Although the second largest chromosome of the genome, the X chromosome is usually excluded from genome‐wide association studies (GWAS). Considering the presence and importance of genes on this chromosome that are involved in reproduction, the aim of this study was to evaluate the effect of its inclusion in GWAS on reproductive traits (scrotal circumference [SC], early pregnancy [P16] and age at first calving [AFC]) in a Nelore herd. Genotype data from 3,263 animals with the above‐mentioned phenotypes were used. The results showed an increase in the variances explained by the autosomal markers for all traits when the X chromosome was not included. For SC, there was an increase of more than 10% for the windows on chromosomes 2 and 6. For P16, the effect was increased by almost 20% for windows on chromosome 5. The same pattern was found for AFC, with an increase of more than 10% for the most important windows. The results indicate that the noninclusion of the X chromosome can overestimate the effects of autosomes on SC, P16 and AFC not only because of the additive effect of the X chromosome itself but also because of its epistatic effect on autosomal genes.

中文翻译：

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肉牛繁殖性状的基因组区域定位：X染色体的包含。

尽管X染色体是基因组的第二大染色体，但X染色体通常被排除在全基因组关联研究（GWAS）中。考虑到该染色体上与生殖有关的基因的存在和重要性，本研究的目的是评估将其包含在GWAS中对生殖特征（阴囊周长[SC]，早孕[P16]和最初的年龄）的影响在内罗尔牛群中产犊[AFC]。使用来自3263只具有上述表型的动物的基因型数据。结果显示，当不包括X染色体时，所有性状的常染色体标记所解释的方差增加。对于SC，在2号和6号染色体上的窗​​口增加了10％以上。对于P16，在5号染色体上的窗​​口的影响增加了近20％。最重要的窗户增加了10％以上。结果表明，不包含X染色体可以高估常染色体对SC，P16和AFC的作用，这不仅是由于X染色体本身的累加作用，而且还因为其对常染色体基因的上位性作用。