芯片和重测序在猪遗传结构研究中的应用比较

doi:10.11843/j.issn.0366-6964.2023.07.011

Abstract

Abstract: This study aimed to compare the effects of SNP genotyping techniques (array and sequencing) and marker densities on the analysis results of genetic diversity, phylogenetic tree and genomic inbreeding coefficient, and explore low-cost and efficient genotyping method and appropriate SNP density in genetic structure study. The data of the CAUPorcine SNP50 array and the resequencing data of 35 Zaozhuang Heigai pigs were used in this study. In this study, using resequencing data as "raw materials", 4 SNP panels of random 34K, even 34K, even 340K and even 3 400K were constructed. The genetic diversity, phylogenetic tree and genomic inbreeding coefficient of Zaozhuang Heigai pigs were analyzed using SNP data of CAUPorcine SNP50 array and several sequencing panels. The results showed that:1) The index values of genetic diversity, including observed heterozygosity (H_O) (0.385 9 vs. 0.320 0-0.324 1), expected heterozygosity (H_E) (0.381 3 vs. 0.333 5-0.334 6), and genetic distance (0.305 7 vs. 0.279 8-0.280 6), estimated by array SNPs were higher than those by the SNPs of sequencing panels, and the phylogenetic tree constructed by array SNPs was of much difference from those by the SNPs of sequencing panels. These may be caused by the tendency of choosing higher minor allele frequency (MAF) SNPs in array design. 2) All sequencing panels had small impact on the analysis results of H_O (0.320 0-0.324 1), H_E (0.333 5-0.334 6), genetic distance (0.279 8-0.280 6) and phylogenetic tree, but had great impact on the number (784-106 547) and length (0.20-13.51 Mb) of runs of homozygosity (ROH) and genomic inbreeding coefficient (F_ROH) (0.127-0.263). Currently used 50 K genome-wide SNP arrays in the analysis of inbreeding coefficient of livestock and poultry is good at detection of large fragments of ROHs, but weak in identification small and medium ones. So the genomic inbreeding coefficient estimated by them may be lower than the actual value. In summary, different SNP genotyping techniques have a significant impact on the analysis results of genetic diversity, phylogenetic tree, and ROH. In the sequencing group, different SNP densities had a small impact on genetic diversity and phylogenetic tree analysis results, but had a significant impact on ROH and F_ROH analysis results.

Key words: SNP array, resequencing, genetic diversity, phylogenetic tree, genomic inbreeding coefficient

CLC Number:

S828.2

YANG Qing, GONG Jing, ZHAO Xueyan, ZHU Xiaodong, GENG Liying, ZHANG Chuansheng, WANG Jiying. Comparison of Array and Resequencing in Pig Genetic Structure Studies[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2772-2782.

