
---|---|---|---|---|
麦洼牦牛Maiwa yak | 279.211~2456.350 | 279.210~2456.340 | 99.990~100.000 | 0.040~0.060 |
共计Toal | 327.517 | 327.512 | - | - |
平均Mean | 806.690 | 806.680 | 99.990 | 0.044 |
类型 Type | Q20 (%) | GC (%) | 有效读长数Clean reads (Mb) | 有效读长数比对率Mapping rate (%) | 测序深度Average depth (×) | 覆盖度 Coverage (%) |
---|---|---|---|---|---|---|
麦洼牦牛Maiwa yak | 93.83~97.58 | 36.56~40.28 | 1.94~17.08 | 92.60~99.68 | 5.65~31.64 | 2.03~6.13 |
平均Mean | 95.73 | 38.88 | 5.60 | 98.75 | 14.33 | 3.46 |
表3 测序数据质量评估
Table 3 Quality assessment of sequencing
类型 Type | Q20 (%) | GC (%) | 有效读长数Clean reads (Mb) | 有效读长数比对率Mapping rate (%) | 测序深度Average depth (×) | 覆盖度 Coverage (%) |
---|---|---|---|---|---|---|
麦洼牦牛Maiwa yak | 93.83~97.58 | 36.56~40.28 | 1.94~17.08 | 92.60~99.68 | 5.65~31.64 | 2.03~6.13 |
平均Mean | 95.73 | 38.88 | 5.60 | 98.75 | 14.33 | 3.46 |
群体 Population | 观测杂合度Ho | 期望杂合度He | 核苷酸多样度π | 近交系数Fis |
---|---|---|---|---|
全黑群QH | 0.3029 | 0.3030 | 0.3030 | 0.0144 |
粉嘴群FZ | 0.3042 | 0.3025 | 0.3020 | 0.0152 |
弗洛群FL | 0.3044 | 0.3052 | 0.3009 | 0.0209 |
平均Mean | 0.3038 | 0.3036 | 0.3020 | 0.0168 |
表4 麦洼牦牛3个育种群遗传多样性参数
Table 4 Genetic diversity parameters of three preserved populations of Maiwa yak
群体 Population | 观测杂合度Ho | 期望杂合度He | 核苷酸多样度π | 近交系数Fis |
---|---|---|---|---|
全黑群QH | 0.3029 | 0.3030 | 0.3030 | 0.0144 |
粉嘴群FZ | 0.3042 | 0.3025 | 0.3020 | 0.0152 |
弗洛群FL | 0.3044 | 0.3052 | 0.3009 | 0.0209 |
平均Mean | 0.3038 | 0.3036 | 0.3020 | 0.0168 |
群体Population | 粉嘴群FZ | 弗洛群FL | 全黑群QH |
---|---|---|---|
粉嘴群FZ | - | 0.02760 | 0.03580 |
弗洛群FL | 0.02726 | - | 0.02540 |
全黑群QH | 0.03513 | 0.02504 | - |
表5 群体间的遗传分化系数(Fst)(对角线下)和遗传距离(DR)(对角线上)
Table 5 Genetic differentiation index (below diagonal) and genetic distance (above diagonal) among three populations of Maiwa yak
群体Population | 粉嘴群FZ | 弗洛群FL | 全黑群QH |
---|---|---|---|
粉嘴群FZ | - | 0.02760 | 0.03580 |
弗洛群FL | 0.02726 | - | 0.02540 |
全黑群QH | 0.03513 | 0.02504 | - |
图5 麦洼牦牛structure群体遗传结构A:3个群体不同K值下的群体结构,每个颜色代表1个分组;B:不同K值下群体结构的CV值曲线。A: The population structure of three groups with different K values, each color represents a group; B: The CV curve of the population structure with different K values.
