Population Genetic Parameters Research Articles

Development of microsatellite markers for the American species Vachellia aroma (Fabac

Background and aims: There are currently no microsatellite markers available for any American species of Vachellia, and particularly, for V. aroma. Then the aims of this study were to develop SSR markers specific for V. aroma, for the first time, and test its amplification in a close related species. M&M: For the development of the SSR in V. aroma, total genomic DNA was extracted and it was sequenced in a one-fourth run on a Roche 454 GS FLX+ platform. The study area included two Argentinean populations: San José and Robles, Santiago del Estero province.  Results: We detected 422 sequences containing SSR loci. A set of 39 primer pairs presented amplified products in V. aroma and V. caven, but 12 revealed clear, replicable and polymorphic loci in V. aroma. Conclusions: The results of this work indicate that a new set of SSR markers was developed for V. aroma and their transferability to V. caven was assessed. The analysis of variability, showed that these 12 polymorphic markers are highly informative, and a powerful tool to investigate population genetics parameters in V. aroma and related species.

Mutation rate and effective population size of the model cooperative bacterium Myxococcus xanthus.

Intrinsic rates of genetic mutation have diverged greatly across taxa and exhibit statistical associations with several other parameters and features. These include effective population size (Ne), genome size, and gametic multicellularity, with the latter being associated with both increased mutation rates and decreased effective population sizes. However, data sufficient to test for possible relationships between microbial multicellularity and mutation rate (µ) are lacking. Here we report estimates of two key population-genetic parameters, Ne and µ, for Myxococcus xanthus, a bacterial model organism for the study of aggregative multicellular development, predation, and social swarming. To estimate µ, we conducted an ∼400-day mutation-accumulation (MA) experiment with 46 lineages subjected to regular single colony bottlenecks prior to clonal regrowth. Upon conclusion, we sequenced one clonal-isolate genome per lineage. Given collective evolution for 85,323 generations across all lines, we calculate a per base-pair mutation rate of ∼5.5 × 10-10 per site per generation, one of the highest mutation rates among free-living eubacteria. Given our estimate of µ, we derived Ne at ∼107 from neutral diversity at four-fold degenerate sites across two dozen M. xanthus natural isolates. This estimate is below average for eubacteria and strengthens an already clear negative correlation between µ and Ne in prokaryotes. The higher and lower than average mutation rate and Ne for M. xanthus, respectively, amplify the question of whether any features of its multicellular life-cycle - such as group-size reduction during fruiting-body development - or its highly structured spatial distribution have significantly influenced how these parameters have evolved.

How Does Selfing Affect the Pace and Process of Speciation?

Surprisingly little attention has been given to the impact of selfing on speciation, even though selfing reduces gene flow between populations and affects other key population genetics parameters. Here we review recent theoretical work and compile empirical data from crossing experiments and genomic and phylogenetic studies to assess the effect of mating systems on the speciation process. In accordance with theoretical predictions, we find that accumulation of hybrid incompatibilities seems to be accelerated in selfers, but there is so far limited empirical support for a predicted bias toward underdominant loci. Phylogenetic evidence is scarce and contradictory, including studies suggesting that selfing either promotes or hampers speciation rate. Further studies are therefore required, which in addition to measures of reproductive barrier strength and selfing rate should routinely include estimates of demographic history and genetic divergence as a proxy for divergence time.

Polymorphisms in two key anthocyanic genes of clivia (Clivia miniata L.) reveal evidence of selection and possible association with flower pigmentation.

