Genomic selection signatures in Brazilian sheep breeds reared in a tropical environment

Leveraging Agri-advocacy to promote animal genetic diversity for climate change mitigation: Kenya and Tanzania perspective

The role that genetic diversity in animal genetic resources (AnGR) plays in mitigating the effects of climate change on the global protein supply is of the utmost significance. East Africa historically played a pivotal role in the dispersal of domesticated livestock species across the African continent. At present, it maintains a substantial contribution to worldwide biodiversity as a result of its reservoir of a diverse array of AnGR, characterized by genetic and species diversity. A considerable reduction in the genetic diversity of AnGR has been documented in numerous studies, giving rise to concerns regarding the sustainability of animal protein supply in the face of climate change. The objective of this article is to outline prospective roles that advocacy and management organizations specializing in AnGRs may undertake to aid in the conservation of AnGR genetic diversity in East Africa. Moreover, it provides a prospective framework and structure for advocacy that extends from the farmers, to the higher-level (regional farmers association). We believe that advocating for the promotion of genetic diversity at the regional level will have a significant impact at the national and further at global scale.

Combined Use of Univariate and Multivariate Approaches to Detect Selection Signatures Associated with Milk or Meat Production in Cattle

OBJECTIVES

The aim of this study was to investigate the genomic structure of the cattle breeds selected for meat and milk production and to identify selection signatures between them.

METHODS

A total of 391 animals genotyped at 41,258 SNPs and belonging to nine breeds were considered: Angus (N = 62), Charolais (46), Hereford (31), Limousin (44), and Piedmontese (24), clustered in the Meat group, and Brown Swiss (42), Holstein (63), Jersey (49), and Montbéliarde (30), clustered in the Milk group. The population stratification was analyzed by principal component analysis (PCA), whereas selection signatures were identified by univariate (Wright fixation index, FST) and multivariate (canonical discriminant analysis, CDA) approaches. Markers with FST values larger than three standard deviations from the chromosomal mean were considered interesting. Attention was focused on markers selected by both techniques.

RESULTS

A total of 10 SNPs located on seven different chromosomes (7, 10, 14, 16, 17, 18, and 24) were identified. Close to these SNPs (±250 kb), 165 QTL and 51 genes were found. The QTL were grouped in 45 different terms, of which three were significant (Bonferroni correction < 0.05): milk fat content, tenderness score, and length of productive life. Moreover, genes mainly associated with milk production, immunity and environmental adaptation, and reproduction were mapped close to the common SNPs.

CONCLUSIONS

The results of the present study suggest that the combined use of univariate and multivariate approaches can help to better identify selection signatures due to directional selection.

Genome-Wide Scan for Selective Sweeps Reveals Novel Loci Associated with Prolificacy in Iranian Sheep Breeds in Comparison with Highly Prolific Exotic Breed

Domestication and selection significantly changed phenotypic traits in modern domestic animals. To identify the genomic regions associated with prolificacy in this study, 837 ewes from three Iranian indigenous sheep breeds, consisting of Baluchi, Lori-Bakhtiari, and Zandi uniparous breeds, and one Greek highly prolific dairy sheep, namely Chios, were genotyped using OvineSNP50K arrays. Statistical tests were then performed using different and complementary methods based on either site frequency (FST) and haplotype (hapFLK) between populations, followed by a pathway analysis of the genes contained in the selected regions. The results revealed that for the top 0.01 percentile of the obtained FST values, 16 genomic regions on chromosomes 2, 3, 4, 7, 8, 9, 13, 14, 16, 18, 19, and 20, and for hapFLK values, 3 regions located on chromosomes 3, 7, and 13, were under selection. A bioinformatic analysis of these genomic regions showed that these loci overlapped with potential candidate genes associated with prolificacy in sheep including GNAQ, COL5A2, COL3A1, HECW1, FBN1, COMMD3, RYR1, CCL28, SERPINA14, and HSPA2. These regions also overlapped with some quantitative trait loci (QTLs) linked to prolificacy traits, milk yield, and body weight. These findings suggest that future research could further link these genomic regions to prolificacy traits in sheep.

Genome-wide discovery of selection signatures in four Anatolian sheep breeds revealed by ddRADseq

