Integrating genome-wide association study and pathway analysis reveals physiological aspects affecting heifer early calving defined at different ages in Nelore cattle

Mota, Lúcio Flávio Macêdo; Carvajal, Alejandro B.; Bernardes, Priscila Arrigucci; Buzanskas, Marcos Eli; Baldi, Fernando; Lôbo, Raysildo Barbosa; Munari, Danísio Prado

doi:10.1016/j.ygeno.2022.110395

Cited by 11 publications

(7 citation statements)

References 89 publications

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“…Para se ter ideia de quão baixa seria a herança de características reprodutivas precoces, estes autores observaram estimativa de herdabilidade média para a característica idade ao primeiro parto igual a 0,11± 0,03. Porém, outros autores trabalhando com novilhas Nelore de 14 a 16 meses observaram estimativas de herdabilidade variando de 0,44 a 0,55 (MOTA et al, 2022;TERAKADO et al, 2015) podendo responder positivamente a seleção. Segundo Borba et al (2011), característica de prenhez precoce exibe maiores estimativas de herdabilidade chegando a aproximadamente 73%.…”

Section: Resultsunclassified

Impacto da idade da vaca ao parto sobre o peso à desmama e ao sobreano de animais da raça Nelore

Jesus,

Venturini,

Figueiredo

et al. 2023

PRW

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O Brasil é um grande produtor de carne bovina, porém, o aumento constante da produção, e melhoria da eficiência produtiva e reprodutiva da raça Nelore, deve ser o foco. O objetivo deste trabalho foi avaliar a existência de interação da idade da vaca sobre o peso a desmama e ao sobreano de seus produtos. Foram analisadas 1.039 progenitoras da raça Nelore, divididas em três grupos, provenientes da região de Bonito-MS. Em relação ao perfil produtivo destes animais 66,8% (694/1039) pariram. A taxa de parição foi significativamente superior nos animais com idade de 17 a 36 meses. Em relação aos índices produtivos vacas de 36 meses, entregaram bezerros mais pesados e vacas de 17 a 36 meses entregaram bezerro ao sobreano quando comparadas com os demais grupos. Interações entre a idade das mães e os pesos são de suma importância, visto que isso facilitar na escolha das vacas para determinada característica almejada. Com base nos dados obtidos, pode-se concluir que a idade das vacas é um fator importante a ser levado em consideração pois, influencia diretamente no peso dos seus produtos na desmama e consequentemente ao sobreano sendo este, devido possivelmente ao ganho compensatório.

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Section: Resultsunclassified

Impacto da idade da vaca ao parto sobre o peso à desmama e ao sobreano de animais da raça Nelore

Jesus,

Venturini,

Figueiredo

et al. 2023

PRW

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“…EXD2 for example, it has been involved in reproductive performance of cattle under heat stress [ 42 ]. In addition, overlapping ROHs comprise genes affecting pregnancy and fertility ( FZD9 ) [ 43 ], heifer early calving ( PHF20 and RBM39 ) [ 44 ], resistance to uterine disease traits in first parity ( ERC2 ) [ 45 ] and ovulation rate ( BCL7B ) [ 46 ]. Finally, signals of selection were found in ARFGEF2 , a candidate gene associated with low fertility in single kid cashmere goat [ 47 ].…”

