Identification of breed-specific SNP panel in nine different cattle genomes.

Kumar, Harshit; Panigrahi, Manjit; Chhotaray, Supriya; Pal, D. K.; Bhanuprakash, V.; KA, Saravanan; Shandilya, Rahul; Parida, Subhashree; Bhushan, Bharat

doi:10.35841/biomedicalresearch.30-18-1195

Cited by 14 publications

(11 citation statements)

References 15 publications

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“…Variants mapping on unplaced scaffolds were discarded. Breed-specific SNP files were obtained for the six subspecies from the vcf file containing the total SNPs with vcftools [ 29 ], and filtered according to Kumar et al [ 30 ]. Each breed-specific file was filtered with plink2 (--geno 0.05 --max-alleles 2 --maf 0.36) [ 31 , 32 ].…”

Section: Methodsmentioning

confidence: 99%

Whole-Genome Sequence Analysis of Italian Honeybees (Apis mellifera)

Minozzi

Lazzari²,

Iorio

et al. 2021

Animals

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At the end of the last glaciation, Apis mellifera was established in northern Europe. In Italy, Apis melliferaligustica adapted to the mild climate and to the rich floristic biodiversity. Today, with the spread of Varroa destructor and with the increasing use of pesticides in agriculture, the Ligustica subspecies is increasingly dependent on human action for its survival. In addition, the effects of globalization of bee keeping favored the spread in Italy of other honeybee stocks of A. mellifera, in particular the Buckfast bee. The purpose of this study was to characterize the Italian honeybee’s population by sequencing the whole genome of 124 honeybees. Whole genome sequencing was performed by Illumina technology, obtaining a total coverage of 3720.89X, with a mean sample coverage of 29.77X. A total of 4,380,004 SNP variants, mapping on Amel_HAv3.1 chromosomes, were detected. Results of the analysis of the patterns of genetic variation allowed us to identify and subgroup bees according to their type. The investigation revealed the genetic originality of the Sicula, and in A.m. ligustica limited genetic introgression from the other breeds. Morphometric analysis of 5800 worker bees was in agreement with genomic data.

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Section: Methodsmentioning

confidence: 99%

Whole-Genome Sequence Analysis of Italian Honeybees (Apis mellifera)

Minozzi

Lazzari²,

Iorio

et al. 2021

Animals

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“…Several studies have shown that a small set of SNPs, if accurately chosen, is sufficient to differentiate the genetic origin of breeds [ 15 , 21 ]. In the case of the estimation of breed composition, Kumar et al [ 22 ] showed that a subset of 470 informative SNPs could discriminate six Indian indigenous and European dairy breeds. Using a combination of principal component analysis (PCA) and random forest, Hulsegge et al [ 23 ] identified 133 SNPs that allowed to differentiate local Dutch cattle breeds.…”

Section: Introductionmentioning

confidence: 99%

SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

et al. 2021

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Background Understanding the relationship between genetic admixture and phenotypic performance is crucial for the optimization of crossbreeding programs. The use of small sets of informative ancestry markers can be a cost-effective option for the estimation of breed composition and for parentage assignment in situations where pedigree recording is difficult. The objectives of this study were to develop small single nucleotide polymorphism (SNP) panels that can accurately estimate the total dairy proportion and assign parentage in both West and East African crossbred dairy cows. Methods Medium- and high-density SNP genotype data (Illumina BovineSNP50 and BovineHD Beadchip) for 4231 animals sampled from African crossbreds, African Bos taurus, European Bos taurus, Bos indicus, and African indigenous populations were used. For estimating breed composition, the absolute differences in allele frequency were calculated between pure ancestral breeds to identify SNPs with the highest discriminating power, and different combinations of SNPs weighted by ancestral origin were tested against estimates based on all available SNPs. For parentage assignment, informative SNPs were selected based on the highest minor allele frequency (MAF) in African crossbred populations assuming two Scenarios: (1) parents were selected among all the animals with known genotypes, and (2) parents were selected only among the animals known to be a parent of at least one progeny. Results For the medium-density genotype data, SNPs selected for the largest differences in allele frequency between West African indigenous and European Bos taurus breeds performed best for most African crossbred populations and achieved a prediction accuracy (r2) for breed composition of 0.926 to 0.961 with 200 SNPs. For the high-density dataset, a panel with 70% of the SNPs selected on their largest difference in allele frequency between African and European Bos taurus performed best or very near best across all crossbred populations with r2 ranging from 0.978 to 0.984 with 200 SNPs. In all African crossbred populations, unambiguous parentage assignment was possible with ≥ 300 SNPs for the majority of the panels for Scenario 1 and ≥ 200 SNPs for Scenario 2. Conclusions The identified low-cost SNP assays could overcome incomplete or inaccurate pedigree records in African smallholder systems and allow effective breeding decisions to produce progeny of desired breed composition.

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“…Small sets, or panels, of ancestry informative markers (AIMs) have been developed and used to infer population genetic parameters in several species. AIM panels have been used to estimate biogeographical ancestry and structure in human populations [19][20][21][22], to discriminate among breeds and geographical origin of Italian sheep breeds [23], to identify cattle breeds [24][25][26], to trace the origin of animal products [27,28], and for breed assignment and analysis of individual ancestry in cattle [29][30][31][32] and pig populations [33]. Moreover, AIM panels have been developed to identify hybrids in wildlife conservation projects on wolf [34], wild cat [9], and mule deer [35].…”

Section: Introductionmentioning

confidence: 99%

Identification of Ancestry Informative Marker (AIM) Panels to Assess Hybridisation between Feral and Domestic Sheep

Somenzi

Ajmone‐Marsan

Barbato

2020

Animals

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Hybridisation of wild populations with their domestic counterparts can lead to the loss of wildtype genetic integrity, outbreeding depression, and loss of adaptive features. The Mediterranean island of Sardinia hosts one of the last extant autochthonous European mouflon (Ovis aries musimon) populations. Although conservation policies, including reintroduction plans, have been enforced to preserve Sardinian mouflon, crossbreeding with domestic sheep has been documented. We identified panels of single nucleotide polymorphisms (SNPs) that could act as ancestry informative markers able to assess admixture in feral x domestic sheep hybrids. The medium-density SNP array genotyping data of Sardinian mouflon and domestic sheep (O. aries aries) showing pure ancestry were used as references. We applied a two-step selection algorithm to this data consisting of preselection via Principal Component Analysis followed by a supervised machine learning classification method based on random forest to develop SNP panels of various sizes. We generated ancestry informative marker (AIM) panels and tested their ability to assess admixture in mouflon x domestic sheep hybrids both in simulated and real populations of known ancestry proportions. All the AIM panels recorded high correlations with the ancestry proportion computed using the full medium-density SNP array. The AIM panels proposed here may be used by conservation practitioners as diagnostic tools to exclude hybrids from reintroduction plans and improve conservation strategies for mouflon populations.

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Identification of breed-specific SNP panel in nine different cattle genomes.

Cited by 14 publications

References 15 publications

Whole-Genome Sequence Analysis of Italian Honeybees (Apis mellifera)

Whole-Genome Sequence Analysis of Italian Honeybees (Apis mellifera)

SNP panels for the estimation of dairy breed proportion and parentage assignment in African crossbred dairy cattle

Identification of Ancestry Informative Marker (AIM) Panels to Assess Hybridisation between Feral and Domestic Sheep

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