SNP遗传力估计方法、影响因素及其在畜禽育种中的应用

doi:10.11843/j.issn.0366-6964.2024.05.004

摘要/Abstract

摘要： 遗传力是衡量由遗传因素解释的表型方差的比例，在实际遗传力估计中多只考虑加性遗传效应。由于畜禽传统遗传力估计需要的系谱信息完整性和准确性较难以实现，随着基因组学的发展，以全基因组单核苷酸多态性(SNP)进行遗传力估计的方法得到广泛应用。而对SNP遗传力的准确估计有利于了解遗传变异对表型的作用程度，目前已有不少SNP遗传力估计模型被开发利用。本文主要综述了SNP遗传力的概念、常用估计方法及其影响因素，并与传统遗传力估计进行比较，探究了SNP遗传力在畜禽育种中的应用潜力。

关键词: SNP遗传力, 遗传力缺失, 影响因素, 估计模型, 畜禽育种

Abstract: Heritability is a measure of the proportion of phenotypic variance explained by genetic factors. In actual heritability evaluation, only additive genetic effects are considered. With the development of genomics, genome-wide single nucleotide polymorphisms (SNPs) have been widely used to evaluate heritability because of the difficulty in achieving the integrity and accuracy of genealogy information that traditional heritability estimation relies on. However, accurate evaluation of SNP heritability is helpful in understanding the extent of genetic variation’s effect on phenotype. Currently, many SNP heritability evaluation models have been developed and utilized. In this paper, the concept, common evaluation methods and influencing factors of SNP heritability are reviewed, and a comparison was made between SNP heritability and the traditional heritability estimation, in order to explore the potential application of SNP heritability in livestock breeding.

Key words: SNP heritability, loss of heritability, influencing factors, estimation model, farmer animal breeding

中图分类号:

S813

段益欣, 张林云, 赵永聚. SNP遗传力估计方法、影响因素及其在畜禽育种中的应用[J]. 畜牧兽医学报, 2024, 55(5): 1854-1865.

DUAN Yixin, ZHANG Linyun, ZHAO Yongju. The Evaluated Methods and Influencing Factors of SNP Heritability and Its Application in Farmer Animal Breeding[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(5): 1854-1865.

