全基因組掃描篩選德保矮馬矮小性狀相關(guān)候選基因研究
發(fā)布時(shí)間：2019-06-09 20:41
【摘要】：德保矮馬分布于我國(guó)南方廣西山區(qū)的體型顯著矮小的馬品種,是全世界矮馬品種里比較古老的矮馬資源之一。它的矮小體型是長(zhǎng)期馴化過(guò)程中人類(lèi)的定向培育和適應(yīng)自然環(huán)境的結(jié)果。對(duì)德保矮馬來(lái)說(shuō),矮小體型是適應(yīng)山路托運(yùn)的優(yōu)勢(shì)性狀,因此對(duì)德保矮馬的長(zhǎng)期培育和保護(hù)十分重要。目前,對(duì)德保矮馬的歷史起源以及矮小性的分子遺傳機(jī)理的研究起步比較晚,尤其是在基因組水平上研究報(bào)道極為稀少。本研究利用馬高密度基因芯片(GeneSeek Equine SNP 65K)對(duì)中國(guó)體高差異較大的三個(gè)品種(德保矮馬,蒙古馬,伊犁馬)進(jìn)行選擇信號(hào)篩選,單拷貝序列(CNV)以及體高關(guān)聯(lián)分析研究。同時(shí)整合了來(lái)32個(gè)國(guó)外馬品種729個(gè)個(gè)體的50K基因芯片分型數(shù)據(jù)。進(jìn)一步確認(rèn)了德保矮馬與國(guó)外馬品種系統(tǒng)進(jìn)化關(guān)系以及對(duì)矮小性狀的遺傳機(jī)理提供了分子遺傳學(xué)依據(jù)。本研究利用普氏野馬做為外群,構(gòu)建國(guó)內(nèi)外馬品種的進(jìn)化樹(shù),結(jié)果發(fā)現(xiàn)中國(guó)三個(gè)馬品種在進(jìn)化樹(shù)上形成獨(dú)立的分支。從遺傳距離來(lái)看中國(guó)馬品種和國(guó)外蒙古馬比較近。這對(duì)理解中國(guó)三個(gè)馬品種系統(tǒng)進(jìn)化提供了分子基礎(chǔ)。為進(jìn)一步了解中國(guó)三個(gè)馬品種和國(guó)外32個(gè)馬品種之間的系統(tǒng)發(fā)生關(guān)系以及群體遺傳結(jié)構(gòu)情況同樣進(jìn)行主成分分析(PCA)和遺傳結(jié)構(gòu)分析,發(fā)現(xiàn)中國(guó)馬品種和國(guó)外蒙古馬及北西伯利亞(TUVA)馬聚在一起屬于古老的小型馬品種。連鎖不平衡分析結(jié)果也支持了中國(guó)馬屬于比較古老品種。為了解中國(guó)三個(gè)馬品種遺傳關(guān)系和遺傳結(jié)構(gòu),進(jìn)行主成分分析(PCA)和遺傳結(jié)構(gòu)分析。結(jié)果顯示德保矮馬與其它兩個(gè)中國(guó)馬品種(伊犁馬和蒙古馬)明顯分離。說(shuō)明德保矮馬遺傳背景與中國(guó)這兩個(gè)馬品種有比較大的差別。本研究在中國(guó)三個(gè)馬品種全基因組上通過(guò)基于群體分化系數(shù)FST為基礎(chǔ)的di分析,基于單倍型為基礎(chǔ)的XP-EHH分析以及德保矮馬與伊犁馬體高全基因組關(guān)聯(lián)分析(GWAS),在德保矮馬基因組上分別檢測(cè)到523個(gè)和505個(gè)顯著的di和XP-EHH值的選擇信號(hào)位點(diǎn)。結(jié)合兩種方法篩選到了與體高顯著相關(guān)的SNP位點(diǎn)進(jìn)行關(guān)聯(lián)分析。最終篩選了與體高顯著相關(guān)的22個(gè)SNP位點(diǎn)。通過(guò)基因注釋確認(rèn)了兩個(gè)候選基因HMGA2和TBX3基因與德保矮馬體高顯著相關(guān)。其中HMGA2基因是以前人和馬研究中報(bào)道過(guò)的體高相關(guān)的基因,但是TBX3基因在國(guó)外馬品種沒(méi)有報(bào)道過(guò)。并且我們沒(méi)有檢測(cè)到德保矮馬與國(guó)外矮馬的基因交流情況。因此,我們認(rèn)為德保矮馬很可能經(jīng)歷了與國(guó)外矮馬不同的獨(dú)立的矮化馴化過(guò)程。說(shuō)明德保矮馬矮小性分子遺傳機(jī)理不同于國(guó)外矮馬品種。本研究將會(huì)為世界矮馬矮小遺傳機(jī)理解提供一些新的分子證據(jù)。最近研究表明尋找直接影響個(gè)體表型差異的DNA變異的研究中,僅關(guān)注單核苷酸多態(tài)性(SNPs)是不夠的,在基因組中有重要功能意義的變異還有其他形式,如拷貝數(shù)變異(copy number variation,CNV)。我們?cè)诘卤０R以及其他國(guó)內(nèi)兩個(gè)品種馬全基因組水平上進(jìn)行單拷貝序列(CNV)多態(tài)性分析,發(fā)現(xiàn)只有在11號(hào)染色上包含生長(zhǎng)發(fā)育相關(guān)基因的CNVR。這可能與我們檢測(cè)CNV方法的單一性或者芯片密度的限制檢測(cè)不到更多的CNVR的原因。將來(lái)更高密度芯片以及重測(cè)序技術(shù)的開(kāi)發(fā)會(huì)進(jìn)一步發(fā)現(xiàn)在德保矮馬體高相關(guān)CNVR的可能。綜上所述,本研究發(fā)現(xiàn)德保矮馬體高相關(guān)正向選擇位點(diǎn)與國(guó)外馬品種選擇位點(diǎn)有所不同。說(shuō)明德保矮馬矮小性可能存在獨(dú)立的的分子遺傳學(xué)機(jī)理。
[Abstract]:The dwarf horse of Debao is a kind of large and small horse variety in the mountainous area of Guangxi, and is one of the ancient dwarf horse resources in the world's short horse variety. Its short stature is the result of the directional cultivation and adaptation of the natural environment in the process of long-term domestication. The short stature is the dominant character to adapt to the consignment of the mountain road, so it is very important for the long-term cultivation and protection of the Dwara. At present, the research on the historical origin and the molecular genetic mechanism of the dwarf horse is relatively late, especially at the genomic level. In this study, the selection signal screening, single copy sequence (CNV) and high correlation analysis of three varieties (Debao Dwarf, Mongolian horse and Ili horse) with a large difference in Chinese body height were studied by using a high-density gene chip (Genetek Equine SNP 65K). At the same time, the data of 50 K gene chips of 729 individuals from 32 foreign horses were also integrated. The genetic mechanism of the dwarf horse and the foreign horse variety system is further confirmed, and the molecular genetic basis is provided for the genetic mechanism of the small characters. In this study, the wild Mustang was used