基于全基因组重测序技术的狮头鹅Indel标记分析

doi:10.11843/j.issn.0366-6964.2021.03.010

摘要/Abstract

摘要： 旨在利用重测序技术分析狮头鹅基因Indel差异并探讨其产蛋调控通路。本研究选用产蛋量有差异的成年狮头鹅和吉林白鹅母鹅各5只，采用全基因组重测序方法，对两个品种基因组水平的插入缺失突变情况进行比较分析。结果表明，测序共得到350.35 Gb数据，其中Q20与Q30平均值分别为96.74%、92.19%；通过注释分析发现了748 821.2个Indel变异位点。10只试验鹅的Indel位点在编码区（CDS）的分布趋势和数量与参考基因组相似，其中有11 737个Indel位点导致了插入或删除；在此基础上，进一步分析筛选产蛋相关通路，发现在GnRH信号通路、雌激素信号通路、催产素信号通路、催乳素信号通路以及孕酮介导的卵母细胞成熟通路中分别有15、1、1、1、18个变异基因参与狮头鹅产蛋调控。结果显示，通过Indel位点分析表明，GnRH信号通路、雌激素信号通路、催产素信号通路、催乳素信号通路和孕酮介导的卵母细胞成熟通路均与狮头鹅产蛋有关，并进一步筛选出可能的产蛋相关基因。这些数据将为我们研究狮头鹅繁殖性能提供有效基础和依据。

关键词: 狮头鹅, 重测序, Indel, 信号通路, 产蛋

Abstract: This study aimed to use resequencing technology to analyze the differences in Shitou goose gene Indel and to explore its egg production regulatory pathway. Five adult Shitou geese and five Jilin white geese with different egg production were selected, and the whole genome resequencing method was used to compare and analyze the indel mutations at the genome level of the two breeds. The results showed that 350.35 Gb data was obtained by sequencing, among which the average values of Q20 and Q30 reached 96.74% and 92.19%, respectively. Annotation analysis found 748 821.2 Indel mutation sites. The distribution trend and the number of Indel loci in the coding region (CDS) of 10 experimental geese were similar to those of the reference genome. Among them, 11 737 Indel loci resulted in insertion or deletion. On the basis, egg-laying related pathways were further analyzed and screened, and 15, 1, 1, 1, and 18 variant genes in the GnRH, estrogen, oxytocin, prolactin signaling pathways and progesterone-mediated oocyte maturation pathway, respectively involved in the regulation of goose egg-laying were found. The results suggest that the GnRH, estrogen, oxytocin, prolactin signaling pathways and progesterone-mediated oocyte maturation pathway are all related to Shitou goose egg-laying, and egg-laying related genes were further screened. These data will provide an effective basis for studying the reproductive performance of Shitou geese.

Key words: Shitou goose, resequencing, Indel, signaling pathway, egg-laying

中图分类号:

S835.2

王慧芳, 周光现, 孙永峰, 陈新企, 雷栩斌, 张锐毅, 贾汝敏, 赵志辉. 基于全基因组重测序技术的狮头鹅Indel标记分析[J]. 畜牧兽医学报, 2021, 52(3): 662-675.

WANG Huifang, ZHOU Guangxian, SUN Yongfeng, CHEN Xinqi, LEI Xubin, ZHANG Ruiyi, JIA Rumin, ZHAO Zhihui. Analysis of Indel Markers of Shitou Goose Based on Whole Genome Resequencing Technology[J]. Acta Veterinaria et Zootechnica Sinica, 2021, 52(3): 662-675.

