Inbreeding depression on production and reproduction traits of buffaloes from Brazil

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.

Genealogical analysis of European bison population revealed a growing up population despite very low genetic diversity

In 1919, the European bison population became extinct in the wild. The rescue of the lowland subspecies and the whole species was achieved mainly thanks to individuals from the Białowieża Forest (Polish-Belarusian border). There are currently two breeding lines—the lowland (purebred B. b. Bonasus) founded by 7 individuals and the lowland-Caucasian (hybrids of B. b. Bonasus and B. b. caucasicus) founded by 12 individuals. This genealogical study was conducted on 15,071 individuals recorded in the pedigree book between 1881 and 2020. Its objective was to determine the level of genetic variability and inbreeding almost 100 years after the rescue measures were initiated. The completeness of the pedigree of the reference population was 77% in the fifth generation backwards. A maximum of 23 generations can be traced back in the pedigree. The average inbreeding coefficient and the mean average relatedness of the reference population were very high, about 17% and 16% respectively. No significant amount of new inbreeding was discovered. The reference population has lost 9.11% of the total genetic diversity compared to the population of founders. A male of the Caucasian subspecies Kaukasus was discovered among the ancestors of the lowland lineage reference population. The effective population size calculated based on the increase in inbreeding was 23.93 individuals, based on complete generations equivalent it was 16.1 individuals. Wright’s F-statistics showed very small differences in genotypic frequencies between individuals within the two lineages in the reference population (FIS = 0.10), between individuals and the total population (FIT = 0.04) and low differentiation between lineages (FST = 0.06). The population of the European bison from the Białowieża Forest is generally very uniform but still shows good fitness.

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.

Genetic and genomic evaluation of different breeding strategies using stochastic simulation in Iranian buffalo (Bubalus bubalis)

Context Despite the importance of buffalos to income and food needs, there has been little attention to the simulation of breeding programs using different strategies in the Iranian buffalo population. Aims The present study aimed to evaluate different breeding strategies in Iranian native buffalo by using stochastic simulation, and to determine the most appropriate strategy for Iranian buffalo breeding. Methods Different breeding scenarios were simulated for sensitivity of outcomes to the nucleus population size and selection design. Two systems of closed and open nucleus breeding schemes were simulated. Three different nucleus sizes, the optimal fraction of nucleus dams born in the base, and the appropriate fraction of base sires born in the nucleus were considered. Four selection designs were considered: random, phenotypic, best linear unbiased prediction (BLUP), and genomic selection. Key results The results indicated that in different population sizes and both open and closed nuclei, the average total genetic value was higher in genomic selection than in other selection designs. The total genetic value was higher in open nucleus than closed nucleus breeding schemes regardless of selection design. The highest mean of total genetic value was estimated at 91.53 in the optimal nucleus size of 15% of base population for the genomic selection approach and the open nucleus breeding system. In all nucleus population sizes, the highest inbreeding was obtained for selection based on BLUP, followed by genomic, phenotype and then random selection. Conclusions Overall, the application of open nucleus breeding schemes along with genomic selection is recommended for improving buffalo productivity. Implications Selection strategies used in Iranian buffaloes have so far been based on phenotypic information; however, obtaining genetic information could improve genetic progress in the Iranian buffalo population.

Effect of controlling future rate of inbreeding on expected genetic gain and genetic variability in small livestock populations

Context In the present study we assessed the use of average relationship as a means to control future rates of inbreeding in small cattle closed nucleus and its effect on genetic gain for milk yield as a means of managing genetic variability in livestock improvement programs. Aim The aim was to strike an ideal balance between genetic gain and loss of genetic variability for Sahiwal population. Methods A total of 8452 milk yield records of Sahiwal cows from National Sahiwal Stud, Kenya, were used to estimate breeding values and 19315 records used to estimate average relatedness of all individuals. The estimated breeding values and genetic relationships were then used to optimise individual genetic contributions between the best two males and the top 210 females in 2000–2008-year group, as well as between the best four, six and eight males and top, 420, 630 and 840 females based on estimated breeding values for lactation milk yield. Weights on genetic merit and average relationship considered in this study were (1, 0), (1, −300), (1, −500), (1, −1000) and (0, −1). Key results When the best sires were selected and used for mating disregarding average relationship with their mates i.e. (0, –1), genetic gain of up to 213 kg was realised accompanied by a rate of inbreeding per generation of 4%. Restricting average relationship alone i.e. (0, –1), resulted in a future rate of inbreeding of 1.6% and average merit of 154 when top two sires were used for breeding. At the same restriction level but using eight top sires, the rate of inbreeding per generation was 0.9% accompanied by an average merit of 128.2 kg. Controlling average relationship between mates resulted in increased genetic variability i.e. lower rate of inbreeding though average merit declined. Conclusion A rate of inbreeding per generation of <1% is required for a population to maintain its long-term viability. For this level to be attained, the size of the breeding population should be increased from the current two sires vs 210 dams to eight sires vs 840 dams. Implications Practical implications for closed nucleus programs such as the Sahiwal program in Kenya should include expanding the nucleus to comprise other institutional and privately-owned herds.

Population genetic structure in the Holstein breed in Brazil

We evaluated the population genetic structure of the Holstein breed in Brazil through pedigree analysis with the aim of supporting genetic management of extant herds. We used data from genealogical records of 204,511 animals in farms from south and southeast Brazil. Pedigree records between 1943 and 2005 were divided into seven periods of 8 years to estimate the effective population size (N e ). N e varied during the study periods, ranging from 0.19 to 3016.25. There was an increase in the percentage of inbred animals over time, from 0.18 to 5.0 %. However, this figure may be an underestimate due to the low completeness of pedigree, primarily related to paternal pedigree. The effective number of founders (fe) was 473 animals and ancestors (fa) was 471. The genetic contribution of 260 ancestors (founders or not) accounted for 50 % of the genetic variability in the population. The average relatedness coefficient (AR) and inbreeding coefficient indicate that the Holstein breed in Brazil is being effectively managed, despite a moderate founder effect and the low number of animals that are responsible for the population variance.