High-density genotyping reveals signatures of selection related to acclimation and economically important traits in 15 local sheep breeds from Russia

Domestication and centuries of selective breeding have changed genomes of sheep breeds to respond to environmental challenges and human needs. The genomes of local breeds, therefore, are valuable sources of genomic variants to be used to understand mechanisms of response to adaptation and artificial selection. As a step toward this we performed a high-density genotyping and comprehensive scans for signatures of selection in the genomes from 15 local sheep breeds reared across Russia

Evaluation of current gene pool of Kholmogor and Black-and-white cattle breeds based on whole genome SNP analysis

Conservation of local cattle genetic resources is an important strategy for achieving Russia’s food security. During last decades, in the Russian Federation, local livestock populations were either crossbred or replaced by highly productive imported breeds, which led to a loss of the major part of original breeds identities. The objective of our study was to identify genetic differences between the populations of Kholmogor and Black-and-white cattle with varying degrees of admixture with the Holstein breed. The aforementioned breeds were studied using their whole-genome single nucleotide polymorphism (SNP) genotypes. The Kholmogor breed was subdivided into three groups: purebred (KHLM, n = 3), admixed with Holsteins (KHLM-HLST, n = 4) and representatives of old-type breed (KHLM-INTA, n = 15). Blackand-white was subdivided into four groups: purebred (BLWT, n = 9), with a low (BLWT-75, n = 8) and a high (BLWT-HLST, n = 10) level of admixture with Holstein, and represented by archival samples from the 1970s and 1980s (BLWT-OLD, n = 15). The Holsteins genetic profiles (HLST, n = 27) were taken as a comparison group. PLINK 1.07, Admixture 1.3, SplitsTree 4.14.6 and R package StAMPP were used to infer genetic relationship between the studied groups. After quality control, 29 688 SNPs were selected for analysis. Multidimensional scaling (MDS), Admixture analysis and a dendrogram constructed using the Neighbor-Net method, revealed the presence of three clusters belonging to the Kholmogor, Black-and-white and Holstein breeds. The first one included KHLM and KHLM-INTA, the second – BLWT and BLWT-OLD, and the third – HLST, KHLM-HLST and BLWT-HLST. The BLWT-75 samples were placed between HLST and BLWT. Thus, our results showed that currently the populations of native cattle breeds with valuable genotypes still exist. The populations with a high level of admixture with Holsteins could be considered neither as the Kholmogor nor as Blackand-white breeds, and would rather be referred as the Holstein breed of local breeding

Genomic assessment and phenotypic characteristics of F2 resource sheep population

The article presents the results of assessment of genetic diversity and Principal Component Analysis (PCA) in the re-source sheep population, originated from crossing of fast-growing (Katahdin) and slow growing (Romanov) breeds for QTL mapping and search for candidate genes associated with growth rate. The study was conducted on 88 sheep from the resource population, including two unrelated families that have been reared in the Moscow region since 2017. Each family consists of a Katahdin ram (founder), Romanov’s ewes (mothers), F1 hybrids, and two groups of backcrosses. All sheep were genotyped using a high-density DNA chip Illumina Ovine Infinium® HD SNP BeadChip (~ 600 thousand SNP markers). SNP markers were filtered in the PLINK v.1.90. PCA was performed in PLINK v.1.90 and visualized in R package ggplot2. The genetic diversity indices (Ho, uHe, Ar, FIS) were calculated in R package “diveRsity”. It was established that both crosses had higher level of genetic diversity in comparison with the mother breed. F1 hybrids were characterized by the highest level of observed heterozygosity (Ho = 0.409-0.407), while Ho ranged from 0.382 to 0.396 for the backcrosses, respectively. The expected heterozygosity ranged from 0.329 to 0.356 in the groups from the resource population. Allelic richness was high in all studied groups (more than 1.849). PCA showed that the mated parent breeds were highly differentiated, as it should be in successful establishment of the resource population. The phenotypic characteristic of the backcrosses on live weight and nine body measurements at 9, 42 and 90 days is given. The coefficients of variation were the highest by live weight (17.0-19.0%), body length (15.5-22.3%) and oblique body length (16.2% and 22.7%) at 90 days. The results are intermediate and create a geno-typic and phenotypic base to perform GWAS at the next stage of our study

Eggology and mathematics of a quail egg: an innovative non-destructive technology for evaluating egg parameters in Japanese quail

Quail eggs, the smallest ones among poultry species, require special methodological aspects for their non-destructive examination and quality analysis. Using eggs from a cross between the Japanese and Texas breeds, we devised a methodology for defining the main geometric parameters of quail eggs. Calculation formulae were proposed to estimate indirectly egg volume and surface area. Our findings on the weights of structural egg components enabled to obtain mathematical equations for computing the weights of shell, yolk and albumen, depending on the complex of measured parameters including the egg weight, its volume and surface area. When taken as a whole, the results of our study can be regarded as the most thorough methodological approach to date for the execution of comprehensive investigations of quail egg quality. They will be applicable and instrumental in areas of food research and emerging technologies, including the aspects of storage, packing, and processing of quail eggs