Members of the genus Clivia show considerable variation in flower pigmentation and morphology. Such variation is effected by mutations that emerge in candidate flower development genes over time. Besides population history, mutations can further illuminate the effects of demographic events in populations in addition to population genetic parameters including selection, recombination, and linkage disequilibrium (LD). The current study aimed to find sequence variants in two anthocyanin biosynthetic genes (DFR and bHLH) of Clivia miniata and use the data to assess population genetic factors from a random collection of orange/red- and yellow-flowered specimens. Overall, average nucleotide diversity in the two anthocyanin genes was moderate (π = 0.00646), whereas haplotypes differed significantly (Hd ≥ 0.9). Gene evolution was seemingly driven by mutations (CmiDFR) or recombination (CmibHLH001). LD decayed swiftly within the analyzed gene regions and supported the feasibility of assessing trait-variant associations via the association/linkage mapping approach. In the end, most associations were found to be spurious, but one haplotype in CmibHLH001 showed a promising correlation to the orange/red flower phenotype in Clivia specimens. In all, the present study is the first to measure gene-level diversity in C. miniata - data that had never been reported so far. Further, the study also identified allelic and haplotypic variants that may be beneficial in future association genetic studies of Clivia. Such studies, however, consider large diverse populations to control for statistical bias intrinsic to the analysis of small datasets.

Influence of molecular marker type on estimating effective population size and other genetic parameters in a critically endangered parrot

AbstractGenetics is a fast‐moving field, and for conservation practitioners or ecologists, it can be bewildering. The choice of marker used in studies is fundamental; in the literature, preference has recently shifted from microsatellites to single nucleotide polymorphism (SNP) loci. Understanding how marker type affects estimates of population genetic parameters is important in the context of conservation, especially because the accuracy of estimates has a bearing on the actions taken to protect threatened species. We compare parameter estimates between seven microsatellites, 3761 SNP loci, and a random subset of 100 SNPs for the exact same 324 individual swift parrots, Lathamus discolor, and also use 457 additional samples from subsequent years to compare SNP estimates. Both marker types estimated a lower HO than HE. We show that microsatellites and SNPs mainly indicate a lack of spatial genetic structure, except when a priori collection locations were used on the SNP data in a discriminant analysis of principal components (DAPC). The 100‐SNP subset gave comparable results to when the full dataset was used. Estimates of effective population size (Ne) were comparable between markers when the same individuals were considered, but SNPs had narrower confidence intervals. This is reassuring because conservation assessments that rely on population genetic estimates based on a few microsatellites are unlikely to be nullified by the general shift toward SNPs in the literature. However, estimates between markers and datasets varied considerably when only adult samples were considered; hence, including samples of all age groups is recommended to be used when available. The estimated Ne was higher for the full SNP dataset (2010–2019) than the smaller comparison data (2010–2015), which might be a better reflection of the species status. The lower precision of microsatellites may not necessarily be a barrier for most conservation applications; however, SNPs will improve confidence limits, which may be useful for practitioners.

TRAILS: Tree reconstruction of ancestry using incomplete lineage sorting.

Genome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny. Here, we introduce TRAILS, a hidden Markov model that accurately infers time-resolved population genetics parameters, such as ancestral effective population sizes and speciation times, for ancestral branches using a multi-species alignment of three species and an outgroup. TRAILS leverages the information contained in incomplete lineage sorting fragments by modelling genealogies along the genome as rooted three-leaved trees, each with a topology and two coalescent events happening in discretized time intervals within the phylogeny. Posterior decoding of the hidden Markov model can be used to infer the ancestral recombination graph for the alignment and details on demographic changes within a branch. Since TRAILS performs posterior decoding at the base-pair level, genome-wide scans based on the posterior probabilities can be devised to detect deviations from neutrality. Using TRAILS on a human-chimp-gorilla-orangutan alignment, we recover speciation parameters and extract information about the topology and coalescent times at high resolution.

Sequence-based population structure, relatedness, and inbreeding estimates for forensic autosomal STR markers

Population data have become available for sequence data to aid forensic investigations and prepare the forensic community in the move towards implementing NGS methods. This comes with a need for updated population genetic parameters estimates to allow DNA evidence evaluations using sequence data. Initial work has been done on a small sample and here we expand this work by providing estimates of population structure and relatedness for autosomal STR data generated by sequencing technologies. We also discuss the effect of inbreeding on forensic calculations and discuss why the use of genotypic-based estimates may be preferred over allelic-based estimates.