as the outer group to construct the wild tree of the horse variety at home and abroad. The results showed that the three horses in China form an independent branch on the evolutionary tree. From the genetic distance, the Chinese horse variety is close to the other Mongolian horse. This provides a molecular basis for understanding the evolution of three Chinese species systems. The main component analysis (PCA) and the genetic structure analysis were also carried out in order to further understand the relationship between the three horses in China and the 32 horses in the country and the genetic structure of the population. It is found that the Chinese horse variety and the overseas Mongolian horse and the North Siberia (TUVA) horse come together to belong to the ancient small-scale horse variety. The results of the linkage disequilibrium analysis also support the Chinese horse as a relatively old variety. In order to understand the genetic relationship and the genetic structure of the three horses in China, the principal component analysis (PCA) and the genetic structure analysis were carried out. The results show that Debao Dwarf is obviously separated from the other two Chinese horse breeds (Ili horse and Mongolian horse). There is a great difference between the genetic background and the two kinds of horses in China. Based on the population differentiation factor (FST) based on the population differentiation factor (FST) based on the population differentiation factor (FST), this study is based on the haplotype-based XP-EHH analysis and the high-genome association analysis (GWAS) of the Debao dwarf horse and the Ili horse. The selection signal sites of 523 and 505 significant di and XP-EHH values were respectively detected on the genome of the Debao Dwarf horse. The association analysis of SNP sites associated with a significant body height was screened in combination with two methods. The 22 SNP sites associated with the body height were finally screened. Two candidate genes, such as HMGA2 and TBX3, were confirmed to be highly correlated with DPPH. The HMGA2 gene is the body-high-related gene reported in the previous human and horse studies, but the TBX3 gene has not been reported in the foreign horse variety. And we didn't have a sense of the gene exchange between Dbao Dwarf and the foreign dwarf. Therefore, we think that Debao Dwarf is very likely to experience a separate, dwarfed, acclimatization process that is different from that of a foreign dwarf. The genetic mechanism of dwarfed dwarf horse is different from that of foreign dwarf horse. The study will provide some new molecular evidence for the understanding of the world's dwarf genetic machine. Recent studies have shown that it is not sufficient to look for DNA variants that directly affect the individual phenotypic differences, and there are other forms, such as copy number variation (CNV), that are important in the genome. We carried out a single copy sequence (CNV) polymorphism analysis on both German and other domestic two breeds, and found that only CNVR with the development-related genes was included in the No.11 staining. This may not be the cause of more CNVR than we can detect the uniformity of the CNV method or the limitation of the chip density. The development of higher density chips and heavy sequencing techniques in the future will further identify the potential for high-related CNVR in Debao dwarfs. In conclusion, the present study found that the highly correlated forward selection site of Densin Dwarf is different from that of the foreign horse. It is suggested that there may be an independent molecular genetic mechanism in the dwarfism of Densin.
