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Bantam chicken, known as an exquisite form of dwarfism, has been used for crossbreeding to create corresponding dwarf counterparts for native fowls in the Dutch populations. Here, we demonstrate the heterogeneity of the bantam trait in Dutch chickens and reveal the underlying genetic causes, using whole\u2010genome sequence data from matching pairs of bantam and normal\u2010sized breeds. During the bantam\u2010oriented crossbreeding, various bantam origins were used to introduce the bantam phenotype, and three major bantam sources were identified and clustered. The genome\u2010wide association studies revealed multiple genetic variants and genes associated with bantam phenotype, including <jats:italic>HMGA2<\/jats:italic> and <jats:italic>PRDM16<\/jats:italic>, genes involved in body growth and stature. The comparison of associated variants among studies illustrated differences related to divergent bantam origins, suggesting a clear heterogeneity among bantam breeds. We show that in neo\u2010bantam breeds, the bantam\u2010related regions underwent a strong haplotype introgression from the bantam source, outcompeting haplotypes from the normal\u2010sized counterpart. The bantam heterogeneity is further confirmed by the presence of multiple haplotypes comprising associated alleles, which suggests the selection of the bantam phenotype is likely subject to a convergent direction across populations. Our study demonstrates that the diverse history of human\u2010mediated crossbreeding has contributed to the complexity and heterogeneity of the bantam phenotype.<\/jats:p>","DOI":"10.1111\/eva.13183","type":"journal-article","created":{"date-parts":[[2020,12,12]],"date-time":"2020-12-12T08:11:58Z","timestamp":1607760718000},"page":"1095-1108","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":20,"title":["Heterogeneity of a dwarf phenotype in Dutch traditional chicken breeds revealed by genomic analyses"],"prefix":"10.1111","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-8840-9630","authenticated-orcid":false,"given":"Zhou","family":"Wu","sequence":"first","affiliation":[{"name":"Wageningen University &amp; Research, Animal Breeding and Genomics Wageningen The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6589-6635","authenticated-orcid":false,"given":"Chiara","family":"Bortoluzzi","sequence":"additional","affiliation":[{"name":"Wageningen University &amp; Research, Animal Breeding and Genomics Wageningen The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martijn F. 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