Determinação do perfil transcriptômico associados à eficiência alimentar de bovinos Nelore (Bos taurus indicus)
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Data
2022-04-29
Autores
Serna‐garcía, Marta [UNESP]
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Universidade Estadual Paulista (Unesp)
Resumo
– A população mundial deverá atingir 9,8 milhões pessoas em 2050. Essa tendência ameaça a sustentabilidade dos sistemas e preocupa quanto a capacidade de suprir necessidades alimentares do planeta. Devido à crescente demanda dos produtos pecuários, é necessário estar preparados para os impactos na produção, mas fazê-lo de maneira inclusiva e sustentável exigirá grandes transformações. O consumo alimentar residual (CAR) permite identificar e selecionar animais mais eficientes sem prejuízo do crescimento e reprodução, ou da qualidade da carne. Além disso, o aumento da eficiência alimentar diminui o impacto ambiental, uma vez que animais mais eficientes tendem a consumir menos e produzir mais quando comparados aos menos eficientes. A característica é de difícil mensuração e a busqueda pelo entendimento genético e biológico se tornou uma alternativa na investigação de animais superiores, e dentre as técnicas moleculares, o RNA-Seq, tem sido uma das mais utilizadas, pois permite o sequenciamento e a quantificação dos transcritos com uma grande resolução, detecção de eventos de splicing alternativo e ncRNAs (non-coding RNA), que podem ter diversas funções na arquitetura regulatória. Visando entender melhor os processos genéticos envolvidos na expressão do Consumo Alimentar Residual (CAR), foram analisados dois grupos genéticos (G1 e G2) de bovinos Nelore. No G1, animais (n=60) do mesmo grupo de contemporâneos foram submetidos a uma avaliação do CAR e dentre eles, 24 animais extremos para a característica foram abatidos. Amostras de tecido hepático foram coletadas e sequenciadas por meio da plataforma HiSeq 2500 System (Illumina). Para G2, foram utilizados dados públicos, provenientes do sequenciamento de 20 amostras de tecido hepático de animais divergentes para CAR, também do mesmo grupo de contemporâneos, obtidos por meio HiSeq 2000 System (Illumina). Os objetivos do estudo foram identificar os genes diferencialmente expressos, descrever eventos de splicing alternativo, traçar um perfil dos transcritos de ncRNA comparando duas populações de Nelore (Bos taurus indicus), classificados de forma divergente para CAR, em tecido hepático usando RNA-Seq. Foram encontrados 1.811 genes de expressão diferencial (DEGs) e 2.054 DEGs (p-valor 0,05) para G1 e G2, respectivamente. Quanto aos DEG comumente identicados nas duas populações, foram encontrados 88, dos quais 33 estavam envolvidos na resposta imune e no bloqueio do estresse oxidativo. Foram encontrados sete (B2M, ADSS, SNX2, TUBA4A, ARHGAP18, MECR, ABCF3) possíveis biomarcadores, considerando AUC > 0,70. O gene B2M foi mais expresso no grupo mais eficiente [CAR negativo] comparado com o grupo ineficiente [CAR positivo] atua regulando o turnover proteico, metabolismo lipídico e inibe a morte celular. Em ambos os grupos genéticos, o grupo CAR negativo apresentou genes com capacidade antioxidante, maior capacidade de proliferação celular e proteção contra a morte. Os genes BoLA-DRA, BoLA-DRB3 e CD74 foram preditos como hub, e estão envolvidos na melhoria da resposta imune. Os fatores de transcrição LRRFIP1 e NR4A2 foram detectados e estão envolvidos na promoção da angiogênese e diminuição da apoptose. A análise de redes de interação física mediante dados públicos (BioGRID) detectou 7 possíveis nodes; DDB2, ACTB, PAK1, VIM, PRC1, RPS6KA1 e PKM regulando positivamente proliferação celular, lipólise, organização do citoesqueleto e sobrevivência celular no grupo CAR negativo. No capítulo 4, com os mesmos animais do capítulo 2 (fenotipicamente divergentes para RFI), foram identificados eventos de splicing alternativos diferencialmente expressos (DAS) a partir da abordagem exon-centric. Os DAS encontrados foram transcritos para 67 e 75 genes (p-value ≤ 0,05) respectivamente para G1 e para G2. Identificamos 9 comuns genes DAS, no geral, desempenham um papel no metabolismo lipídico e do sistema imunológico, destacando SAT1 como gene hub. Os RNAs não codificantes significativos encontrados foram; MIR25 and SNORD16 para G1 RNase_MRP e SCARNA10 e para G2 em RLFI. Destacamos o MIR25 sendo capaz de atuar bloqueando a citotoxicidade e o estresse oxidativo e o RNase_MRP como bloqueador do dano mitocondrial. Os resultados relatados neste estudo indicam genes candidatos e mecanismos moleculares reguladores do CAR em dois grupos geneticos em bovinos Nelore, o que irá melhorar a compreensão da eficiência alimentar, auxiliar em futuras abordagens dos métodos quantitativos de melhoramento para aumentar da produtividade e a diminuição do impacto ambiental da pecuária através da identificação de animais com alta eficiência alimentar com rapidez e menor custo.
