A comprehensive genome-wide scan detects genomic regions related to local adaptation and climate resilience in Mediterranean domestic sheep

Abstract

Background The management of farm animal genetic resources and the adaptation of animals to climate change will probably have major effects on the long-term sustainability of the livestock sector. Genomic data harbour useful relevant information that needs to be harnessed for effectively managing genetic resources. In this paper, we report the genome characterization of the highly productive Mediterranean Chios dairy sheep and focus on genetic diversity measures related with local adaptation and selection and the genetic architecture of animal resilience to weather fluctuations as a novel adaptative trait linked to climate change. Results We detected runs of homozygosity (ROH) and heterozygosity (ROHet) that revealed multiple highly homozygous and heterozygous hotspots across the Chios sheep genome. A particularly highly homozygous region was identified on chromosome 13 as a candidate of directional genetic selection associated with milk traits, which includes annotated genes that were previously shown to be linked to local adaptation to harsh environmental conditions. Favourable heterozygosity related with a potentially protective role against livestock diseases and enhanced overall fitness was revealed in heterozygous-rich regions on sheep chromosomes 3, 10, 13 and 19. Furthermore, genomic analyses were conducted on sheep resilience phenotypes that display changes in milk production in response to weather variation. Sheep resilience to heat stress was a significantly heritable trait (h2 = 0.26) and genetically antagonistic to milk production. Genome-wide association and regional heritability mapping analyses revealed novel genomic markers and regions on chromosome 5 that were significantly associated with sheep resilience to climate change. Subsequently, an annotation analysis detected a set of genes on chromosome 5 that were associated with olfactory receptor complexes that could participate in heat stress mitigation through changes in respiration rate and respiratory evaporation. Other genes were grouped in previously reported biological processes relevant to livestock heat dissipation, including stress and immune response. Conclusions Our results may contribute to the optimal management of sheep genetic resources and inform modern selective breeding programmes that aim at mitigating future environmental challenges towards sustainable farming, while better balancing animal adaptation and productivity. Our results are directly relevant to the studied breed and the respective environmental conditions; however, the methodology may be extended to other livestock species of interest.

Genome-Wide Estimates of Runs of Homozygosity, Heterozygosity, and Genetic Load in Two Chinese Indigenous Goat Breeds

“…Considering the estimated statistics using a window or sliding window can cause some analytical bias; hence, the consecutive run test was applied, which has been suggested to be more accurate ( Santos et al, 2021 ) to detect genome-wide ROH and ROHet. Due to diverse computational parameters, tested populations, SNP arrays, and the number and length of ROH and ROHet obtained herein were different than those obtained from previous studies in cattle ( Biscarini et al, 2020 ), turkeys ( Marras et al, 2018 ), horses ( Santos et al, 2021 ), and sheep ( Tsartsianidou et al, 2021 ). For example, the average number of ROHet detected per animal (45.50 in this study) was higher than that detected by other studies in cattle (9.87) ( Biscarini et al, 2020 ) and sheep (28.28) ( Tsartsianidou et al, 2021 ) and lower than that detected in turkeys (57.80) ( Marras et al, 2018 ) and horses (52.17) ( Santos et al, 2021 ).…”

“…Due to diverse computational parameters, tested populations, SNP arrays, and the number and length of ROH and ROHet obtained herein were different than those obtained from previous studies in cattle ( Biscarini et al, 2020 ), turkeys ( Marras et al, 2018 ), horses ( Santos et al, 2021 ), and sheep ( Tsartsianidou et al, 2021 ). For example, the average number of ROHet detected per animal (45.50 in this study) was higher than that detected by other studies in cattle (9.87) ( Biscarini et al, 2020 ) and sheep (28.28) ( Tsartsianidou et al, 2021 ) and lower than that detected in turkeys (57.80) ( Marras et al, 2018 ) and horses (52.17) ( Santos et al, 2021 ). Nevertheless, our results were consistent with these studies wherein the short segment of ROH (<2 Mb) and ROHet (<1 Mb) showed the largest proportion, and ROHet were much rarer and shorter than ROH.…”

“…In comparison, we did not find a persuasive threshold of ROHet in previous studies ( Williams et al, 2016 ; Biscarini et al, 2020 ; Santos et al, 2021 ). In this study, the observed SNPs in ROHet at the top 0.1% level were identified as ROHet hotspots ( Tsartsianidou et al, 2021 ). In addition, Tajima’s D values and β scores were calculated using VCFtools ( Danecek et al, 2011 ) and BetaScan2 ( Siewert and Voight, 2020 ) software, respectively, to validate candidate regions that may have undergone balancing selection.…”

“…This discrepancy may be due to the limitation of SNP density and the few missing and homozygous genotypes allowed in ROHet segments. It is worth mentioning that the detection of ROHet and the selected parameters have not been extensively studied yet ( Tsartsianidou et al, 2021 ). Therefore, further analyses are required to improve the parameter settings of ROHet detection using high-density SNPs, more parameters, and populations.…”

Tecnologías moleculares ómicas aplicadas al estudio del estrés por calor en ganado

“…Estas tecnologías han permitido la identificación de marcadores moleculares en genes candidatos asociados a indicadores de termo-tolerancia (Luna-Nevárez et al, 2020, fertilidad (Luna-Nevárez et al, 2011;Angulo-Valenzuela et al, 2021), crecimiento (Weng et al, 2016) y caracteres de calidad de la canal (Peters et al, 2013). Regiones genómicas han sido reportadas como asociadas a procesos de adaptación y resistencia a los efectos del cambio climático en ovinos (Tsartsianidou et al, 2021). Además, la tecnología de secuenciación de ARN (RNA-Seq) ha facilitado el descubrimiento de nuevos transcritos (transcriptómica), la identificación de sus genes correspondientes, así como la medición de su expresión a través de métodos como la reacción en cadena de la polimerasa cuantitativa (qPCR; Kukurba y Montgomery, 2015).…”