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Nevertheless, the genetic mechanisms responsible for its short-legged phenotype have yet to be elucidated.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      In this study, Yunlong Short-Leg chickens with different shank lengths\u2014Long-legged and Short-legged phenotypes\u2014were selected as experimental subjects (\n                      <jats:italic>n<\/jats:italic>\n                      \u2009=\u200960, 30 males and 30 females). We performed genome-wide analyses of single nucleotide polymorphisms (SNPs) and insertion\/deletion variants (InDels), followed by genome-wide association studies (GWAS) correlating these variants with body weight and morphometric traits. Population genetic analysis indicated no significant differences in genetic background between the Long\u2011legged and Short\u2011legged groups, confirming they belong to the same population. GWAS identified shank length as the only trait significantly associated with eight genes on chromosome 7, including\n                      <jats:italic>IHH<\/jats:italic>\n                      ,\n                      <jats:italic>NHEJ1<\/jats:italic>\n                      , and\n                      <jats:italic>MNR2<\/jats:italic>\n                      . A comparison of variants on chromosome 7 revealed that the Long\u2011legged samples exhibited no structural changes, whereas Short-legged samples were categorized as creeper phenotype, exhibiting two non-contiguous deletions and an inversion on chromosome 7: a 13,480\u00a0bp deletion (positions 22,287,390\u201322,300,869\u00a0bp) and an 11,559\u00a0bp deletion (positions 22,301,448\u201322,313,006\u00a0bp), totaling 25,039\u00a0bp, as well as a 578\u00a0bp inversion (positions 22,300,870\u201322,301,447\u00a0bp). Lethal samples carried a homozygous deletion and the same inversion in this region on chromosome 7. Multiplex PCR with different primers was performed to genotype shank-length phenotypes based on structural genomic variants. Finally, qRT\u2011PCR analysis confirmed that the relative mRNA expression levels of\n                      <jats:italic>IHH<\/jats:italic>\n                      and\n                      <jats:italic>NHEJ1<\/jats:italic>\n                      correlated with corresponding locus variation and shank-length phenotypes in Yunlong Short-Leg chicken.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>These findings provide insight into the genetic basis of the short\u2011leg phenotype in Yunlong Short-Leg chicken and offer theoretical support for genetic resource conservation and future breeding programs.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1186\/s12864-026-12943-0","type":"journal-article","created":{"date-parts":[[2026,5,18]],"date-time":"2026-05-18T13:12:16Z","timestamp":1779109936000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["A heterozygous deletion and inversion at the NHEJ1\u2011IHH locus associated with shank length in Yunlong short-leg chicken"],"prefix":"10.1186","volume":"27","author":[{"given":"Kuowei","family":"Xu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kai","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinyan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuxin","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junlan","family":"Gou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jielong","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fenfen","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ping","family":"Xiao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,5,18]]},"reference":[{"key":"12943_CR1","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1016\/j.tvjl.2017.05.014","volume":"224","author":"IJM Boegheim","year":"2017","unstructured":"Boegheim IJM, Leegwater PaJ, Van Lith HA, et al. 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