High-density genomic data analyzed by accurate statistical methods are of potential to enlighten past breeding practices such as selection by unraveling fixed regions. In this study, four native Turkish sheep breeds (80 samples) were genotyped via 296.097 single nucleotide polymorphisms (SNPs) detected by double-digest restriction site-associated DNA (ddRADseq) library preparation combined with the Illumina HiSeq X Ten instrument in order to identify genes under selection pressure. A total of 32, 136, 133, and 119 protein-coding genes were detected under selection pressure by runs of homozygosity (ROH), integrated haplotype score (iHS), the ratio of extended haplotype homozygosity (Rsb), and fixation index (FST) approaches, respectively. Of these, a total of 129 genes were identified by at least two statistical models which overlapped with a total of 52 quantitative trait loci (QTL)-associated SNPs, known to be related to fiber diameter, milk content, body weight, carcass traits, some blood parameters, and entropion. A total of six genes under selection pressure were validated by three statistical approaches five of which are of potential to be integrated into animal breeding since they were associated with wool fiber diameter (ZNF208B), behaviors related to neurocognitive development (CBX1 and NFE2L1), adaptation to high-altitude (SDK1), and anxiety causing internal stress (GSG1L). The sixth gene (COPZ1) turned out to play an important role in coping with different types of cancer in mammals. In particular, ROH analysis uncovered significant findings that the Güney Karaman (GKR) had experienced different selection practices than the Akkaraman (AKR) breed. Moreover, some genes specifically under selection in the GKR breed turned out to be associated with olfaction (OR6K6, OR6N1, OR6N2, and OR4C16), survival during the gestation period (PRR15L), and heat stress (CDK5RAP9). The results of this study imply that GKR may become genetically different from the AKR breed at the genome level due to most probably experiencing different adaptation processes occurring in raised climatic conditions. These differences should be conserved to face future challenges, while other native Turkish sheep breeds could be monitored via genome-wide high-density SNP data to obtain deeper knowledge about the effects of natural selection.

Performance, carcass characteristics and non-carcass components of Santa Ines and crossbred (Santa Ines x Dorper) lambs finished in different confinement strategies

Genetic group, age at entry into confinement and at slaughter, are characteristics that have an important influence on lamb performance and carcass. The aim of this study was to evaluate the performance, carcass characteristics and non-carcass components from different genetic groups (Santa Inês and ½ Dorper x ½ Santa Inês) sheep, submitted to different feedlot entry and exit strategies. Were used 72 lambs males and castrated; 36 Santa Inês (SI) and 36 crossbred (Dorper x Santa Inês-DSI), with 6 months of average initial age. The groups were established in a completely randomized experimental design, in a 2x3x4 factorial arrangement, from the combination of genetic groups (GG), body weight at the beginning of confinement (WBC) and length of stay in confinement (LSC). The body weight classes at the beginning of confinement were: light (25 kg), intermediate (28 kg) and heavy (31 kg), for Santa Inês and crossbreeds, respectively. Slaughters were carried out every 28 days of confinement, in four LSC: 0, 28, 56 and 84 days. The GG did not influence performance, carcass and non-carcass component traits of lambs (p > 0.05). There was an effect of the WBC on the weights: final (FW), metabolic (MW), body at slaughter (BWS), empty body (EBW), hot carcass (HCY) and cold (CCW), loin, shoulder, leg musculature; loin eye area (LEA) and loin fat (p < 0.05). There was also an effect on LSC, for FW, average daily weight gain (ADG), MW, weight and yield of body components, weight of cuts and tissue ratio components of cuts (p < 0.05). In non-carcass components, effect on full and empty weight of: omasum, rumen-reticulum, small intestine; empty large intestine, liver and kidneys, paws and skin, and perirenal, pelvic and inguinal fat (p < 0.05). Interaction double effect on the tissue muscle/fat:bone ratio (MF:B) and for the full omasal component (p < 0.05). And triple interaction effect for ADG, full omasum and perirenal fat (p < 0.05). Weight at the beginning of confinement and confinement time are the characteristics that most influence performance, quantitative characteristics of carcass and non-carcass components. Regardless of the genetic group and age class, the animals reach the same weight after 84 days of confinement. Thus, the confinement of heavier lambs (31 kg) can be a profitable alternative, as they presented the highest weights for the most commercially valued cuts (shank and loin). The confinement strategy must adapt to market situations.

Validation of SNP markers for thermotolerance adaptation in Ovis aries adapted to different climatic regions using KASP-PCR technique

A study on 51 SNPs belonging to 29 genes related to heat stress was carried out in 720 sheep from 17 different breeds adapted to different climates from Hungary, Bosnia and Herzegovina, Morocco and Romania, using Kompetitive Allele-Specific Polymerase Chain Reaction. Genotype frequency and the Hardy-Weinberg equilibrium were calculated, followed by a clustering using the Principal Component Analysis. We analyzed the polymorphisms in the following genes analyzed: HSPA12A, HSP90AA1, IL33, DIO2, BTNL2, CSN2, ABCG1, CSN1S1, GHR, HSPA8, STAT3, and HCRT. We emphasized on HSPA12A and HSPA8 genes as they were successfully genotyped in all studied flocks in which genotype frequency patterns were identified. Contrary to previous findings, the A allele for HSPA8 SNP was not observed in the heat tolerant breeds, being found exclusively in cold-tolerant breeds. The principal component analysis could not clearly differentiate the breeds, while plot concentration was slightly varied among the three groups, with HSP90AA1 and IL33 SNPs' loading values significantly contributing to PC1 and PC2. We confirmed previous works that the HSPA12A, HSPA8, HSP90AA1 and IL33 SNPs are potential candidate markers for thermotolerance adaptation in sheep. This research contributes to the genetic variability of SNPs for thermotolerance adaptability in sheep.