Comparison of haplotype method using for genomic prediction versus single SNP genotypes in sheep breeding programs

Sharifi, Reza; Noshahr, F. Ala; Seifdavati, Jamal; Evrigh, Nemat Hedayat; Cipriano‐Salazar, Moisés; Mariezcurrena-Berasain, María Antonia

doi:10.1016/j.smallrumres.2021.106380

Cited by 3 publications

(2 citation statements)

References 17 publications

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“…It is well-established that DNA-based inheritance enables the transmission of selected phenotypes across generations either without changes in the DNA sequence through epigenetic inheritance [31] or through functional mutations involving changes in only one base pair (single nucleotide polymorphisms-SNP). Through next-generation sequencing, SNP are valuable for detecting genetic variability and genomic prediction in sheep breeding programs [32], developing breed-specific DNA markers for breed identification [33,34], animal productivity [35], parentage assignment [36,37], forensics [38], and prediction of meat quality traits [39][40][41].…”

Section: Discussionmentioning

confidence: 99%

Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb

Pewan

Otto

Huerlimann

et al. 2021

Foods

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Meat quality data can only be obtained after slaughter when selection decisions about the live animal are already too late. Carcass estimated breeding values present major precision problems due to low accuracy, and by the time an informed decision on the genetic merit for meat quality is made, the animal is already dead. We report for the first time, a targeted next-generation sequencing (NGS) of single nucleotide polymorphisms (SNP) of lipid metabolism genes in Tattykeel Australian White (TAW) sheep of the MARGRA lamb brand, utilizing an innovative and minimally invasive muscle biopsy sampling technique for directly quantifying the genetic worth of live lambs for health-beneficial omega-3 long-chain polyunsaturated fatty acids (n-3 LC-PUFA), intramuscular fat (IMF), and fat melting point (FMP). NGS of stearoyl-CoA desaturase (SCD), fatty acid binding protein-4 (FABP4), and fatty acid synthase (FASN) genes identified functional SNP with unique DNA marker signatures for TAW genetics. The SCD g.23881050T>C locus was significantly associated with IMF, C22:6n-3, and C22:5n-3; FASN g.12323864A>G locus with FMP, C18:3n-3, C18:1n-9, C18:0, C16:0, MUFA, and FABP4 g.62829478A>T locus with IMF. These add new knowledge, precision, and reliability in directly making early and informed decisions on live sheep selection and breeding for health-beneficial n-3 LC-PUFA, FMP, IMF and superior meat-eating quality at the farmgate level. The findings provide evidence that significant associations exist between SNP of lipid metabolism genes and n-3 LC-PUFA, IMF, and FMP, thus underpinning potential marker-assisted selection for meat-eating quality traits in TAW lambs.

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Section: Discussionmentioning

confidence: 99%

Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb

Pewan

Otto

Huerlimann

et al. 2021

Foods

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“…The number of SNP markers a haploblock should contain and for which regions of the genome the haploblocks should be defined are needed to be considered when building haplotype blocks. Some methods to define haploblock for GS are simply setting windows with a fixed number of contiguous SNPs ( Hayes et al, 2007 ), a fixed range of base pairs on the genome ( Hess et al, 2017 ; Sharifi et al, 2021 ), and a fixed-length in centimorgans ( Sun et al, 2015 ), collectively termed as fixed-length haploblocks, which are in equal sizes of segments in the genome. Some complicated methods to define haploblock for GS attempt to incorporate the LD pattern across the genome ( Cuyabano et al, 2015a ; Won et al, 2021 ), for example, setting minimum pairwise LD cutoffs to group SNPs into haplotypes, termed variable-length haploblocks, which are in unequal sizes of the segments in the genome and may result in less explanatory variables than fixed-length haploblocks ( Cuyabano et al, 2014 ).…”

Section: Introductionmentioning

confidence: 99%

Genomic Prediction Using LD-Based Haplotypes in Combined Pig Populations

Zhang

Ren

et al. 2022

Front. Genet.

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The size of reference population is an important factor affecting genomic prediction. Thus, combining different populations in genomic prediction is an attractive way to improve prediction ability. However, combining multireference population roughly cannot increase the prediction accuracy as well as expected in pig. This may be due to different linkage disequilibrium (LD) pattern differences between population. In this study, we used the imputed whole-genome sequencing (WGS) data to construct LD-based haplotypes for genomic prediction in combined population to explore the impact of different single-nucleotide polymorphism (SNP) densities, variant representation (SNPs or haplotype alleles), and reference population size on the prediction accuracy for reproduction traits. Our results showed that genomic best linear unbiased prediction (GBLUP) using the WGS data can improve prediction accuracy in multi-population but not within-population. Not only the genomic prediction accuracy of the haplotype method using 80 K chip data in multi-population but also GBLUP for the multi-population (3.4–5.9%) was higher than that within-population (1.2–4.3%). More importantly, we have found that using the haplotype method based on the WGS data in multi-population has better genomic prediction performance, and our results showed that building haploblock in this scenario based on low LD threshold (r2 = 0.2–0.3) produced an optimal set of variables for reproduction traits in Yorkshire pig population. Our results suggested that whether the use of the haplotype method based on the chip data or GBLUP (individual SNP method) based on the WGS data were beneficial for genomic prediction in multi-population, while simultaneously combining the haplotype method and WGS data was a better strategy for multi-population genomic evaluation.

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Haplotype analysis of genomic prediction by incorporating genomic pathway information based on high-density SNP marker in Chinese yellow-feathered chicken

Bello

et al. 2023

Poultry Science

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Comparison of haplotype method using for genomic prediction versus single SNP genotypes in sheep breeding programs

Cited by 3 publications

References 17 publications

Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb

Next Generation Sequencing of Single Nucleotide Polymorphic DNA-Markers in Selecting for Intramuscular Fat, Fat Melting Point, Omega-3 Long-Chain Polyunsaturated Fatty Acids and Meat Eating Quality in Tattykeel Australian White MARGRA Lamb

Genomic Prediction Using LD-Based Haplotypes in Combined Pig Populations

Haplotype analysis of genomic prediction by incorporating genomic pathway information based on high-density SNP marker in Chinese yellow-feathered chicken

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