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. 2023 Jan 3:101:skac383.
doi: 10.1093/jas/skac383.

Design and characterization of a high-resolution multiple-SNP capture array by target sequencing for sheep

Yingwei Guo  1 , Fengting Bai  1 , Jintao Wang  1 , Shaoyin Fu  2 , Yu Zhang  1 , Xiaoyi Liu  1 , Zhuangbiao Zhang  1 , Junjie Shao  1 , Ran Li  1 , Fei Wang  1 , Lei Zhang  1 , Huiling Zheng  1 , Xihong Wang  1 , Yongbin Liu  3 , Yu Jiang  1
Affiliations

Design and characterization of a high-resolution multiple-SNP capture array by target sequencing for sheep

Yingwei Guo et al. J Anim Sci. .

Abstract

The efficiency of molecular breeding largely depends on inexpensive genotyping arrays. In this study, we aimed to develop an ovine high-resolution multiple-single-nucleotide polymorphism (SNP) capture array, based on genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology. All the markers were from 40K captured regions, including genes located within selective sweep regions, breed-specific regions, quantitative trait loci (QTL), and the potential functional SNPs on the sheep genome. The results showed that a total of 210K high-quality SNPs were identified in the 40K regions, indicating a high average capture ratio (99.7%) for the target genomic regions. Using genotyped data (n = 317) from liquid chip technology, we further performed genome-wide association studies (GWAS) to detect the genetic loci affecting sheep hair types and teat number. A single significant association signal for hair types was identified on 6.7-7.1 Mb of chromosome 25. The IRF2BP2 gene (chr25: 7,067,974-7,071,785), which is located within this genomic region, has been previously known to be involved in hair/wool traits in sheep. The results further showed a new candidate region around 26.4 Mb of chromosome 13, between the ARHGAP21 and KIAA1217 genes, that was significantly related to teat number in sheep. The haplotype patterns of this region also showed differences in animals with 2, 3, or 4 teats. Advances in using the high-accuracy and low-cost liquid chip are expected to accelerate sheep genomic and breeding studies in the coming years.

Keywords: GWAS; chip design; genotyping by target sequencing; sheep breeding.

Plain language summary

Large-scale genotyping platforms are valuable tools for animal selection and breeding programs. The bead chip has been widely used in both research and commercial applications for a long time. A highly efficient and economical genotyping platform has been developed recently. In the present study, by combining the advantages of resequencing and bead chips, we developed a high-resolution capture array based on target sequencing with capture-in-solution technology (liquid chip), including updated functional probes according to the latest research. We further evaluated this approach by using 317 individuals and found that 210K single-nucleotide polymorphisms can be accurately genotyped, confirming the ratio of the captured regions compared with the designed rations is around 99.7%. Genome-wide association studies conducted using this chip suggested IRF2BP2 gene may be involved in hair types and ARHGAP21-KIAA1217 locus may be related to teats number. The liquid chip with high accuracy and low cost can be widely used in genome-wide association studies and genome selection, supporting efforts in molecular breeding and genetic improvement of sheep.

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Conflict of interest statement

The authors declare no real or perceived conflicts of interest.

Figures

Figure 1.
Figure 1.
Roadmap and characterization of the SNPs on the chip. (A) Roadmap for the design of sheep liquid chip. (B) Distribution of the designed sites on the genome with 1Mb window size. (C) The frequency distribution of the spaces between adjacent SNPs.
Figure 2.
Figure 2.
Validation of the sheep liquid chip. (A) Distribution of the capture ratio of the 317 sheep. (B) Distribution of the MAF of the SNPs on the chip and their flanking regions. (C) Read depth of designed SNPs and their flanking regions. (D) Depth of SNPs on the autosome, X chromosome, and Y chromosome, respectively.
Figure 3.
Figure 3.
Manhattan and quantile-quantile plot of GWAS for hair types and teat number. (A, B) Manhattan and quantile-quantile plot for hair types. (C, D) Manhattan and quantile-quantile plot for teat number.
See this image and copyright information in PMC

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