Investigation of genetic diversity and selection signatures between Sarda and Sardinian Ancestral black, two related sheep breeds with evident morphological differences

Cesarani, Alberto; Sechi, Tiziana; Gaspa, Giustino; Usai, Mario Graziano; Sorbolini, Silvia; Macciotta, N.P.P.; Carta, Antonello

doi:10.1016/j.smallrumres.2019.06.014

Cited by 24 publications

(21 citation statements)

References 60 publications

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“…Only Switzerland and Italy had animals in the upper inbreeding class (>20%), with 3 and 5 bulls, respectively. As expected, average F ROH obtained in the present study were lower than those reported for cosmopolitan highly selected breeds: between 12.7% and 15.6% for Brown Swiss (Cesarani et al, 2019; Ferencakovic et al, 2013; Marras et al., 2015), and 11.6% for Holstein (Marras et al., 2015; Szmatola et al, 2016). Signer‐Hasler et al (2017) reported F ROH values for Swiss Fleckvieh (2.9 ± 2.1%) and Simmental (3.9 ± 2.3%), lower than those calculated in the present work for the Swiss population (12.6 ± 2.9%).…”

Section: Discussionsupporting

confidence: 58%

“…One of them is represented by the detection of Runs of Homozyogosity (ROH), uninterrupted sequences of homozygous genotypes, that have been widely investigated for many livestock species (Peripolli et al., 2017). Since the ROHs' occurrence could be ascribed to the inheritance from a common ancestor (Gurgul et al., 2014; Keller, Visscher, & Goddard, 2011; Purfield, Berry, McParland, & Bradley, 2012), these homozygous segments are useful for analysing the degree of relatedness among individuals belonging to different livestock populations (Bertolini et al., 2018; Cesarani et al., 2019; Mastrangelo et al., 2016). Moreover, the ROH length is related to the time distance of the inbreeding event: long ROH segments are likely to occur when the mating between relatives had taken place recently (Curik, Ferencakovic, & Solkner, 2014).…”

Section: Introductionmentioning

confidence: 99%

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Genome‐wide analysis of homozygosity regions in european simmental bulls

Cesarani

Gaspa

Pauciullo

et al. 2020

J Animal Breeding Genetics

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The study of Runs of Homozygosity (ROH) is a useful approach for the characterization of the genome of livestock populations. Due to their high relationship with autozygosity, ROH allow to make inference about population genetic history, to estimate the level of inbreeding, to assess within breed heterogeneity and to detect the footprints of selection on livestock genomes. Aim of this study was to investigate the distribution of runs of homozygosity in bulls belonging to five European Simmental populations and to assess the relationship between three production traits (milk yield, fat and protein contents) and autozygosity. ROH count, distribution and ROH‐based coefficient of inbreeding (FROH) were calculated for 3,845 Simmental bulls of five different European countries: Austria (AT), Switzerland (CH), Czech Republic (CZ), Germany (DE) and Italy (IT). Average values of ROH number per animal, and total genome length covered by ROH were 77.8 ± 20.7 and 205 ± 74.4 Mb, respectively. Bulls from AT, DE and IT exhibited similar ROH characteristics. Swiss animals showed the highest (12.6%), while CZ the lowest (4.6%) FROH coefficient. The relationship between ROH occurrence and milk production traits was investigated through a genome‐wide ROH‐traits association analysis (GWRA). A total of 34 regions previously associated with milk traits (yield and/or composition) were identified by GWRA. Results of the present research highlight a mixed genetic background in the 5 European Simmental populations, with the possible presence of three subgroups. Moreover, a strong relationship between autozygosity and production traits has been detected.

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Section: Discussionsupporting

confidence: 58%

Section: Introductionmentioning

confidence: 99%

Genome‐wide analysis of homozygosity regions in european simmental bulls

Cesarani

Gaspa

Pauciullo

et al. 2020

J Animal Breeding Genetics

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“…F ST interpretation was improved by removing noise from the raw signals with a locally weighed scatterplot smoothing (LOWESS) procedure [ 33 ]. A threshold based on F ST distribution was adopted [ 33 – 35 ], and SNPs that were three standard deviations from the mean were considered relevant.…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2021

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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.

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“…Interestingly, the combined use of case-control GWAS, F ST , and CDA highlighted several markers potentially associated with the investigated syndromes. The use of multiple approaches is generally advised in genome-wide analysis [ 17 , 23 , 24 ]. The use of CDA was recently proposed as an effective tool for improving the discovery rate either alone or in a combination with GWAS, especially when the sample size is reduced [ 25 ].…”

Section: Discussionmentioning

confidence: 99%

Genetics of Arthrogryposis and Macroglossia in Piemontese Cattle Breed

Stasio

Albera²,

Pauciullo

et al. 2020

Animals

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Arthrogryposis and macroglossia are congenital pathologies known in several cattle breeds, including Piemontese. As variations in single genes were identified as responsible for arthrogryposis in some breeds, we decided: (i) to test the hypothesis of a similar genetic determinism for arthrogryposis in the Piemontese breed by genotyping affected and healthy animals with a high-density chip and applying genome-wide association study (GWAS), FST and canonical discriminant analysis (CDA) procedures, and (ii) to investigate with the same approach the genetic background of macroglossia, for which no genetic studies exist so far. The study included 125 animals (63 healthy, 30 with arthrogryposis, and 32 with macroglossia). Differently from what reported for other breeds, the analysis did not evidence a single strong association with the two pathologies. Rather, 23 significant markers on different chromosomes were found (7 associated to arthrogryposis, 11 to macroglossia, and 5 to both pathologies), suggesting a multifactorial genetic mechanism underlying both diseases in the Piemontese breed. In the 100-kb interval surrounding the significant SNPs, 20 and 26 genes were identified for arthrogryposis and macroglossia, respectively, with 12 genes in common to both diseases. For some genes (NTN3, KCNH1, KCNH2, and KANK3), a possible role in the pathologies can be hypothesized, being involved in processes related to muscular or nervous tissue development. The real involvement of these genes needs to be further investigated and validated.

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Investigation of genetic diversity and selection signatures between Sarda and Sardinian Ancestral black, two related sheep breeds with evident morphological differences

Cited by 24 publications

References 60 publications

Genome‐wide analysis of homozygosity regions in european simmental bulls

Genome‐wide analysis of homozygosity regions in european simmental bulls

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

Genetics of Arthrogryposis and Macroglossia in Piemontese Cattle Breed

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