参考文献 46

[1]	PROSSER D J,WU J X,ELLIS E C,et al.Modelling the distribution of chickens,ducks,and geese in China[J].Agric Ecosyst Environ,2011,141(3-4):381-389.
[2]	ZHENG R B,SMITH L M,PROSSER D J,et al.Investigating home range,movement pattern,and habitat selection of bar-headed geese during breeding season at Qinghai Lake,China[J].Animals (Basel),2018,8(10):182.
[3]	ZHANG P Y,ZOU Y A,XIE Y H,et al.Shifts in distribution of herbivorous geese relative to hydro-logical variation in East Dongting Lake wetland,China[J].Sci Total Environ,2018,636:30-38.
[4]	刘思扬,刘秋翔.饶平狮头鹅[J].广东畜牧兽医科技,2019,44(6):10-13.LIU S Y,LIU Q X.Lion-head goose from Raoping[J].Guangdong Journal of Animal and Veterinary Science, 2019, 44(6):10-13.(in Chinese)
[5]	YANG Y Z,YAO Y,CAO Z F,et al.Histological characteristics of follicles and reproductive hormone secretion during ovarian follicle development in laying geese[J].Poult Sci,2019,98(11):6063-6070.
[6]	YAO Y,YANG Y Z,GU T T,et al.Comparison of the broody behavior characteristics of different breeds of geese[J].Poult Sci,2019,98(11):5226-5233.
[7]	LIU G J,CHEN Z F,ZHAO X H,et al.Meta-analysis:Supplementary artificial light and goose reproduction[J].Anim Reprod Sci,2020,214:106278.
[8]	MA W Q,CHENG H Z,ZHAO D H,et al.Effects of dietary Enteromorpha powder supplementation on productive performance,egg quality,and antioxidant performance during the late laying period in Zi geese[J].Poult Sci,2020,99(2):1062-1068.
[9]	LAMERIS T K,DE JONG M E,BOOM M P,et al.Climate warming may affect the optimal timing of reproduction for migratory geese differently in the low and high Arctic[J].Oecologia,2019,191(4):1003-1014.
[10]	罗艺,刘作兰,王启贵,等.饲粮能量水平对初产期四川白鹅生产性能、蛋品质和孵化性能的影响[J].畜牧兽医学报,2018,49(2):439-448.LUO Y,LIU Z L,WANG Q G,et al.Effects of dietary energy concentrations on growth perfor-mance,egg quality and hatching performance in primiparous laying Sichuan white geese[J].Acta Veterinaria et Zootechnica Sinica,2018,49(2):439-448.(in Chinese)
[11]	林潮佳.世界鹅王——狮头鹅[J].生物学通报,1986(11):42.LIN C J.King of world goose-Lion head goose[J].Bulletin of Biology,1986(11):42.(in Chinese)
[12]	包海缘,欧阳宏佳,唐军,等.不同生长期狮头鹅体尺性状、屠宰性能和种蛋品质的测定与分析[J].养禽与禽病防治,2019(6):36-39.BAO H Y,OUYANG H J,TANG J,et al.Determination and analysis of traits,slaughter performance and egg quality of lion head goose in different growth stages[J].Poultry Husbandry and Disease Control,2019(6):36-39.(in Chinese)
[13]	林树欣,潘育璇,黄靓,等.狮头鹅种鹅的饲养管理[J].广东畜牧兽医科技,2019,44(5):26-27,35.LIN S X,PAN Y X,HUANG L,et al.Feeding and management of Shitou Goose for breeding[J].Guangdong Journal of Animal and Veterinary Science,2019,44(5):26-27,35.(in Chinese)
[14]	孙永泰.狮头鹅的饲养技术[J].水禽世界,2016(2):59.SUN Y T.Breeding technology of lion head goose[J].Waterfowl World,2016(2):59.(in Chinese)
[15]	王雪丽,孙姝芬.吉林白鹅简介[J].农村科学实验,2006(12):28.WANG X L,SUN S F.Introduction of Jilin white goose[J].Rural Science Experiment,2006(12):28.(in Chinese)
[16]	GAO G,ZHANG K,ZHAO X,et al.Molecular cloning of the goose GnRH gene and identification of GnRH polymorphisms associated with laying traits[J].Br Poult Sci,2020,61(5):502-507.
