Cosmochemical Derivation of the Composition of Chondrite Material.

第2回極域科学シンポジウム/第34回南極隕石シンポジウム 11月17日（木） 国立国語研究所 2階講

Ordinary Chondrites and the Origin of the Earth

第3回極域科学シンポジウム/第35回南極隕石シンポジウム 11月29日（木）、30日（金） 国立国語研究所 2階講

Biotechnological bases of the development of cloned pig embryos

The term ‘clone’ in animal biotechnology refers to an organism derived from non-sexual reproduction, which is both a direct offspring and a genetic copy of the parent organism. To date, the pig appears to be the most interesting object in cloning research. Somatic cell nuclear transfer in pigs has a wide range of potential applications in various fields of human scientific and economic activities. However, the efficiency of producing cloned embryos in swine is still lower than that of other livestock species, in particular horses and cattle. Somatic cell nuclear transfer is a technically complex multi-stage technology, at each stage of which the pig oocytes, which are more susceptible to changes of surrounding conditions, are affected by various factors (mechanical, physical, chemical). At the stage of oocyte maturation, changes in the cell ultrastructures of the ooplasm occur, which play an important role in the subsequent nuclear reprogramming of the transferred donor cell. Before transfer to the oocyte donor somatic cells are synchronized in the G0/G1 stage of the cell cycle to ensure the normal ploidy of the cloned embryo. When removing the nucleus of pig oocytes maturated in vitro, it is necessary to pay attention to the problem of preserving the viability of cells, which were devoid of their own nuclear material. To perform the reconstruction, a somatic cell is placed, using micro-tools, in the perivitelline space, where the first polar body was previously located, or in the cytoplasm of an enucleated oocyte. The method of manual cloning involves the removal of the oocyte nucleus with subsequent fusion with the donor cell without the use of micromanipulation techniques. The increased sensitivity of oocytes to the environmental conditions causes special requirements for the choice of the system for in vitro culture of cloned pig embryos. In this work, we have reviewed the modern methods used for the production of cloned embryos and identified the technological issues that prevent improving the efficiency of somatic cloning of pigs

Dynamics of the biodiversity of black and white cattle influenced by cross-breeding

The inter-breed crossing (crossbreeding) permits one to introduce new alleles, extend genetic diversity, and achieve desired phenotypic characteristics of initial breeds. On the other hand, crossbreeding may cause a decrease in genetic differentiation of indigenous breeds due to loss of the part of their unique allele pool. The objective of the present work was to investigate the effect of crossbreeding on the allele pool variability of Russian Black and White cattle by using 10 microsatellite loci (BM1818, BM2113, ETH10, ETH225, TGLA122, TGLA126, TGLA227, ILST005, ETH185, and ILST006). The study was performed with purebred pedigree bulls of the Russian Black and White breed (BW_PB, n = 14) and two groups of their crosses with Holsteins carrying 25,0–62,5 % (BW_KR1, n = 16) and less than 12,5 % of the Black and White gene pool (BW_KR2, n = 67). Purebred Holstein bulls (HOLST, n = 42) were used as a reference group. It was found that the increase in Holstein’s blood could lead to the observed decrease in genetic diversity evaluated by the average number of effective alleles per loci (from 4,59 ± 0,46 to 3,87 ± 0,53), by the value of the Shannon index (from 1,60 ± 0,13 to 1,46 ± 0,14) and by the observed heterozygosity degree (from 0,779 ± 0,053 to 0,687 ± 0,055). It is shown that crossbreeding with Holsteins increases the genetic similarity to HOLST: Fst = 0,058, 0,036, and 0,026; Rst = 0,088, 0,060, and 0,050; DNei = 0,306, 0,178, and 0,123 for BW_PB, BW_KR1, and BW_KR2, respectively. Decrease in the genetic difference between the Black and White breed and Holsteins due to crossbreeding is confirmed by cluster analysis. Thus, evaluation of the allele pool and the level of genetic variability in populations are necessary for the efficient management of farm animal genetic recourses

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

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

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

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