The world population is expected to reach 9.8 million by 2050. This trend threatens the sustainability of the systems in place and concerns the ability to meet the requirements of our planet. Due to the growing demand for livestock products, it is necessary to be prepared for the impact on production but doing so in an inclusive and sustainable way will require major transformations. Residual Feed Intake (RFI) indicates how to identify and select more efficient animals without detriment to growth and reproduction or compromising meat quality. In addition, increased feed efficiency reduces environmental impact, as more efficient animals tend to consume less and produce more compared to less efficient ones. The search for genetic and biological understanding of this type of characteristics has become an alternative in the investigation of more efficient animals and, among molecular techniques, RNA-seq is one of the most used. It allows sequencing and quantifying transcripts with high resolution, detection of alternative splicing events, and ncRNAs (non-coding RNAs), which may have multiple roles in regulatory architecture. To gain a better understanding of the genetic processes involved in RFI expression, two genetic groups (G1 and G2) of Nelore cattle were analyzed. In G1, animals (n = 60) from the same contemporaneous group underwent RFI evaluation. Twenty-four extreme animals were selected for this population, low RFI (N = 12) and high RFI (N = 12); they were subsequently slaughtered. Liver tissue was collected and sequenced using the HiSeq 2500 System (Illumina). Public data was used for G2, which includes RNA-seq data from 20 samples of liver tissue from animals divergent for RFI. These animals belong to the same contemporary group and the data were obtained by the HiSeq 2000 system (Illumina). The study aimed to identify differentially expressed genes, alternative splicing events and the ncRNA transcript profile by comparing two populations of Nelore cattle (Bos taurus indicus) classified divergently for RFI using RNA-seq data. We found 1,811 differentially expressed genes (DEGs) and 2,054 DEGs (p-value 0.05) in low RFI (LRFI) group compared with high RFI (HRFI) group for G1 and G2, respectively. Analyses found 88 common genes between the genetic groups, and 33 of these were involved in immune response and blocking of oxidative stress. Seven possible markers (B2M, ADSS, SNX2, TUBA4A, ARHGAP18, MECR, ABCF3) were found, considering AUC > 0.70. The B2M gene was overexpressed in the efficient group (LRFI) when compared with the inefficient group (HRFI); this gene acts by regulating protein turnover, lipid metabolism and inhibition of cell death. For both genetic groups, the LRFI group includes genes that could have an antioxidant capacity, increased cell proliferation capacity and protection against death. The BoLA-DRA, BoLA-DRB3 and CD74 have been predicted to be hub genes and are involved in enhancing the immune response. Transcription factors LRRFIP1 and NR4A2 are involved in the promotion of angiogenesis and decreasing apoptosis. Physical interaction network analysis using public data (BioGRID) detected seven possible nodes: DDB2, ACTB, PAK1, VIM, PRC1, RPS6KA1 and PKM. In chapter 4, with the same animals selected in chapter 2 (phenotypically divergent for RFI), differentially expressed alternative splicing events (DAS) were identified from the exon-centric approach. The DAS found were transcribed for 67 and 75 genes, respectively for G1 and for G2. We identified 9 common DAS genes, in general, play a role in lipid metabolism and the immune system, highlighting SAT1 as the hub gene. The significant non-coding RNAs found were MIR25 and SNORD16 for G1 RNase_MRP and SCARNA10 and for G2 in RLFI group. We highlight MIR25 being able to act by blocking cytotoxicity and oxidative stress and RNase_MRP as a blocker of mitochondrial damage.These genes were positively regulated for cell proliferation, lipolysis, cytoskeletal organization and cell survival in the efficient group. The results reported in this study indicate candidate genes and regulatory molecular mechanisms for RFI in the two genetic groups of Nelore cattle, which will improve the understanding of feed efficiency, help in future approaches of quantitative breeding methods to increase productivity and reduce the environmental impact of livestock through rapid identification of animals with high feed efficiency and low cost.
