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

Mota, Rodrigo Reis; Guimarães, Simone Eliza Facioni; Fortes, M. R. S.; Hayes, Ben J.; Silva, F.F.; Verardo, Lucas Lima; Kelly, Matthew; Campos, Carolina; Guimarães, José Domingos; Wenceslau, Raphael Rocha; Penitente-Filho, Jurandy Mauro; Garcia, José Fernando; Moore, S. S.

doi:10.1111/jbg.12299

Cited by 44 publications

(36 citation statements)

References 29 publications

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“…Among the genes identified in this study, NMNAT1 and NCOA2 appear to be associated with female fertility via regulation of the secretion of luteinizing hormone and follicle development in cattle (Mota et al . ). Experiments on mice revealed that Arntl ( Bmal1 ) knockout individuals were infertile and that the genes were required for testosterone production (Alvarez et al .…”

Section: Resultsmentioning

confidence: 97%

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

Edea

Dadi

Dessie³

et al. 2018

Animal Genetics

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In this study, to identify genomic signatures of divergent selection, we genotyped 10 cattle breeds/populations (n = 275), representing eight Ethiopian cattle populations (n = 229) and two zebu populations (n = 46) adapted to tropical and sub-tropical environments, using the high-density single-nucleotide polymorphisms (SNPs) derived mainly from Bos indicus breeds, and using five reference taurine breeds (n = 212). Population genetic differentiation (F ST ) values across sliding windows were estimated between zebu and reference combined taurine breeds. The most differentiated regions (F ST ≥ 0.53), representing the top 1% smoothed F ST values, were considered to represent regions under diversifying selection. In total, 285 and 317 genes were identified in the comparisons of Ethiopian cattle with taurine and Asian zebu with taurine respectively. Some of these genes are involved in stress responses/thermo-tolerance and DNA damage repair (HSPA4, HSF1, CMPK1 and EIF2AK4), pigmentation (ERBB3 and MYO1A), reproduction/fertility (UBE2D3, ID3 and PSPC1), immune response (PIK3CD and AKIRIN2) and body stature and size (MBP2, LYN and NPM1). Additionally, the candidate genes were associated with functional terms (e.g. cellular response to stress, DNA repair, inflammatory response) important for physiological adaptation to environmental stresses. The results of our study may shed light on the influence of artificial and natural selection in shaping the genomic diversity of modern cattle breeds and also may serve as a basis for further genetic investigation of traits of tropical adaptation in cattle.

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Section: Resultsmentioning

confidence: 97%

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

Edea

Dadi

Dessie³

et al. 2018

Animal Genetics

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“…Non-overlapping islands within the lineages were explored for gene content and among the genes identified within the regions we can highpoint those described in Table 5 . Remarkably, six genes were also reported in Nellore-specific studies associated with carcass traits [ 64 ] ( PPM1 ), age at first calving [ 65 ] ( NPBWR1, OPRK1, and MRPL1 ), and birth weight [ 66 ] ( RPS20 and TGS1 ).…”

Section: Discussionmentioning

confidence: 98%

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits

et al. 2018

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BackgroundThe aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED).ResultsThe average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands.ConclusionsLow FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5060-8) contains supplementary material, which is available to authorized users.

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“…The region presents tropical climate with dry winter season, commonly known as a savannah climate, in which each month has an average temperature above 18°C and a rainfall index of up to 1,200 mm (Sá Júnior, Carvalho, Silva, & Carvalho Alves, ). Contemporary groups were composed by the combination of year and season of birth as proposed by Mota et al ().…”

Section: Methodsmentioning

confidence: 99%

Genetic parameters for fertility traits in Nellore bulls

Filho

Marques

Campos

et al. 2019

Reprod Domestic Animals

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Nellore is the main cattle breed used in Brazil, being the largest commercial herd in the world. Beyond the importance of male reproductive efficiency for farm profit, the use of reproductive techniques, mainly artificial insemination, turns the evaluation of male reproductive traits even more important. Estimation of genetic parameters increases the knowledge on traits variances and allows envisaging the possibility of the inclusion of new traits as selection criterion. Genetic parameters for fifteen traits that can be classified as testicular biometry or physical and morphological semen traits were estimated for a Nellore bull population ranging from 18 to 36 months.Single-trait and bi-trait animal models were used for (co)variance components estimation. The contemporary group was considered as fixed effect and age at measurement as covariable. Scrotal circumference presented heritability of 0.47 ± 0.12. This value is similar to the heritabilities found for all testicular biometry traits (0.34-0.48).Sperm progressive motility, which has a direct effect on bull fertility, presented low heritability (0.07 ± 0.08). Major and total sperm defects presented moderate to high heritabilities (0.49 ± 0.18 and 0.39 ± 0.15, respectively), indicating that great genetic gain can be obtained through selection against sperm defects. High and positive genetic correlations were observed among testicular biometry traits, which also presented favourable genetic correlations with physical and morphological traits of the semen with magnitude ranging from high to low. Scrotal circumference presented moderate to high and favourable genetic correlations with sperm progressive motility, sperm turbulence, major sperm defects and total sperm defects. Thus, the selection for scrotal circumference results in favourable correlated genetic response for semen quality. The results show that the use of scrotal circumference as reference trait for bull fertility is appropriate, since it presents high heritability and favourable genetic correlation with semen quality. K E Y W O R D S genetic correlation, heritability, semen quality, testicular biometry, Zebu | 39 CARVALHO FILHO et AL. S U PP O RTI N G I N FO R M ATI O N Additional supporting information may be found online in the Supporting Information section. How to cite this article: Carvalho Filho I, Marques DBD, de Campos CF, et al. Genetic parameters for fertility traits in Nellore bulls. Reprod Dom Anim. 2020;55:38-43. https ://doi.

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

Cited by 44 publications

References 29 publications

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

Genome‐wide scan reveals divergent selection among taurine and zebu cattle populations from different regions

Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits

Genetic parameters for fertility traits in Nellore bulls

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