Association of 20 candidate gene markers with milk production and composition traits in sires of Reggiana breed, a local dairy cattle population

Scotti, Emilio; Samoré, A.B.; Bagnato, A.; Russo, Vincenzo

doi:10.1016/j.livsci.2015.03.022

Cited by 19 publications

(20 citation statements)

References 52 publications

(48 reference statements)

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“…In particular, Cinisara and Modicana are two ancient Sicilian breeds that are not subject to breeding programs (Mastrangelo et al, 2014), whereas Reggiana is characterized by limited selection program. For this breed, only few studies have been carried out so far with the aim to identify associations with production traits that might be useful to refine selection and conservation programs (Fontanesi et al, 2015). Holstein dairy cattle has dominated the milk production industry over decades.…”

Section: Resultsmentioning

confidence: 99%

“…Consequently, the genetic diversity stored in each of them should be treated with great care and management strategies that insure the viability, and maintenance of the population should be implemented. Selection programs in local breeds with small population size are limited by the low number of animals (families) and by the need to control inbreeding (Fontanesi et al, 2015), which represent one of the most important problems. The individual inbreeding coefficient (F) is defined as the proportion of an individual's genome that is autozygous, that has homozygous identical by descent (IBD) status, or equivalently the probability of a randomly sampled locus in the genome to be autozygous (Ferenčaković et al, 2013a).…”

Section: Introductionmentioning

confidence: 99%

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Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Mastrangelo

Tolone

Gerlando

et al. 2016

Animal

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In the local breeds with small population size, one of the most important problems is the increase of inbreeding coefficient ( F). High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. The availability of high-density single nucleotide polymorphism (SNP) arrays has facilitated the quantification of F by genomic markers in farm animals. Runs of homozygosity (ROH) are contiguous lengths of homozygous genotypes and represent an estimate of the degree of autozygosity at genome-wide level. The current study aims to quantify the genomic F derived from ROH ( F ROH ) in three local dairy cattle breeds. F ROH values were compared with F estimated from the genomic relationship matrix ( F GRM ), based on the difference between observed v. expected number of homozygous genotypes ( F HOM ) and the genomic homozygosity of individual i ( F MOL i ). The molecular coancestry coefficient ( f MOL ij ) between individuals i and j was also estimated. Individuals of Cinisara (71), Modicana (72) and Reggiana (168) were genotyped with the 50K v2 Illumina BeadChip. Genotypes from 96 animals of Italian Holstein cattle breed were also included in the analysis. We used a definition of ROH as tracts of homozygous genotypes that were >4 Mb. Among breeds, 3661 ROH were identified. Modicana showed the highest mean number of ROH per individual and the highest value of F ROH , whereas Reggiana showed the lowest ones. Differences among breeds existed for the ROH lengths. The individuals of Italian Holstein showed high number of short ROH segments, related to ancient consanguinity. Similar results showed the Reggiana with some extreme animals with segments covering 400 Mb and more of genome. Modicana and Cinisara showed similar results between them with the total length of ROH characterized by the presence of large segments. High correlation was found between F HOM and F ROH ranged from 0.83 in Reggiana to 0.95 in Cinisara and Modicana. The correlations among F ROH and other estimated F coefficients were generally lower ranged from 0.45 ( F MOL i − F ROH ) in Cinisara to 0.17 ( F GRM − F ROH ) in Modicana. On the basis of our results, recent inbreeding was observed in local breeds, considering that 16 Mb segments are expected to present inbreeding up to three generations ago. Our results showed the necessity of implementing conservation programs to control the rise of inbreeding and coancestry in the three Italian local dairy cattle breeds.Keywords: genomic inbreeding, local cattle breeds, runs of homozygosity ImplicationsIn the local breeds with small population size, one of the most important problems is the increase of inbreeding that leads to different negative effects as a reduction in phenotypic values. The current study aims to quantify the genomic inbreeding derived from runs of homozygosity (ROH) (F ROH ) in three Italian local dairy cattle breeds. According to ROH results, recent inbreeding was well detected in the investigated local dairy cattle breeds. Our results showed the necessity of implementing co...

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Mastrangelo

Tolone

Gerlando

et al. 2016

Animal

Self Cite

136

128

View full text Add to dashboard Cite

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“…Holstein [ 21 ] and Jersey [ 22 ]. However, none of the well-known genes associated with milk-production, such as DGAT1 , GHR and ABCG2 [ 57 ] are intersecting with any of the candidate regions of positive selection identified in these two indigenous African dairy cattle breeds.…”

Section: Discussionmentioning

confidence: 99%

Signatures of positive selection in African Butana and Kenana dairy zebu cattle

et al. 2018

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Butana and Kenana are two types of zebu cattle found in Sudan. They are unique amongst African indigenous zebu cattle because of their high milk production. Aiming to understand their genome structure, we genotyped 25 individuals from each breed using the Illumina BovineHD Genotyping BeadChip. Genetic structure analysis shows that both breeds have an admixed genome composed of an even proportion of indicine (0.75 ± 0.03 in Butana, 0.76 ± 0.006 in Kenana) and taurine (0.23 ± 0.009 in Butana, 0.24 ± 0.006 in Kenana) ancestries. We also observe a proportion of 0.02 to 0.12 of European taurine ancestry in ten individuals of Butana that were sampled from cattle herds in Tamboul area suggesting local crossbreeding with exotic breeds. Signatures of selection analyses (iHS and Rsb) reveal 87 and 61 candidate positive selection regions in Butana and Kenana, respectively. These regions span genes and quantitative trait loci (QTL) associated with biological pathways that are important for adaptation to marginal environments (e.g., immunity, reproduction and heat tolerance). Trypanotolerance QTL are intersecting candidate regions in Kenana cattle indicating selection pressure acting on them, which might be associated with an unexplored level of trypanotolerance in this cattle breed. Several dairy traits QTL are overlapping the identified candidate regions in these two zebu cattle breeds. Our findings underline the potential to improve dairy production in the semi-arid pastoral areas of Africa through breeding improvement strategy of indigenous local breeds.

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“…The cortisol hormone stimulates gluconeogenesis in liver and lipolysis in adipose tissue, and inhibits glucose consumption in adipose tissue and muscle [59]. Polymorphisms in the CRH gene are associated with marbling score [59], growth and carcass yield [60], and milk production [61,62], which suggests a pleiotropic effect of this gene. FOXA2 is another identified gene that is known to be one of the important transcriptional activators and plays a role in the regulation of energy homeostasis and feeding.…”

Section: Signatures Of Potential Human-mediated Selectionmentioning

confidence: 99%

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

et al. 2020

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Background: Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. Results: Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8,

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Association of 20 candidate gene markers with milk production and composition traits in sires of Reggiana breed, a local dairy cattle population

Cited by 19 publications

References 52 publications

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Genomic inbreeding estimation in small populations: evaluation of runs of homozygosity in three local dairy cattle breeds

Signatures of positive selection in African Butana and Kenana dairy zebu cattle

Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds

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