The world population is expected to reach 9.8 million by 2050. This trend threatens the sustainability of the systems in place and concerns the ability to meet the requirements of our planet. Due to the growing demand for livestock products, it is necessary to be prepared for the impact on production but doing so in an inclusive and sustainable way will require major transformations. Residual Feed Intake (RFI) indicates how to identify and select more efficient animals without detriment to growth and reproduction or compromising meat quality. In addition, increased feed efficiency reduces environmental impact, as more efficient animals tend to consume less and produce more compared to less efficient ones. The search for genetic and biological understanding of this type of characteristics has become an alternative in the investigation of more efficient animals and, among molecular techniques, RNA-seq is one of the most used. It allows sequencing and quantifying transcripts with high resolution, detection of alternative splicing events, and ncRNAs (non-coding RNAs), which may have multiple roles in regulatory architecture. To gain a better understanding of the genetic processes involved in RFI expression, two genetic groups (G1 and G2) of Nelore cattle were analyzed. In G1, animals (n = 60) from the same contemporaneous group underwent RFI evaluation. Twenty-four extreme animals were selected for this population, low RFI (N = 12) and high RFI (N = 12); they were subsequently slaughtered. Liver tissue was collected and sequenced using the HiSeq 2500 System (Illumina). Public data was used for G2, which includes RNA-seq data from 20 samples of liver tissue from animals divergent for RFI. These animals belong to the same contemporary group and the data were obtained by the HiSeq 2000 system (Illumina). The study aimed to identify differentially expressed genes, alternative splicing events and the ncRNA transcript profile by comparing two populations of Nelore cattle (Bos taurus indicus) classified divergently for RFI using RNA-seq data. We found 1,811 differentially expressed genes (DEGs) and 2,054 DEGs (p-value 0.05) in low RFI (LRFI) group compared with high RFI (HRFI) group for G1 and G2, respectively. Analyses found 88 common genes between the genetic groups, and 33 of these were involved in immune response and blocking of oxidative stress. Seven possible markers (B2M, ADSS, SNX2, TUBA4A, ARHGAP18, MECR, ABCF3) were found, considering AUC > 0.70. The B2M gene was overexpressed in the efficient group (LRFI) when compared with the inefficient group (HRFI); this gene acts by regulating protein turnover, lipid metabolism and inhibition of cell death. For both genetic groups, the LRFI group includes genes that could have an antioxidant capacity, increased cell proliferation capacity and protection against death. The BoLA-DRA, BoLA-DRB3 and CD74 have been predicted to be hub genes and are involved in enhancing the immune response. Transcription factors LRRFIP1 and NR4A2 are involved in the promotion of angiogenesis and decreasing apoptosis. Physical interaction network analysis using public data (BioGRID) detected seven possible nodes: DDB2, ACTB, PAK1, VIM, PRC1, RPS6KA1 and PKM. In chapter 4, with the same animals selected in chapter 2 (phenotypically divergent for RFI), differentially expressed alternative splicing events (DAS) were identified from the exon-centric approach. The DAS found were transcribed for 67 and 75 genes, respectively for G1 and for G2. We identified 9 common DAS genes, in general, play a role in lipid metabolism and the immune system, highlighting SAT1 as the hub gene. The significant non-coding RNAs found were MIR25 and SNORD16 for G1 RNase_MRP and SCARNA10 and for G2 in RLFI group. We highlight MIR25 being able to act by blocking cytotoxicity and oxidative stress and RNase_MRP as a blocker of mitochondrial damage.These genes were positively regulated for cell proliferation, lipolysis, cytoskeletal organization and cell survival in the efficient group. The results reported in this study indicate candidate genes and regulatory molecular mechanisms for RFI in the two genetic groups of Nelore cattle, which will improve the understanding of feed efficiency, help in future approaches of quantitative breeding methods to increase productivity and reduce the environmental impact of livestock through rapid identification of animals with high feed efficiency and low cost.
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Palavras-chave
Bovine, Genes, Nodes, Pecuária