Section: Discussionmentioning

confidence: 99%

Genome-wide scan for runs of homozygosity in South American Camelids

Pallotti,

Picciolini,

Antonini

et al. 2023

BMC Genomics

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Background Alpaca (Vicugna pacos), llama (Lama glama), vicugna (Vicugna vicugna) and guanaco (Lama guanicoe), are the camelid species distributed over the Andean high-altitude grasslands, the Altiplano, and the Patagonian arid steppes. Despite the wide interest on these animals, most of the loci under selection are still unknown. Using whole-genome sequencing (WGS) data we investigated the occurrence and the distribution of Runs Of Homozygosity (ROHs) across the South American Camelids (SACs) genome to identify the genetic relationship between the four species and the potential signatures of selection. Results A total of 37 WGS samples covering the four species was included in the final analysis. The multi-dimensional scaling approach showed a clear separation between the four species; however, admixture analysis suggested a strong genetic introgression from vicugna and llama to alpaca. Conversely, very low genetic admixture of the guanaco with the other SACs was found. The four species did not show significant differences in the number, length of ROHs (100-500 kb) and genomic inbreeding values. Longer ROHs (> 500 kb) were found almost exclusively in alpaca. Seven overlapping ROHs were shared by alpacas, encompassing nine loci (FGF5, LOC107034918, PRDM8, ANTXR2, LOC102534792, BSN, LOC116284892, DAG1 and RIC8B) while nine overlapping ROHs were found in llama with twenty-five loci annotated (ERC2, FZD9, BAZ1B, BCL7B, LOC116284208, TBL2, MLXIPL, PHF20, TRNAD-AUC, LOC116284365, RBM39, ARFGEF2, DCAF5, EXD2, HSPB11, LRRC42, LDLRAD1, TMEM59, LOC107033213, TCEANC2, LOC102545169, LOC116278408, SMIM15, NDUFAF2 and RCOR1). Four overlapping ROHs, with three annotated loci (DLG1, KAT6B and PDE4D) and three overlapping ROHs, with seven annotated genes (ATP6V1E1, BCL2L13, LOC116276952, BID, KAT6B, LOC116282667 and LOC107034552), were detected for vicugna and guanaco, respectively. Conclusions The signatures of selection revealed genomic areas potentially selected for production traits as well as for natural adaptation to harsh environment. Alpaca and llama hint a selection driven by environment as well as by farming purpose while vicugna and guanaco showed selection signals for adaptation to harsh environment. Interesting, signatures of selection on KAT6B gene were identified for both vicugna and guanaco, suggesting a positive effect on wild populations fitness. Such information may be of interest to further ecological and animal production studies.

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“…The age at first calving, a trait related to female sexual precocity, can be affected by the level of subcutaneous fat in cattle [43]. These findings indicate that both genes (PLCB1 and CTSH) have pleiotropic properties, supporting the occurrence of a favorable effect on subcutaneous fat deposition and precocity/fertility traits in bovine females [44][45][46]. The FUT8 gene on BTA10 encodes an enzyme that transfers fucose from GDP-fucose to glycoconjugates such as glycoproteins [47].…”

Section: Genomic Regions For Rn Coefficients Affecting Afcmentioning

confidence: 91%

Genome-wide association study considering genotype-by-environment interaction for productive and reproductive traits using whole-genome sequencing in Nellore cattle

Carvalho Filho,

Arikawa,

Mota

et al. 2024

BMC Genomics

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Background The genotype-by-environment interaction (GxE) in beef cattle can be investigated using reaction norm models to assess environmental sensitivity and, combined with genome-wide association studies (GWAS), to map genomic regions related to animal adaptation. Including genetic markers from whole-genome sequencing in reaction norm (RN) models allows us to identify high-resolution candidate genes across environmental gradients through GWAS. Hence, we performed a GWAS via the RN approach using whole-genome sequencing data, focusing on mapping candidate genes associated with the expression of reproductive and growth traits in Nellore cattle. For this purpose, we used phenotypic data for age at first calving (AFC), scrotal circumference (SC), post-weaning weight gain (PWG), and yearling weight (YW). A total of 20,000 males and 7,159 females genotyped with 770k were imputed to the whole sequence (29 M). After quality control and linkage disequilibrium (LD) pruning, there remained ∼ 2.41 M SNPs for SC, PWG, and YW and ∼ 5.06 M SNPs for AFC. Results Significant SNPs were identified on Bos taurus autosomes (BTA) 10, 11, 14, 18, 19, 20, 21, 24, 25 and 27 for AFC and on BTA 4, 5 and 8 for SC. For growth traits, significant SNP markers were identified on BTA 3, 5 and 20 for YW and PWG. A total of 56 positional candidate genes were identified for AFC, 9 for SC, 3 for PWG, and 24 for YW. The significant SNPs detected for the reaction norm coefficients in Nellore cattle were found to be associated with growth, adaptative, and reproductive traits. These candidate genes are involved in biological mechanisms related to lipid metabolism, immune response, mitogen-activated protein kinase (MAPK) signaling pathway, and energy and phosphate metabolism. Conclusions GWAS results highlighted differences in the physiological processes linked to lipid metabolism, immune response, MAPK signaling pathway, and energy and phosphate metabolism, providing insights into how different environmental conditions interact with specific genes affecting animal adaptation, productivity, and reproductive performance. The shared genomic regions between the intercept and slope are directly implicated in the regulation of growth and reproductive traits in Nellore cattle raised under different environmental conditions.

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Integrating genome-wide association study and pathway analysis reveals physiological aspects affecting heifer early calving defined at different ages in Nelore cattle

Cited by 11 publications

References 89 publications

Impacto da idade da vaca ao parto sobre o peso à desmama e ao sobreano de animais da raça Nelore

Impacto da idade da vaca ao parto sobre o peso à desmama e ao sobreano de animais da raça Nelore

Genome-wide scan for runs of homozygosity in South American Camelids

Genome-wide association study considering genotype-by-environment interaction for productive and reproductive traits using whole-genome sequencing in Nellore cattle

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