Relationships between hemoglobin type and reproduction, lamb, wool and milk production and health-related traits in crossbred ewes

Genome-wide copy number variant analysis reveals candidate genes associated with milk production traits in water buffalo (Bubalus bubalis)

Buffaloes are vital contributors to the global dairy industry. Understanding the genetic basis of milk production traits in buffalo populations is essential for breeding programs and improving productivity. In this study, we conducted whole-genome resequencing on 387 buffalo genomes from 29 diverse Asian breeds, including 132 river buffaloes, 129 swamp buffaloes, and 126 crossbred buffaloes. We identified 36,548 copy number variants (CNV) spanning 133.29 Mb of the buffalo genome, resulting in 2,100 CNV regions (CNVR), with 1,993 shared CNVR being found within the studied buffalo types. Analyzing CNVR highlighted distinct genetic differentiation between river and swamp buffalo subspecies, verified by evolutionary tree and principal component analyses. Admixture analysis grouped buffaloes into river and swamp categories, with crossbred buffaloes displaying mixed ancestry. To identify candidate genes associated with milk production traits, we employed 3 approaches. First, we used Vst-based population differentiation, revealing 11 genes within CNVR that exhibited significant divergence between different buffalo breeds, including genes linked to milk production traits. Second, expression quantitative loci analysis revealed differentially expressed CNVR-derived genes (DECG) associated with milk production traits. Notably, known milk production-related genes were among these DECG, validating their relevance. Last, a GWAS identified 3 CNVR significantly linked to peak milk yield. Our study provides comprehensive genomic insights into buffalo populations and identifies candidate genes associated with milk production traits. These findings facilitate genetic breeding programs aimed at increasing milk yield and improving quality in this economically important livestock species.

Comparison of ovine β-globin haplotype sequences and a new multiplex PCR for identification

Deletion of pre-adult β^C-globin in sheep harboring BB haplotype of β-globin was associated to decreased tolerance to anemia and hypoxia, and consequently, reduced resistance to Haemonchus contortus infection, which is closely related to severe anemia. Recently, a qPCR using hydrolysis probe was successfully developed for β-globin haplotype identification, and association between resistance against H. contortus and presence of β^A allele was observed in Morada Nova sheep. Thus, this study aimed to better investigate the differences between β-globin haplotypes and to develop a conventional multiplex PCR, as an alternative to qPCR assay for β-globin haplotype identification. A total of 333 Morada Nova lambs had their blood collected and tested by both qPCR and new multiplex PCR, and 100 % of agreement was observed between the results. Since different primers were designed for such assay development, including different target genes, high specificity of both methods may be also highlighted. Three A haplotype samples were submitted to DNA Sanger sequencing of β-globin gene and compared to sequences previously deposited in Genbank. One nucleotide deletion in intronic region was observed only in AA haplotype of Morada Nova animals, while in BB animals the nucleotide remained present. To the best of our knowledge, this is the first report of multiplex conventional PCR for ovine β-globin haplotype identification. The advantages of the developed conventional PCR are reduced reagents costs (less than a half price) and wider reachability, since even labs without real time PCR thermocyclers are able to offer this assay. Therefore, it may become an important tool for sheep producers to improve genetic selection of parasite resistant animals.

Genomic Tools for the Identification of Loci Associated with Facial Eczema in New Zealand Sheep