参考文献

[1] ZHU H H,ZHOU X.Statistical methods for SNP heritability estimation and partition:a review[J].Comput Struct Biotechnol J,2020,18:1557-1568.
[2] TANG M S,WANG T,ZHANG X F.A review of SNP heritability estimation methods[J].Brief Bioinform,2022,23(3):bbac067.
[3] VISSCHER P M,HILL W G,WRAY N R.Heritability in the genomics era-concepts and misconceptions[J].Nat Rev Genet,2008,9(4):255-266.
[4] FRIEDMAN N P,BANICH M T,KELLER M C.Twin studies to GWAS:there and back again[J].Trends Cogn Sci,2021,25(10): 855-869.
[5] MAYHEW A J,MEYRE D.Assessing the heritability of complex traits in humans:methodological challenges and opportunities[J]. Curr Genomics,2017,18(4):332-340.
[6] SRIVASTAVA A K,WILLIAMS S M,ZHANG G.Heritability estimation approaches utilizing genome-wide data[J].Curr Protoc,2023,3(4):e734.
[7] PIZARRO INOSTROZA M G,LANDI V,NAVAS GONZÁLEZ F J,et al.Does the acknowledgement of αS1-casein genotype affect the estimation of genetic parameters and prediction of breeding values for milk yield and composition quality-related traits in Murciano-Granadina?[J].Animals (Basel),2019,9(9):679.
[8] 倪萍,任强,王静,等.仿刺参疣足数量SNP遗传力评估[J].渔业科学进展,2021,42(3):68-76.
NI P,REN Q,WANG J,et al.Estimating SNP heritability for papillae number in sea cucumber[J].Progress in Fishery Sciences,2021,42(3):68-76.(in Chinese)
[9] YANG J,BENYAMIN B,MCEVOY B P,et al.Common SNPs explain a large proportion of the heritability for human height[J]. Nat Genet, 2010,42(7):565-569.
[10] LIN Z T,SEAL S,BASU S.Estimating SNP heritability in presence of population substructure in biobank-scale datasets[J]. Genetics,2022,220(4):iyac015.
[11] UZZAMAN M R,PARK J E,LEE K T,et al.Whole-genome association and genome partitioning revealed variants and explained heritability for total number of teats in a Yorkshire pig population[J].Asian-Australas J Anim Sci,2018,31(4):473-479.
[12] SHIN D,PARK K D,KA S,et al.Heritability estimated using 50K SNPs indicates missing heritability problem in Holstein breeding[J].Genomics Inform,2015,13(4):146-151.
[13] MANOLIO T A,COLLINS F S,COX N J,et al.Finding the missing heritability of complex diseases[J].Nature,2009, 461(7265):747-753.
[14] WITTE J S,VISSCHER P M,WRAY N R.The contribution of genetic variants to disease depends on the ruler[J].Nat Rev Genet,2014,15(11):765-776.
[15] YANG J,BAKSHI A,ZHU Z H,et al.Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index[J].Nat Genet,2015,47(10):1114-1120.
[16] TENESA A,HALEY C S.The heritability of human disease:estimation,uses and abuses[J].Nat Rev Genet,2013,14(2):139-149.
[17] BURCH K S,HOU K C,DING Y,et al.Partitioning gene-level contributions to complex-trait heritability by allele frequency identifies disease-relevant genes[J].Am J Hum Genet,2022,109(4):692-709.
[18] ZHOU Y,ZHANG Z Y,BAO Z G,et al.Graph pangenome captures missing heritability and empowers tomato breeding[J].Nature,2022,606(7914):527-534.
[19] LÓPEZ-CORTEGANO E,CABALLERO A.Inferring the nature of missing heritability in human traits using data from the GWAS catalog[J].Genetics,2019,212(3):891-904.
[20] ALIPANAH M,ROUDBARI Z,MOMEN M,et al.Impact of inclusion non-additive effects on genome-wide association and variance’s components in Scottish black sheep[J].Anim Biotechnol,2023,34(8):3765-3773.
[21] CHEN X,KUJA-HALKOLA R,RAHMAN I,et al.Dominant genetic variation and missing heritability for human complex traits:insights from twin versus genome-wide common SNP models[J].Am J Hum Genet,2015,97(5):708-714.
[22] LI Z C,SIMIANER H.Pan-genomic open reading frames:a potential supplement of single nucleotide polymorphisms in estimation of heritability and genomic prediction[J].PLoS Genet,2020,16(8):e1008995.
[23] SPEED D,O’BRIEN T J,PALOTIE A,et al.Describing the genetic architecture of epilepsy through heritability analysis[J].Brain,2014,137(10):2680-2689.
[24] 常瑶,苏国生,李艳华,等.基于系谱和基因组信息估计荷斯坦青年母牛体重性状遗传参数[J].畜牧兽医学报,2022,53(11):3759-3768.
CHANG Y,SU G S,LI Y H,et al.Estimating genetic parameters for body weights using pedigree and genotype-pedigree based approaches in Holstein heifers[J].Acta Veterinaria et Zootechnica Sinica,2022,53(11):3759-3768.(in Chinese)
