家驴40K液相芯片开发及其初步应用

doi:10.11843/j.issn.0366-6964.2024.12.019

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (12): 5538-5548.doi: 10.11843/j.issn.0366-6964.2024.12.019

家驴40K液相芯片开发及其初步应用

李聪¹(), 刘书琴², 高峰¹, 苏江天¹, 王朝飞¹, 拓少华³, 孙玉江²^,*(), 党瑞华¹^,*()

1. 西北农林科技大学动物科技学院, 杨凌 712100
2. 青岛农业大学动物科技学院, 青岛 266109
3. 延安市安塞区科学技术局, 延安 717400

收稿日期:2024-06-17 出版日期:2024-12-23 发布日期:2024-12-27
通讯作者: 孙玉江,党瑞华 E-mail:lc863749946@163.com;s36s@163.com;dangruihua@nwsuaf.edu.cn
作者简介:李聪(1996-), 女, 河南鹤壁人, 博士, 主要从事动物遗传资源与育种研究, E-mail: lc863749946@163.com
基金资助:
山东省农业重大应用技术创新项目(SD2019XM008);山东省现代农业产业技术体系驴创新团队建设专项基金(SDAIT-27);中央引导地方项目(K3030922098);陕西省创新能力支持计划项目(2018XY-021);陕西省科技厅“科学家+工程师”项目(2020)

Development and Preliminary Application of Domestic Donkey 40K Liquid Chip

LI Cong¹(), LIU Shuqin², GAO Feng¹, SU Jiangtian¹, WANG Zhaofei¹, TUO Shaohua³, SUN Yujiang²^,*(), DANG Ruihua¹^,*()

1. College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
2. College of Animal Science and Technology, Qingdao Agricultural University, Qingdao 266109, China
3. Science and Technology Bureau of Ansai District, Yan'an 717400, China

Received:2024-06-17 Online:2024-12-23 Published:2024-12-27
Contact: SUN Yujiang, DANG Ruihua E-mail:lc863749946@163.com;s36s@163.com;dangruihua@nwsuaf.edu.cn

摘要/Abstract

摘要：

为加快我国家驴的分子选育进展，本研究收集国内外27个驴品种，共251头成年驴的全基因组重测序数据，结合国内外家驴重要性状遗传变异研究结果，设计了一款基于靶向测序基因型检测技术的家驴40K液相芯片。结果表明，家驴40K液相芯片中的变异位点(45 893个SNPs和1个InDel)在家驴基因组范围内的平均间距为61.8 kb。利用该芯片对210头成年德州驴母驴进行基因分型测试，所有测试样本的位点检出率为98.4%~99.2%，位点平均测序深度为133×，共有42 575个位点的次等位基因频率大于0.35。使用芯片对20张驴皮样本进行了品种鉴定，初步验证了芯片的可用性。综上，本研究开发的家驴40K液相芯片作为首款大规模家驴基因型检测工具，具有位点密度高、多态性好、检出率高、应用性强等优势，可用于家驴早期的分子标记辅助选择、品种鉴定等方面，进一步提高家驴的育种效率。

关键词: 家驴, 靶向测序基因型检测, 液相芯片, 育种

Abstract:

To accelerate the progress of molecular breeding of Chinese donkeys, this study collected whole genome resequencing data from 251 adult donkeys across 27 donkey breeds and combined it with the results of genetic variation research on important traits of domestic donkeys at home and abroad, designed a 40K liquid chip based on targeted sequencing genotype detection technology for domestic donkeys. The results showed that the variation sites (45 893 SNPs and 1 InDel) in the 40K liquid chip of the domestic donkey were distributed within the domestic donkey genome, with an average spacing of 61.8 kb. Genotyping test was performed on 210 adult Dezhou female donkeys, achieving a detection rate of 98.4%-99.2% across all samples. The average sequencing depth of the loci was 133×, and 42 575 loci had minor allele frequency greater than 0.35. The chip was used for breed identification in 20 donkey-hide samples and preliminarily verified its usability. In summary, the 40K liquid chip developed in this study, the first large-scale genotype detection tool for domestic donkeys, has the advantages of high loci density, good polymorphism, high detection rate, and strong application. It can be used for early molecular marker-assisted selection and breed identification of domestic donkeys, further improving the breeding efficiency.

Key words: domestic donkey, genotyping detection by target sequencing, liquid chip, breeding

中图分类号:

S822.2

李聪, 刘书琴, 高峰, 苏江天, 王朝飞, 拓少华, 孙玉江, 党瑞华. 家驴40K液相芯片开发及其初步应用[J]. 畜牧兽医学报, 2024, 55(12): 5538-5548.

LI Cong, LIU Shuqin, GAO Feng, SU Jiangtian, WANG Zhaofei, TUO Shaohua, SUN Yujiang, DANG Ruihua. Development and Preliminary Application of Domestic Donkey 40K Liquid Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(12): 5538-5548.