Characteristic of allele pool of sheep of the southern meat breed using microsatellite markers

Purpose: to characterize the allele pool of sheep of the southern beef breed using microsatellites.Materials and methods. The biomaterial was ear’s plucks from 80 sheep of the southern meat breed, selected from the Ladozhsky Breeding Plant. 20 East Friesian sheep, 33 Dorset sheep and 63 Romanov sheep were used for comparison. Nine microsatellite loci (INRA005, SPS113, INRA23, MAF65, McM527, OarCP49, HSC, OarAE129, MAF214) were selected as DNA markers. Microsatellite variability was analyzed using the ABI3130x1 Genetic Analyzer. The results were processed in the GenAIEx 6.503 program, with the help of which the main indicators characterizing the state of the allele pool and genetic diversity were calculated.Results. Analysis of the population genetic parameters of sheep of the southern meat breed showed that the average number of alleles per locus (Na) and the effective number of alleles per locus (Ne) exceed the sample average by 1,72 and 0,58 alleles, respectively. The expected heterozygosity (He) was 0,766, while the observed heterozygosity (Ho) was 0,741. The coefficient of inbreeding (Fis) was 0,03. The analysis of the principal components, carried out for the studied breeds in the planes of the first and third principal components, did not fundamentally change the nature of the spatial clustering of the studied groups of sheep. Analysis of the principal coordinates, performed on the basis of calculation of pairwise Fst values, showed that the southern meat breed is located in the upper left quadrant and is isolated from other breeds. The values of the Fst indicator indicate that there is moderate genetic differentiation between the southern meat and dorset breeds (Fst=0,116), and significant genetic differentiation between the southern meat and romanov breeds (Fst=0,161).Conclusion. An analysis of the population genetic parameters of sheep of the southern meat breed, in comparison with the east friesian, dorset and romanov breeds, showed that, in general, in terms of the total number of alleles per locus and the number of effective alleles per locus, it is characterized by a high level of genetic diversity. The presence of a tendency towards a deficiency of heterozygotes is probably explained by the limited population, represented by the only relict gene pool in Russia.

Parthenogenomics: Insights on mutation rates and nucleotide diversity in parthenogenetic Panagrolaimus nematodes.

Asexual reproduction is assumed to lead to the accumulation of deleterious mutations, and reduced heterozygosity due to the absence of recombination. Panagrolaimid nematode species display different modes of reproduction. Sexual reproduction with distinct males and females, asexual reproduction through parthenogenesis in the genus Panagrolaimus, and hermaphroditism in Propanagrolaimus. Here, we compared genomic features of free-living nematodes in populations and species isolated from geographically distant regions to study diversity, and genome-wide differentiation under different modes of reproduction. We firstly estimated genome-wide spontaneous mutation rates in a triploid parthenogenetic Panagrolaimus, and a diploid hermaphroditic Propanagrolaimus via long-term mutation accumulation lines. Secondly, we calculated population genetic parameters including nucleotide diversity, and fixation index (F ST) between populations of asexually and sexually reproducing nematodes. Thirdly, we used phylogenetic network methods on sexually and asexually reproducing Panagrolaimus populations to understand evolutionary relationships between them. The estimated mutation rate was slightly lower for the asexual population, as expected for taxa with this reproductive mode. Natural polyploid asexual populations revealed higher nucleotide diversity. Despite their common ancestor, a gene network revealed a high level of genetic differentiation among asexual populations. The elevated heterozygosity found in the triploid parthenogens could be explained by the third genome copy. Given their tendentially lower mutation rates it can be hypothesized that this is part of the mechanism to evade Muller's ratchet. Our findings in parthenogenetic triploid nematode populations seem to challenge common expectations of evolution under asexuality.

