Selection of discriminant SNP markers for breed and geographic assignment of Italian sheep

Dimauro, Corrado; Nicoloso, L.; Cellesi, Massimo; Macciotta, N.P.P.; Ciani, Elena; Moioli, B.; Pilla, Fabio; Crepaldi, P.

doi:10.1016/j.smallrumres.2015.05.001

Cited by 19 publications

(22 citation statements)

References 31 publications

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“…Principal component analysis and k-means using this subset of SNPs showed a lack of ability to discriminate among the breeds and the presence of overlapped areas. Recently, Dimauro et al (2015) using three complementary multivariate statistical techniques (discriminant analysis) and using two reduced pools of 110 and 108 SNPs, respectively, obtained a separation among divergent sheep breeds.…”

Section: Discussionmentioning

confidence: 99%

Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds

Sottile

Sardina

Mastrangelo

et al. 2018

Animal

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The identification of individuals' breed of origin has several practical applications in livestock and is useful in different biological contexts such as conservation genetics, breeding and authentication of animal products. In this paper, penalized multinomial regression was applied to identify the minimum number of single nucleotide polymorphisms (SNPs) from high-throughput genotyping data for individual assignment to dairy sheep breeds reared in Sicily. The combined use of penalized multinomial regression and stability selection reduced the number of SNPs required to 48. A final validation step on an independent population was carried out obtaining 100% correctly classified individuals. The results using independent analysis, such as admixture, F st , principal component analysis and random forest, confirmed the ability of these methods in selecting distinctive markers. The identified SNPs may constitute a starting point for the development of a SNP based identification test as a tool for breed assignment and traceability of animal products.

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Section: Discussionmentioning

confidence: 99%

Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds

Sottile

Sardina

Mastrangelo

et al. 2018

Animal

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“…In our study, SNPs g.1837C>G and g.3195G>A located in the GnIH gene are interesting markers for litter size in both goat breeds, but nothing indicates that these SNPs are more than simple markers. Reproductive traits are complex quantitative traits involving multiple genes, loci, and their interactions (Dimauro et al 2015); therefore, the combined effects of multiple genes or loci on reproductive traits should be analyzed. In the present study, associations between both loci and litter size were analyzed from the first to fourth parities.…”

Section: Discussionmentioning

confidence: 99%

Two single nucleotide polymorphisms in the caprine GnIH gene are associated with litter size

An¹,

Bao²,

Hou³

et al. 2017

CZECH J ANIM SCI

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An X., Bao L., Hou J., Bai Y., Zhao X., Song Y., Cao B. . (2017): Two single nucleotide polymorphisms in the caprine GnIH gene are associated with litter size. Czech J. Anim. Sci., 62, 269-275.Gonadotropin-inhibitory hormone (GnIH) can decrease luteinizing hormone and/or follicle-stimulating hormone levels in rat, mouse, sheep, and cattle by the direct suppression of gonadotropin-releasing hormone (GnRH). The present study investigated polymorphisms in the GnIH genes of two dairy goat breeds and their association with litter size. Single nucleotide polymorphisms (SNPs) g.1837C>G and g.3195G>A (GenBank Accession Nos. KR778885 and KR819142) were detected in the GnIH genes of Xinong Saanen and Guanzhong dairy goat breeds using DNA sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Furthermore, the g.1837C>G and g.3195G>A loci were closely linked in both breeds (r 2 > 0.33). Association analysis showed that these SNPs had significant effects on the litter size of goats (P < 0.05). In both breeds, individuals with the CC/GG (g.1837C>G/g.3195G>A) genotype showed larger litter sizes in the second and average parities than individuals with the GG/AA genotype (P < 0.05). Known biochemical and physiological functions, along with our results, indicate that the CC/GG genotype may be used in marker-assisted selection to choose individuals with a larger litter size from both breeds.

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“…Precise breed identification is a key step in genetic and genomic studies as accurate breed assignment can improve accuracy of the genomic breeding value estimation, especially when mixed-breed populations are used for developing or applying prediction equations (Kachman et al, 2013;Vandenplas et al, 2016). Moreover, many examples of protected denomination of origin (PDO) and protected geographical indications (PGI) for animal-derived products are directly associated with specific breeds (Dimauro et al, 2015;Mateus & Russo-Almeida, 2015), and proper certification is therefore dependent on the correct identification of livestock breed. Issuing of PDO and PGI certifications, associated with robust methods to monitor marketed Pesq.…”

Section: Termos Para Indexaçãomentioning

confidence: 99%

“…Mateus & Russo-Almeida (2015) identified 12 microsatellite markers able to correctly classify animals into their respective breeds, while Di Stasio et al (2017) used 15 microsatellite markers for breed certification in Italian sheep breeds. Other studies (Bertolini et al, 2015;Dimauro et al, 2015) showed that at minimum of 100 SNPs are required for correct and accurate breed assignment of cattle and sheep breeds. Table 1.…”

Section: Termos Para Indexaçãomentioning

confidence: 99%

Validation of a customized subset of SNPs for sheep breed assignment in Brazil

Paim

McManus

Vieira

et al. 2019

Pesq. agropec. bras.

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The objective of this work was to evaluate the usefulness of a subset of 18 single nucleotide polymorphisms (SNPs) for breed identification of Brazilian Crioula, Morada Nova (MN), and Santa Inês (SI) sheep. Data of 588 animals were analyzed with the Structure software. Assignments higher than 90% confidence were observed in 82% of the studied samples. Most of the low-value assignments were observed in MN and SI breeds. Therefore, although there is a high reliability in this subset of 18 SNPs, it is not enough for an unequivocal assignment of the studied breeds, mainly of hair breeds. A more precise panel still needs to be developed for the widespread use in breed assignment.

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Selection of discriminant SNP markers for breed and geographic assignment of Italian sheep

Cited by 19 publications

References 31 publications

Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds

Penalized classification for optimal statistical selection of markers from high-throughput genotyping: application in sheep breeds

Two single nucleotide polymorphisms in the caprine GnIH gene are associated with litter size

Validation of a customized subset of SNPs for sheep breed assignment in Brazil

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