Scientia Agricultura Sinica ›› 2023, Vol. 56 ›› Issue (8): 1585-1593.doi: 10.3864/j.issn.0578-1752.2023.08.013

• ANIMAL SCIENCE·VETERINARY SCIENCE • Previous Articles     Next Articles

Comparison of Imputation Accuracy for Different Low-Density SNP Selection Strategies

LIN YuNong1,2(), WANG ZeZhao2, CHEN Yan2, ZHU Bo2, GAO Xue2, ZHANG LuPei2, GAO HuiJiang2, XU LingYang2, CAI WenTao2, LI YingHao3, LI JunYa2(), GAO ShuXin1()   

  1. 1 College of Animal Science and Technology, Inner Mongolia University for the Nationalities, Tongliao 028042, Inner Magnolia
    2 Institute of Animal Sciences, Chinese Academy of Agriculture Sciences, Beijing 100193
    3 Tongliao Jingyuan Breeding Cattle Breeding LLC, Tongliao 028006, Inner Magnolia
  • Received:2021-12-13 Accepted:2022-03-24 Online:2023-04-16 Published:2023-04-23

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Abstract:

【Objective】 To facilitate the low-cost genomic selection in Huaxi Cattle, the present study represented the first attempt to designed a new low-density Genotype chip to support imputation to higher density genotypes. The representative SNP markers with different density gradients were selected from high-density SNP chips in the Huaxi cattle reference population by using two SNP selection methods. And then, these marker sets were imputed to high-density sets with the same imputation parameters for subsequent genomic studies. Meanwhile, the current study compared the differences in imputation accuracy and concordance among SNP panels and illustrated the effects of four factors on imputation results, including marker screening method, marker density, minor allele frequency, and the number of reference population. This study could provide insights about the methods to select the low-density SNP markers for imputation in the current population and the representative SNPs, and aid in designing low-density SNP chip for Huaxi cattle.【Method】Totally 1,233 Huaxi cattle after genotypes filtered was randomly divided into reference (986) and validation (247) populations., Based on Equidistance (EQ) and high MAF (HM), two SNP selection strategies were used to make 16 SNP sets with different densities from the Illumina Bovine HD chip in the reference population, respectively. Each of the 32 low-density set was then imputed to the 770K density level in the validation population by using Beagle (v5.1), while the imputation accuracy and concordance were calculated as the mean correlation between true and imputed genotypes. Finally, a comprehensive set of factors that influence the imputation performance were analyzed.【Result】The number of markers in the 32 low-density SNP sets ranged from 100 to 16 000, with a maximum window of 24 176 kb and a minimum window of 151 kb. The imputation accuracy and concordance of both EQ and HM methods went up with increasing marker densities. The imputation accuracy of both methods was the highest at 16k SNP density (r2 EQ=0.8801, r2 MAF=0.8696). When the marker density was below 11k, the imputation concordance of HM was higher than EQ for all marker density gradients. However, when the SNP density exceeded 11 k, EQ showed an imputation accuracy advantage over HM. Similar to the imputation concordance results, the HM method still had higher imputation accuracy when the SNP density was lower than 10 k, but the EQ method had higher imputation accuracy when the SNP pool density was higher than 10 k, and the EQ imputation accuracy tended to be stable after the SNP density was greater than 12 k. It was also found that the imputation accuracy of high MAF locus was higher. During the imputation process, it was found that the imputation accuracy and concordance increased with the increase of the reference panel. The imputation accuracy and concordance of loci were higher when the population of the reference panel was 600-800. 【Conclusion】In the Huaxi cattle population, the imputation accuracy and concordance increased with increasing marker density, and a better imputation effect could be obtained in the marker density of 10 k-12 k interval. The HM method was preferred when the marker density was less than 10 k, and the EQ method was better at high marker density. High MAF loci were more accurate for imputation. When the imputation strategy for low-density marker imputation was used, the number of reference panel should be at least 400 heads for better imputation effect.

Key words: imputation accuracy, low density SNP array, Chinese Simmental cattle, linkage disequilibrium, MAF

Table 1

The window size and the number of SNP different marker densities"

组号
No.		 窗口大小
Window size(kb)		 SNP标记数量
SNPs amount		 组号
No.		 窗口大小
Window size (kb)		 SNP标记数量
SNPs amount
1 24176 100 9 268 90 000
2 4835 500 10 242 10 000
3 2417 1000 11 220 11000
4 805 3000 12 201 12000
5 483 50000 13 186 13000
6 403 60000 14 173 14000
7 345 70000 15 161 15000
8 302 80000 16 151 16000

Fig. 1

The imputation concordance rate (A) and the imputation accuracy (B) of different selection strategies"

Fig. 2

Imputation accuracy and concordance rate with minor allele frequency for two selection strategies with the 16k-density A: Concordance rate of EQ selection strategy; B: Imputation accuracy of EQ selection strategy; C: Concordance rate of HM selection strategy; D: Imputation accuracy of HM selection strategy. Red points indicate more identical markers, and points blue indicates fewer identical markers"

Fig. 3

Mean concordance rate (A) and mean imputation accuracy (B) with minor allele frequency of two selection strategies with the 16 k-density"

Fig. 4

Effects of reference population size on concordance rate (A, C) and imputation accuracy (B, D)"

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