Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle
A haplotype is defined as a combination of alleles at adjacent loci belonging to the same chromosome that can be transmitted as a unit. In this study, we used both the Illumina BovineHD chip (HD chip) and imputed whole-genome sequence (WGS) data to explore haploblocks and assess haplotype effects, a...
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2021-07-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2021.665382/full |
| id |
doaj-be6c6d0968524f1d8280665486bdce6d |
|---|---|
| record_format |
Article |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Hongwei Li Bo Zhu Bo Zhu Ling Xu Zezhao Wang Lei Xu Peinuo Zhou Han Gao Peng Guo Yan Chen Xue Gao Lupei Zhang Huijiang Gao Huijiang Gao Wentao Cai Lingyang Xu Junya Li Junya Li |
| spellingShingle |
Hongwei Li Bo Zhu Bo Zhu Ling Xu Zezhao Wang Lei Xu Peinuo Zhou Han Gao Peng Guo Yan Chen Xue Gao Lupei Zhang Huijiang Gao Huijiang Gao Wentao Cai Lingyang Xu Junya Li Junya Li Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle Frontiers in Genetics genomic prediction prediction accuracy LD haplotype Chinese Simmental beef cattle |
| author_facet |
Hongwei Li Bo Zhu Bo Zhu Ling Xu Zezhao Wang Lei Xu Peinuo Zhou Han Gao Peng Guo Yan Chen Xue Gao Lupei Zhang Huijiang Gao Huijiang Gao Wentao Cai Lingyang Xu Junya Li Junya Li |
| author_sort |
Hongwei Li |
| title |
Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle |
| title_short |
Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle |
| title_full |
Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle |
| title_fullStr |
Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle |
| title_full_unstemmed |
Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef Cattle |
| title_sort |
genomic prediction using ld-based haplotypes inferred from high-density chip and imputed sequence variants in chinese simmental beef cattle |
| publisher |
Frontiers Media S.A. |
| series |
Frontiers in Genetics |
| issn |
1664-8021 |
| publishDate |
2021-07-01 |
| description |
A haplotype is defined as a combination of alleles at adjacent loci belonging to the same chromosome that can be transmitted as a unit. In this study, we used both the Illumina BovineHD chip (HD chip) and imputed whole-genome sequence (WGS) data to explore haploblocks and assess haplotype effects, and the haploblocks were defined based on the different LD thresholds. The accuracies of genomic prediction (GP) for dressing percentage (DP), meat percentage (MP), and rib eye roll weight (RERW) based on haplotype were investigated and compared for both data sets in Chinese Simmental beef cattle. The accuracies of GP using the entire imputed WGS data were lower than those using the HD chip data in all cases. For DP and MP, the accuracy of GP using haploblock approaches outperformed the individual single nucleotide polymorphism (SNP) approach (GBLUP_In_Block) at specific LD levels. Hotelling’s test confirmed that GP using LD-based haplotypes from WGS data can significantly increase the accuracies of GP for RERW, compared with the individual SNP approach (∼1.4 and 1.9% for GHBLUP and GHBLUP+GBLUP, respectively). We found that the accuracies using haploblock approach varied with different LD thresholds. The LD thresholds (r2 ≥ 0.5) were optimal for most scenarios. Our results suggested that LD-based haploblock approach can improve accuracy of genomic prediction for carcass traits using both HD chip and imputed WGS data under the optimal LD thresholds in Chinese Simmental beef cattle. |
| topic |
genomic prediction prediction accuracy LD haplotype Chinese Simmental beef cattle |
| url |
https://www.frontiersin.org/articles/10.3389/fgene.2021.665382/full |
| work_keys_str_mv |
AT hongweili genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT bozhu genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT bozhu genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT lingxu genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT zezhaowang genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT leixu genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT peinuozhou genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT hangao genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT pengguo genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT yanchen genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT xuegao genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT lupeizhang genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT huijianggao genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT huijianggao genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT wentaocai genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT lingyangxu genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT junyali genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle AT junyali genomicpredictionusingldbasedhaplotypesinferredfromhighdensitychipandimputedsequencevariantsinchinesesimmentalbeefcattle |
| _version_ |
1721251829494317056 |
| spelling |
doaj-be6c6d0968524f1d8280665486bdce6d2021-07-29T08:45:39ZengFrontiers Media S.A.Frontiers in Genetics1664-80212021-07-011210.3389/fgene.2021.665382665382Genomic Prediction Using LD-Based Haplotypes Inferred From High-Density Chip and Imputed Sequence Variants in Chinese Simmental Beef CattleHongwei Li0Bo Zhu1Bo Zhu2Ling Xu3Zezhao Wang4Lei Xu5Peinuo Zhou6Han Gao7Peng Guo8Yan Chen9Xue Gao10Lupei Zhang11Huijiang Gao12Huijiang Gao13Wentao Cai14Lingyang Xu15Junya Li16Junya Li17Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaNational Centre of Beef Cattle Genetic Evaluation, Beijing, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaCollege of Computer and Information Engineering, Tianjin Agricultural University, Tianjin, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaNational Centre of Beef Cattle Genetic Evaluation, Beijing, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaLaboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaNational Centre of Beef Cattle Genetic Evaluation, Beijing, ChinaA haplotype is defined as a combination of alleles at adjacent loci belonging to the same chromosome that can be transmitted as a unit. In this study, we used both the Illumina BovineHD chip (HD chip) and imputed whole-genome sequence (WGS) data to explore haploblocks and assess haplotype effects, and the haploblocks were defined based on the different LD thresholds. The accuracies of genomic prediction (GP) for dressing percentage (DP), meat percentage (MP), and rib eye roll weight (RERW) based on haplotype were investigated and compared for both data sets in Chinese Simmental beef cattle. The accuracies of GP using the entire imputed WGS data were lower than those using the HD chip data in all cases. For DP and MP, the accuracy of GP using haploblock approaches outperformed the individual single nucleotide polymorphism (SNP) approach (GBLUP_In_Block) at specific LD levels. Hotelling’s test confirmed that GP using LD-based haplotypes from WGS data can significantly increase the accuracies of GP for RERW, compared with the individual SNP approach (∼1.4 and 1.9% for GHBLUP and GHBLUP+GBLUP, respectively). We found that the accuracies using haploblock approach varied with different LD thresholds. The LD thresholds (r2 ≥ 0.5) were optimal for most scenarios. Our results suggested that LD-based haploblock approach can improve accuracy of genomic prediction for carcass traits using both HD chip and imputed WGS data under the optimal LD thresholds in Chinese Simmental beef cattle.https://www.frontiersin.org/articles/10.3389/fgene.2021.665382/fullgenomic predictionprediction accuracyLDhaplotypeChinese Simmental beef cattle |