跳转到内容

连续性纯合片段：修订间差异

维基百科，自由的百科全书
以互动方式浏览历史
←上一版本下一版本→
删除的内容 添加的内容
可视化wikitext
小 Heihaheihaha移动页面User:Heihaheihaha/沙盒至连续性纯合片段：​发布草稿：​移出沙盒
内容扩充 增加或调整参考来源 调整格式、排版 修正笔误
第3行： 第3行：
| doi-access = free }}</ref><ref>{{Cite journal |last=Chen |first=Chujie |last2=Zhu |first2=Bo |last3=Tang |first3=Xiangwei |last4=Chen |first4=Bin |last5=Liu |first5=Mei |last6=Gao |first6=Ning |last7=Li |first7=Sheng |last8=Gu |first8=Jingjing |date=2023-06 |title=Genome-Wide Assessment of Runs of Homozygosity by Whole-Genome Sequencing in Diverse Horse Breeds Worldwide |url=https://www.mdpi.com/2073-4425/14/6/1211 |journal= |language=en |volume=14 |issue=6 |doi=10.3390/genes14061211 |issn=2073-4425 |al=genes |access-date=2024-01-24 |archive-date=2023-07-23 |archive-url=https://web.archive.org/web/20230723090356/https://www.mdpi.com/2073-4425/14/6/1211 |dead-url=no }}</ref>
| doi-access = free }}</ref><ref>{{Cite journal |last=Chen |first=Chujie |last2=Zhu |first2=Bo |last3=Tang |first3=Xiangwei |last4=Chen |first4=Bin |last5=Liu |first5=Mei |last6=Gao |first6=Ning |last7=Li |first7=Sheng |last8=Gu |first8=Jingjing |date=2023-06 |title=Genome-Wide Assessment of Runs of Homozygosity by Whole-Genome Sequencing in Diverse Horse Breeds Worldwide |url=https://www.mdpi.com/2073-4425/14/6/1211 |journal= |language=en |volume=14 |issue=6 |doi=10.3390/genes14061211 |issn=2073-4425 |al=genes |access-date=2024-01-24 |archive-date=2023-07-23 |archive-url=https://web.archive.org/web/20230723090356/https://www.mdpi.com/2073-4425/14/6/1211 |dead-url=no }}</ref>


高于特定长度连续性纯合片段在常染色体基因组的比例，称为''F<sub>roh</sub>''，可用于预测或估计一个亚群的个体[[Autozygosity|自合性]]的潜力，可用作[[近交系数]]<ref>{{Cite journal |last=胡 |first=紫平 |title=基于基因组SNP和ROH的剑白香猪群体遗传结构解析 |url=https://doi.org/10.11843/j.issn.0366-6964.2023.10.011 |journal=畜牧兽医学报 |page=4117-4125 |doi=10.11843/j.issn.0366-6964.2023.10.011 |access-date=2024-1-24 |via=中国知网}}</ref>。''<ref>{{cite journal |display-authors=6 |vauthors=McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, Macleod AK, Farrington SM, Rudan P, Hayward C, Vitart V, Rudan I, Wild SH, Dunlop MG, Wright AF, Campbell H, Wilson JF |date=September 2008 |title=Runs of homozygosity in European populations |journal=American Journal of Human Genetics |volume=83 |issue=3 |pages=359–72 |doi=10.1016/j.ajhg.2008.08.007 |pmc=2556426 |pmid=18760389}}</ref>''
高于特定长度连续性纯合片段在常染色体基因组的比例，称为''F<sub>ROH</sub>''，可用于预测或估计一个亚群的个体[[Autozygosity|自合性]]的潜力，可用作[[近交系数]]<ref>{{Cite journal |last=胡 |first=紫平 |title=基于基因组SNP和ROH的剑白香猪群体遗传结构解析 |url=https://doi.org/10.11843/j.issn.0366-6964.2023.10.011 |journal=畜牧兽医学报 |page=4117-4125 |doi=10.11843/j.issn.0366-6964.2023.10.011 |access-date=2024-1-24 |via=中国知网}}</ref>。''<ref>{{cite journal |display-authors=6 |vauthors=McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, Smolej-Narancic N, Janicijevic B, Polasek O, Tenesa A, Macleod AK, Farrington SM, Rudan P, Hayward C, Vitart V, Rudan I, Wild SH, Dunlop MG, Wright AF, Campbell H, Wilson JF |date=September 2008 |title=Runs of homozygosity in European populations |journal=American Journal of Human Genetics |volume=83 |issue=3 |pages=359–72 |doi=10.1016/j.ajhg.2008.08.007 |pmc=2556426 |pmid=18760389}}</ref>''