Fig.5 Genetic structure of Maiwa yak structure populations
图7 受选择基因的GO富集条目1.有丝分裂细胞周期G1/S转换;2.氯离子跨膜运输;3.节律过程;4.细胞DNA损伤的刺激反应;5.细胞信号转导;6.神经元凋亡过程的负调控;7.细胞黏着;8.趋化性;9.细胞分裂;10.细胞表面受体信号通路;11.氯离子通道复合体;12.细胞间连接;13.膜的锚固组分;14.树突;15.细胞连接;16.线粒体;17.质膜的整体组分;18.突触后膜;19.蛋白质复合体;20.胞质;21.氯离子通道活性;22.酶结合;23.蛋白质二聚化活性;24.锌离子结合;25.镁离子结合;26.细胞因子活性;27.蛋白质同源二聚体化活性;28.蛋白质异源二聚体化活性;29.RNA结合;30.金属离子结合。1. G1/S transition of mitotic cell cycle; 2. Chloride transmembrane transport; 3. Rhythmic process; 4. Cellular response to DNA damage stimulus; 5. Cell-cell signaling; 6. Negative regulation of neuron apoptotic process; 7. Cell adhesion; 8. Chemotaxis; 9. Cell division; 10. Cell surface receptor signaling pathway; 11. Chloride channel complex; 12. Cell-cell junction; 13. Anchored component of membrane; 14. Dendrite; 15. Cell junction; 16. Mitochondrion; 17. Integral component of plasma membrane; 18. Postsynaptic membrane; 19. Protein complex; 20. Cytosol; 21. Chloride channel activity; 22. Enzyme binding; 23. Protein dimerization activity; 24. Zinc ion binding; 25. Magnesium ion binding; 26. Cytokine activity; 27. Protein homodimerization activity; 28. Protein heterodimerization activity; 29. RNA binding; 30. Metal ion binding.
Fig.7 GO enrichment items of selected gene
KEGG通路KEGG pathway | 分类号ID | 基因名Gene name |
---|---|---|
催产素信号通路Oxytocin signaling pathway | bom04921 | GNAQ; MAP2K5; PPP3CC; MEF2C; KCNJ3; ROCK2; ITPR2; CACNB4 |
缝隙连接Gap junction | bom04540 | GNAQ; MAP2K5; PRKG1; PDGFRB; ITPR2 |
雌激素信号通路Estrogen signaling pathway | bom04915 | ITPR1; GNAQ; OPRM1; KCNJ3; ITPR2 |
钙信号通路Calcium signaling pathway | bom04020 | GNAQ; ADORA2B; GNA14; PTAFR; PPP3CC; PDGFRB; ITPR2 |
cGMP-PKG信号通路cGMP-PKG signaling pathway | bom04022 | GNAQ; PRKG1; KCNMA1; MEF2C; ROCK2; ITPR2 |
血管平滑肌收缩Vascular smooth muscle contraction | bom04270 | GNAQ; ADORA2B; PRKG1; KCNMA1; ROCK2; ITPR2 |
逆行神经的信号Retrograde endocannabinoid signaling | bom04723 | ITPR1; GNAQ; GABRA1; KCNJ3; ITPR2 |
果糖和甘露糖代谢Fructose and mannose metabolism | bom00051 | ENOSF1; SORD; MPI |
肾素分泌Renin secretion | bom04924 | GNAQ; KCNMA1; PPP3CC; ITPR2 |
内分泌等因素调节钙的重吸收Endocrine and other factor-regulated calcium reabsorption | bom04961 | GNAQ; CLTC; CALB1 |
唾液分泌Salivary secretion | bom04970 | GNAQ; PRKG1; KCNMA1; ITPR2 |
胰腺分泌Pancreatic secretion | bom04972 | GNAQ; SLC4A4; KCNMA1; ITPR2 |
Rap1信号通路Rap1 signaling pathway | bom04015 | ADORA2B; KIT; VEGFC; NGF; PDGFRB |
谷氨酸突触Glutamatergic synapse | bom04724 | GNAQ; PPP3CC; KCNJ3; ITPR2 |
卵母细胞减数分裂Oocyte meiosis | bom04114 | ANAPC10; YWHAQ; PPP3CC; ITPR2 |
甲状腺激素的合成Thyroid hormone synthesis | bom04918 | GNAQ; PAX8; ITPR2 |
MAPK信号通路MAPK signaling pathway | bom04010 | NGF; PPP3CC; MEF2C; PDGFRB; CACNB4 |
