{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T06:04:44Z","timestamp":1789538684703,"version":"build-2803163510"},"reference-count":63,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T00:00:00Z","timestamp":1789516800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Adipose deposition is a complex trait shaped by both host genetics and environmental factors, including the gut microbiota. While quantitative trait loci (QTLs) and candidate genes underlying fat accumulation have been extensively identified in diverse pig breeds, the hologenomic regulatory networks integrating host genetic variation and microbial signals remain to be fully deciphered.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>In this study, we utilized a strictly controlled dietary cross-fostering model involving Jinhua and Landrace\u00d7Yorkshire pigs across developmental stages (day60, day90 and day180). We integrated population genetics, eQTL analysis, transcriptomics, metagenomics and metabolomics to elucidate the host-metabolite-microbe axis.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Phenotypic analysis revealed a robust genetic trait for high backfat thickness in Jinhua pigs, independent of dietary intervention. Through\n                      <jats:italic>F<\/jats:italic>\n                      <jats:sub>ST<\/jats:sub>\n                      analysis and eQTL mapping, we pinpointed a strongly differentiated locus (13_133481393_A_G) that was nearly fixed in JH pigs (allele frequency 0.95) and was associated with upregulation of\n                      <jats:italic>APOD<\/jats:italic>\n                      . In our multi-omics dataset, this locus was linked to shifts in cecal gene expression that were consistent with a pro-adipogenic program, which coincided with an intestinal metabolic profile marked by elevated oleic acid and reduced oleoylethanolamide. This metabolic niche, in turn, directionally recruited synergistic microbes, specifically\n                      <jats:italic>Eubacterium<\/jats:italic>\n                      sp.\n                      <jats:italic>AM28-29<\/jats:italic>\n                      and\n                      <jats:italic>Blautia<\/jats:italic>\n                      , which functioned as biochemical amplifiers to further accelerate lipid accumulation.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>\n                      Our study establishes a hologenomic framework demonstrating how foundational genetic selection (\n                      <jats:italic>APOD<\/jats:italic>\n                      ) shapes the host-microbe metabolic interplay to drive complex production traits. This study offers novel molecular targets and a theoretical framework for precision breeding and nutritional modulation of meat quality in livestock.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1915318","type":"journal-article","created":{"date-parts":[[2026,9,16]],"date-time":"2026-09-16T05:31:35Z","timestamp":1789536695000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Integrative hologenomic analysis reveals apolipoprotein D\u2013associated host\u2013microbe metabolic crosstalk linked to fat deposition in Jinhua pigs"],"prefix":"10.3389","volume":"17","author":[{"given":"Ran","family":"Shen","sequence":"first","affiliation":[{"name":"Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, College of Animal Sciences, Zhejiang University","place":["Hangzhou, China"]},{"name":"Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuang","family":"Liu","sequence":"additional","affiliation":[{"name":"Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, College of Animal Sciences, Zhejiang University","place":["Hangzhou, China"]},{"name":"Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengfei","family":"Yu","sequence":"additional","affiliation":[{"name":"Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, College of Animal Sciences, Zhejiang University","place":["Hangzhou, China"]},{"name":"Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shuyan","family":"Xie","sequence":"additional","affiliation":[{"name":"Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, College of Animal Sciences, Zhejiang University","place":["Hangzhou, China"]},{"name":"Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs","place":["Hangzhou, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qinqin","family":"Xie","sequence":"additional","affiliation":[{"name":"Zhejiang Key Laboratory of Nutrition and Breeding for High-Quality Animal Products, College of Animal Sciences, Zhejiang University","place":["Hangzhou, China"]},{"name":"Key Laboratory of Livestock and Poultry Resources Evaluation and Utilization, Ministry of Agriculture and Rural Affairs","place":["Hangzhou, 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