Genomic Prediction Using LD-Based Haplotypes in Combined Pig Populations

Ye, Haoqiang; Zhang, Zipeng; Ren, Duanyang; Cai, Xiaodian; Zhu, Qianghui; Ding, Xiangdong; Zhang, Hao; Zhang, Zhe; Li, Jiaqi

doi:10.3389/fgene.2022.843300

Cited by 3 publications

(1 citation statement)

References 55 publications

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“…As shown in a large number of studies, high-density SNP markers and imputed data are not more accurate than medium-density markers. Therefore, this study directly used more economical and convenient 50k chips [26,39]. The implications of our findings hold significant relevance for the pragmatic aspects of Chinese pig breeding.…”

Section: Discussionmentioning

confidence: 78%

Genomic Prediction of Growth Traits in Yorkshire Pigs of Different Reference Group Sizes Using Different Estimated Breeding Value Models

Yin,

Shi,

Zhou

et al. 2024

Animals

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The need for sufficient reference population data poses a significant challenge in breeding programs aimed at improving pig farming on a small to medium scale. To overcome this hurdle, investigating the advantages of combing reference populations of varying sizes is crucial for enhancing the accuracy of the genomic estimated breeding value (GEBV). Genomic selection (GS) in populations with limited reference data can be optimized by combining populations of the same breed or related breeds. This study focused on understanding the effect of combing different reference group sizes on the accuracy of GS for determining the growth effectiveness and percentage of lean meat in Yorkshire pigs. Specifically, our study investigated two important traits: the age at 100 kg live weight (AGE100) and the backfat thickness at 100 kg live weight (BF100). This research assessed the efficiency of genomic prediction (GP) using different GEBV models across three Yorkshire populations with varying genetic backgrounds. The GeneSeek 50K GGP porcine high-density array was used for genotyping. A total of 2295 Yorkshire pigs were included, representing three Yorkshire pig populations with different genetic backgrounds—295 from Danish (small) lines from Huaibei City, Anhui Province, 500 from Canadian (medium) lines from Lixin County, Anhui Province, and 1500 from American (large) lines from Shanghai. To evaluate the impact of different population combination scenarios on the GS accuracy, three approaches were explored: (1) combining all three populations for prediction, (2) combining two populations to predict the third, and (3) predicting each population independently. Five GEBV models, including three Bayesian models (BayesA, BayesB, and BayesC), the genomic best linear unbiased prediction (GBLUP) model, and single-step GBLUP (ssGBLUP) were implemented through 20 repetitions of five-fold cross-validation (CV). The results indicate that predicting one target population using the other two populations yielded the highest accuracy, providing a novel approach for improving the genomic selection accuracy in Yorkshire pigs. In this study, it was found that using different populations of the same breed to predict small- and medium-sized herds might be effective in improving the GEBV. This investigation highlights the significance of incorporating population combinations in genetic models for predicting the breeding value, particularly for pig farmers confronted with resource limitations.

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Section: Discussionmentioning

confidence: 78%

Genomic Prediction of Growth Traits in Yorkshire Pigs of Different Reference Group Sizes Using Different Estimated Breeding Value Models

Yin,

Shi,

Zhou

et al. 2024

Animals

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Genomic prediction within and across maize landrace derived populations using haplotypes

Lin,

Mayer,

Valle Torres

et al. 2024

Front. Plant Sci.

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Genomic prediction (GP) using haplotypes is considered advantageous compared to GP solely reliant on single nucleotide polymorphisms (SNPs), owing to haplotypes’ enhanced ability to capture ancestral information and their higher linkage disequilibrium with quantitative trait loci (QTL). Many empirical studies supported the advantages of haplotype-based GP over SNP-based approaches. Nevertheless, the performance of haplotype-based GP can vary significantly depending on multiple factors, including the traits being studied, the genetic structure of the population under investigation, and the particular method employed for haplotype construction. In this study, we compared haplotype and SNP based prediction accuracies in four populations derived from European maize landraces. Populations comprised either doubled haploid lines (DH) derived directly from landraces, or gamete capture lines (GC) derived from crosses of the landraces with an inbred line. For two different landraces, both types of populations were generated, genotyped with 600k SNPs and phenotyped as lines per se for five traits. Our study explores three prediction scenarios: (i) within each of the four populations, (ii) across DH and GC populations from the same landrace, and (iii) across landraces using either DH or GC populations. Three haplotype construction methods were evaluated: 1. fixed-window blocks (FixedHB), 2. LD-based blocks (HaploView), and 3. IBD-based blocks (HaploBlocker). In within population predictions, FixedHB and HaploView methods performed as well as or slightly better than SNPs for all traits. HaploBlocker improved accuracy for certain traits but exhibited inferior performance for others. In prediction across populations, the parameter setting from HaploBlocker which controls the construction of shared haplotypes between populations played a crucial role for obtaining optimal results. When predicting across landraces, accuracies were low for both, SNP and haplotype approaches, but for specific traits substantial improvement was observed with HaploBlocker. This study provides recommendations for optimal haplotype construction and identifies relevant parameters for constructing haplotypes in the context of genomic prediction.

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Development and Validation of a 54K Genome-Wide Liquid SNP Chip Panel by Target Sequencing for Dairy Goat

Guan

Jin

et al. 2023

Genes

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As an important genotyping platform, SNP chips are essential for implementing genomic selection. In this article, we introduced the development of a liquid SNP chip panel for dairy goats. This panel contains 54,188 SNPs based on genotyping by targeted sequencing (GBTS) technology. The source of SNPs in the panel were from the whole-genome resequencing of 110 dairy goats from three European and two Chinese indigenous dairy goat breeds. The performance of this liquid SNP chip panel was evaluated by genotyping 200 additional goats. Fifteen of them were randomly selected for whole-genome resequencing. The average capture ratio of the panel design loci was 98.41%, and the genotype concordance with resequencing reached 98.02%. We further used this chip panel to conduct genome-wide association studies (GWAS) to detect genetic loci that affect coat color in dairy goats. A single significant association signal for hair color was found on chromosome 8 at 31.52–35.02 Mb. The TYRP1 gene, which is associated with coat color in goats, was identified to be located at this genomic region (chromosome 8: 31,500,048-31,519,064). The emergence of high-precision and low-cost liquid microarrays will improve the analysis of genomics and breeding efficiency of dairy goats.

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Genomic Prediction Using LD-Based Haplotypes in Combined Pig Populations

Cited by 3 publications

References 55 publications

Genomic Prediction of Growth Traits in Yorkshire Pigs of Different Reference Group Sizes Using Different Estimated Breeding Value Models

Genomic Prediction of Growth Traits in Yorkshire Pigs of Different Reference Group Sizes Using Different Estimated Breeding Value Models

Genomic prediction within and across maize landrace derived populations using haplotypes

Development and Validation of a 54K Genome-Wide Liquid SNP Chip Panel by Target Sequencing for Dairy Goat

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