References 40

[1]	JIN S H, XIA J J, JIA F M, et al. Complete mitochondrial genome, genetic diversity and phylogenetic analysis of Pingpu Yellow chicken (Gallus gallus)[J]. Animals(Basel), 2022, 12(21):3037.
[2]	MACHOVA K, MARINA H, ARRANZ J J, et al. Genetic diversity of two native sheep breeds by genome-wide analysis of single nucleotide polymorphisms[J]. Animal, 2022, 17(1):100690.
[3]	SUN X L, GUO J Z, LI L, et al. Genetic diversity and selection signatures in Jianchang Black goats revealed by whole-genome sequencing data[J]. Animals(Basel), 2022, 12(18):2365.
[4]	CHEN Y G, WU X D, WANG J L, et al. Detection of selection signatures in Anqing Six-End-White pigs based on resequencing data[J]. Genes, 2022, 13(12):2310.
[5]	ZHAO Y X, GAO G X, ZHOU Y, et al. Genome-wide association studies uncover genes associated with litter traits in the pig[J]. Animal, 2022, 16(12):100672.
[6]	SUN Y X, SANG Q Q, YIN Z T, et al. Genome-wide association study identified the candidate genes associated with angel wing trait in Pekin duck[J]. Anim Genet, 2023, 54(2):211-215.
[7]	FERNANDES J G A, PERIPOLLI E, SCHMIDT P I, et al. Current applications and perspectives of genomic selection in Bos indicus (Nellore) cattle[J]. Livest Sci, 2022, 263(1):105001.
[8]	ZHENG X, ZHANG T L, WANG T Z, et al. Long-term impact of genomic selection on genetic gain using different SNP density[J]. Agriculture, 2022, 12(9):1463.
[9]	董磊. 基于全基因组重测序技术发掘晋汾白猪特异SNP位点[D]. 晋中:山西农业大学, 2020.DONG L. Discovery of specific SNP sites in Jinfen White pig based on whole genome resequencing[D]. Jinzhong:Shanxi Agricultural University, 2020.(in Chinese)
[10]	刘继强, 郝晓东, 武丽娜, 等. 全基因组SNP分型技术在畜禽遗传育种研究中的应用[J]. 畜牧兽医学报, 2022, 53(12):1-16.LIU J Q, HAO X D, WU L N, et al. Application of whole genome SNP genotyping technology in livestock and poultry genetics and breeding[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(12):1-16. (in Chinese)
[11]	李富. 奶山羊泌乳量GWAS分析及候选基因的筛选[D]. 杨凌:西北农林科技大学, 2022.LI F. GWAS analysis of milk production traits and screening of candidate genes in dairy goats[D]. Yangling:Northwest A&F University, 2022.(in Chinese)
[12]	陈美佳. 不同密度SNP和低密度填充面板对凡纳滨对虾收获体重基因组预测准确性的影响[D]. 上海:上海海洋大学, 2021.CHEN M J.Effects of SNPs with different densities and low-density imputation panels on genomic prediction accuracy of harvest weight trait in Litopenaeus vannamei[D]. Shanghai:Shanghai Ocean University, 2021.(in Chinese)
[13]	曾浩南, 钟展明, 徐志婷, 等. 3款猪50K SNP芯片基因型填充至序列数据的效果评估[J]. 华南农业大学学报, 2022, 43(4):5-10.ZENG H N, ZHONG Z M, XU Z T, et al. Evaluation on genotype imputation performance of three porcine 50K SNP chips from chip data to sequencing data[J]. Journal of South China Agricultural University, 2022, 43(4):5-10.(in Chinese)
[14]	陈宇, 邱奥, 张梓鹏, 等. 猪SNP液相芯片10K~50K基因型填充效果研究[J]. 畜牧兽医学报, 2022, 53(10):3368-3376.CHEN Y, QIU A, ZHANG Z P, et al. Study on the genotype imputation effect of 10 K~50 K genotype of pig SNP liquid chip[J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(10):3368-3376.(in Chinese)
[15]	LI H, DURBIN R. Fast and accurate long-read alignment with Burrows-Wheeler transform[J]. Bioinformatics, 2010, 26(5):589-595.
[16]	YANG J, LEE S, GODDARD M, et al. GCTA:a tool for genome-wide complex trait analysis[J]. Am J Hum Genet, 2011, 88(1):76-82.
[17]	LI H, HANDSAKER B, WYSOKER A, et al. The sequence alignment/map format and SAMtools[J]. Bioinformatics, 2009, 25(16):2078-2079.
[18]	NARASIMHAN V, DANECEK P, SCALLY A, et al. BCFtools/RoH:a hidden Markov model approach for detecting autozygosity from next-generation sequencing data[J]. Bioinformatics, 2016, 32(11):1749-1751.