[17]	WU Y P,ZHAO X Y,CHEN L,et al.Transcriptomic analyses of the hypothalamic-pituitary-gonadal axis identify candidate genes related to egg production in Xinjiang Yili geese[J].Animals (Basel),2020,10(1):90.
[18]	ZHAO Q Q,CHEN J P,ZHANG X H,et al.Genome-wide association analysis reveals key genes responsible for egg production of lion head goose[J].Front Genet,2020,10(1):1391.
[19]	LI X P,LU Y L,LIU X F,et al.Identification of chicken FSHR gene promoter and the correlations between polymorphisms and egg production in Chinese native hens[J].Reprod Domest Anim,2019,54(4):702-711.
[20]	CABANILLAS R,DIÑEIRO M,CIFUENTES G A,et al.Comprehensive genomic diagnosis of non-syndromic and syndromic hereditary hearing loss in Spanish patients[J].BMC Med Genomics,2018,11(1):58.
[21]	LI X J,YE J W,HAN X L,et al.Whole-genome sequencing identifies potential candidate genes for reproductive traits in pigs[J].Genomics,2020,112(1):199-206.
[22]	唐莹王金玉,张跟喜,等.Myf5基因8个SNPs位点与京海黄鸡生长和繁殖性状的关联分析[J].畜牧兽医学报, 2014, 45(6):863-870.TANG Y,WANG J Y,ZHANG G X,et al.Eight SNPs of the Myf5 gene and its relationship with growth and reproductive traits in Jinghai yellow chicken[J].Acta Veterinaria et Zootechnica Sinica,2014,45(6):863-870.(in Chinese)
[23]	HARDISON R C.Comparative genomics[J].PLoS Biol,2003,1(2):E58.
[24]	吕敏娜,陈伟峰,廖申权.狮头鹅之健康养殖[J].畜牧兽医科技信息,2019(9):143-145.LÜ M N,CHEN W F,LIAO S Q.Healthy breeding of lion head goose[J].Chinese Journal of Animal Husbandry and Veterinary Medicine,2019(9):143-145.(in Chinese)
[25]	TANG J,SHEN X,OUYANG H J,et al.Transcriptome analysis of pituitary gland revealed candidate genes and gene networks regulating the growth and development in goose[J/OL].Anim Biotechnol,2020, doi:10.1080/10495398.2020.1801457.
[26]	隋玉健,杨薇,许云鹏,等.复合中草药添加剂对吉林白鹅生产性能的影响[J].黑龙江畜牧兽医,2020(20):106-108,113.SUI Y J,YANG W,XU Y P,et al.Effect of compound Chinese herbal medicine additive on the production performance of Jilin white goose[J].Heilongjiang Animal Science and Veterinary Medicine,2020(20):106-108,113.(in Chinese)
[27]	甄霆,张响英,张海波,等.光照对浙东白鹅产蛋和相关基本表达量的影响[J].黑龙江畜牧兽医,2018(8):67-68.ZHEN T,ZHANG X Y,ZHANG H B,et al.Effects of light treatments on egg production and related gene expression level in Eastern Zhejiang White Goose[J].Heilongjiang Animal Science and Veterinary Medicine,2018(8):67-68.(in Chinese)
[28]	姚颖,曹正锋,杨耀宗,等.浙东白鹅产蛋与就巢行为学研究[J].中国畜牧杂志,2018,54(4):113-116.YAO Y,CAO Z F,YANG Y Z,et al.Study on egg laying and nesting behavior of eastern Zhejiang White Goose[J].Chinese Journal of Animal Science,2018,54(4):113-116.(in Chinese)
[29]	OUYANG Q Y,HU S Q,WANG G S,et al.Comparative transcriptome analysis suggests key roles for 5-hydroxytryptamlne receptors in control of goose egg production[J].Genes (Basel),2020,11(4):455.
[30]	LIU H H,WANG J W,LI L,et al.Transcriptome analysis revealed the possible regulatory pathways initiating female geese broodiness within the hypothalamic-pituitary-gonadal axis[J].PLoS One,2018,13(2):e0191213.
[31]	CAO Z,MENG B,FAN R,et al.Comparative proteomic analysis of ovaries from Huoyan geese between pre-laying and laying periods using an iTRAQ-based approach[J].Poult Sci,2018,97(6):2170-2182.
[32]	张泽宾.利用全基因组重测序研究家鸭驯化的选择信号及驯化时间[D].北京:中国农业大学,2018.ZHANG Z B.Whole-genome resequencing reveals signatures of selection and timing of duck domestication[D]. Beijing:China Agricultural University,2018.(in Chinese)