== 影响因素 ==
对于较大的种群，通常具有较短的ROH，而对于封闭的或孤立的或规模较小的或是近亲繁殖的种群，则具有较长的ROH。在人类中，有研究认为美洲原住民可能拥有世界上最高的ROH负担。ROH在人类基因组中普遍存在。<ref>{{Cite journal |last=Ceballos |first=Francisco C. |last2=Joshi |first2=Peter K. |last3=Clark |first3=David W. |last4=Ramsay |first4=Michèle |last5=Wilson |first5=James F. |date=2018-04 |title=Runs of homozygosity: windows into population history and trait architecture |url=https://www.nature.com/articles/nrg.2017.109 |journal=Nature Reviews Genetics |language=en |volume=19 |issue=4 |doi=10.1038/nrg.2017.109 |issn=1471-0056}}</ref>

较早的一些研究认为，非遗传因素也可能对ROH的水平产生影响，如受教育水平<ref name=":0">{{Cite journal |last=Abdellaoui |first=Abdel |last2=Hottenga |first2=Jouke-Jan |last3=Willemsen |first3=Gonneke |last4=Bartels |first4=Meike |last5=Beijsterveldt |first5=Toos van |last6=Ehli |first6=Erik A. |last7=Davies |first7=Gareth E. |last8=Brooks |first8=Andrew |last9=Sullivan |first9=Patrick F. |last10=Penninx |first10=Brenda W. J. H. |last11=Geus |first11=Eco J. de |date=2015-03-03 |title=Educational Attainment Influences Levels of Homozygosity through Migration and Assortative Mating |url=https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0118935 |journal=PLOS ONE |language=en |volume=10 |issue=3 |doi=10.1371/journal.pone.0118935 |issn=1932-6203 |pmc=PMC4347978 |pmid=25734509}}</ref><ref>{{Cite journal |last=The BioBank Japan Project |last2=Joshi |first2=Peter K. |last3=Esko |first3=Tonu |last4=Mattsson |first4=Hannele |last5=Eklund |first5=Niina |last6=Gandin |first6=Ilaria |last7=Nutile |first7=Teresa |last8=Jackson |first8=Anne U. |last9=Schurmann |first9=Claudia |last10=Smith |first10=Albert V. |last11=Zhang |first11=Weihua |date=2015-07 |title=Directional dominance on stature and cognition in diverse human populations |url=https://www.nature.com/articles/nature14618 |journal=Nature |language=en |volume=523 |issue=7561 |doi=10.1038/nature14618 |issn=0028-0836 |pmc=PMC4516141 |pmid=26131930}}</ref>，这可能和受过高等教育的人更有可能移民有关<ref name=":0" />。之后的一项研究则否认非遗传因素对ROH的影响。<ref>{{Cite journal |last=Clark |first=David W |last2=Okada |first2=Yukinori |last3=Moore |first3=Kristjan H S |last4=Mason |first4=Dan |last5=Pirastu |first5=Nicola |last6=Gandin |first6=Ilaria |last7=Mattsson |first7=Hannele |last8=Barnes |first8=Catriona L K |last9=Lin |first9=Kuang |last10=Zhao |first10=Jing Hua |last11=Deelen |first11=Patrick |date=2019-10-31 |title=Associations of autozygosity with a broad range of human phenotypes |url=https://www.nature.com/articles/s41467-019-12283-6 |journal=Nature Communications |language=en |volume=10 |issue=1 |doi=10.1038/s41467-019-12283-6 |issn=2041-1723 |pmc=PMC6823371 |pmid=31673082}}</ref>

