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

Macciotta, N.P.P.; Colli, Licia; Cesarani, Alberto; Ajmone‐Marsan, Paolo; Low, Wai Yee; Tearle, Rick; Williams, J. L.

doi:10.1186/s12711-021-00616-3

Cited by 26 publications

(24 citation statements)

References 107 publications

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“…As mentioned by Biscarini et al [16], few studies aimed to evaluate the impact of different parameters on ROH detection, with such parameters still not well established. This de nition is of crucial importance, as it has a direct effect on the results obtained [23]; not only in ROH detection, but also in the secondary analyses (e.g., inbreeding coe cient based on ROH).…”

Section: Discussionmentioning

confidence: 99%

Characterization of Runs of Homozygosity, Heterozygosity-Enriched Regions, and Population Structure in Cattle Populations Selected for Different Breeding Goals

Mulim

Brito

Pinto

et al. 2021

Preprint

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Background: A decline in the level of genetic diversity can result in reduced response to selection, greater incidence of genetic defects, and inbreeding depression. In this context, some metrics have been proposed to assess the levels of populational genetic diversity in selected populations. The main goals of this study were to: 1) investigate the population structure of 16 cattle populations from 15 different pure breeds or composite populations, which have been selected for different breeds goals; and, 2) identify and compare runs of homozygosity (ROH) and heterozygosity-enriched regions (HER) based on different single nucleotide polymorphism (SNP) panels and whole-genome sequence data (WGS), followed by functional genomic analyses. Results: A total of 24,187 ROH were found across all cattle populations, with 55% classified in the 2-4 Mb size group. Fourteen homozygosity islands were found in five populations, where four islands located on BTA1, BTA5, BTA16, and BTA19 overlapped between the Brahman (BRM) and Gyr (GIR) breeds. A functional analysis of the genes found in these islands revealed candidate genes known to play a role in the melanogenesis, prolactin signaling, and calcium signaling pathways. The correlations between inbreeding metrics ranged from 0.02 to 0.95, where the methods based on homozygous genotypes (FHOM), uniting of gametes (FUNI), and genotype additive variance (FGRM) showed strong correlations among them. All methods yielded low to moderate correlations with the inbreeding coefficients based on runs of homozygosity (FROH). For the HER, 3,576 runs and 26 islands, distributed across all autosomal chromosomes, were found in regions containing genes mainly related to the immune system. Although the analyses with WGS did not enable detection of the same island patterns, it unraveled novel regions not captured when using SNP panel data.Conclusions: The cattle populations that showed the largest amount of ROH and HER were Senepol (SEN) and Montana (MON), respectively. Overlapping ROH islands were identified between GIR and BRM breeds, indicating a possible historical connection between the populations. The distribution and pattern of ROH and HER are population specific, indicating that different breeds have experienced divergent selection processes or different genetic processes.

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Section: Discussionmentioning

confidence: 99%

Characterization of Runs of Homozygosity, Heterozygosity-Enriched Regions, and Population Structure in Cattle Populations Selected for Different Breeding Goals

Mulim

Brito

Pinto

et al. 2021

Preprint

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“…We performed two linear mixed models to evaluate the statistical significance of the difference between the ROH parameters identified for each population group [ 23 ] using the statistical software JMP 16 [ 24 ]. We modelized two variables ( ): (i) a standardized ratio between the length of single ROH in each individual and the length of the corresponding chromosome , and (ii) a standardized ratio between the number of ROH on each chromosome of each individual and the length of the chromosome ; both of these models included the same factors: where is the mean, is the fixed effect of the autosome (chromosomes 1 to 29), is the fixed effect of the population group (CSD vs NRD), is the fixed effect of the breed nested within the population groups (n = 20 in CSD and n = 10 in NRD), is the interaction between population group and autosome, is the random effect of the animal, and is the random residual.…”

Section: Methodsmentioning

confidence: 99%

Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

et al. 2021

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Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (FROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged FST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations.

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“…In a population with high inbreeding levels for a long time, such as Line 1 Hereford, the effects of inbreeding depression could be moderate because of selection against deleterious alleles in the population [ 31 ]. As an illustration of that in a bubaline population, Macciota et al [ 32 ] used ROH islands to identify genes associated with environmental adaptation, fitness, and reproduction. In this sense, positive and negative inbreeding may counterbalance, leading to small or no inbreeding depression, as found by Sumreddee [ 7 ] for reproduction traits.…”

Section: Resultsmentioning

confidence: 99%

“…Studies with ROH in dairy cattle have shown that chromosomal ROH vary widely [ 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 ]. Similarly, in beef cattle the contributions of different chromosomes also fluctuate [ 7 , 34 , 35 ].…”

Section: Resultsmentioning

confidence: 99%

Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford

Pilon

Hinterneder

Hay

et al. 2021

Animals

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The goal of this study was to evaluate inbreeding in a closed beef cattle population and assess phenotype prediction accuracy using inbreeding information. Effects of inbreeding on average daily gain phenotype in the Line 1 Hereford cattle population were assessed in this study. Genomic data were used to calculate inbreeding based on runs of homozygosity (ROH), and pedigree information was used to calculate the probability of an allele being identical by descent. Prediction ability of phenotypes using inbreeding coefficients calculated based on pedigree information and runs of homozygosity over the whole genome was close to 0, even in the case of significant inbreeding coefficient effects. On the other hand, inbreeding calculated per individual chromosomes’ ROH yielded higher accuracies of prediction. Additionally, including only ROH from chromosomes with higher predicting ability further increased prediction accuracy. Phenotype prediction accuracy, inbreeding depression, and the effects of chromosome-specific ROHs varied widely across the genome. The results of this study suggest that inbreeding should be evaluated per individual regions of the genome. Moreover, mating schemes to avoid inbreeding depression should focus more on specific ROH with negative effects. Finally, using ROH as added information may increase prediction of the genetic merit of animals in a genomic selection program.

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

Cited by 26 publications

References 107 publications

Characterization of Runs of Homozygosity, Heterozygosity-Enriched Regions, and Population Structure in Cattle Populations Selected for Different Breeding Goals

Characterization of Runs of Homozygosity, Heterozygosity-Enriched Regions, and Population Structure in Cattle Populations Selected for Different Breeding Goals

Runs of homozygosity in the Italian goat breeds: impact of management practices in low-input systems

Inbreeding Calculated with Runs of Homozygosity Suggests Chromosome-Specific Inbreeding Depression Regions in Line 1 Hereford

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