绒山羊Y染色体的BAC筛选、鉴定与序列分析
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摘要
绒山羊是经过若干世纪的自然选择与人工选育，逐步分化出的、分布于特定生态环境中的山羊品种，具有多种用途及极高的经济价值，是重要的家畜资源，其所产羊绒稀有而珍贵。但目前，由于绒山羊生存环境逐步恶化，其生长发育受到生态条件制约，良种化程度较低、优质种羊匮乏，而且羊绒品质下降。因此，加强绒山羊优良基因的保护、提高繁殖力、增加羊绒产量、提高羊绒品质成为迫切的任务。
雄性绒山羊在繁殖中具有重要的作用，不仅具有繁殖能力，而且产绒量也较高。所以，大力培育良种种公羊势在必行。而种公羊的培育和繁殖主要取决于Y染色体上分布的许多与繁殖性状相关基因的作用机制。由于至今还没有完成山羊Y染色体测序工作，因此，繁殖相关基因的作用机制无法清楚地了解。
为此，本研究通过PCR技术对绒山羊基因组BAC文库进行了Y染色体序列的筛选、FISH鉴定和测序组装及序列分析，主要结果如下：
1.本研究通过PCR技术从绒山羊基因组BAC文库中筛选出10个BAC，经克隆测序和BAC末端测序比对初步确定为绒山羊Y染色体BAC。
2.利用FISH技术对614B22、516O16、405D22及570A194个BAC进行了Y染色体的进一步鉴定，从而确定其为Y染色体BAC。
3.应用软件对4个BAC进行测序拼接，得到contig335个，其中614B22103个，516O16135个，405D2267个，570A1930个；scaffold314个，其中614B2298个，516O16126个，405D2262个，570A1928个。4个BAC中516O16最长，405D22最短。
4.对570A19和516O16两个BAC部分序列的转录因子起始位点和结合位点进行预测，分别得到了4个和1个起始位点、多个结合位点及转录结合因子。
5.预测到570A19和516O16两个BAC具有多个ORF，而且通过蛋白质编码序列比对，确定其分别为TSPY和USP9Y蛋白编码框。
6.对所有编码框进行蛋白质结构域预测，570A19只预测到一个保守的跨膜螺旋区域；516O16预测到一个保守的跨膜螺旋区域和一个高度保守的结构域-UCH，表明TSPY和USP9Y基因在物种间的保守性较低。
7. TSPY和USP9Y蛋白质的三级结构预测显示，两种蛋白三级结构均由多个α螺旋和β-折叠组成。
8. USP9Y基因的进化树表明，绒山羊、牛、人、恒河猴、狐猴等9个物种间的亲缘关系同其在分类学中的位置基本一致，其中绒山羊与牛的亲缘关系最近，聚为一类。
此研究为后续深入研究绒山羊Y染色体基因功能、时空调控及基因间的相互关系，进一步促进绒山羊遗传资源的保护利用、实施性别控制、缩短公羊选育时间和提高其生产效率提供理论依据。
After several centuries of natural selection and artificial selection, Cashmere goatis differentiated gradually from a goat variety and lives in a specific ecologicalenvironment. It has kinds of uses and high economic value, and has become animportant livestock resource, which it can produce rare and valuable cashmere. Atpresent, because of the gradual deterioration of the survival environment, the growthand development of cashmere goat are restricted by the ecological conditions.Thisleads to the lower degree of improved varieties, lack of high-quality stud and declinedcashmere quality. Therefore, the urgent task is to strengthen the good gene protectionof the cashmere goat, improve breeding force, increase cashmere production andimprove cashmere quality.
Male cashmere goat plays an important role in the process of breeding.Not onlyit has the ability to reproduce, but also has higher cashmere yield. So, cultivating goodrams vigorously is necessary.However, ram breeding capacity mainly depends on themechanism of the genes related to reproductive traits on the Y chromosome. Becausegoat Y chromosome sequencing work has not completed, the mechanism of the genesrelated to reproduction can not be clearly understood.
