Genome-wide association study and predictive ability for growth traits in Nellore cattle

Carvalho, Fabrício Kitazono de; Espigolan, Rafael; Berton, Mariana Piatto; Neto, José Braccini; Silva, R.P.; Grigoletto, Laís; Silva, R.M.O.; Ferraz, José Bento Sterman; Eler, Joanir Pereira; Aguilar, Ignácio; Lôbo, Raysildo Barbosa; Baldi, Fernando

doi:10.1016/j.livsci.2019.103861

Cited by 5 publications

(4 citation statements)

References 162 publications

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“…On the other hand, DP had an almost significant signal on BTA1: the gene closest to the SNP was SIM2 , already known to be associated with carcass quality, differentiation of longissimus, and semimembranosus muscle ( De Las Heras-Saldana et al, 2019 ; Edea et al, 2020 ). To conclude, the strongest of the remaining suggestively associated signals for DP came from BTA4, within LOC112446424 , a non-coding RNA close to candidate gene SLC13A4 , a cationic canal important both for muscle traits in sheep and growth and development in cattle ( Carvalho et al, 2020 ; Kaur et al, 2020 ).…”

Section: Resultsmentioning

confidence: 97%

Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification

et al. 2022

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Knowledge of the genetic architecture of key growth and beef traits in livestock species has greatly improved worldwide thanks to genome-wide association studies (GWAS), which allow to link target phenotypes to Single Nucleotide Polymorphisms (SNPs) across the genome. Local dual-purpose breeds have rarely been the focus of such studies; recently, however, their value as a possible alternative to intensively farmed breeds has become clear, especially for their greater adaptability to environmental change and potential for survival in less productive areas. We performed single-step GWAS and post-GWAS analysis for body weight (BW), average daily gain (ADG), carcass fleshiness (CF) and dressing percentage (DP) in 1,690 individuals of local alpine cattle breed, Rendena. This breed is typical of alpine pastures, with a marked dual-purpose attitude and good genetic diversity. Moreover, we considered two of the target phenotypes (BW and ADG) at different times in the individuals’ life, a potentially important aspect in the study of the traits’ genetic architecture. We identified 8 significant and 47 suggestively associated SNPs, located in 14 autosomal chromosomes (BTA). Among the strongest signals, 3 significant and 16 suggestive SNPs were associated with ADG and were located on BTA10 (50–60 Mb), while the hotspot associated with CF and DP was on BTA18 (55–62 MB). Among the significant SNPs some were mapped within genes, such as SLC12A1, CGNL1, PRTG (ADG), LOC513941 (CF), NLRP2 (CF and DP), CDC155 (DP). Pathway analysis showed great diversity in the biological pathways linked to the different traits; several were associated with neurogenesis and synaptic transmission, but actin-related and transmembrane transport pathways were also represented. Time-stratification highlighted how the genetic architectures of the same traits were markedly different between different ages. The results from our GWAS of beef traits in Rendena led to the detection of a variety of genes both well-known and novel. We argue that our results show that expanding genomic research to local breeds can reveal hitherto undetected genetic architectures in livestock worldwide. This could greatly help efforts to map genomic complexity of the traits of interest and to make appropriate breeding decisions.

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Section: Resultsmentioning

confidence: 97%

Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification

et al. 2022

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“…The heritability estimated for W450 (0.35) was moderate (Table 4), pointing out that genetic progress for this trait is feasible when phenotypic records for W450 are available in selection candidates. High heritability estimates for W450 were reported by Yokoo et al (2007), Lira et al (2013), Kluska, Lemos et al (2018a), Kluska, Olivieri et al (2018b) and Carvalho et al (2020) also in Nelore cattle with values ranging from 0.42 to 0.64.…”

Section: Resultsmentioning

confidence: 79%

Weighted genomic prediction for growth and carcass‐related traits in Nelore cattle

et al. 2023

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This study aimed to assess the impact of differential weighting in genomic regions harboring candidate causal loci on the genomic prediction accuracy and dispersion for growth and carcass‐related traits in Nelore cattle. The dataset contained 168 793 phenotypic records for adjusted weight at 450 days of age (W450), 83 624 for rib eye area (REA), 24 480 for marbling (MAR) and 82 981 for subcutaneous backfat thickness (BFT) and rump fat thickness (RFT). The pedigree harbored information from 244 254 animals born between 1977 and 2016, including 6283 sires and 50 742 dams. Animals (n = 7769) were genotyped with the low‐density panel (Clarifide® Nelore 3.0), and the genotypes were imputed to a panel containing 735 044 markers. A linear animal model was applied to estimate the genetic parameters and to perform the weighted single‐step genome‐wide association study (WssGWAS). A total of seven models for genomic prediction were evaluated combining the SNP weights obtained in the iterations of the WssGWAS and the candidate QTL. The heritability estimated for W450 (0.35) was moderate, and for carcass‐related traits, the estimates were moderate for REA (0.27), MAR (0.28) and RFT (0.28), and low for BFT (0.18). The prediction accuracy for W450 incorporating reported QTL previously described in the literature along with different SNPs weights was like those described for the default ssGBLUP model. The use of the ssGWAS to weight the SNP effects displayed limited advantages for the REA prediction accuracy. Comparing the ssGBLUP with the BLUP model, a meaningful improvement in the prediction accuracy from 0.09 to 0.63 (700%) was observed for MAR. The highest prediction accuracy was obtained for BFT and RFT in all evaluated models. The application of information obtained from the WssGWAS is an alternative to reduce the genomic prediction dispersion for growth and carcass‐related traits, except for MAR. Furthermore, the results obtained herein pointed out that is possible to improve the prediction accuracy and reduce the genomic prediction dispersion for growth and carcass‐related traits in young animals.

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“…Similarly, Seroussi et al ( 59 ) highlighted this gene in the local Awassi breed, which has white body and brick-red face and resembles the distinguishing phenotype of Comisana and Noticiana breeds. This island also enclosed PSIP1 and FREM1 that were reported as candidate genes for growth, muscle and adipose tissue metabolism and development ( 60 , 61 ). The island OAR2:121.83–123.24 was identified by Purfield et al ( 49 ) in three commercial meat sheep breeds, and by Cesarani et al ( 62 ) in Sarda breed.…”

Section: Discussionmentioning

confidence: 99%

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context

et al. 2023

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Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise FST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and FST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.

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Genome-wide association study and predictive ability for growth traits in Nellore cattle

Abstract: Carvalho, F. E. Genome-wide association study and predictive ability for growth traits in Nellore cattle. 2019. 67 f. Dissertação (Mestrado) -Faculdade

Cited by 5 publications

References 162 publications

Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification

Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification

Weighted genomic prediction for growth and carcass‐related traits in Nelore cattle

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context

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