Inbreeding coefficients and runs of homozygosity islands in Brazilian water buffalo

Genomic insights into selection signatures and candidate genes for milk production traits in buffalo population

Genetic variability in livestock driven by selection leaves distinct signatures within the genome. However, the comprehensive landscape of the selection responses for milk production traits in the Chinese buffalo population remains elusive. This study employed an integrated haplotype score (iHS) and runs of homozygosity (ROH) analyses of whole-genome sequence data from 100 Chinese buffaloes to decipher selection signatures. Using iHS and ROH, we identified 1 046 and 1 045 significant genomic regions, containing 717 and 263 candidate genes, respectively. The integration of iHS and ROH revealed 258 candidate regions and 108 overlapping genes, representing true selection signatures. Additionally, 94 candidate regions overlapped with 672 previously reported quantitative trait loci associated with key economically important traits. Annotation of the genomic regions highlighted candidate genes linked to milk production traits, including SNORD42, COX18, ANKRD17, ALB, RASSF6, CXCL8, TMEM232, ARHGAP26, and NR3C1. Transcriptome-wide association analysis supported ANKRD17 and CEP41 as potential candidates for affecting milk traits. This study unveils a comprehensive selection signature profile for the Chinese buffalo population by integrating iHS and ROH methods. The findings have broad implications for improving milk production traits in buffalo populations globally, contributing to more sustainable livestock systems. The identified candidate genes shed light on the selection response for milk production traits, offering crucial insights into optimising the breeding strategies for Chinese buffaloes.

Variability of PRDM9 in buffaloes

The buffalo population raised in Brazil tend to show loss of genetic variability over generations, with significant estimates of inbreeding depression. Besides mating genetically distant individuals, other tools can be used to maintain/increase the genetic variability of the population, such as the use of PRDM9 genotypes. The PRDM9 gene promotes the creation of crossing-over points across the genome, with each allele promoting the creation of a different hotspot. Thus, increasing the frequency of less frequent alleles in the population, allows the emergence of new haplotypes and increases genetic variability. So, this study aimed to characterize the alleles of the PRDM9 gene circulating in the Murrah, Jaffarabadi, and Mediterranean breeds and verify their potential impact on genetic diversity management within the populations. The three alleles (B, C and D) were found in the three breeds at different frequencies, as well as the genotypic frequencies. The mating of different homozygous genotypes and genotypes carrying less frequent alleles may increase recombination rates and population variability. Four described variants and one new variant for allele D were found by sequencing. It was verified that it is possible to mate sires and dams with different PRDM9 genotypes in order to try to increase genetic variability in buffalo populations, improving the matings choices in buffalo breeding, helping to maintain production levels.

Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data

The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.

Runs of homozygosity and cross-generational inbreeding of Iranian fat-tailed sheep

The Lori-Bakhtiari fat-tailed sheep is one of the most important heavyweight native breeds of Iran. The breed is robust and well-adapted to semi-arid regions and an important resource for smallholder farms. An established nucleus-based breeding scheme is used to improve their production traits but there is an indication of inbreeding depression and loss of genetic diversity due to selection. Here, we estimated the inbreeding levels and the distribution of runs of homozygosity (ROH) islands in 122 multi-generational female Lori-Bakhtiari from different half-sib families selected from a breeding station that were genotyped on the 50k array. A total of 2404 ROH islands were identified. On average, there were 19.70 ± 1.4 ROH per individual ranging between 6 and 41. The mean length of the ROH was 4.1 ± 0.14 Mb. There were 1999 short ROH of length 1-6 Mb and another 300 in the 6-12 Mb range. Additionally long ROH indicative of inbreeding were found in the ranges of 12-24 Mb (95) and 24-48 Mb (10). The average inbreeding coefficient (FROH) was 0.031 ± 0.003 with estimates varying from 0.006 to 0.083. Across generations, FROH increased from 0.019 ± 0.012 to 0.036 ± 0.007. Signatures of selection were identified on chromosomes 2, 6, and 10, encompassing 55 genes and 23 QTL associated with production traits. Inbreeding coefficients are currently within acceptable levels but across generations, inbreeding is increasing due to selection. The breeding program needs to actively monitor future inbreeding rates and ensure that the breed maintains or improves on its current levels of environmental adaptation.

Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle

Runs of homozygosity (ROH) and signatures of selection are the results of selection processes in livestock species that have been shown to affect several traits in cattle. The aim of the current work was to verify the profile of ROH and inbreeding depression in the number of total (TO) and viable oocytes (VO) and the number of embryos (EMBR) in Gir Indicine cattle. In addition, we aim to identify signatures of selection, genes, and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2093 animals and 420,718 SNP markers. Breeding values used to sort Gir animals were previously obtained. ROH and signature of selection analyses were performed using PLINK software, followed by ROH-based (F_ROH) and pedigree-based inbreeding (F_ped) and a search for genes and their functions. An average of 50 ± 8.59 ROHs were found per animal. ROHs were separated into classes according to size, ranging from 1 to 2 Mb (ROH_1-2Mb: 58.17%), representing ancient inbreeding, ROH_2-4Mb (22.74%), ROH_4-8Mb (11.34%), ROH_8-16Mb (5.51%), and ROH_>16Mb (2.24%). Combining our results, we conclude that the increase in general F_ROH and F_ped significantly decreases TO and VO; however, in different chromosomes traits can increase or decrease with F_ROH. In the analysis for signatures of selection, we identified 15 genes from 47 significant genomic regions, indicating differences in populations with high and low breeding value for the three traits.

Effect of Boron Supplementation on Nutrient Utilization and Productive Performance of Peripartum Murrah Buffaloes

Boron (B) has been established as a beneficial micronutrient for some farm animals. However, its impact on coping negative energy balance during transition and subsequent production performance needs critical perusal. Therefore, the present study was undertaken to determine the effect of B supplementation on productive performance, apparent nitrogen (N), and mineral utilization in peripartum Murrah buffaloes. Thirty advanced pregnant buffaloes (60 days prior to expected date of calving) were allocated into three groups, i.e. control, B-200, and B-400, and supplemented with pharmacological concentration of B at 0, 200, and 400 ppm, respectively, from 45 days prior to expected date of calving till 120 days post calving. Two metabolism trials were conducted (with animals having similar expected date of calving), one during prepartum (30 days prior to the expected date of calving) and another during postpartum (90 days post calving) phase to evaluate nutrient utilization and balance of N as well as minerals. Results revealed that B supplementation decreased (P < 0.05) overall plasma nonesterified fatty acids (NEFA), whereas plasma level of β-hydroxybutyric acid, insulin, triglyceride, and glucose did not differ (P > 0.05) among the groups. Dry matter intake, nutrient digestibility, and N balance remained unaffected with B supplementation. Higher (P < 0.05) apparent absorption coefficient for magnesium (Mg) and zinc (Zn) was observed in pregnant animals, while during lactation, absorption coefficient of calcium, Mg, and Zn was increased (P < 0.05) in B-supplemented groups. Hence, it can be concluded that alteration in NEFA concentration and variation in apparent absorption coefficient of minerals with B supplementation suggest its role in energy and mineral metabolism. However, further investigations are required to determine the underlying mechanism of action for the present findings.

Genome-wide analysis of runs of homozygosity in Italian Mediterranean buffalo

Runs of homozygosity (ROH) are a powerful tool to explore patterns of genomic inbreeding in animal populations and detect signatures of selection. The present study used ROH analysis to evaluate the genome-wide patterns of homozygosity, inbreeding levels, and distribution of ROH islands using the SNP data sets from 899 Mediterranean buffaloes. A total of 42,433 ROH segments were identified, with an average of 47.20 segments per individual. The ROH comprising mostly shorter segments (1-4 Mb) accounted for approximately 72.29% of all ROH. In contrast, the larger ROH (>8 Mb) class accounted for only 7.97% of all ROH segments. Estimated inbreeding coefficients from ROH (F_ROH) ranged from 0.0201 to 0.0371. Pearson correlations between F_ROH and genomic relationship matrix increased with the increase of ROH length. We identified ROH hotspots in 12 genomic regions, located on chromosomes 1, 2, 3, 5, 17, and 19, harboring a total of 122 genes. Protein-protein interaction (PPI) analysis revealed the clustering of these genes into 7 PPI networks. Many genes located in these regions were associated with different production traits. In addition, 5 ROH islands overlapped with cattle quantitative trait loci that were mainly associated with milk traits. These findings revealed the genome-wide autozygosity patterns and inbreeding levels in Mediterranean buffalo. Our study identified many candidate genes related to production traits that could be used to assist in selective breeding for genetic improvement of buffalo.

The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events

Background

Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types.

Results

The SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction.

Conclusions

Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00616-3.