[19]	PURCELL S, NEALE B, TODD-BROWN K, et al. PLINK:A tool set for whole-genome association and population-based linkage analyses[J]. Am J Hum Genet, 2007, 81(3):559-575.
[20]	TSAIRIDOU S, HAMILTON A, ROBLEDO D, et al. Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon[J]. G3 (Bethesda), 2020, 10(2):581-590.
[21]	FELSENSTEIN J. PHYLIP (Phylogeny Inference Package) version3.6[M]. Seattle:Department of Genome Science, University of Washington, 2004.
[22]	KUHNER M K, FELSENSTEIN J. A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates[J]. Mol Biol Evol, 1994, 11(3):459-468.
[23]	BISCARINI F, COZZI P, GASPA G, et al. detectRUNS:Detect Runs of Homozygosity and Runs of Heterozygosity in Diploid Genomes[DB/OL]. https://cran.case.edu/web/packages/detectRUNS/index.html, 2019-10-24.
[24]	MCQUILLAN R, LEUTENEGGER A L, ABDEL-RAHMAN R, et al. Runs of homozygosity in European populations[J]. Am J Hum Genet, 2008, 83(3):359-372.
[25]	PERIPOLLI E, MUNARI D P, SILVA M V G B, et al. Runs of homozygosity:current knowledge and applications in livestock[J]. Anim Genet, 2017, 48(3):255-271.
[26]	詹慧雯. 基于重测序数据的不同猪品种群体遗传学参数估计与ROH分析[D]. 武汉:华中农业大学, 2021.ZHAN H W. The assessment of population genetic paramenters and genome-wide patterns of homozygosity in various swine breeds[D]. Wuhan:Huazhong Agricultural University, 2021.(in Chinese)
[27]	ABECASIS G, AUTON A, BROOKS L, et al. An integrated map of genetic variation from 1, 092 human genomes[J]. Nature, 2012, 491(7422):56-65.
[28]	AI H S, FANG X D, YANG B, et al. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing[J]. Nat Genet, 2015, 47(3):217-225.
[29]	EYNARD S, WINDIG J, LEROY G, et al. The effect of rare alleles on estimated genomic relationships from whole genome sequence data[J]. BMC Genet, 2015, 16:24.
[30]	PEREZ-ENCISO M. Genomic relationships computed from either next-generation sequence or array SNP data[J]. J Anim Breed Genet, 2014, 131(2):85-96.
[31]	WANG X Q, WANG L G, SHI L Y, et al. GWAS of reproductive traits in Large White pigs on chip and imputed whole-genome sequencing data[J]. Int J Mol Sci, 2022, 23(21):13338.
[32]	ALBRECHTSEN A, NIELSEN F C, NIELSEN R. Ascertainment biases in SNP chips affect measures of population divergence[J]. Mol Biol Evol, 2010, 27(11):2534-2547.
[33]	NIELSEN R, SIGNOROVITCH J. Correcting for ascertainment biases when analyzing SNP data:applications to the estimation of linkage disequilibrium[J]. Theor Popul Biol, 2003, 63(3):245-255.
[34]	GEIBEL J, REIMER C, WEIGEND S, et al. How array design creates SNP ascertainment bias[J]. PloS One, 2021, 16(3):e0245178.
[35]	DOKAN K, KAWAMURA S, TESHIMA K M. Effects of single nucleotide polymorphism ascertainment on population structure inferences[J]. G3 (Bethesda), 2021, 11(9):128.
[36]	POLAK G, GURGUL A, JASIELCZUK, et al. Suitability of pedigree information and genomic methods for analyzing inbreeding of Polish Cold-Blooded horses covered by conservation programs[J]. Genes, 2021, 12(3):429.
[37]	ALEMU S, KADRI N, HARLAND C, et al. An evaluation of inbreeding measures using a whole-genome sequenced cattle pedigree[J]. Heredity, 2021, 126(3):410-423.
[38]	PURFIELD D, BERRY D, MCPARLAND S, et al. Runs of homozygosity and population history in cattle[J]. BMC Genetics, 2012, 13:70.
[39]	FEREN AČG AKOVIĆ M, SOLKNER J, CURIK I. Estimating autozygosity from high-throughput information:effects of SNP density and genotyping errors[J]. Genet Sel Evol, 2013, 45(1):42.
[40]	ZHANG Q Q, CALUS M, GULDBRANDTSEN B, et al. Estimation of inbreeding using pedigree, 50k SNP chip genotypes and full sequence data in three cattle breeds[J]. BMC Genetics, 2015, 16:88.

Comparison of Array and Resequencing in Pig Genetic Structure Studies

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