The growth of animals is a complex trait, in chicken resulting in a diverse variety of forms, caused by a heterogeneous genetic basis. 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‐genome sequence data from matching pairs of bantam and normal‐sized breeds. During the bantam‐oriented crossbreeding, various bantam origins were used to introduce the bantam phenotype, and three major bantam sources were identified and clustered. The genome‐wide association studies revealed multiple genetic variants and genes associated with bantam phenotype, including HMGA2 and PRDM16, 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‐bantam breeds, the bantam‐related regions underwent a strong haplotype introgression from the bantam source, outcompeting haplotypes from the normal‐sized 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‐mediated crossbreeding has contributed to the complexity and heterogeneity of the bantam phenotype.

中文翻译：

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基因组分析揭示荷兰传统鸡品种矮化表型的异质性


动物的生长是一个复杂的性状，鸡的生长形态多种多样，这是由异质的遗传基础造成的。矮脚鸡被称为一种精致的侏儒鸡，已被用于杂交育种，为荷兰当地的家禽创造出相应的侏儒鸡。在这里，我们利用匹配的矮脚鸡和正常体型品种的全基因组序列数据，证明了荷兰鸡矮脚鸡性状的异质性，并揭示了潜在的遗传原因。在以矮脚鸡为导向的杂交育种过程中，使用不同的矮脚鸡起源来引入矮脚鸡表型，并鉴定和聚类了三个主要的矮脚鸡来源。全基因组关联研究揭示了与 bantam 表型相关的多种遗传变异和基因，包括HMGA2和PRDM16 ，这些基因涉及身体生长和身材。研究之间相关变异的比较说明了与不同矮脚鸡起源相关的差异，表明矮脚鸡品种之间存在明显的异质性。我们发现，在新矮脚鸡品种中，矮脚鸡相关区域经历了来自矮脚鸡来源的强烈单倍型渗入，击败了来自正常大小对应区域的单倍型。包含相关等位基因的多个单倍型的存在进一步证实了矮脚鸡异质性，这表明矮脚鸡表型的选择可能受到群体间趋同方向的影响。我们的研究表明，人类介导的杂交育种的不同历史导致了矮脚鸡表型的复杂性和异质性。