血小板激活Platelet activation | bom04611 | GNAQ; PRKG1; ROCK2; ITPR2 |
多巴胺能神经突触Dopaminergic synapse | bom04728 | GNAQ; PPP3CC; KCNJ3; ITPR2 |
胆汁分泌Bile secretion | bom04976 | NCEH1; SLC5A1 |
促性腺激素信号通路GnRH signaling pathway | bom04912 | GNAQ; ITPR2 |
节律导引Circadian entrainment | bom04713 | GNAQ; PRKG1; KCNJ3 |
炎症介质调节TRP通道Inflammatory mediator regulation of TRP channels | bom04750 | GNAQ; NGF; ITPR2 |
Ras信号通路Ras signaling pathway | bom04014 | KIT; VEGFC; NGF; PDGFRB |
磷脂酰肌醇信号系统Phosphatidylinositol signaling system | bom04070 | PI4KA; ITPK1; ITPR2 |
表6 受选择基因的KEGG通路
Table 6 KEGG pathway of differential expression genes
KEGG通路KEGG pathway | 分类号ID | 基因名Gene name |
---|---|---|
催产素信号通路Oxytocin signaling pathway | bom04921 | GNAQ; MAP2K5; PPP3CC; MEF2C; KCNJ3; ROCK2; ITPR2; CACNB4 |
缝隙连接Gap junction | bom04540 | GNAQ; MAP2K5; PRKG1; PDGFRB; ITPR2 |
雌激素信号通路Estrogen signaling pathway | bom04915 | ITPR1; GNAQ; OPRM1; KCNJ3; ITPR2 |
钙信号通路Calcium signaling pathway | bom04020 | GNAQ; ADORA2B; GNA14; PTAFR; PPP3CC; PDGFRB; ITPR2 |
cGMP-PKG信号通路cGMP-PKG signaling pathway | bom04022 | GNAQ; PRKG1; KCNMA1; MEF2C; ROCK2; ITPR2 |
血管平滑肌收缩Vascular smooth muscle contraction | bom04270 | GNAQ; ADORA2B; PRKG1; KCNMA1; ROCK2; ITPR2 |
逆行神经的信号Retrograde endocannabinoid signaling | bom04723 | ITPR1; GNAQ; GABRA1; KCNJ3; ITPR2 |
果糖和甘露糖代谢Fructose and mannose metabolism | bom00051 | ENOSF1; SORD; MPI |
肾素分泌Renin secretion | bom04924 | GNAQ; KCNMA1; PPP3CC; ITPR2 |
内分泌等因素调节钙的重吸收Endocrine and other factor-regulated calcium reabsorption | bom04961 | GNAQ; CLTC; CALB1 |
唾液分泌Salivary secretion | bom04970 | GNAQ; PRKG1; KCNMA1; ITPR2 |
胰腺分泌Pancreatic secretion | bom04972 | GNAQ; SLC4A4; KCNMA1; ITPR2 |
Rap1信号通路Rap1 signaling pathway | bom04015 | ADORA2B; KIT; VEGFC; NGF; PDGFRB |
谷氨酸突触Glutamatergic synapse | bom04724 | GNAQ; PPP3CC; KCNJ3; ITPR2 |
卵母细胞减数分裂Oocyte meiosis | bom04114 | ANAPC10; YWHAQ; PPP3CC; ITPR2 |
甲状腺激素的合成Thyroid hormone synthesis | bom04918 | GNAQ; PAX8; ITPR2 |
MAPK信号通路MAPK signaling pathway | bom04010 | NGF; PPP3CC; MEF2C; PDGFRB; CACNB4 |
血小板激活Platelet activation | bom04611 | GNAQ; PRKG1; ROCK2; ITPR2 |
多巴胺能神经突触Dopaminergic synapse | bom04728 | GNAQ; PPP3CC; KCNJ3; ITPR2 |
胆汁分泌Bile secretion | bom04976 | NCEH1; SLC5A1 |
促性腺激素信号通路GnRH signaling pathway | bom04912 | GNAQ; ITPR2 |
节律导引Circadian entrainment | bom04713 | GNAQ; PRKG1; KCNJ3 |
炎症介质调节TRP通道Inflammatory mediator regulation of TRP channels | bom04750 | GNAQ; NGF; ITPR2 |
Ras信号通路Ras signaling pathway | bom04014 | KIT; VEGFC; NGF; PDGFRB |
磷脂酰肌醇信号系统Phosphatidylinositol signaling system | bom04070 | PI4KA; ITPK1; ITPR2 |
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