連續性純合片段

連續性純合片段 (Runs of homozygosity, ROH)^[1] 是來自共同祖先的相同單倍型遺傳產生的長段純合基因型。^[2]^[3]ROH在人類基因組中普遍存在，在非近交人群中也是如此。^[4]

在基因組中，ROH多見於高連鎖不平衡和低重組的區域，這可以用近交缺乏重組打破ROH或是該區域本身高連鎖不平衡而低重組解釋。^[4]

高於特定長度連續性純合片段在常染色體基因組的比例，稱為F_ROH，可用於預測或估計一個亞群的個體自合性的潛力，可用作基因組近交係數（Genomic inbreeding coefficient）^[5]。^[6]

影響因素

對於較大的種群中的個體，其所有的ROH通常較短，而對於封閉的或孤立的或規模較小的或是近親繁殖的種群的個體，則其所有的ROH較長。在人類中，有研究認為美洲原住民可能擁有世界上最高的ROH負擔。^[7]

較早的一些研究認為，非遺傳因素也可能對ROH的水平產生影響，如受教育水平^[8]^[9]，這可能和受過高等教育的人更有可能移民有關^[8]。之後的一項研究則否認非遺傳因素對ROH的影響。^[10]

檢測方法

PLINK等工具等的算法在SNP微陣列的數據中，沿染色體移動固定大小的「窗口」來掃描每條染色體，如果一個窗口內的純合SNPs的比例高於預設值，則認定為ROH；^[11]此外採用隱馬爾可夫模型（HMM）的具有較高計算成本的方法^[7]，綜合考慮血緣同源（IBD）狀態和連鎖不平衡（LD）效應並處理基因型錯誤，使用該算法的軟件有 Beagle^[12]、Garlic^[13]等。

應用

該技術可以用來識別保護生物學中的近親繁殖的基因組足跡，因為最近經歷近親繁殖後的生物將表現出較長的連續性純合片段。例如，在瑞士阿爾卑斯山分步驟重新引入阿爾卑斯羱羊（Capra ibex）的策略造成了數個嚴重的種群瓶頸，降低了新引入群體的遺傳多樣性。可以通過測量不同個體的連續性純合片段來研究近親繁殖對亞群所產生的影響。^[14]

參考文獻

[1]
孫, 麗俠. ROH及其在绵羊遗传育种中的应用研究进展. China Animal Husbandry & Veterinary Medicine. 2023-08-23, 50 (08): 3258-3266 [2024-01-24]. doi:10.16431/j.cnki.1671-7236.2023.08.023. （原始內容存檔於2024-01-24） –透過中國知網.
[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 . PMID 22888858. doi:10.1186/1471-2156-13-70 .
[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. （原始內容存檔於2023-07-23）（英語）.
[4]
Gibson, Jane; Morton, Newton E.; Collins, Andrew. Extended tracts of homozygosity in outbred human populations. Human Molecular Genetics. 2006-01-25, 15 (5). ISSN 1460-2083. doi:10.1093/hmg/ddi493.
[5]
胡, 紫平. 基于基因组SNP和ROH的剑白香猪群体遗传结构解析. 畜牧獸醫學報: 4117-4125. [2024-01-24]. doi:10.11843/j.issn.0366-6964.2023.10.011 –透過中國知網.
[6]
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 . PMID 18760389. doi:10.1016/j.ajhg.2008.08.007.
[7]
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) [2024-01-26]. ISSN 1471-0056. doi:10.1038/nrg.2017.109. （原始內容存檔於2024-01-18）（英語）.
[8]
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) [2024-01-26]. ISSN 1932-6203. PMC 4347978 . PMID 25734509. doi:10.1371/journal.pone.0118935. （原始內容存檔於2023-09-27）（英語）.
[9]
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) [2024-01-26]. ISSN 0028-0836. PMC 4516141 . PMID 26131930. doi:10.1038/nature14618. （原始內容存檔於2023-10-10）（英語）.
[10]
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) [2024-01-26]. ISSN 2041-1723. PMC 6823371 . PMID 31673082. doi:10.1038/s41467-019-12283-6. （原始內容存檔於2023-06-04）（英語）.
[11]
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) [2024-01-26]. PMC 1950838 . PMID 17701901. doi:10.1086/519795. （原始內容存檔於2024-01-19）（英語）.
[12]
Browning, Sharon R.; Browning, Brian L. High-Resolution Detection of Identity by Descent in Unrelated Individuals. The American Journal of Human Genetics. 2010-04, 86 (4) [2024-01-26]. PMC 2850444 . PMID 20303063. doi:10.1016/j.ajhg.2010.02.021. （原始內容存檔於2024-04-11）（英語）.
[13]
Szpiech, Zachary A; Blant, Alexandra; Pemberton, Trevor J. Berger, Bonnie , 編. GARLIC : Genomic Autozygosity Regions Likelihood-based Inference and Classification. Bioinformatics. 2017-07-01, 33 (13) [2024-01-26]. ISSN 1367-4803. PMC 5870576 . PMID 28205676. doi:10.1093/bioinformatics/btx102. （原始內容存檔於2024-04-10）（英語）.
[14]
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 . PMID 29387150. doi:10.1111/eva.12490.