Metabolic rate and egg production in Japanese quails can be predicted by assessing growth parameters of laying hens

Simple Summary: Quails are becoming increasingly popular for their meat and eggs, and thus, the productivity of laying hens, and how that can be predicted, is of growing interest to quail producers. Because of this, we wanted to find out whether we could predict the performance of laying hens (typically expressed as the number of eggs produced multiplied by the egg weight—the so-called total egg mass) simply by looking at certain growth traits (i.e., body weight, surface area, and volume), as well as the metabolic rate among eight Japanese quail breeds. To succeed in this analysis, we developed a novel method for calculating the volume and surface area of a quail body. As a result, we derived a new mathematical formula called the metabolic index, which included the measurements of body weight, surface area, and volume. We discovered that the total egg mass in quails can be judged from these growth parameters, particularly when we examined the slope angles of the trend lines in the graphs pertaining to these parameters. Abstract: The aim of the current study was to assess the female metabolic rate and test the hypothesis that there is a relationship between the egg productivity of Japanese quails from eight breeds and their morphometric, or growth, parameters. Parameters measured were body weight (B), volume (V), and surface area (S), as well as the metabolism level expressed by the ratio S/V. The collected egg performance traits were as follows: the number of eggs produced (N), the average egg weight (W), and the total egg mass (M) (i.e., N multiplied by W). To measure the S and V values, a novel technique was developed that takes into account the similarity of the quail’s body to an ellipsoid. An analysis of the relationships between productivity indicators allowed us to introduce a new index called the metabolic index, B·S/V, based on all three main growth parameters in quails. Using the values of this index, we were then able to judge indirectly the level of quails’ egg productivity. We went on to assess the N, W, and M values, not only depending on the size of the bird’s growth parameters but also according to the degree of their changes during quail growth. These changes were expressed as the slope angles of trend lines describing the growth process data. This approach produced more accurate results for predicting the egg productivity in terms of W and M

Dissecting selective signatures and candidate genes in grandparent lines subject to high selection pressure for broiler production and in a local Russian chicken breed of Ushanka

Breeding improvements and quantitative trait genetics are essential to the advancement of broiler production. The impact of artificial selection on genomic architecture and the genetic markers sought remains a key area of research. Here, we used whole-genome resequencing data to analyze the genomic architecture, diversity, and selective sweeps in Cornish White (CRW) and Plymouth Rock White (PRW) transboundary breeds selected for meat production and, comparatively, in an aboriginal Russian breed of Ushanka (USH). Reads were aligned to the reference genome bGalGal1.mat.broiler.GRCg7b and filtered to remove PCR duplicates and low-quality reads using BWA-MEM2 and bcftools software; 12,563,892 SNPs were produced for subsequent analyses. Compared to CRW and PRW, USH had a lower diversity and a higher genetic distinctiveness. Selective sweep regions and corresponding candidate genes were examined based on ZFST, hapFLK, and ROH assessment procedures. Twenty-seven prioritized chicken genes and the functional projection from human homologs suggest their importance for selection signals in the studied breeds. These genes have a functional relationship with such trait categories as body weight, muscles, fat metabolism and deposition, reproduction, etc., mainly aligned with the QTLs in the sweep regions. This information is pivotal for further executing genomic selection to enhance phenotypic traits

Whole-genome analysis of introgressive hybridization and characterization of the bovine legacy of Mongolian yaks

The yak is remarkable for its adaptation to high altitude and occupies a central place in the economies of the mountainous regions of Asia. At lower elevations, it is common to hybridize yaks with cattle to combine the yak’s hardiness with the productivity of cattle. Hybrid males are sterile, however, preventing the establishment of stable hybrid populations, but not a limited introgression after backcrossing several generations of female hybrids to male yaks. Here we inferred bovine haplotypes in the genomes of 76 Mongolian yaks using high-density SNP genotyping and whole-genome sequencing. These yaks inherited ~1.3% of their genome from bovine ancestors after nearly continuous admixture over at least the last 1,500 years. The introgressed regions are enriched in genes involved in nervous system development and function, and particularly in glutamate metabolism and neurotransmission. We also identified a novel mutation associated with a polled (hornless) phenotype originating from Mongolian Turano cattle. Our results suggest that introgressive hybridization contributed to the improvement of yak management and breeding

Genotyping-by-sequencing strategy for integrating genomic structure, diversity and performance of various Japanese quail (Coturnix japonica) breeds