We screened Y chromosome sequences in cashmere goat genomic BAC libraryby PCR, identified Y chromosome sequences by FISH tecnology, assembled andanalysized sequences in this study, the main results are as follows:
1.10BACs are screened out from cashmere goat genomic BAC library by PCRand identified, cloned and sequenced. At last,they are initially identified as cashmeregoat Y chromosome BAC in this study.
2.614B22,516O16,405D22and570A19BAC are further mapped to cashmeregoat Y chromosome by FISH.
3. After four BACs original sequencing data was first assebled by software,weobtained335contigs.103contigs of them are from614B22,135contigs are from516O16,67contigs contigs are from405D22and30contigs are from570A19. Andwe obtained314scaffolds too,98scaffolds of them are from614B22,126scaffoldsare from516O16,62scaffolds are from405D22and28scaffolds are from570A19.The sequence length of516O16BAC is the longest,while405D22BAC isthe shortest.
4. Predicting the start site and the binding sites of the transcription factor ofpartial sequences of570A19BAC and516O16BAC,we obtained four start sites anda start site and many binding sites and transcription binding factors respectively.
5. Both570A19BAC and516O16BAC have multiple ORFs predicted.By theprotein-coding sequences alignment, we determined they are TSPY and USP9Yprotein coding frame respectively.
6. The protein structure domains are searched in all coding frames and a conserved transmembrane helix region in570A19is only predicted and a conservedtransmembrane helix region and a highly conserved domain-UCH are in516O16. Itshowed TSPY and USP9Y are less conserved among the species.
7. TSPY and USP9Y protein tertiary structure prediction showed that both ofthem are composed of multiple α-helix and β-fold.
8. NJ phylogenetic tree based on USP9Y genes showed that the kinships of goat,cattle, homo sapiens,macaca mulutta,eulemur fulus and other species are consistentwith the positions in the taxonomy，and cashmere goat and cattle are the closestgenetic relation and belong to a class.
This research provided a theoretical basis for follow-up in-depth study oncashmere goat Y chromosome gene function, regulation of time and space, therelationships of genes and further promoting cashmere goat genetic resourceprotection and utilization,implementing sex control,shortening the ram breeding timeand improving its production efficiency.
雄性绒山羊在繁殖中具有重要的作用，不仅具有繁殖能力，而且产绒量也较高。所以，大力培育良种种公羊势在必行。而种公羊的培育和繁殖主要取决于Y染色体上分布的许多与繁殖性状相关基因的作用机制。由于至今还没有完成山羊Y染色体测序工作，因此，繁殖相关基因的作用机制无法清楚地了解。
为此，本研究通过PCR技术对绒山羊基因组BAC文库进行了Y染色体序列的筛选、FISH鉴定和测序组装及序列分析，主要结果如下：
1.本研究通过PCR技术从绒山羊基因组BAC文库中筛选出10个BAC，经克隆测序和BAC末端测序比对初步确定为绒山羊Y染色体BAC。
2.利用FISH技术对614B22、516O16、405D22及570A194个BAC进行了Y染色体的进一步鉴定，从而确定其为Y染色体BAC。
3.应用软件对4个BAC进行测序拼接，得到contig335个，其中614B22103个，516O16135个，405D2267个，570A1930个；scaffold314个，其中614B2298个，516O16126个，405D2262个，570A1928个。4个BAC中516O16最长，405D22最短。
4.对570A19和516O16两个BAC部分序列的转录因子起始位点和结合位点进行预测，分别得到了4个和1个起始位点、多个结合位点及转录结合因子。
5.预测到570A19和516O16两个BAC具有多个ORF，而且通过蛋白质编码序列比对，确定其分别为TSPY和USP9Y蛋白编码框。
6.对所有编码框进行蛋白质结构域预测，570A19只预测到一个保守的跨膜螺旋区域；516O16预测到一个保守的跨膜螺旋区域和一个高度保守的结构域-UCH，表明TSPY和USP9Y基因在物种间的保守性较低。
7. TSPY和USP9Y蛋白质的三级结构预测显示，两种蛋白三级结构均由多个α螺旋和β-折叠组成。
8. USP9Y基因的进化树表明，绒山羊、牛、人、恒河猴、狐猴等9个物种间的亲缘关系同其在分类学中的位置基本一致，其中绒山羊与牛的亲缘关系最近，聚为一类。
此研究为后续深入研究绒山羊Y染色体基因功能、时空调控及基因间的相互关系，进一步促进绒山羊遗传资源的保护利用、实施性别控制、缩短公羊选育时间和提高其生产效率提供理论依据。
