Autochthonous cattle breeds constitute important reservoirs of genetic diversity. Reggiana is an Italian local cattle breed reared in the north of Italy for the production of a mono-breed Parmigiano–Reggiano cheese. Reggiana cattle usually have a classical solid red coat colour and pale muzzle. As part of the strategies designed for the sustainable conservation of this genetic resource, we investigated at the genome-wise level the within-breed detected variability of three pigmentation-related traits (intensity of red coat colour, based on three classes – light/diluted, normal and dark; spotted patterns/piebaldism that sometime emerge in the breed; muzzle colour – pink/pale, grey and black), stature, presence/absence and number of supernumerary teats and teat length. A total of 1776 Reggiana cattle (about two-thirds of the extant breed population) were genotyped with the GeneSeek GGP Bovine 150k SNP array and single-marker and haplotype-based GWASs were carried out. The results indicated that two main groups of genetic factors affect the intensity of red coat colour: darkening genes (including EDN3 and a few other genes) and diluting genes (including PMEL and a few other genes). Muzzle colour was mainly determined by MC1R gene markers. Piebaldism was mainly associated with KIT gene markers. Stature was associated with BTA6 markers upstream of the NCAPG–LCORL genes. Teat defects were associated with TBX3/TBX5, MCC and LGR5 genes. Overall, the identified genomic regions not only can be directly used in selection plans in the Reggiana breed, but also contribute to clarifying the genetic mechanisms involved in determining exterior traits in cattle.

中文翻译：

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利用本土 Reggiana 品种的品种内变异性确定了几个影响牛的色素沉着相关性状、身材和乳房缺陷的候选基因

本土牛品种构成了重要的遗传多样性库。Reggiana 是一种在意大利北部饲养的意大利本地牛品种，用于生产单一品种的 Parmigiano-Reggiano 奶酪。Reggiana 牛通常具有经典的纯红色毛色和苍白的口吻。作为为可持续保护这一遗传资源而设计的战略的一部分，我们在基因组层面调查了三个与色素沉着相关的特征（红色毛色的强度，基于三类——浅色/稀释、正常和深色；有时出现在该品种中的斑点图案/花斑；口吻颜色 - 粉红色/苍白、灰色和黑色）、身高、多余乳头的存在/缺失和数量以及乳头长度。共有 1776 头 Reggiana 牛（约占现存品种种群的三分之二）使用 GeneSeek GGP 牛 150k SNP 阵列进行基因分型，并进行了基于单标记和单倍型的 GWAS。结果表明，影响红色毛色强度的遗传因素主要有两类：变黑基因（包括EDN3和其他一些基因）和稀释基因（包括PMEL和其他一些基因）。口吻颜色主要由MC1R基因标记决定。花斑主要与KIT基因标记有关。身高与NCAPG – LCORL基因上游的 BTA6 标记相关。乳头缺陷与TBX3 / TBX5、MCC和LGR5基因有关。总的来说，确定的基因组区域不仅可以直接用于 Reggiana 品种的选择计划，而且有助于阐明确定牛外部性状所涉及的遗传机制。