Runs of homozygosity (ROH) are chromosomal stretches that in a diploid genome appear in a homozygous state and display identical alleles at multiple contiguous loci. This study aimed to systematically compare the genomic distribution of the ROH islands among five populations of wild vs. commercial chickens of both layer and broiler type. To this end, we analyzed whole genome sequences of 115 birds including white layer (WL, n = 25), brown layer (BL, n = 25), broiler line A (BRA, n = 20), broiler line B (BRB, n = 20) and Red Junglefowl (RJF, n = 25). The ROH segments varied in size markedly among populations, ranging from 0.3 to 21.83 Mb reflecting their past genealogy. White layers contained the largest portion of the genome in homozygous state with an average ROH length of 432.1 Mb (±18.7) per bird, despite carrying it in short segments (0.3-1 Mb). Population-wise inbreeding measures based on Wright’s (F_is) and genomic (F_ROH) metrics revealed highly inbred genome of layer lines relative to the broilers and Red Junglefowl. We further revealed the ROH islands, among commercial lines overlapped with QTL related to limb development (GREM1, MEOX2), body weight (Meis2a.1, uc_338), eggshell color (GLCCI1, ICA1, UMAD1), antibody response to Newcastle virus (ROBO2), and feather pecking. Comparison of ROH landscape in sequencing resolution demonstrated that a sizable portion of genome of commercial lines segregates in homozygote state, reflecting many generations of assortative mating and intensive selection in their recent history. In contrary, wild birds carry shorter ROH segments, likely suggestive of older evolutionary events.

纯合性（ROH）运行是在二倍体基因组中以纯合状态出现并在多个连续基因座处显示相同等位基因的染色体延伸。本研究旨在比较系统地野生五个种群间的ROH岛屿的基因组分布VS。蛋鸡和肉鸡类型的商业鸡。为此，我们分析了115羽鸟类的全基因组序列，包括白色层（WL，n = 25），棕色层（BL，n = 25），肉鸡A系（BRA，n = 20），肉鸡B系（BRB， n = 20）和红色丛林鸟（RJF，n = 25）。ROH片段的大小在人群中明显不同，从0.3到21.83 Mb不等，反映了他们过去的族谱。白色层以纯合子状态包含基因组的最大部分，每只鸟的平均ROH长度为432.1 Mb（±18.7），尽管携带的片段很短（0.3-1 Mb）。基于赖特（F _is）和基因组（F _ROH）指标显示出相对于肉鸡和红色丛林禽来说，层系的高度近交基因组。我们还揭示了ROH岛，在与肢体发育（GREM1，MEOX2），体重（Meis2a.1，uc_338），蛋壳颜色（GLCCI1，ICA1，UMAD1），对新城疫病毒（ROBO2）的抗体反应有关的QTL重叠的商业品系中）和羽毛啄。ROH景观在测序分辨率上的比较表明，商品系基因组的相当一部分以纯合子状态分离，反映了近代的许多代交配和密集选择。相反，野生鸟类携带的ROH片段更短，可能暗示了较早的进化事件。