Facial eczema (FE) is a significant metabolic disease that affects New Zealand ruminants. Ingestion of the mycotoxin sporidesmin leads to liver and bile duct damage, which can result in photosensitisation, reduced productivity and death. Strategies used to manage the incidence and severity of the disease include breeding. In sheep, there is considerable genetic variation in the response to FE. A commercial testing program is available for ram breeders who aim to increase tolerance, determined by the concentration of the serum enzyme, gamma-glutamyltransferase 21 days after a measured sporidesmin challenge (GGT21). Genome-wide association studies were carried out to determine regions of the genome associated with GGT21. Two regions on chromosomes 15 and 24 are reported, which explain 5% and 1% of the phenotypic variance in the response to FE, respectively. The region on chromosome 15 contains the β-globin locus. Of the significant SNPs in the region, one is a missense variant within the haemoglobin subunit β (HBB) gene. Mass spectrometry of haemoglobin from animals with differing genotypes at this locus indicated that genotypes are associated with different forms of adult β-globin. Haemoglobin haplotypes have previously been associated with variation in several health-related traits in sheep and warrant further investigation regarding their role in tolerance to FE in sheep. We show a strategic approach to the identification of regions of importance for commercial breeding programs with a combination of discovery, statistical and biological validation. This study highlights the power of using increased density genotyping for the identification of influential genomic regions, combined with subsequent inclusion on lower density genotyping platforms.

Ovine β-globin gene: A new qPCR for rapid haplotype identification and association with susceptibility to Haemonchus contortus infection

Two β-globin allelic haplotypes (A and B) were identified in domestic sheep, wherein animals which are homozygous for β^B allele (BB haplotype) have a deletion of pre-adult β^C-globin and consequently are less tolerant to anemia and hypoxia. Since Haemonchus contortus infection, is associated with severe anemia, studies performed from 1960s to 1990s investigated the association between β-globin haplotype and resistance against this parasite. However, the findings were controversial, pointing out from increased resistance in animals harboring the β^A allele to inexistence of association. Thus, our study aimed to develop a qPCR for β-globin haplotype identification, and to evaluate the association between β-globin haplotype and resistance against H. contortus in a group of sheep submitted to artificial infection with this parasite. A total of 286 lambs of Morada Nova breed were experimentally challenged with 4000 H. contortus L3 and monitored for 112 days from weaning. Significantly improved (p < 0.05) phenotypic profiles (lower fecal egg counts, higher packed cell volume and birthweight) were observed for AA haplotype animals, especially when compared to BB animals, while AB animals were similar to BB. This is the first report of a qPCR assay for ovine β-globin haplotype identification. In view of significant differences of phenotypic profiles between haplotype groups, the developed qPCR may constitute an important tool for sheep producers to improve genetic selection of parasite resistant animals.

Beta-globin gene evolution in the ruminants: evidence for an ancient origin of sheep haplotype B

Domestic sheep (Ovis aries) can be divided into two groups with significantly different responses to hypoxic environments, determined by two allelic beta-globin haplotypes. Haplotype A is very similar to the goat beta-globin locus, whereas haplotype B has a deletion spanning four globin genes, including beta-C globin, which encodes a globin with high oxygen affinity. We surveyed the beta-globin locus using resequencing data from 70 domestic sheep from 42 worldwide breeds and three Ovis canadensis and two Ovis dalli individuals. Haplotype B has an allele frequency of 71.4% in O. aries and was homozygous (BB) in all five wild sheep. This shared ancestry indicates haplotype B is at least 2-3 million years old. Approximately 40 kb of the sequence flanking the ~37-kb haplotype B deletion had unexpectedly low identity between haplotypes A and B. Phylogenetic analysis showed that the divergent region of sheep haplotype B is remarkably distinct from the beta-globin loci in goat and cattle but still groups with the Ruminantia. We hypothesize that this divergent ~40-kb region in haplotype B may be from an unknown ancestral ruminant and was maintained in the lineage to O. aries, but not other Bovidae, evolving independently of haplotype A. Alternatively, the ~40-kb sequence in haplotype B was more recently acquired by an ancestor of sheep from an unknown non-Bovidae ruminant, replacing part of haplotype A. Haplotype B has a lower nucleotide diversity than does haplotype A, suggesting a recent bottleneck, whereas the higher frequency of haplotype B suggests a subsequent spread through the global population of O. aries.

