Research Note: Evaluation of Resequencing Technologies Parameters for CNV Genotyping

Whole genome (re)sequencing provides new opportunities to discover Copy Number Variation (CNV) on the genome. Due to the continuous reduction in sequencing costs, it has become as the principal methodology to detect CNV in livestock. One parameter that increases the genotyping cost is the depth of the coverage during sequencing. The main aim of this note was to assess the variation on CNV identification with different depth coverage and readlength on genome sequencing. The results point out that sequences coming from short read-length require less depth coverage than those obtained with long read-length. In addition, small CNV require deeper coverage to be detected. These results can reduce the discovering and genotyping costs since sequencing technologies with short read-lengths are often less costly. Finally, a general formula was derived to optimize the sequencing costs

Copy number variation mapping and genomic variation of autochthonous and commercial turkey populations

This study aims at investigating genomic diversity of several turkey populations using Copy Number Variants (CNVs). A total of 115 individuals from six Italian breeds (Colle Euganei, Bronzato Comune Italiano, Parma e Piacenza, Brianzolo, Nero d\u2019Italia, and Ermellinato di Rovigo), seven Narragansett, 38 commercial hybrids, and 30 Mexican turkeys, were genotyped with the Affymetrix 600K single nucleotide polymorphism (SNP) turkey array. The CNV calling was performed with the Hidden Markov Model of PennCNV software and with the Copy Number Analysis Module of SVS 8.4 by Golden Helix\uae. CNV were summarized into CNV regions (CNVRs) at population level using BEDTools. Variability among populations has been addressed by hierarchical clustering (pvclust R package) and by principal component analysis (PCA). A total of 2,987 CNVs were identified covering 4.65% of the autosomes of the Turkey_5.0/melGal5 assembly. The CNVRs identified in at least two individuals were 362\u2014189 gains, 116 losses, and 57 complexes. Among these regions the 51% contain annotated genes. This study is the first CNV mapping of turkey population using 600K chip. CNVs clustered the individuals according to population and their geographical origin. CNVs are known to be indicators also of adaptation, as some researches in different species are suggesting

Análisis de variables morfológicas de pavos de traspatio mexicanos (Meleagris gallopavo gallopavo) = Analysis of morphological variables in Mexican backyard turkeys (Meleagris gallopavo gallopavo)

The objective was to evaluate some morphological characteristics of backyard Turkeys (n=248) coming from 126 rural production units located in 75 municipalities of 24 States of the Mexican Republic. The statistical model included sex, state, and municipality within state. The three explanatory variables affected all the response variables (P0.05). Male Turkeys had greater (P0.05). Body weight increased 143 g in males (P<0.01) and 113 g in females (P<0.01) for each centimeter increment in breast circumference. The predominant colors in the plumage, skin and tarsus were black, white and brown, respectively. The Mexican backyard Turkey presented significant sexual dimorphism and strong phenotypic correlation between breast circumference and body weight

Few mitochondrial DNA sequences are inserted into the turkey (Meleagris gallopavo) nuclear genome: evolutionary analyses and informativity in the domestic lineage

Mitochondrial DNA (mtDNA) insertions have been detected in the nuclear genome of many eukaryotes. These sequences are pseudogenes originated by horizontal transfer of mtDNA fragments into the nuclear genome, producing nuclear DNA sequences of mitochondrial origin (numt). In this study we determined the frequency and distribution of mtDNA-originated pseudogenes in the turkey (Meleagris gallopavo) nuclear genome. The turkey reference genome (Turkey_2.01) was aligned with the reference linearized mtDNA sequence using last. A total of 32 numt sequences (corresponding to 18 numt regions derived by unique insertional events) were identified in the turkey nuclear genome (size ranging from 66 to 1415\ua0bp; identity against the modern turkey mtDNA corresponding region ranging from 62% to 100%). Numts were distributed in nine chromosomes and in one scaffold. They derived from parts of 10 mtDNA protein-coding genes, ribosomal genes, the control region and 10 tRNA genes. Seven numt regions reported in the turkey genome were identified in orthologues positions in the Gallus gallus genome and therefore were present in the ancestral genome that in the Cretaceous originated the lineages of the modern crown Galliformes. Five recently integrated turkey numts were validated by PCR in 168 turkeys of six different domestic populations. None of the analysed numts were polymorphic (i.e. absence of the inserted sequence, as reported in numts of recent integration in other species), suggesting that the reticulate speciation model is not useful for explaining the origin of the domesticated turkey lineage

Genetic (CO)variances between milk yield and growth traits in a multibreed population in the tropical regions of Mexico

The objective of this study was to estimate genetic parameters for milk yield (MY), birth weight (BW) and weights adjusted to 205 and 365 days of age (P205 and P365, respectively) and to evaluate the genetic relationship between first lactation milk yield (MY1) and P205 using restricted maximum likelihood methodology. Estimates of direct heritability were 0.120.04, 0.400.09, 0.280.05 and 0.250.05 for MY, BW, P205 and P365, respectively. Repeatability for MY was 0.340.02. The correlation between MY1 and P205 was 0.1980.45, thus both traits need to be considered in selection improvement programs

Copy number variants reveal genomic diversity in a Mexican Creole cattle population

Mexican Creole Cattle (MCC) derived from cattle of the Iberian Peninsula, mainly from Andaluc\ueda and Extremadura, and were introduced in central America the 16th century. Copy Number Variants (CNVs) are structural variants contributing to the genetic diversity among populations and related to variation in phenotypic expression. More than half of the identified CNVs regions in human and livestock include protein-coding genes involved in essential function, as cellular functionality, metabolic pathways and disease susceptibility. The aim of this study is to investigate the CNVs genomic variation in the MCC population. A total of 48 unrelated individuals (5 males and 43 females) were genotyped with the BovineHD Genotyping BeadChip Illumina, containing 7,77,962 polymorphic SNPs. A total of 2170 CNVs were detected in 40 individuals, summarized into 733 CNV regions, covering 32.1 Mb of the bovine autosome genome. Functional analysis of the CNVRs identified 131 genes mainly involved in immune response and inflammation, and 923 overlapping QTL classified in six difference QTL-term categories. Cluster and PCA analyses showed a samples distribution in concordance with the geographical origins of the sub-populations, highlighting both a sharing genetic background together with a diversification of populations as a response to adaptation to different and adverse environments