[25] JOERGENSEN D,MADSEN P,ROPSTAD E O,et al.Heritability estimates of distichiasis in Staffordshire bull terriers using pedigrees and genome-wide SNP data[J].Acta Vet Scand,2022,64(1):30.
[26] GUO H B,ZENG Q F,LI Y P,et al.Estimating realized heritability for growth in Zhikong scallop (Chlamys farreri) using genome-wide complex trait analysis[J].Aquaculture,2018,497:103-108.
[27] BÉRÉNOS C,ELLIS P A,PILKINGTON J G,et al.Estimating quantitative genetic parameters in wild populations:a comparison of pedigree and genomic approaches[J].Mol Ecol,2014,23(14):3434-3451.
[28] KHANZADEH H,GHAVI HOSSEIN-ZADEH N,GHOVVATI S.A meta-analysis of the gap between pedigree-based and genomic heritability estimates for production traits in dairy cows[J].Livest Sci,2022,263:105000.
[29] ZIMMERMANN E,DISTL O.SNP-based heritability of osteochondrosis dissecans in hanoverian warmblood horses[J].Animals (Basel),2023,13(9):1462.
[30] PERRIER C,DELAHAIE B,CHARMANTIER A.Heritability estimates from genomewide relatedness matrices in wild populations:application to a passerine,using a small sample size[J].Mol Ecol Resour,2018,18(4):838-853.
[31] OGAWA S,MATSUDA H,TANIGUCHI Y,et al.Estimation of the autosomal contribution to total additive genetic variability of carcass traits in Japanese Black cattle[J].Anim Sci J,2022,93(1):e13710.
[32] AASE K,JENSEN H,MUFF S.Genomic estimation of quantitative genetic parameters in wild admixed populations[J].Methods Ecol Evol,2022,13(5):1014-1026.
[33] BÉRÉNOS C,ELLIS P A,PILKINGTON J G,et al.Heterogeneity of genetic architecture of body size traits in a free-living population[J].Mol Ecol,2015,24(8):1810-1830.
[34] SPEED D,KAPHLE A,BALDING D J.SNP-based heritability and selection analyses:improved models and new results[J]. Bioessays,2022,44(5):2100170.
[35] MIN A L,THOMPSON E,BASU S.Comparing heritability estimators under alternative structures of linkage disequilibrium[J]. G3 (Bethesda),2022,12(8):jkac134.
[36] SCHWARTZMAN A,SCHORK A J,ZABLOCKI R,et al.A simple,consistent estimator of SNP heritability from genome-wide association studies[J].Ann Appl Stat,2019,13(4):2509-2538.
[37] YANG J,LEE S H,GODDARD M E,et al.GCTA:a tool for genome-wide complex trait analysis[J].Am J Hum Genet,2011,88(1): 76-82.
[38] YANG J,ZENG J,GODDARD M E,et al.Concepts,estimation and interpretation of SNP-based heritability[J].Nat Genet,2017,49(9):1304-1310.
[39] GUAN Y T,STEPHENS M.Bayesian variable selection regression for genome-wide association studies and other large-scale problems[J].Ann Appl Stat,2011,5(3):1780-1815.
[40] KRAG K,JANSS L L,SHARIATI M M,et al.SNP-based heritability estimation using a Bayesian approach[J]. Animal,2013,7(4):531-539.
[41] ZHOU X,CARBONETTO P,STEPHENS M.Polygenic modeling with Bayesian sparse linear mixed models[J].PLoS Genet, 2013, 9(2):e1003264.
[42] SPEED D,HEMANI G,JOHNSON M R,et al.Improved heritability estimation from genome-wide SNPs[J].Am J Hum Genet, 2012, 91(6):1011-1021.
[43] SPEED D,CAI N,The UCLEB Consortium,et al.Reevaluation of SNP heritability in complex human traits[J].Nat Genet,2017, 49(7):986-992.
[44] BULIK-SULLIVAN B K,LOH P R,FINUCANE H K,et al.LD Score regression distinguishes confounding from polygenicity in genome-wide association studies[J].Nat Genet,2015,47(3):291-295.
[45] HOU K C,BURCH K S,MAJUMDAR A,et al.Accurate estimation of SNP-heritability from biobank-scale data irrespective of genetic architecture[J].Nat Genet,2019,51(8):1244-1251.
[46] YOUNG A I,FRIGGE M L,GUDBJARTSSON D F,et al.Relatedness disequilibrium regression estimates heritability without environmental bias[J].Nat Genet,2018,50(9):1304-1310.
[47] ARJAS A,HAUPTMANN H,SILLANPÄÄ M J.Estimation of dynamic SNP-heritability with Bayesian Gaussian process models[J].Bioinformatics,2020,36(12):3795-3802.
[48] LEE S H,WRAY N R,GODDARD M E,et al.Estimating missing heritability for disease from genome-wide association studies[J].Am J Hum Genet,2011,88(3):294-305.
[49] GOLAN D,LANDER E S,ROSSET S.Measuring missing heritability:inferring the contribution of common variants[J].Proc Natl Acad Sci U S A,2014,111(49):E5272-E5281.