After several centuries of natural selection and artificial selection, Cashmere goatis differentiated gradually from a goat variety and lives in a specific ecologicalenvironment. It has kinds of uses and high economic value, and has become animportant livestock resource, which it can produce rare and valuable cashmere. Atpresent, because of the gradual deterioration of the survival environment, the growthand development of cashmere goat are restricted by the ecological conditions.Thisleads to the lower degree of improved varieties, lack of high-quality stud and declinedcashmere quality. Therefore, the urgent task is to strengthen the good gene protectionof the cashmere goat, improve breeding force, increase cashmere production andimprove cashmere quality.
Male cashmere goat plays an important role in the process of breeding.Not onlyit has the ability to reproduce, but also has higher cashmere yield. So, cultivating goodrams vigorously is necessary.However, ram breeding capacity mainly depends on themechanism of the genes related to reproductive traits on the Y chromosome. Becausegoat Y chromosome sequencing work has not completed, the mechanism of the genesrelated to reproduction can not be clearly understood.
We screened Y chromosome sequences in cashmere goat genomic BAC libraryby PCR, identified Y chromosome sequences by FISH tecnology, assembled andanalysized sequences in this study, the main results are as follows:
1.10BACs are screened out from cashmere goat genomic BAC library by PCRand identified, cloned and sequenced. At last,they are initially identified as cashmeregoat Y chromosome BAC in this study.
2.614B22,516O16,405D22and570A19BAC are further mapped to cashmeregoat Y chromosome by FISH.
3. After four BACs original sequencing data was first assebled by software,weobtained335contigs.103contigs of them are from614B22,135contigs are from516O16,67contigs contigs are from405D22and30contigs are from570A19. Andwe obtained314scaffolds too,98scaffolds of them are from614B22,126scaffoldsare from516O16,62scaffolds are from405D22and28scaffolds are from570A19.The sequence length of516O16BAC is the longest,while405D22BAC isthe shortest.
4. Predicting the start site and the binding sites of the transcription factor ofpartial sequences of570A19BAC and516O16BAC,we obtained four start sites anda start site and many binding sites and transcription binding factors respectively.
5. Both570A19BAC and516O16BAC have multiple ORFs predicted.By theprotein-coding sequences alignment, we determined they are TSPY and USP9Yprotein coding frame respectively.
6. The protein structure domains are searched in all coding frames and a conserved transmembrane helix region in570A19is only predicted and a conservedtransmembrane helix region and a highly conserved domain-UCH are in516O16. Itshowed TSPY and USP9Y are less conserved among the species.
7. TSPY and USP9Y protein tertiary structure prediction showed that both ofthem are composed of multiple α-helix and β-fold.
8. NJ phylogenetic tree based on USP9Y genes showed that the kinships of goat,cattle, homo sapiens,macaca mulutta,eulemur fulus and other species are consistentwith the positions in the taxonomy，and cashmere goat and cattle are the closestgenetic relation and belong to a class.
This research provided a theoretical basis for follow-up in-depth study oncashmere goat Y chromosome gene function, regulation of time and space, therelationships of genes and further promoting cashmere goat genetic resourceprotection and utilization,implementing sex control,shortening the ram breeding timeand improving its production efficiency.
引文
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