Assessment of genetic diversity, population structure and wolf-dog hybridisation in the Eastern Romanian Carpathian wolf population

The Carpathian Mountains have been constantly inhabited by grey wolves and present one of the largest distribution areas in Europe, comprising between 2300 and 2700 individuals in Romania. To date, however, relatively little is known about the Romanian wolf population. We aimed to provide a first assessment of genetic diversity, population structure and wolf-dog hybridisation based on 444 mostly non-invasively collected samples in the Eastern Romanian Carpathians. Pack reconstruction and analysis of population genetic parameters were performed with mitochondrial DNA control-region sequencing and microsatellite genotyping. We found relatively high levels of genetic diversity, which is similar to values found in previous studies on Carpathian wolves from Poland and Slovakia, as well as to the long-lasting Dinaric-Balkan wolf population. We found no significant population structure in our study region, suggesting effective dispersal and admixture. Analysis of wolf-dog hybridisation using a Single Nucleotide Polymorphism panel optimised for hybrid detection revealed low rates of admixture between wolves and domestic dogs. Our results provide evidence for the existence of a genetically viable wolf population in the Romanian Carpathians. The genetic data obtained in this study may serve as valuable baseline information for the elaboration of monitoring standards and management plans for wolves in Romania.

Genetic evaluation for production and body size traits using different animal models in purebred-Duroc pigs.

Duroc pigs are popular crossbred terminal sires, and accurate assessment of genetic parameters in the population can help to rationalize breeding programmes. The principle aim of this study were to evaluate the genetic parameters of production (birth weight, BW; age at 115 kg, AGE; feed conversion ratio, FCR) and body size (body length, BL; body height, BH; front cannon circumference, FCC) traits of Duroc pigs. The second objective was to analyze the fit of different genetic assessment models. The variance components and correlations of BW (28,348 records), AGE (28,335 records), FCR (11,135 records), BL (31,544 records), BH (21,862 records), and FCC (14,684 records) traits were calculated by using DMU and AIREMLF90 from BLUPF90 package. In the common environment model, the heritability of BW, AGE, FCR, BL, BH, and FCC traits were 0.17 ± 0.014, 0.30 ± 0.019, 0.28 ± 0.024, 0.16 ± 0.013, 0.14 ± 0.017, and 0.081 ± 0.016, with common litter effect values of 0.25, 0.20, 0.18, 0.23, 0.19, and 0.16, respectively. According to the results of the Akaike information criterion (AIC) calculations, models with smaller AIC values have a better fit. We found that the common environment model with litter effects as random effects for estimating genetic parameters had a better fit. In this Model, the estimated genetic correlations between AGE with BW, FCR, BL, BH, and FCC traits were -0.28 (0.040), 0.76 (0.038), -0.71 (0.036), -0.44 (0.060), and -0.60 (0.073), respectively, with phenotypic correlations of -0.17, 0.52, -0.22, -0.13 and -0.24, respectively. In our analysis of genetic trends for six traits in the Duroc population from 2012 to 2021, we observed significant genetic trends for AGE, BL, and BH. Particularly noteworthy is the rapid decline in the genetic trend for AGE, indicating an enhancement in the pig's growth rate through selective breeding. Therefore, we believe that some challenging-to-select traits can benefit from the genetic correlations between traits. By selecting easily measurable traits, they can gain from synergistic selection effects, leading to genetic progress. Conducting population genetic parameter analysis can assist us in devising breeding strategies.

Whole genome resequencing revealed genomic variants and functional pathways related to adaptation in Indian yak populations

The present study aims to identify genomic variants through a whole genome sequencing (WGS) approach and uncover biological pathways associated with adaptation and fitness in Indian yak populations. A total of 30 samples (10 from each population) were included from Arunachali, Himachali and Ladakhi yak populations. WGS analysis revealed a total of 32171644, 27260825, and 32632460 SNPs and 4865254, 4429941, and 4847513 Indels in the Arunachali, Himachali, and Ladakhi yaks, respectively. Genes such as RYR2, SYNE2, BOLA, HF1, and the novel transcript ENSBGRG00000011079 were found to have the maximum number of high impact variants in all three yak populations, and might play a major role in local adaptation. Functional enrichment analysis of genes harboring high impact SNPs revealed overrepresented pathways related to response to stress, immune system regulation, and high-altitude adaptation. This study provides comprehensive information about genomic variants and their annotation in Indian yak populations, thus would serve as a data resource for researchers working on the yaks. Furthermore, it could be well exploited for better yak conservation strategies by estimating population genetics parameters viz., effective population size, inbreeding, and observed and expected heterozygosity.

