Dataset Information

Factors Affecting the Accuracy of Genomic Selection for Agricultural Economic Traits in Maize, Cattle, and Pig Populations.

ABSTRACT: Genomic Selection (GS) has been proved to be a powerful tool for estimating genetic values in plant and livestock breeding. Newly developed sequencing technologies have dramatically reduced the cost of genotyping and significantly increased the scale of genotype data that used for GS. Meanwhile, state-of-the-art statistical methods were developed to make the best use of high marker density genotype data. In this study, 14 traits from four data sets of three species (maize, cattle, and pig) and five influential factors that affect the prediction accuracy were evaluated, including marker density (from 1 to ~600 k), statistical method (GBLUP-A, GBLUP-AD, and BayesR), minor allele frequency (MAF), heritability, and genetic architecture. Results indicate that in the GBLUP method, higher marker density leads to a higher prediction accuracy. In contrast, BayesR method needs more Monte Carlo Markov Chain (MCMC) iterations to reach the convergence and get reliable prediction values. BayesR outperforms GBLUP in predicting high or medium heritability trait that affected by one or several genes with large effects, while GBLUP performs similarly or slightly better than BayesR in predicting low heritability trait that controlled by a large amount of genes with minor effects. Prediction accuracy of trait with complex genetic architecture can be improved by increasing the marker density. Interestingly, for simple traits that controlled by one or several genes with large effects, higher marker density can cause a lower prediction accuracy if the QTN is included, but leads to a higher prediction accuracy if the QTN is excluded. The quantity of genetic markers with low MAF would not significantly affect the prediction accuracy of GBLUP, but results in a bad prediction accuracy performance of BayesR method. Compared with GBLUP-A, GBLUP-AD didn't show any advantages in capturing the non-additive variance for the traits with high heritability. The factors that affected prediction accuracy are discussed in this study and indicate that a combination of either GBLUP or BayesR method with moderate marker density and favorable polymorphism single nucleotide polymorphisms (SNPs) (~25 k SNPs) would always produce a good and stable prediction accuracy with acceptable breeding and computational costs.

SUBMITTER: Zhang H

PROVIDER: S-EPMC6426750 | biostudies-literature | 2019

REPOSITORIES: biostudies-literature

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Factors Affecting the Accuracy of Genomic Selection for Agricultural Economic Traits in Maize, Cattle, and Pig Populations.

Zhang Haohao H Yin Lilin L Wang Meiyue M Yuan Xiaohui X Liu Xiaolei X

Frontiers in genetics 20190314

Genomic Selection (GS) has been proved to be a powerful tool for estimating genetic values in plant and livestock breeding. Newly developed sequencing technologies have dramatically reduced the cost of genotyping and significantly increased the scale of genotype data that used for GS. Meanwhile, state-of-the-art statistical methods were developed to make the best use of high marker density genotype data. In this study, 14 traits from four data sets of three species (maize, cattle, and pig) and f ...[more]

PMID: 30923535

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Project description:BackgroundThousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions.ResultsFive statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR?<?5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8, PPP1R12A, SLC16A3, UCP2, UCP3, TIGAR), cold acclimation (AQP3, AQP7, HSPB8), body size and stature (PLAG1, KCNA6, NDUFA9, AKAP3, C5H12orf4, RAD51AP1, FGF6, TIGAR, CCND2, CSMD3), resistance to disease and bacterial infection (CHI3L2, GBP6, PPFIBP1, REP15, CYP4F2, TIGD2, PYURF, SLC10A2, FCHSD2, ARHGEF17, RELT, PRDM2, KDM5B), reproduction (PPP1R12A, ZFP36L2, CSPP1), milk yield and components (NPC1L1, NUDCD3, ACSS1, FCHSD2), growth and feed efficiency (TMEM68, TGS1, LYN, XKR4, FOXA2, GBP2, GBP5, FGD6), and polled phenotype (URB1, EVA1C).ConclusionsWe identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p-values of different statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses.

Project description:BACKGROUND: Genotype imputation is a cost efficient alternative to use of high density genotypes for implementing genomic selection. The objective of this study was to investigate variables affecting imputation accuracy from low density tagSNP (average distance between tagSNP from 100kb to 1Mb) sets in swine, selected using LD information, physical location, or accuracy for genotype imputation. We compared results of imputation accuracy based on several sets of low density tagSNP of varying densities and selected using three different methods. In addition, we assessed the effect of varying size and composition of the reference panel of haplotypes used for imputation. RESULTS: TagSNP density of at least 1 tagSNP per 340kb (~7000 tagSNP) selected using pairwise LD information was necessary to achieve average imputation accuracy higher than 0.95. A commercial low density (9K) tagSNP set for swine was developed concurrent to this study and an average accuracy of imputation of 0.951 based on these tagSNP was estimated. Construction of a haplotype reference panel was most efficient when these haplotypes were obtained from randomly sampled individuals. Increasing the size of the original reference haplotype panel (128 haplotypes sampled from 32 sire/dam/offspring trios phased in a previous study) led to an overall increase in imputation accuracy (IA = 0.97 with 512 haplotypes), but was especially useful in increasing imputation accuracy of SNP with MAF below 0.1 and for SNP located in the chromosomal extremes (within 5% of chromosome end). CONCLUSION: The new commercially available 9K tagSNP set can be used to obtain imputed genotypes with high accuracy, even when imputation is based on a comparably small panel of reference haplotypes (128 haplotypes). Average imputation accuracy can be further increased by adding haplotypes to the reference panel. In addition, our results show that randomly sampling individuals to genotype for the construction of a reference haplotype panel is more cost efficient than specifically sampling older animals or trios with no observed loss in imputation accuracy. We expect that the use of imputed genotypes in swine breeding will yield highly accurate predictions of GEBV, based on the observed accuracy and reported results in dairy cattle, where genomic evaluation of some individuals is based on genotypes imputed with the same accuracy as our Yorkshire population.

Dataset Information

Factors Affecting the Accuracy of Genomic Selection for Agricultural Economic Traits in Maize, Cattle, and Pig Populations.

Publications

Factors Affecting the Accuracy of Genomic Selection for Agricultural Economic Traits in Maize, Cattle, and Pig Populations.

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