Xie Rui, Shi Liangyu, Liu Jiaxin, Deng Tianyu, Wang Lixian, Liu Yang, Zhao Fuping
Department of Animal Genetics, Breeding and Reproduction, National Experimental Teaching Demonstration Center of Animal Science, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
Animals (Basel). 2019 Aug 1;9(8):518. doi: 10.3390/ani9080518.
Runs of homozygosity (ROH) are contiguous homozygous genotype segments in the genome that are present in an individual since the identical haplotypes are inherited from each parent. The aim of this study was to investigate the frequency and distribution of ROH in the genomes of Landrace, Songliao black and Yorkshire pigs. We calculated two types of genome inbreeding coefficients and their correlation, including the inbreeding coefficient based on ROH () and the inbreeding coefficient based on the difference between the observed and expected number of homozygous genotypes (). Furthermore, we identified candidate genes in the genomic region most associated with ROH. We identified 21,312 ROH in total. The average number of ROH per individual was 32.99 ± 0.38 and the average length of ROH was 6.40 ± 0.070 in the three breeds. The results showed that Yorkshire pigs exhibited the highest level of inbreeding (0.092 ± 0.0015) and that Landrace pigs exhibited the lowest level of inbreeding (0.073 ± 0.0047). The average correlation between and was high (0.94) within three breeds. The length of ROH provides insight into the inbreeding history of these three pig breeds. In this study, Songliao black pigs presented a higher frequency and average length of long ROH (>40 Mb) compared with those of Landrace and Yorkshire pigs, which indicated greater inbreeding in recent times. Genes related to reproductive traits (, meat quality traits ( and energy conversion () were identified within genomic regions with a high frequency of ROH. These genes could be used as target genes for further marker-assisted selection and genome selection.
纯合子连续片段（ROH）是基因组中连续的纯合基因型片段，由于个体从每个亲本继承相同的单倍型，所以这些片段存在于个体中。本研究的目的是调查长白猪、松辽黑猪和大白猪基因组中ROH的频率和分布。我们计算了两种类型的基因组近交系数及其相关性，包括基于ROH的近交系数（）和基于观察到的纯合基因型数量与预期数量之差的近交系数（）。此外，我们在与ROH最相关的基因组区域中鉴定了候选基因。我们总共鉴定出21312个ROH。在这三个品种中，个体的ROH平均数量为32.99±0.38，ROH的平均长度为6.40±0.070。结果表明，大白猪的近交水平最高（0.092±0.0015），长白猪的近交水平最低（0.073±0.0047）。在三个品种中，与的平均相关性较高（0.94）。ROH的长度为了解这三个猪品种的近交历史提供了线索。在本研究中，与长白猪和大白猪相比，松辽黑猪的长ROH（>40 Mb）频率和平均长度更高，这表明近期的近交程度更高。在ROH频率较高的基因组区域中鉴定出了与繁殖性状（）、肉质性状（）和能量转换（）相关的基因。这些基因可作为进一步进行标记辅助选择和基因组选择的目标基因。
