{"id":11558,"date":"2026-04-13T11:53:17","date_gmt":"2026-04-13T11:53:17","guid":{"rendered":"https:\/\/www.proefschriftmaken.nl\/portfolio\/xiaofei-yu\/"},"modified":"2026-04-22T14:39:58","modified_gmt":"2026-04-22T14:39:58","slug":"xiaofei-yu","status":"publish","type":"us_portfolio","link":"https:\/\/www.proefschriftmaken.nl\/en\/portfolio\/xiaofei-yu\/","title":{"rendered":"Xiaofei Yu"},"content":{"rendered":"","protected":false},"excerpt":{"rendered":"","protected":false},"author":8,"featured_media":12016,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"us_portfolio_category":[45],"class_list":["post-11558","us_portfolio","type-us_portfolio","status-publish","has-post-thumbnail","hentry","us_portfolio_category-new-template"],"acf":{"naam_van_het_proefschift":"Genomic architecture of selection for adaptation to challenging environments in Aquaculture","samenvatting":"Er is geen Nederlandse samenvatting beschikbaar. De Engelse samenvatting vind je <a href=\"https:\/\/www.proefschriftmaken.nl\/en\/portfolio\/xiaofei-yu\/\">hier<\/a>.","summary":"Aquaculture is a sustainable way to meet the increased human demand for animal food. However, sustainability is threatened by the increasing effect of climate change. The most important threats to aquaculture resulting from climate change are high water temperatures that fall outside of the physiological tolerance range, increase of and rapid change in salinity due to drought and flooding, acidification of seawater due to carbon dioxide uptake, and last but not least oxygen shortage caused by any combination of the above that could result in algal blooms. Although a reasonable genetic gain can be achieved by traditional selective breeding, aquaculture may not grow sufficiently due to the complexity of traits underlying adaptation to these environmental stressors. However, the development of genomic technologies enabled us to investigate the genomic architecture of traits of interest. The aim of this thesis is to provide an insight into the genomic architecture of adaptation to challenging environments of aquaculture species under farming conditions and the underlying essential biological processes and metabolic pathways.\n\nIn Chapter 2 we used two groups of the Genetic Improvement of Farmed Tilapia strain that originated from the same genetic background. The Nile tilapia were raised in aerated (normoxic) and non-aerated (hypoxic) ponds, respectively. We observed different genomic architectures associated with early and later growth in hypoxic and normoxic environments, indicating a transition in metabolism. We highlighted that MAPK and VEGF signalling are significantly involved in the regulation of later-stage growth under hypoxia. Furthermore, by a meta-analysis of GWAS results, we identified thirty-three SNPs that are significantly associated with growth across two environments, while the genes linked to these SNPs were mostly involved in nervous system development, organ growth and oocyte maturation. These findings suggest a possible shared effect independent of the two environments.\n\nIn Chapter 3, critical swimming performance (U crit) is studied as a potential indicator trait for hypoxia tolerance. Fish with higher U crit are not only supposed to perform better in cardio-respiratory health, but also to cope with hypoxia better. We found slightly negative correlations between swimming performance in early life and growth traits based on the genomic relationship matrix, suggesting that fish with better swimming performance have a slower growth tendency later in life. We also identified the genomic architecture associated with U crit early in life and identified several potential target genes such as hip1, hectd1, elna, smyd1b, rrp12 and pprc. Moreover, a clear pleiotropic effect of three SNPs was found between swimming performance and growth traits, while the remaining six SNPs only affect swimming performance, but not growth. The genetic markers identified in the study can be used to select fish with cardio-respiratory health and growth that can potentially grow well in a hypoxic environment.\n\nThe results described in Chapter 4 are based on a saline-tolerant and highly productive tilapia strain that was developed by the aquaculture research institute and named \u201cSukamandi\u201d. We show that the Sukamandi genome is predominantly of Nile tilapia origin, with about 9% of the genome derived from blue tilapia. We further show that eight salinity tolerance genes, including caprin1a, nucb2a, abcb10, slc12a10.1, cacna1ab, ulk2, slc25a24 and cdh1, were strongly selected after a four-generation breeding program. Moreover, the genomic architecture that was introgressed from blue tilapia also confers the observed salinity tolerance. Collectively, the results help us understand fish adaptation in a saline environment.\n\nIn Chapter 5 we study the same genetic background of gilthead seabream that grew out in two distinct commercial sites (Spain and Greece). We describe a region between 19.66 Mb to 46.84 Mb on chromosome 22 that is strongly associated with growth traits in Spain. However, none of the SNPs within this region are associated with growth in Greece. Moreover, a similar pattern was found for organ weight, suggesting a divergent genomic architecture under genotype-by-environment interaction. By performing gene ontology and KEGG enrichment analyses for the target QTLs region, we show that cell adhesion, light absorption, and ECM-receptor interaction are the most prominent terms related to growth in Spain but not in Greece. Also, we show that ATP binding activity and response to stimulus are more prominent processes for organ weight in Spain than in Greece. The QTLs identified in this study provide insight into the genomic basis of fish growth traits and organ weight under a temperature challenging environment.\n\nIn Chapter 6, the general discussion, I discuss the genomic basis of environmental adaptation using forward and reverse approaches, suggesting a schematic diagram of combining two approaches to study the genetic mechanism of adaptation. To further strengthen our understanding of genotype-by-environment interaction, I discuss QTL by environment interaction from a genomic perspective. I also discuss the advantages and disadvantages of current genomic technologies from SNP array, genotype-by-sequencing to whole genome sequencing used in the studies described in this thesis. Lastly, I give concluding remarks and suggest the inclusion of regulatory network (gene expression, methylation status) and environmental data in future studies.","auteur":"Xiaofei Yu","auteur_slug":"xiaofei-yu","publicatiedatum":"13 december 2022","taal":"EN","url_flipbook":"https:\/\/ebook.proefschriftmaken.nl\/ebook\/xiaofeiyu?iframe=true","url_download_pdf":"","url_epub":"","ordernummer":"FTP-202604131151","isbn":"978-94-6447-469-5","doi_nummer":"","naam_universiteit":"Wageningen University","afbeeldingen":12016,"naam_student:":"","binnenwerk":"","universiteit":"Wageningen University","cover":"","afwerking":"","cover_afwerking":"","design":""},"_links":{"self":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/11558","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio"}],"about":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/types\/us_portfolio"}],"author":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/users\/8"}],"replies":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/comments?post=11558"}],"version-history":[{"count":1,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/11558\/revisions"}],"predecessor-version":[{"id":11559,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio\/11558\/revisions\/11559"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/media\/12016"}],"wp:attachment":[{"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/media?parent=11558"}],"wp:term":[{"taxonomy":"us_portfolio_category","embeddable":true,"href":"https:\/\/www.proefschriftmaken.nl\/en\/wp-json\/wp\/v2\/us_portfolio_category?post=11558"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}