== 检测方法 ==

=== 观察基因型计数 ===
PLINK等工具等的算法在基因分型（genotyped）后全基因组SNP（SNVs）数据或是SNP微阵列的数据中，沿染色体长度移动固定大小的窗口来扫描每条染色体，如果一个窗口内的纯合SNPs的比例高于预设值，则认定为ROH。<ref>{{Cite journal |last=Purcell |first=Shaun |last2=Neale |first2=Benjamin |last3=Todd-Brown |first3=Kathe |last4=Thomas |first4=Lori |last5=Ferreira |first5=Manuel A.R. |last6=Bender |first6=David |last7=Maller |first7=Julian |last8=Sklar |first8=Pamela |last9=de Bakker |first9=Paul I.W. |last10=Daly |first10=Mark J. |last11=Sham |first11=Pak C. |date=2007-09 |title=PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses |url=https://linkinghub.elsevier.com/retrieve/pii/S0002929707613524 |journal=The American Journal of Human Genetics |language=en |volume=81 |issue=3 |doi=10.1086/519795 |pmc=PMC1950838 |pmid=17701901}}</ref>


== 应用 ==
== 应用 ==

2024年1月26日 (五) 03:31的版本

连续性纯合片段 (Runs of homozygosity, ROH)[1] 是来自共同祖先的相同单倍型遗传产生的长段纯合基因型。[2][3]

高于特定长度连续性纯合片段在常染色体基因组的比例，称为FROH，可用于预测或估计一个亚群的个体自合性的潜力，可用作近交系数[4]。[5]

影响因素

对于较大的种群，通常具有较短的ROH，而对于封闭的或孤立的或规模较小的或是近亲繁殖的种群，则具有较长的ROH。在人类中，有研究认为美洲原住民可能拥有世界上最高的ROH负担。ROH在人类基因组中普遍存在。[6]

较早的一些研究认为，非遗传因素也可能对ROH的水平产生影响，如受教育水平[7][8]，这可能和受过高等教育的人更有可能移民有关[7]。之后的一项研究则否认非遗传因素对ROH的影响。[9]

检测方法

观察基因型计数

PLINK等工具等的算法在基因分型（genotyped）后全基因组SNP（SNVs）数据或是SNP微阵列的数据中，沿染色体长度移动固定大小的窗口来扫描每条染色体，如果一个窗口内的纯合SNPs的比例高于预设值，则认定为ROH。[10]

应用

该技术可以用来识别保护生物学中的近亲繁殖的基因组足迹，因为最近经历近亲繁殖后的生物将表现出较长的纯合片段。例如，在瑞士阿尔卑斯山分步骤重新引入阿尔卑斯羱羊（Capra ibex）的策略造成了数个严重的种群瓶颈，降低了新引入群体的遗传多样性。可以通过测量不同个体的连续性纯合片段来研究近亲繁殖对亚群所产生的影响。[11]