[50] SUN S Q,ZHU J Q,MOZAFFARI S,et al.Heritability estimation and differential analysis of count data with generalized linear mixed models in genomic sequencing studies[J].Bioinformatics,2019,35(3):487-496.
[51] ZHOU X.A unified framework for variance component estimation with summary statistics in genome-wide association studies[J].Ann Appl Stat,2017,11(4):2027-2051.
[52] GE T,CHEN C Y,NEALE B M,et al.Phenome-wide heritability analysis of the UK Biobank[J].PLoS Genet,2017,13(4): e1006711.
[53] PALLA L,DUDBRIDGE F.A fast method that uses polygenic scores to estimate the variance explained by genome-wide marker panels and the proportion of variants affecting a trait[J].Am J Hum Genet,2015,97(2):250-259.
[54] VISSCHER P M,GODDARD M E.A general unified framework to assess the sampling variance of heritability estimates using pedigree or marker-based relationships[J].Genetics,2015,199(1):223-232.
[55] UEMOTO Y,SASAKI S,KOJIMA T,et al.Impact of QTL minor allele frequency on genomic evaluation using real genotype data and simulated phenotypes in Japanese Black cattle[J].BMC Genet,2015,16:134.
[56] EVANS L M,TAHMASBI R,VRIEZE S I,et al.Comparison of methods that use whole genome data to estimate the heritability and genetic architecture of complex traits[J].Nat Genet,2018,50(5):737-745.
[57] DANDINE-ROULLAND C,BELLENGUEZ C,DEBETTE S,et al.Accuracy of heritability estimations in presence of hidden population stratification[J].Sci Rep,2016,6:26471.
[58] GODDARD M E,HAYES B J.Mapping genes for complex traits in domestic animals and their use in breeding programmes[J].Nat Rev Genet,2009,10(6):381-391.
[59] JAMES C,PEMBERTON J M,NAVARRO P,et al.The impact of SNP density on quantitative genetic analyses of body size traits in a wild population of Soay sheep[J].Ecol Evol,2022,12(12):e9639.
[60] MATHEW B,LÉON J,SILLANPÄÄ M J.A novel linkage-disequilibrium corrected genomic relationship matrix for SNP-heritability estimation and genomic prediction[J].Heredity (Edinb),2018,120(4):356-368.
[61] REN D Y,CAI X D,LIN Q,et al.Impact of linkage disequilibrium heterogeneity along the genome on genomic prediction and heritability estimation[J].Genet Sel Evol,2022,54(1):47.
[62] GUL S,ARZIK Y,KIZILASLAN M,et al.Heritability and environmental influence on pre-weaning traits in Kilis goats[J].Trop Anim Health Prod,2023,55(2):85.
[63] 阮栋林,陈悦,庄站伟,等.基于SNP芯片的杜洛克种猪生长和体尺性状遗传参数估计及相关分析[J].家畜生态学报,2023,44(2):19-24.
RUAN D L,CHEN Y,ZHUANG Z W,et al.Genetic parameter estimation and correlation analysis of growth traits and body traits in Duroc pigs based on SNP chip[J].Journal of Domestic Animal Ecology,2023,44(2):19-24.(in Chinese)
[64] ARZIK Y,KIZILASLAN M,BEHREM S,et al.Genome-wide scan of wool production traits in akkaraman sheep[J].Genes (Basel),2023,14(3):713.
[65] 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.
[66] ZHANG F,ZHU F,YANG F X,et al.Genomic selection for meat quality traits in Pekin duck[J].Anim Genet,2022,53(1):94-100.
[67] ROSTAMZADEH MAHDABI E,TIAN R G,LI Y,et al.Genomic heritability and correlation between carcass traits in Japanese Black cattle evaluated under different ceilings of relatedness among individuals[J].Front Genet,2023,14:1053291.
[68] TUSELL L,GILBERT H,VITEZICA Z G,et al.Dissecting total genetic variance into additive and dominance components of purebred and crossbred pig traits[J].Animal,2019,13(11):2429-2439.
[69] WU Z Y,DOU T F,BAI L Y,et al.Genomic prediction and genome-wide association studies for additive and dominance effects for body composition traits using 50 K and imputed high-density SNP genotypes in Yunong-black pigs[J].J Anim Breed Genet,2023,doi:10.1111/jbg.12830.
[70] HAYES B J,COPLEY J,DODD E,et al.Multi-breed genomic evaluation for tropical beef cattle when no pedigree information is available[J].Genet Sel Evol,2023,55(1):71.
[71] SUTERA A M,TOLONE M,MASTRANGELO S,et al.Detection of genomic regions underlying milk production traits in Valle del Belice dairy sheep using regional heritability mapping[J].J Anim Breed Genet,2021,138(5):552-561.
[72] MOGHADDAR N,BROWN D J,SWAN A A,et al.Genomic prediction in a numerically small breed population using prioritized genetic markers from whole-genome sequence data[J].J Anim Breed Genet,2021,139(1):71-83.