Population genetics of the endangered Clanwilliam sandfish Labeo seeberi: considerations for conservation management

The Cape Fold Ecoregion (CFE) is one of southern Africa’s unique aquatic ecoregions and its freshwater fish fauna is characterized by high levels of endemism. As with many other Mediterranean-type ecosystems, the region is also a hotspot for threatened and range-restricted freshwater fish. Many of the CFE’s endemic species are at risk for extinction, with declines in population sizes and distribution ranges. The Clanwilliam sandfish Labeo seeberi is an example of such a species and is considered one of South Africa’s most endangered large migratory cyprinids. This species is endemic to the Olifants/Doring river system in the CFE and has been subject to a major population decline, mainly as a result of invasive alien fish and adverse climate events. Little is known of the genetics of the Clanwilliam sandfish, thus this study aimed to provide basic population genetic parameters to inform future conservation interventions. Both microsatellite and mitochondrial DNA (mtDNA) markers were used to assess populations from three sites within the Olifants/Doring river system. Genetic diversity was moderate to low and did not reflect the drastic decline expected on the basis of previous relative abundance data. This is likely due to a lag effect between ecological/life history demographics (due to juvenile recruitment failures) and population genetic composition. Furthermore, there was limited genetic differentiation between the sampling locations, suggesting a single breeding population, but mtDNA haplotype distribution and slight divergence of the smaller populations does suggest that the population might have become recently fragmented. The results show that the effective population size of the current breeding population might still be sufficient to maintain evolutionary potential in the short term, which could act as a buffer until conservation strategies focusing on protecting breeding animals and maximizing juvenile survival can restore population numbers.

The variation in the beta-casein genotypes and its effect on milk yield and genomic values in Holstein-Friesian cows

The A2 milk marker is gaining popularity worldwide; thus, many farms plan to convert their dairy cattle herds to the A2A2 genotype. Variation in beta-casein genotypes needs to be monitored in large dairy cattle populations. Therefore we aimed to evaluate the genotypic distributions, population genetics, and diversity parameters in Holstein-Friesian cows. A total of 1200 cattle were genotyped using the Affymetrix® Axiom® array system. We performed an association analysis regarding the CSN2 genotypes and phenotypic traits, including lactation and test-day milk yield. We next evaluated the effects of the genotypes considering the genetic merit of the animals. Animals were grouped based on their PTAs for milk production, fat, protein, and daughter pregnancy rate. Thus, we tested the genotype × genetic merit interaction for significance. The A2 allele frequency is remarkably high (0.68), and the heterozygous genotype is predominant (46.25%). The marker showed intermediate variability and diversity levels, indicating a considerable frequency of the A1A1 genotype (9.33%) remains in the population. ANOVA results showed no significant association between the CSN2 genotypes and milk yield traits. A similar finding is valid for the genotype × genetic merit regarding the genomic test results. The data presented here may be helpful for further investigations and applications on A2 milk production.

Developmental validation of a novel multiple genotyping assay with 24 Canine STR loci

Canine individual identification and parentage testing are essential in various fields, including forensics and breeding programs. This study aimed to develop and validate the Canine 25 A kit, a multiplex polymerase chain reaction (PCR) system designed to address these critical requirements. This novel system enables the simultaneous amplification of 24 canine autosomal short tandem repeat (STR) loci and one sex-determining marker. Validation of the Canine 25 A kit was conducted following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines, demonstrating significant sensitivity, high inhibitor tolerance, canine specificity within a mixture, species specificity, and precision in genotype determination. The Canine 25 A kit was crucial in resolving several forensic cases, such as casework samples from a dog attack incident and parentage determination. Its effectiveness in genotyping these samples highlights its significance in forensic applications. Population genetic parameter analysis revealed a high discriminatory power, as indicated by the calculated combined discrimination power (CDP) values for each breed exceeding 0.999 999 999 999, while the combined power of exclusion (CPE) surpassed 0.9999. Overall, the Canine 25 A kit offers a precise and dependable tool for canine individual identification and parentage determination.

