Analyses of reaction norms reveal new chromosome regions associated with tick resistance in cattle

Mota, Rodrigo Reis; Silva, Fabyano Fonseca e; Lopes, Paulo Sávio; Tempelman, Robert J.; Sollero, B. P.; Aguilar, Ignácio; Cardoso, F. F.

doi:10.1017/s1751731117001562

Cited by 15 publications

(15 citation statements)

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“…Higher dispersion of SNP marker effects was observed when EC level became less restrictive, and the highest percentage of the genetic variance explained by an SNP was 1.029% for SC and 1.04% for HP. Mota et al (2017) observed the same trend using RNM, i.e. the range and variance of the SNP effects increased with the EC level.…”

Section: G9e Interactionssupporting

confidence: 60%

Genomic reaction norm models exploiting genotype × environment interaction on sexual precocity indicator traits in Nellore cattle

et al. 2020

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Summary Brazilian beef cattle are raised predominantly on pasture in a wide range of environments. In this scenario, genotype by environment (G×E) interaction is an important source of phenotypic variation in the reproductive traits. Hence, the evaluation of G×E interactions for heifer’s early pregnancy (HP) and scrotal circumference (SC) traits in Nellore cattle, belonging to three breeding programs, was carried out to determine the animal’s sensitivity to the environmental conditions (EC). The dataset consisted of 85 874 records for HP and 151 553 records for SC, from which 1800 heifers and 3343 young bulls were genotyped with the BovineHD BeadChip. Genotypic information for 826 sires was also used in the analyses. EC levels were based on the contemporary group solutions for yearling body weight. Linear reaction norm models (RNM), using pedigree information (RNM_A) or pedigree and genomic information (RNM_H), were used to infer G×E interactions. Two validation schemes were used to assess the predictive ability, with the following training populations: (a) forward scheme—dataset was split based on year of birth from 2008 for HP and from 2011 for SC; and (b) environment‐specific scheme—low EC (−3.0 and −1.5) and high EC (1.5 and 3.0). The inclusion of the H matrix in RNM increased the genetic variance of the intercept and slope by 18.55 and 23.00% on average respectively, and provided genetic parameter estimates that were more accurate than those considering pedigree only. The same trend was observed for heritability estimates, which were 0.28–0.56 for SC and 0.26–0.49 for HP, using RNM_H, and 0.26–0.52 for SC and 0.22–0.45 for HP, using RNM_A. The lowest correlation observed between unfavorable (−3.0) and favorable (3.0) EC levels were 0.30 for HP and −0.12 for SC, indicating the presence of G×E interaction. The G×E interaction effect implied differences in animals’ genetic merit and re‐ranking of animals on different environmental conditions. SNP marker–environment interaction was detected for Nellore sexual precocity indicator traits with changes in effect and variance across EC levels. The RNM_H captured G×E interaction effects better than RNM_A and improved the predictive ability by around 14.04% for SC and 21.31% for HP. Using the forward scheme increased the overall predictive ability for SC (20.55%) and HP (11.06%) compared with the environment‐specific scheme. The results suggest that the inclusion of genomic information combined with the pedigree to assess the G×E interaction leads to more accurate variance components and genetic parameter estimates.

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Section: G9e Interactionssupporting

confidence: 60%

Genomic reaction norm models exploiting genotype × environment interaction on sexual precocity indicator traits in Nellore cattle

et al. 2020

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“…Including genomic regions having environment-dependent sensitivity in statistical methods represents an additional biological insight to obtain more accurate genomic predictions and thus select Nellore heifers with greater genetic potential for sexual precocity and tolerance to harsh conditions. Streit et al 11 , in dairy cattle, and Mota et al 10 , in beef cattle,…”

Section: Resultsmentioning

confidence: 99%

“…Integrating genotypic information with reaction norm (RN) models lead to the evaluation of GxE interaction more accurately compared to only pedigree-based analysis 3,8,9 . In addition, RN models can be combined with genome-wide association studies (GWAS) allowing to uncover genomic regions involved in animal adaptation by estimating SNP effects across environmental conditions 8,10 . In this context, a greater understanding can be obtained on how genetic variants are associated with reproductive traits and the environmental sensitivity by physiological adaptation.…”

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confidence: 99%

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Genome-wide scan highlights the role of candidate genes on phenotypic plasticity for age at first calving in Nellore heifers