[33]	刘杰.利用高通量测序技术挖掘影响鸡剩余采食量的遗传变异和功能基因[D].北京:中国农业科学院,2017.LIU J.Exploring genomic variants and genes related to residual feed intake in chickens by high-throughput sequencing[D].Beijing:Chinese Academy of Agricultural Sciences,2017.(in Chinese)
[34]	章双杰,王靖,杨建生,等.长江下游地区地方鸭种全基因组序列测定及遗传多样性分析[J].中国家禽,2016,38(23):5-9.ZHANG S J,WANG J,YANG J S,et al.Analysis on complete genome sequencing and genetic diversity of native duck breeds in the lower reaches of Yangtze River[J].China Poultry,2016,38(23):5-9.(in Chinese)
[35]	RADWAN L M.Genetic improvement of egg laying traits in Fayoumi chickens bred under conditions of heat stress through selection and gene expression studies[J].J Therm Biol,2020,89:102546.
[36]	WOLC A,JANKOWSKI T,ARANGO J,et al.Investigating the genetic determination of clutch traits in laying hens[J].Poult Sci,2019,98(1):39-45.
[37]	ROSIŃSKI A,NOWACZEWSKI S,KONTECKA H,et al.Analysis of the laying rhythm and reproductive traits of geese[J].Folia Biol (Krakow),2006,54(3-4):145-152.
[38]	DUBOIS E A,ZANDBERGEN M A,PEUTE J,et al.Evolutionary development of three gonadotropin-releasing hormone (GnRH) systems in vertebrates[J].Brain Res Bull,2002,57(3-4):413-418.
[39]	胡彦竞科,张克山,钟航,等.鹅GnIH基因多态性及其与产蛋量的关联性研究[J].中国畜牧杂志,2016,52(21):17-19,104.HUYAN J K,ZHANG K S,ZHONG H,et al.Study on GnIH gene polymorphism of goose and its association with egg production[J].Chinese Journal of Animal Science,2016,52(21):17-19,104.(in Chinese)
[40]	GOFFIN V,BINART N,TOURAINE P,et al.Prolactin:the new biology of an old hormone[J].Annu Rev Physiol, 2002, 64:47-67.
[41]	郭军,汤青萍,章双杰,等.利用抑制消减杂交技术筛选鹅就巢行为相关基因[J].畜牧兽医学报,2011,42(10):1477-1484.GUO J,TANG Q P,ZHANG S J,et al.Identification of broodiness-related geese genes by suppression subtractive hybridization[J].Acta Veterinaria et Zootechnica Sinica,2011,42(10):1477-1484.(in Chinese)
[42]	张响英,唐现文,王利刚,等.实时荧光定量RT-PCR检测狮头鹅繁殖周期中PRL mRNA的表达[J].江苏农业科学,2012,40(9):50-52.ZHANG X Y,TANG X W,WANG L G,et al.Real-time fluorescence quantitative RT-PCR detection of PRL mRNA expression during the reproductive cycle of lion head goose[J].Jiangsu Agricultural Sciences,2012,40(9):50-52.(in Chinese)
[43]	张克山,胡彦竞科,韩笑哲,等.鹅不同繁殖时期GnRH和GnIH基因表达和激素浓度变化分析[J].畜牧兽医学报,2016,47(8):1720-1726.ZHANG K S,HUYAN J K,HAN X Z,et al.Analysis of the serum concentrations and mRNA expression levels of GnRH and GnIH in geese during different reproductive periods[J].Acta Veterinaria et Zootechnica Sinica,2016, 47(8):1720-1726.(in Chinese)
[44]	贾汝敏,吴慧英,刘铀,等.狮头鹅PRL基因的克隆及原核表达[J].畜牧兽医学报,2011,42(3):343-348.JIA R M,WU H Y,LIU Y,et al.Cloning and prokaryotic expression of PRL gene in Shitou Goose[J].Acta Veterinaria et Zootechnica Sinica,2011,42(3):343-348.(in Chinese)
[45]	CHEN J,LIU H L,CAI Y F,et al.Mutations in the exon 10 of prolactin receptor gene change the egg production performance in Wanjiang white goose[J].Mol Biol Rep,2012,39(1):475-483.
[46]	XIAO Y Q,NI Y D,HUANG Y B,et al.Effects of kisspeptin-10 on progesterone secretion in cultured chicken ovarian granulosa cells from preovulatory (F1-F3) follicles[J].Peptides,2011,32(10):2091-2097.