Characteristics of meat production traits in the Hungarian Simmental herd selected for the simultaneous improvement of milk and meat production.

Phenotypic and genetic trends, population genetic parameters, and the heritability and breeding values of the fattening and slaughter traits - namely muscularity score (MUS), final fattening weight (FFW), weight gain per day of life (WGD), slaughter weight (SLW), carcass weight (CAR), dressing percentage (DRP), bone-meat production per day of life (BMP), SEUROP conformation and fat coverage score (EUR, FAT), and meat percentage (MEP) - of 1162 Hungarian Simmental bulls were evaluated with the progeny test database of the Association of Hungarian Simmental Breeders. Trends were calculated by weighted linear regression analysis, while the population genetic parameters and breeding values used the BLUP (best linear unbiased prediction) animal model and general linear model (GLM). According to the results, the lowest heritability value () was found in FAT. In the case of MUS, EUR and MEP, the values were moderate (, 0.26 and 0.32), and in the case of the other traits, high heritability values (  0.42-0.52) were estimated. The phenotypic trends of the fattening and slaughter traits of bull progeny born between 2001 and 2019 showed a stagnant direction. Between the sires, the differences in the breeding values for some traits (WDG, CAR and BMP) were large, and with other traits (DRP, EUR and FAT), small differences were found. According to the data of the genetic-trend calculation, the steepness values of the evaluated traits were positive, and the genetic trends showed a slightly improving direction in the estimated period.

De Novo Mutation Rates in Sticklebacks.

Mutation rate is a fundamental parameter in population genetics. Apart from being an important scaling parameter for demographic and phylogenetic inference, it allows one to understand at what rate new genetic diversity is generated and what the expected level of genetic diversity is in a population at equilibrium. However, except for well-established model organisms, accurate estimates of de novo mutation rates are available for a very limited number of organisms from the wild. We estimated mutation rates (µ) in two marine populations of the nine-spined stickleback (Pungitius pungitius) with the aid of several 2- and 3-generational family pedigrees, deep (>50×) whole-genome resequences and a high-quality reference genome. After stringent filtering, we discovered 308 germline mutations in 106 offspring translating to µ = 4.83 × 10-9 and µ = 4.29 × 10-9 per base per generation in the two populations, respectively. Up to 20% of the mutations were shared by full-sibs showing that the level of parental mosaicism was relatively high. Since the estimated µ was 3.1 times smaller than the commonly used substitution rate, recalibration with µ led to substantial increase in estimated divergence times between different stickleback species. Our estimates of the de novo mutation rate should provide a useful resource for research focused on fish population genetics and that of sticklebacks in particular.