[1] [1]
孫, 麗俠. ROH及其在绵羊遗传育种中的应用研究进展. China Animal Husbandry & Veterinary Medicine. 2023-08-23, 50 (08): 3258-3266 [2024-01-24]. doi:10.16431/j.cnki.1671-7236.2023.08.023. （原始內容存檔於2024-01-24） –透過中國知網.

[2] [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 . PMID 22888858. doi:10.1186/1471-2156-13-70 .

[3] [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. （原始內容存檔於2023-07-23）（英語）.

[:2-4] [4]
Gibson, Jane; Morton, Newton E.; Collins, Andrew. Extended tracts of homozygosity in outbred human populations. Human Molecular Genetics. 2006-01-25, 15 (5). ISSN 1460-2083. doi:10.1093/hmg/ddi493.

[5] [5]
胡, 紫平. 基于基因组SNP和ROH的剑白香猪群体遗传结构解析. 畜牧獸醫學報: 4117-4125. [2024-01-24]. doi:10.11843/j.issn.0366-6964.2023.10.011 –透過中國知網.

[6] [6]
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 . PMID 18760389. doi:10.1016/j.ajhg.2008.08.007.

[:1-7] [7]
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) [2024-01-26]. ISSN 1471-0056. doi:10.1038/nrg.2017.109. （原始內容存檔於2024-01-18）（英語）.

[:0-8] [8]
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) [2024-01-26]. ISSN 1932-6203. PMC 4347978 . PMID 25734509. doi:10.1371/journal.pone.0118935. （原始內容存檔於2023-09-27）（英語）.

[9] [9]
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) [2024-01-26]. ISSN 0028-0836. PMC 4516141 . PMID 26131930. doi:10.1038/nature14618. （原始內容存檔於2023-10-10）（英語）.

[10] [10]
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) [2024-01-26]. ISSN 2041-1723. PMC 6823371 . PMID 31673082. doi:10.1038/s41467-019-12283-6. （原始內容存檔於2023-06-04）（英語）.

[11] [11]
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) [2024-01-26]. PMC 1950838 . PMID 17701901. doi:10.1086/519795. （原始內容存檔於2024-01-19）（英語）.

[12] [12]
Browning, Sharon R.; Browning, Brian L. High-Resolution Detection of Identity by Descent in Unrelated Individuals. The American Journal of Human Genetics. 2010-04, 86 (4) [2024-01-26]. PMC 2850444 . PMID 20303063. doi:10.1016/j.ajhg.2010.02.021. （原始內容存檔於2024-04-11）（英語）.

[13] [13]
Szpiech, Zachary A; Blant, Alexandra; Pemberton, Trevor J. Berger, Bonnie , 編. GARLIC : Genomic Autozygosity Regions Likelihood-based Inference and Classification. Bioinformatics. 2017-07-01, 33 (13) [2024-01-26]. ISSN 1367-4803. PMC 5870576 . PMID 28205676. doi:10.1093/bioinformatics/btx102. （原始內容存檔於2024-04-10）（英語）.

[14] [14]
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 . PMID 29387150. doi:10.1111/eva.12490.

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