Simple Summary: Artificial selection has been applied to domesticated birds for many decades. More recently, this selection has made use of so-called single-nucleotide polymorphism (SNP) markers—simple variants in a DNA sequence. These SNPs can be used for whole-genome screening to detect the unique traces of areas of the genome that are subject to selection. Doing this may help to shed light on the evolutionary and family history (phylogeny) of domestic Japanese quails of different breeds and utility types (e.g., egg, meat or dual-purpose breeds). In this study, 99 birds were used, representing eight breeds (11% of the world’s quail gene pool) and various purposes of use to gather genetic (whole-genome) data in the first-ever analysis of its kind performed on domestic quails. We thereby uncovered evolutionary relationships and points of divergence of individual quail breeds, gleaning important insights into the genetic diversity of domestic quail breeds and their future breeding potential. Abstract: Traces of long-term artificial selection can be detected in genomes of domesticated birds via whole-genome screening using single-nucleotide polymorphism (SNP) markers. This study thus examined putative genomic regions under selection that are relevant to the development history, divergence and phylogeny among Japanese quails of various breeds and utility types. We sampled 99 birds from eight breeds (11% of the global gene pool) of egg (Japanese, English White, English Black, Tuxedo and Manchurian Golden), meat (Texas White and Pharaoh) and dual-purpose (Estonian) types. The genotyping-by-sequencing analysis was performed for the first time in domestic quails, providing 62,935 SNPs. Using principal component analysis, Neighbor-Net and Admixture algorithms, the studied breeds were characterized according to their genomic architecture, ancestry and direction of selective breeding. Japanese and Pharaoh breeds had the smallest number and length of homozygous segments indicating a lower selective pressure. Tuxedo and Texas White breeds showed the highest values of these indicators and genomic inbreeding suggesting a greater homozygosity. We revealed evidence for the integration of genomic and performance data, and our findings are applicable for elucidating the history of creation and genomic variability in quail breeds that, in turn, will be useful for future breeding improvement strategies

Гипоксические белки VEGF A и CA IX и резистентность клеток сарком мягких тканей к химиопрепаратам: пилотный опыт ex vivo анализа

Introduction. The identification of predictive factors is a cornerstone task of modern oncology. The development of new targeted drugs determines the need for prediction of chemosensitivity of each patient to the prescribed therapy, in this regard, the search for biomarkers of predictive response to therapy is actively conducted.The study objective to investigate the relationship between tumor cell resistance and the expression levels of CA IX (carbonic anhydrase IX) and VEGF A (vascular endothelial growth factor А) in patient-derived cultures of soft tissue sarcomas.Materials and methods: ex vivo soft tissue sarcoma cell culture, resazurin test, immunoblotting.Results. We obtained 46 ex vivo samples of soft tissue sarcoma cultures for which chemosensitivity to doxorubicin, ifosfamide, docetaxel, gemcitabine, and their combinations was assessed by the resazurin cytotoxicity test. We analyzed the relationship between the expression of hypoxic proteins VEGF A and CA IX and the resistance to drugs. A correlation between the CA IX expression in hypoxia and cell resistance to ifosfamide and its combination with doxorubicin was found. Soft tissue sarcomas with high VEGF A index were resistant to doxorubicin, docetaxel, and its combination with gemcitabine (p <0.05).Conclusion. The data obtained on patient-derived cultures indicate the relationship between hypoxic signaling and resistance of soft tissue sarcomas to chemotherapeutics.Введение. Поиск предиктивных факторов является краеугольной задачей современной онкологии. Разработка большого числа новых таргетных препаратов определяет необходимость четкого предсказания хемочувствительности конкретного пациента к назначаемой терапии. В связи с этим активно ведется поиск биомаркеров прогноза ответа на терапию.Цель исследования – изучение взаимосвязи между резистентностью опухолевых клеток и уровнем экспрессии CA IX (карбоангидразы IX) и VEGF A (фактора роста эндотелия сосудов А) в ex vivo культурах сарком мягких тканей.Материалы и методы. В исследование были включены ex vivo культуры сарком мягких тканей, использованы резазуриновый тест, иммуноблоттинг.Результаты. Получено 46 ex vivo образцов культур сарком мягких тканей, для которых с помощью резазуринового теста на цитотоксичность определена хемочувствительность к доксорубицину, ифосфамиду, доцетакселу, гемцитабину и их комбинациям. Проведен анализ связи экспрессии гипоксических белков VEGF A и CA IX с резистентностью к химиопрепаратам. Обнаружена корреляция уровня экспрессии CA IX в гипоксии с резистентностью клеток к ифосфамиду и его комбинации с доксорубицином. Образцы сарком мягких тканей, обладающие высоким индексом VEGF A, были резистентны к доксорубицину, доцетакселу и его комбинации с гемцитабином (p <0,05).Заключение. Полученные на ex vivo культурах данные свидетельствуют о взаимосвязи гипоксического сигналинга и резистентности сарком мягких тканей к химиотерапии