Characterization of Microsatellite Markers in Crossbred Ducks

Background: Chicken represents a valuable genetic resource and protein source, it remains a potential threat to human health as they serve as a reservoir for diseases and food borne pathogens. Diversification of the poultry production is one of the viable options to enhance the food production with less susceptibility to the threats from the emerging diseases and changing climatic conditions. Ducks are promising species suitable for the diversification and will be complimentary with an adaption potential from small to commercial farming. Majority of ducks in the country are desi type with a meagre proportion of improved duck strains. genetic characterization by developing duck specific microsatellite markers and designing suitable improvement program are required to be undertaken at the earliest. The microsatellite markers are extensively used for assessing genetic structure, diversity, and relationships. Information about genetic diversity of indigenous duck breeds is important to design effective improvement and conservation strategies. Therefore, the current studies aim at genetic characterization and evaluation of growth, production and reproduction traits of the crosses of local duck population besides undertaking a suitable duck improvement program. Methods: Spectrophotometric evaluation of DNA extraction, Electrophoretic evaluation of DNA extraction , microsatellite primers- Presently, a panel of 10 informative duck microsatellite markers were identified from database as reported by Alyethodi and Kumar (2010) and Huang et al., (2006) and used for the studies, Polymerase chain reaction (PCR) , Documentation of PCR products by Agarose Gel Electrophoresis, Metaphor agarose gel electrophoresis(MAGE)of microsatellites alleles, Determination of molecular size of microsatellite alleles and genotypes, Statistical analysis of population genetics data, Data on genotype of all experimental birds at ten microsatellites were compiled and analyzed using POPGENE® 3.1 software (Yeh et al., 1999) for their population genetics parameters. Results: The study was conducted at College of Veterinary Science, Assam Agricultural University, Khanapara, Guwahati, Assam, India. In this study, the genomic DNA was isolated and characterized microsatellite loci in crossbred duck (Pati x White Pekin). Ten microsatellites were used to detect polymorphisms in 50 cross bred ducks. A total of 28 nos of alleles were observed and all loci were polymorphic. The number of alleles ranged from 2 to 5 with an average of 2.6 ±0.08 per microsatellite locus. The observed and expected heterozygosity of these polymorphic makers ranged from 0.00 to 0.42 with an average number of 0.047 and 0.41 to 0.82 with an average number of 0.57, respectively. The Polymorphic markers consist of observed heterozygosities of loci were less than 0.50. The polymorphism information content (PIC) of 10 loci ranged from 0.32 to 0.78 with an average of 0.477. Microsatellite markers will be useful tool for constructing the genetic linkage map of the duck as well as comparative mapping with the chicken.

NgsJulia: population genetic analysis of next-generation DNA sequencing data with Julia language

A sound analysis of DNA sequencing data is important to extract meaningful information and infer quantities of interest. Sequencing and mapping errors coupled with low and variable coverage hamper the identification of genotypes and variants and the estimation of population genetic parameters. Methods and implementations to estimate population genetic parameters from sequencing data available nowadays either are suitable for the analysis of genomes from model organisms only, require moderate sequencing coverage, or are not easily adaptable to specific applications. To address these issues, we introduce ngsJulia, a collection of templates and functions in Julia language to process short-read sequencing data for population genetic analysis. We further describe two implementations, ngsPool and ngsPloidy, for the analysis of pooled sequencing data and polyploid genomes, respectively. Through simulations, we illustrate the performance of estimating various population genetic parameters using these implementations, using both established and novel statistical methods. These results inform on optimal experimental design and demonstrate the applicability of methods in ngsJulia to estimate parameters of interest even from low coverage sequencing data. ngsJulia provide users with a flexible and efficient framework for ad hoc analysis of sequencing data.ngsJulia is available from: https://github.com/mfumagalli/ngsJulia.