【學(xué)位授予單位】：中國(guó)農(nóng)業(yè)科學(xué)院
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2015
【分類(lèi)號(hào)】：S821
本文編號(hào)：2495886
[Abstract]:The dwarf horse of Debao is a kind of large and small horse variety in the mountainous area of Guangxi, and is one of the ancient dwarf horse resources in the world's short horse variety. Its short stature is the result of the directional cultivation and adaptation of the natural environment in the process of long-term domestication. The short stature is the dominant character to adapt to the consignment of the mountain road, so it is very important for the long-term cultivation and protection of the Dwara. At present, the research on the historical origin and the molecular genetic mechanism of the dwarf horse is relatively late, especially at the genomic level. In this study, the selection signal screening, single copy sequence (CNV) and high correlation analysis of three varieties (Debao Dwarf, Mongolian horse and Ili horse) with a large difference in Chinese body height were studied by using a high-density gene chip (Genetek Equine SNP 65K). At the same time, the data of 50 K gene chips of 729 individuals from 32 foreign horses were also integrated. The genetic mechanism of the dwarf horse and the foreign horse variety system is further confirmed, and the molecular genetic basis is provided for the genetic mechanism of the small characters. In this study, the wild Mustang was used as the outer group to construct the wild tree of the horse variety at home and abroad. The results showed that the three horses in China form an independent branch on the evolutionary tree. From the genetic distance, the Chinese horse variety is close to the other Mongolian horse. This provides a molecular basis for understanding the evolution of three Chinese species systems. The main component analysis (PCA) and the genetic structure analysis were also carried out in order to further understand the relationship between the three horses in China and the 32 horses in the country and the genetic structure of the population. It is found that the Chinese horse variety and the overseas Mongolian horse and the North Siberia (TUVA) horse come together to belong to the ancient small-scale horse variety. The results of the linkage disequilibrium analysis also support the Chinese horse as a relatively old variety. In order to understand the genetic relationship and the genetic structure of the three horses in China, the principal component analysis (PCA) and the genetic structure analysis were carried out. The results show that Debao Dwarf is obviously separated from the other two Chinese horse breeds (Ili horse and Mongolian horse). There is a great difference between the genetic background and the two kinds of horses in China. Based on the population differentiation factor (FST) based on the population differentiation factor (FST) based on the population differentiation factor (FST), this study is based on the haplotype-based XP-EHH analysis and the high-genome association analysis (GWAS) of the Debao dwarf horse and the Ili horse. The selection signal sites of 523 and 505 significant di and XP-EHH values were respectively detected on the genome of the Debao Dwarf horse. The association analysis of SNP sites associated with a significant body height was screened in combination with two methods. The 22 SNP sites associated with the body height were finally screened. Two candidate genes, such as HMGA2 and TBX3, were confirmed to be highly correlated with DPPH. The HMGA2 gene is the body-high-related gene reported in the previous human and horse studies, but the TBX3 gene has not been reported in the foreign horse variety. And we didn't have a sense of the gene exchange between Dbao Dwarf and the foreign dwarf. Therefore, we think that Debao Dwarf is very likely to experience a separate, dwarfed, acclimatization process that is different from that of a foreign dwarf. The genetic mechanism of dwarfed dwarf horse is different from that of foreign dwarf horse. The study will provide some new molecular evidence for the understanding of the world's dwarf genetic machine. Recent studies have shown that it is not sufficient to look for DNA variants that directly affect the individual phenotypic differences, and there are other forms, such as copy number variation (CNV), that are important in the genome. We carried out a single copy sequence (CNV) polymorphism analysis on both German and other domestic two breeds, and found that only CNVR with the development-related genes was included in the No.11 staining. This may not be the cause of more CNVR than we can detect the uniformity of the CNV method or the limitation of the chip density. The development of higher density chips and heavy sequencing techniques in the future will further identify the potential for high-related CNVR in Debao dwarfs. In conclusion, the present study found that the highly correlated forward selection site of Densin Dwarf is different from that of the foreign horse. It is suggested that there may be an independent molecular genetic mechanism in the dwarfism of Densin.
【學(xué)位授予單位】：中國(guó)農(nóng)業(yè)科學(xué)院
【學(xué)位級(jí)別】：博士
【學(xué)位授予年份】：2015
【分類(lèi)號(hào)】：S821
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