参考文献

  1. ^ 孙, 丽侠. ROH及其在绵羊遗传育种中的应用研究进展. China Animal Husbandry & Veterinary Medicine. 2023-08-023, 50 (08): 3258-3266 [2024-1-24]. doi:10.16431/j.cnki.1671-7236.2023.08.023. （原始内容存档于2024-01-24） –通过中国知网. 
  2. ^ Purfield DC, Berry DP, McParland S, Bradley DG. Runs of homozygosity and population history in cattle. BMC Genetics. August 2012, 13: 70. PMC 3502433 可免费查阅. PMID 22888858. doi:10.1186/1471-2156-13-70 可免费查阅. 
  3. ^ Chen, Chujie; Zhu, Bo; Tang, Xiangwei; Chen, Bin; Liu, Mei; Gao, Ning; Li, Sheng; Gu, Jingjing. Genome-Wide Assessment of Runs of Homozygosity by Whole-Genome Sequencing in Diverse Horse Breeds Worldwide 14 (6). 2023-06 [2024-01-24]. ISSN 2073-4425. doi:10.3390/genes14061211. （原始内容存档于2023-07-23） （英语）.  已忽略未知参数|al= (帮助)
  4. ^ 胡, 紫平. 基于基因组SNP和ROH的剑白香猪群体遗传结构解析. 畜牧兽医学报: 4117-4125. [2024-1-24]. doi:10.11843/j.issn.0366-6964.2023.10.011 –通过中国知网. 
  5. ^ McQuillan R, Leutenegger AL, Abdel-Rahman R, Franklin CS, Pericic M, Barac-Lauc L, et al. Runs of homozygosity in European populations. American Journal of Human Genetics. September 2008, 83 (3): 359–72. PMC 2556426 可免费查阅. PMID 18760389. doi:10.1016/j.ajhg.2008.08.007. 
  6. ^ Ceballos, Francisco C.; Joshi, Peter K.; Clark, David W.; Ramsay, Michèle; Wilson, James F. Runs of homozygosity: windows into population history and trait architecture. Nature Reviews Genetics. 2018-04, 19 (4). ISSN 1471-0056. doi:10.1038/nrg.2017.109 （英语）. 
  7. ^ 7.0 7.1 Abdellaoui, Abdel; Hottenga, Jouke-Jan; Willemsen, Gonneke; Bartels, Meike; Beijsterveldt, Toos van; Ehli, Erik A.; Davies, Gareth E.; Brooks, Andrew; Sullivan, Patrick F.; Penninx, Brenda W. J. H.; Geus, Eco J. de. Educational Attainment Influences Levels of Homozygosity through Migration and Assortative Mating. PLOS ONE. 2015-03-03, 10 (3). ISSN 1932-6203. PMC 4347978 可免费查阅. PMID 25734509. doi:10.1371/journal.pone.0118935 （英语）. 
  8. ^ The BioBank Japan Project; Joshi, Peter K.; Esko, Tonu; Mattsson, Hannele; Eklund, Niina; Gandin, Ilaria; Nutile, Teresa; Jackson, Anne U.; Schurmann, Claudia; Smith, Albert V.; Zhang, Weihua. Directional dominance on stature and cognition in diverse human populations. Nature. 2015-07, 523 (7561). ISSN 0028-0836. PMC 4516141 可免费查阅. PMID 26131930. doi:10.1038/nature14618 （英语）. 
  9. ^ Clark, David W; Okada, Yukinori; Moore, Kristjan H S; Mason, Dan; Pirastu, Nicola; Gandin, Ilaria; Mattsson, Hannele; Barnes, Catriona L K; Lin, Kuang; Zhao, Jing Hua; Deelen, Patrick. Associations of autozygosity with a broad range of human phenotypes. Nature Communications. 2019-10-31, 10 (1). ISSN 2041-1723. PMC 6823371 可免费查阅. PMID 31673082. doi:10.1038/s41467-019-12283-6 （英语）. 
  10. ^ Purcell, Shaun; Neale, Benjamin; Todd-Brown, Kathe; Thomas, Lori; Ferreira, Manuel A.R.; Bender, David; Maller, Julian; Sklar, Pamela; de Bakker, Paul I.W.; Daly, Mark J.; Sham, Pak C. PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses. The American Journal of Human Genetics. 2007-09, 81 (3). PMC 1950838 可免费查阅. PMID 17701901. doi:10.1086/519795 （英语）. 
  11. ^ Grossen C, Biebach I, Angelone- Alasaad S, Keller LF, Croll D. Population genomics analyses of European ibex species show lower diversity and higher inbreeding in reintroduced populations Evol Appl. 2018;11: 123–139.. Evolutionary Applications. 2018, 11 (2): 123–139. PMC 5775499 可免费查阅. PMID 29387150. doi:10.1111/eva.12490. 
取自“https://zh.wikipedia.org/w/index.php?title=连续性纯合片段&oldid=80655452”