RT Journal Article
SR Electronic
T1 Kinship analysis and pedigree reconstruction by RAD sequencing in cattle
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2024.05.20.595066
DO 10.1101/2024.05.20.595066
A1 Xu, Yiming
A1 Wang, Wanqiu
A1 Xu, Minjie
A1 Wang, Binhu
A1 Huang, Jiefeng
A1 Wu, Yingsong
A1 Xie, Yongzhong
A1 Jian, Jianbo
YR 2024
UL http://biorxiv.org/content/early/2024/05/22/2024.05.20.595066.abstract
AB Kinship and pedigree information, used for estimating inbreeding, heritability, selection, and gene flow, is useful for breeding and animal conservation. However, as the size of the crossbred population increases, inaccurate generation and parentage recoding in livestock farms increases. Restriction-site-associated DNA sequencing (RAD-Seq) is a cost-effective platform for single nucleotide polymorphism (SNP) discovery and genotyping. Here, we performed a kinship analysis and pedigree reconstruction for Angus and Xiangxi yellow cattle, which benefit from good meat quality and yields, providing a basis for livestock management. A total of 975 cattle, including 923 offspring with 24 known sires and 28 known dams, were sampled and subjected to SNP discovery and genotyping. The identified SNPs panel included 7305 SNPs capturing the maximum difference between paternal and maternal genome information allowing us to distinguish between the F1 and F2 generation with 90% accuracy. In addition, parentage assignment software based on different strategies verified that the cross-assignments. In conclusion, we provided a low-cost and efficient SNP panel for kinship analyses and the improvement of local genetic resources, which are valuable for breed improvement, local resource utilization, and conservation.Competing Interest StatementThe authors have declared no competing interest.