图/表 10

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参考文献 36

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品种/产地 Breed/Origin	简称 Abbreviation	样本量 Sample size	样本来源 Sample source
西藏驴Tibetan donkey	XZ	28	西藏墨脱、昌都等
云南驴Yunnan donkey	YUN	7	云南
淮北灰驴Huaibei gray donkey	HB	10	下载
新疆驴Xinjiang donkey	XJ	16	下载
吐鲁番驴Turfan donkey	TLF	5	下载
和田青驴Hetian gray donkey	HT	10	新疆喀什
泌阳驴Biyang donkey	BY	10	河南泌阳
德州驴Dezhou donkey	DZ	7	下载
陕北毛驴Shanbei donkey	GS	7	陕西榆林
关中驴Guanzhong donkey	GZ	10	下载
佳米驴Jiami donkey	JM	11	陕西米脂
青海驴Qinghai donkey	QH	7	青海玉树
庆阳驴Qingyang donkey	QY	9	甘肃庆阳
凉州驴Liangzhou donkey	LZ	10	甘肃河西走廊
太行驴Taihang donkey	TH	5	河北太行
广灵驴Guangling donkey	GL	4	下载
库伦驴Kulun donkey	KUL	6	下载
吉尔吉斯斯坦Kyrgyzstan	Kyrgyz	7	下载
肯尼亚Kenya	Kenya	17	下载
尼日利亚Nigeria	Nigeria	6	下载
埃及Egypt	Egypt	8	下载
埃塞俄比亚Ethiopia	Ethiopia	10	下载
西班牙Spain	Spain	18	下载
伊朗Iran	Iran	8	下载
澳大利亚Australia	Australia	8	下载
藏野驴Equus kiang	KIG	5	下载
亚洲野驴Asiatic wild ass	ASW	2	下载

突变 Variant	名称 ID	染色体 Chromosome	位置 Position	参考 Reference	变异 Variant	基因 Gene	性状 Trait
SNP	15:25408816	15	25 408 816	C	T	ASIP	毛色^[7]
InDel	8:42742556	8	42 742 556	C	CT	TBX3	毛色^[5]

样本产地 Sample origin	样本来源 Sample source	样本数量 Sample size
中国China	国内驴皮供应商1	3
	国内驴皮供应商2	3
埃及Egypt	埃及来源海关货柜	3
尼日利亚Nigeria	尼日利亚来源海关货柜	3
肯尼亚Kenya	肯尼亚来源海关货柜	3
秘鲁Peru	秘鲁来源海关货柜	3
东阿Dong’e	东阿县黑毛驴繁殖中心	2

基因Gene	位点数量Loci number	关联性状Trait
TBX3	17	毛色^[5]
		体长、体高、胸深、胸围、体重、尻宽、尻长^[10]
		体高、体型^[11]
LCORL-NCAPG	45	体高、体长、胸围、体重^[12]
		体高、体型^[11]
		体型^[13]
CDKL5	2	胸围、体长、胸深、尻宽^[14]
IGF1	7	体重、体高、胸围、管围^[15]
IGF2	5	体长、尻高^[16]
ACSL1	2	体高、体长、尻宽、体重^[17]
NR6A1	3	腰椎数、胸腰椎总数、胴体重^[18]
LTBP2	1	腰椎数、胸宽、胴体重^[19]
PRKG2	4	腰椎数、腰椎长、胸腰椎总数、胴体重^[20]
DCAF7	1	胸椎数、其他胴体性状^[21]
CYP4A11	3	耐热性^[22]
DGAT1	1	驴奶脂肪率^[23]
MMP28	2	皮厚度^[12]
KITLG	4	皮肤色素沉着、毛色^[5]
ASIP	1	毛色^[7]
LEPR	6	肌内脂肪、脂肪细胞分化^[24]
MYH1	2	骨骼肌的生长和发育^[25]
ADCY8	31	产奶性状^[26]
NUMB	1
CA8	31
ITGA4	8	精子发生^[27]
ITGA6	7
COL6A2	3
PRKCA	9
ADSL	1	卵母细胞发育^[28]
PIWIL2	1	睾丸发育、精子发生^[29]
CATSPERD	1
CATSPERB	7
SPATA6	1
CD44	4	双胞胎^[30]
SOD2	8
PTPN11	1
BMP7	19	胸椎数、腰椎数^[31]
WNT7A	8
LRP5	7
MAGT1	2	体高、体长^[32]
NKX1-2	1	体高、胴体重^[33]

位点类别Loci category	数量Number
世界家驴的驯化位点Domestication loci of world domestic donkeys	855
中国家驴驯化位点Domestication loci of Chinese domestic donkeys	780
国外家驴驯化位点Domestication loci of foreign domestic donkeys	667
高海拔适应性位点High altitude adaptive loci	540
潜在功能基因位点Potential functional gene loci	257
Y染色体位点Y chromosome loci	115
定制功能位点Customized functional loci	2
其他背景位点Other background loci	42 678
总计Total	45 894

家驴40K液相芯片开发及其初步应用

Development and Preliminary Application of Domestic Donkey 40K Liquid Chip

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