Studies on haemoglobin polymorphism of two breeds of Iranian sheep and its relationship to concentrations of iron, copper, haemoglobin, haematocrit and RBC number

After electrophoresis on cellulose acetate, two haemoglobin phenotypes were detected in Baloochi and Kordi breeds: AA and AB phenotypes. AA was commonest in two breeds. The incidence of type AB haemoglobin in Baloochi and Kordi breeds was 26.5% (9/34) and 9.5% (2/21), respectively. BB phenotype was not seen in Baloochi and Kordi breeds. In sheep with AB phenotype, haemoglobin B was dominant. The mean +/- SD of the two kinds of haemoglobin in sheep with AB phenotype were haemoglobin B percentage 60.5% +/- 9.04%, haemoglobin B absolute 73.84 +/- 5.44 g/L, haemoglobin A percentage 39.5% +/- 9.04%, haemoglobin A absolute 32.88 +/- 2.89 g/L. There were no significant differences for total haemoglobin, haematocrit, red blood cell (RBC) number, iron and copper levels between breed, sex and age groups and also between sheep with AA phenotype and AB phenotype. Pearson's method showed significant correlations for total haemoglobin with packed cell volume (PCV), RBC number, copper concentration and RBC number with PCV, copper level and PCV with copper amount and copper concentration with iron level (p<0.05). In the Kordi breed, significant correlations were seen for total haemoglobin with PCV, RBC number, copper concentration and PCV with RBC number and RBC number with copper level and copper concentration with iron amount (p<0.05). In the Baloochi breed, significant correlations were detected for total haemoglobin with PCV, RBC number and PCV with RBC number (p<0.05).

Characterization of indigenous fat-tailed and fat-rumped hair sheep in Kenya: diversity in blood proteins

This paper reports the variation in five blood proteins from five populations of sheep found in Kenya. Blood samples were collected from a total of 309 adult sheep of both sexes in Kwale, Makueni and Kakamega districts for the fat-tailed sheep and in Isiolo district for the fat-rumped hair sheep. Fine-wooled Merino sheep were used in this study as the reference population. Transferrin, esterase-A and esterase-C were polymorphic in all the populations investigated, while albumin was monomorphic for the S allele in the fat-tailed sheep and haemoglobin was fixed for the B allele in the Kwale, Makueni and Isiolo populations. Phylogenies derived from the pairwise genetic distance estimates showed a clear separation between the indigenous sheep populations and the exotic Merino. However, the topology of the former showed rather poor consistency with their morphological classification based on the localization of their fat deposits, namely fat-tailed or fat-rumped hair sheep.

Blood polymorphism in west African breeds of sheep

This paper reports the blood groups and blood protein distribution in West African sheep breeds. About 100 animals of the Djallonke, Fulani and Touabire breeds were sampled for blood polymorphism analysis. Their blood groups were typed by haemolytic and agglutination reactions, and their blood proteins by starch gel electrophoresis. Almost all the loci analysed showed variability in the three breeds, with the Touabire and Fulani being closer to each other than to the Djallonke.

The influence of haemoglobin types on reproduction and production in Hungarian Merino sheep

Fewer Hb A and AB lambs were born than expected in the investigated Hungarian Merino population but the factors responsible for these differences could not be identified. The Hb A and AB breeding ewes were not inferior to their B type herd mates with respect to average daily weight gain (when lambs), reproductive performance (prolificacy) and survival rate. Their reproductive performance was, in some cases, even better than that of the ewes with other haemoglobin types. The haemoglobin types cannot be used as markers when selecting for higher prolificacy.

Onset and remission of ovine footrot

Sheep exposed to uncontrolled outbreaks of footrot were observed on one farm for 3 successive years and on another for one year. Observations were made from mid-winter to early summer. In each outbreak about 70% or more of sheep exposed to footrot acquired the disease. Natural remission occurred in each outbreak and some cases healed while new cases continued to develop. A feature of all outbreaks observed was that a much higher proportion of late onset cases healed than cases which developed early in the outbreaks. By contrast, 90% of sheep already affected before spring had lesions which persisted into next summer. It is suggested that there is a spectrum of resistance to footrot among sheep. This spectrum includes animals which remain chronically infected and those that do not become infected at all. Intermediate levels of resistance are reflected firstly in the time taken by different groups of sheep, to become affected after exposure and secondly, to heal after becoming affected.