Mota

Lopes²,

Júnior

et al. 2020

Sci Rep

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Age at first calving (AFC) plays an important role in the economic efficiency of beef cattle production. This trait can be affected by a combination of genetic and environmental factors, leading to physiological changes in response to heifers' adaptation to a wide range of environments. Genomewide association studies through the reaction norm model were carried out to identify genomic regions associated with AFC in Nellore heifers, raised under different environmental conditions (EC). The SNP effects for AFC were estimated in three EC levels (Low, Medium, and High, corresponding to average contemporary group effects on yearling body weight equal to 159.40, 228.6 and 297.6 kg, respectively), which unraveled shared and unique genomic regions for AFC in Low, Medium, and High EC levels, that varied according to the genetic correlation between AFC in different EC levels. The significant genomic regions harbored key genes that might play an important biological role in controlling hormone signaling and metabolism. Shared genomic regions among EC levels were identified on BTA 2 and 14, harboring candidate genes associated with energy metabolism (IGFBP2, IGFBP5, SHOX, SMARCAL1, LYN, RPS20, MOS, PLAG1, CHCD7, and SDR16C6). Gene set enrichment analyses identified important biological functions related to growth, hormone levels affecting female fertility, physiological processes involved in female pregnancy, gamete generation, ovulation cycle, and age at puberty. the genomic regions highlighted differences in the physiological processes linked to AFC in different EC levels and metabolic processes that support complex interactions between the gonadotropic axes and sexual precocity in nellore heifers. open Scientific RepoRtS | (2020) 10:6481 | https://doi.org/10.1038/s41598-020-63516-4 www.nature.com/scientificreports www.nature.com/scientificreports/ pathway and gene network analyses from these results can be performed to uncover mechanisms whereby the environment can potentially affect the sexual precocity in cattle. Such knowledge regarding genomic regions and biological pathways involved with GxE interactions in Nellore heifers' sexual precocity is important to identify molecular mechanisms underlying the phenotypic responses to different environments. Hence, this study was carried out to evaluate the changes in the SNP effect estimates, as well as the biological processes associated with age at first calving in three environmental conditions, combining RN models and GWAS. Materials and Methodsethics approval. The animal procedures in this study were approved by Animal Care of the São Paulo State University (UNESP), School of Agricultural and Veterinary Science Ethical Committee (protocol number 18.340/16). All the data sampling was performed in accordance with CEUA/ FCAV-UNESP guidelines and regulations.phenotypic and genotypic data. Age at first calving (AFC) records were obtained from 185,356Nellore heifers belonging to three commercial breeding programs (DeltaGen, Paint -CRV Lagoa and Cia de Melhoramento), which are p...

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“…Another point to be highlighted is that different genes could be pronounced as potential candidates depending upon the environmental gradient, which may suggest a SNP by environment interaction affecting AFC. In a recently paper, Mota et al (2017) reported the presence of SNP by environment interactions for tick resistance in cattle affecting different tick burden levels. Therefore, models that incorporate the genotype by environment interaction should be performed.…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide association study and annotating candidate gene networks affecting age at first calving in Nellore cattle

Mota

Guimarães

Fortes

et al. 2017

J Animal Breeding Genetics

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We performed a genome-wide mapping for the age at first calving (AFC) with the goal of annotating candidate genes that regulate fertility in Nellore cattle. Phenotypic data from 762 cows and 777k SNP genotypes from 2,992 bulls and cows were used. Single nucleotide polymorphism (SNP) effects based on the single-step GBLUP methodology were blocked into adjacent windows of 1 Megabase (Mb) to explain the genetic variance. SNP windows explaining more than 0.40% of the AFC genetic variance were identified on chromosomes 2, 8, 9, 14, 16 and 17. From these windows, we identified 123 coding protein genes that were used to build gene networks. From the association study and derived gene networks, putative candidate genes (e.g., PAPPA, PREP, FER1L6, TPR, NMNAT1, ACAD10, PCMTD1, CRH, OPKR1, NPBWR1 and NCOA2) and transcription factors (TF) (STAT1, STAT3, RELA, E2F1 and EGR1) were strongly associated with female fertility (e.g., negative regulation of luteinizing hormone secretion, folliculogenesis and establishment of uterine receptivity). Evidence suggests that AFC inheritance is complex and controlled by multiple loci across the genome. As several windows explaining higher proportion of the genetic variance were identified on chromosome 14, further studies investigating the interaction across haplotypes to better understand the molecular architecture behind AFC in Nellore cattle should be undertaken.

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Analyses of reaction norms reveal new chromosome regions associated with tick resistance in cattle

Cited by 15 publications

References 53 publications

Genomic reaction norm models exploiting genotype × environment interaction on sexual precocity indicator traits in Nellore cattle

Genomic reaction norm models exploiting genotype × environment interaction on sexual precocity indicator traits in Nellore cattle

Genome-wide scan highlights the role of candidate genes on phenotypic plasticity for age at first calving in Nellore heifers

Genome‐wide association study and annotating candidate gene networks affecting age at first calving in Nellore cattle

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