MILK PRODUCTIVITY AND REPRODUCTIVE CAPACITY OF COWS DEPENDS ON DIFFERENT MILK PRODUCTION TECHNOLOGIES

Introduction. The production of milk from dairy cows in Ukraine is increasingly consistent with the introduction of modern volume-planning and technological solutions, which are based on light-type premises, a tetherless box system for keeping cows of the same type, throughout the year, feeding from the feed table with full-rational fodder mixtures, milking – in milking hall on the "Parallel", "Carousel", "Jalynka" type installations, as well as on robotic milking systems without human participation. But despite the advantages of modern technology, a large number of farms continue to use high-cost traditional technologies for milk production, with a tethered system of keeping cows and milking in stalls into the milk duct.
 Therefore, the aim of the work was to determine the conditions under which cattle of the Ukrainian Black-and-White Dairy breed show the highest level of productivity.
 Research materials and methods. An analysis of methods of keeping and milking of Ukrainian Black-and-White Dairy cows in controlled herds was carried out based on the materials of the information database of the dairy management system of the MS "Intesel-Orsek", which were divided by milk production technologies. Progressive technology is defined as keeping cows untethered throughout the year in pavilion-type premises, with the same type of feeding from feed tables, milking in the milking hall on different types of equipment (n = 4), and traditional – tethered keeping of cows during the stall period in cowsheds, feeding depending on productivity, milking in stalls on UDM "Molokoprovid" type installations (n = 4).
 The level of development of milk productivity and reproductive capacity of cows was determined by population genetic parameters.
 Research results. As a result of a comparative analysis of milk yield, fat content, and milk fat of Ukrainian Black-and-White Dairy breed cows, which produced milk during I–VIII lactations under progressive technology with the same ones, but under traditional technology, it was established that during the first seven lactations, the exploitation of cows in provides higher productivity in comfortable conditions.
 It was established that the yield of cows under industrial technology increased until the third lactation, during which the largest amount of milk was obtained – 6855 kg, and decreased from IV to VIII lactation. In the conditions of progressive technology, cows from the second to the seventh lactation produced a larger amount of milk, compared to the first by 352–789 kg (Р ≤ 0.001), except for VIII.
 Cows of the Ukrainian Black-and-White Dairy breed, which produced milk according to traditional technology, showed a slightly different pattern regarding the level of milk yield with increasing age in lactation. Their hope increased from the first to the fourth lactation by 959 kg (P ≤ 0.001), but tended to decrease from the fifth to the eighth lactation by 411 kg with no significant difference. At the same time, even during the eighth lactation, cows under the conditions of traditional technology produced 548 kg more milk than during the first.
 A comparative analysis of two technologies for the production of milk from of Ukrainian Black-and-White Dairy breed cows established that more milk was obtained with the progressive technology during the I–VII lactations than during similar lactations of cows under the conditions of traditional technology. The difference in I lactation was 414 kg (Р ≤ 0.01), II – 477 (Р ≤ 0.01), III – 254 (Р ≤ 0.01), IV – 119, V – 88, VI – 92 and VII – 75 kg.
 Studies have not established a significant difference in the fat content of cows' milk depending on the difference in the age of cows in lactation and milk production technology.
 The correlation coefficient between milk yield and milk fat content for the studied lactations in the conditions of advanced technology had both a negative and a positive value and varied from -0.215 to +0.083, and in the traditional – from -0.027 to +0.095.
 Peculiarities of the development of the main breeding traits of cows can also be evaluated using variability indicators. Our research has established that the variability of lactation for the studied lactations under the conditions of progressive technology was: 7.26–22.35%, and for the traditional – 19.01–22.35%.
 Irrespective of the existing differentiation of milk yield of cows in the dynamics of age in lactations, we found out the vocative relationship between the trait caused by heredity and environmental factors. The coefficient of repeatability of the yield value for all studied lactations under the conditions of progressive and traditional technology was positive, high or medium level and reliable.
 To determine the impact of milk production technology on the milk productivity of Ukrainian Black-and-White Dairy breed cows, we conducted a one-factor variance analysis, which allowed us to establish that the influence of the technology on milk productivity was.
 The comparative analysis established that the age of first insemination was significantly higher by 3.4 days, the live weight at first insemination by 16.2 kg, and the age of first calving by 2.7 days in cows kept under traditional milk production technology compared to progressive.
 That is, cows for creating comfortable conditions for them came to hunting faster and had an earlier calving age, and therefore were more quickly involved in the milk production process, compared to traditional technology. At the same time, the age of their first insemination significantly correlated with the live weight at the time of the first insemination (r = +0.355). The live weight of the first insemination, as well as after the second and third calving, tended to predominate in cows that produced milk under traditional technology.
 Thus, the comparative analysis of two different technologies of milk production gave the basis for a conclusion about higher milk productivity and better reproductive capacity of Ukrainian Black-and-White Dairy breed cows under progressive technology.
 Conclusions. Exploitation of Ukrainian Black-and-White Dairy breed cows in comfortable conditions provides them with higher productivity, especially yield and milk fat, than under costly traditional ones. At the same time, with progressive technology, the hope of cows increased up to the third lactation, and with the traditional one – up to the fourth. An increase in the age of cows until the eighth lactation was accompanied by a deterioration of their physiological condition and a decrease in the ability to produce milk in large quantities, regardless of the conditions of keeping.