Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus

Abstract Chicken growth traits are economically important, but the relevant genetic mechanisms have not yet been elucidated. Herein, we performed a genome-wide association study to identify the variants associated with growth traits. In total, 860 chickens from a Gushi-Anka F2 resource population were phenotyped for 68 growth and carcass traits, and 768 samples were genotyped based on the genotyping-by-sequencing (GBS) method. Finally, 734 chickens and 321,314 SNPs remained after quality control and removal of the sex chromosomes, and these data were used to carry out a GWAS analysis. A total of 470 significant single-nucleotide polymorphisms (SNPs) for 43 of the 68 traits were detected and mapped on chromosomes (Chr) 1–6, -9, -10, -16, -18, -23, and -27. Of these, the significant SNPs in Chr1, -4, and -27 were found to be associated with more than 10 traits. Multiple traits shared significant SNPs, indicating that the same mutation in the region might have a large effect on multiple growth or carcass traits. Haplotype analysis revealed that SNPs within the candidate region of Chr1 presented a mosaic pattern. The significant SNPs and pathway enrichment analysis revealed that the MLNR, MED4, CAB39L, LDB2, and IGF2BP1 genes could be putative candidate genes for growth and carcass traits. The findings of this study improve our understanding of the genetic mechanisms regulating chicken growth and carcass traits and provide a theoretical basis for chicken breeding programs.

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Identification of genetic loci associated with growth traits at weaning in yak through a genome‐wide association study

Animal Genetics ◽

10.1111/age.12897 ◽

2019 ◽

Vol 51 (2) ◽

pp. 300-305

Author(s):

C. Jia ◽

C. Li ◽

D. Fu ◽

M. Chu ◽

L. Zan ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Growth Traits ◽

Genome Wide Association ◽

Genetic Loci ◽

Genome Wide ◽

A Genome

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Genome‑wide association study and genomic prediction for growth traits in yellow-plumage chicken using genotyping-by-sequencing

Genetics Selection Evolution ◽

10.1186/s12711-021-00672-9 ◽

2021 ◽

Vol 53 (1) ◽

Author(s):

Ruifei Yang ◽

Zhenqiang Xu ◽

Qi Wang ◽

Di Zhu ◽

Cheng Bian ◽

...

Keyword(s):

Association Study ◽

Genomic Prediction ◽

Genetic Background ◽

Prediction Accuracy ◽

Genome Wide Association Study ◽

Growth Traits ◽

Genome Wide Association ◽

Genomic Feature ◽

Genomic Information ◽

Genome Wide

Abstract Background Growth traits are of great importance for poultry breeding and production and have been the topic of extensive investigation, with many quantitative trait loci (QTL) detected. However, due to their complex genetic background, few causative genes have been confirmed and the underlying molecular mechanisms remain unclear, thus limiting our understanding of QTL and their potential use for the genetic improvement of poultry. Therefore, deciphering the genetic architecture is a promising avenue for optimising genomic prediction strategies and exploiting genomic information for commercial breeding. The objectives of this study were to: (1) conduct a genome-wide association study to identify key genetic factors and explore the polygenicity of chicken growth traits; (2) investigate the efficiency of genomic prediction in broilers; and (3) evaluate genomic predictions that harness genomic features. Results We identified five significant QTL, including one on chromosome 4 with major effects and four on chromosomes 1, 2, 17, and 27 with minor effects, accounting for 14.5 to 34.1% and 0.2 to 2.6% of the genomic additive genetic variance, respectively, and 23.3 to 46.7% and 0.6 to 4.5% of the observed predictive accuracy of breeding values, respectively. Further analysis showed that the QTL with minor effects collectively had a considerable influence, reflecting the polygenicity of the genetic background. The accuracy of genomic best linear unbiased predictions (BLUP) was improved by 22.0 to 70.3% compared to that of the conventional pedigree-based BLUP model. The genomic feature BLUP model further improved the observed prediction accuracy by 13.8 to 15.2% compared to the genomic BLUP model. Conclusions A major QTL and four minor QTL were identified for growth traits; the remaining variance was due to QTL effects that were too small to be detected. The genomic BLUP and genomic feature BLUP models yielded considerably higher prediction accuracy compared to the pedigree-based BLUP model. This study revealed the polygenicity of growth traits in yellow-plumage chickens and demonstrated that the predictive ability can be greatly improved by using genomic information and related features.

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PSXI-7 Genomic analysis of heterosis in a composite beef cattle breed

Journal of Animal Science ◽

10.1093/jas/skab235.445 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 244-244

Author(s):

El Hamidi Hay ◽

Andrew Roberts

Keyword(s):

Birth Weight ◽

Beef Cattle ◽

Association Study ◽

Genome Wide Association Study ◽

Growth Traits ◽

Snp Markers ◽

Genome Wide Association ◽

Weaning Weight ◽

Genome Wide ◽

A Genome

Abstract Crossbreeding is widely used in the beef cattle industry to exploit benefits of heterosis. This study evaluated the effects of heterozygosity on growth traits in an Angus x Hereford cross population. Moreover, a genome wide association study was conducted to detect regions in the genome with significant dominance effects on growth traits contributing to heterosis. A total of 1,530 animals, comprised of pure Line 1 Hereford, Angus and Angus x Line 1 Hereford crosses, were evaluated. Phenotypes included birth weight, weaning weight and yearling weight. All animals were genotyped with GeneSeek GGP LD 50k. Effects of genomic heterozygosity on growth traits were estimated. These effects were -0.76 kg (P < 0.001), 4.67 kg (P < 0.0001), 42.39 kg (P < 0.02) on birth weight, weaning weight and yearling weight respectively. A genome wide association study revealed several SNP markers with significant heterotic effects associated with birth weight, weaning weight and yearling weight. These SNP markers were located on chromosomes 1, 2, 14, 19, 13 and 12. Genes in these regions were reported to be involved in growth and other important physiological mechanisms. Our study revealed several regions associated with dominance effects and contributing to heterosis. These results could be beneficial in optimizing crossbreeding.

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