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.

Genotyping-by-Sequencing Strategy for Integrating Genomic Structure, Diversity and Performance of Various Japanese Quail (Coturnix japonica) Breeds

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.

Whole Genome Screening Procures a Holistic Hold of the Russian Chicken Gene Pool Heritage and Demographic History

A study for genomic variation that may reflect putative selective signaling and be associated with economically important traits is instrumental for obtaining information about demographic and selection history in domestic animal species and populations. A rich variety of the Russian chicken gene pool breeds warrants a further detailed study. Specifically, their genomic features can derive implications from their genome architecture and selective footprints for their subsequent breeding and practical efficient exploitation. In the present work, whole genome genotyping of 19 chicken breeds (20 populations with up to 71 samples each) was performed using the Chicken 50 K BeadChip DNA chip. The studied breed sample included six native Russian breeds of chickens developed in the 17th-19th centuries, as well as eight Russian chicken breeds, including the Russian White (RW), created in the 20th century on the basis of improving local chickens using breeds of foreign selection. Five specialized foreign breeds of chickens, including the White Leghorn (WL), were used along with other breeds representing the Russian gene pool. The characteristics of the genetic diversity and phylogenetic relationships of the native breeds of chickens were represented in comparison with foreign breeds. It was established that the studied native breeds demonstrate their own genetic structure that distinguishes them from foreign breeds, and from each other. For example, we previously made an assumption on what could cause the differences between two RW populations, RW1 and RW2. From the data obtained here, it was verified that WL was additionally crossed to RW2, unlike RW1. Thus, inherently, RW1 is a purer population of this improved Russian breed. A significant contribution of the gene pool of native breeds to the global genetic diversity of chickens was shown. In general, based on the results of a multilateral survey of this sample of breeds, it can be concluded that phylogenetic relationships based on their genetic structure and variability robustly reflect the known, previously postulated and newly discovered patterns of evolution of native chickens. The results herein presented will aid selection and breeding work using this gene pool.

Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

BACKGROUND

The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by, and formed due to, past and current admixture events. Adaptation to diverse environments, including acclimation to harsh climatic conditions, has also left selection footprints in breed genomes.

RESULTS

Using the Chicken 50K_CobbCons SNP chip, we genotyped four divergently selected breeds: two aboriginal, cold tolerant Ushanka and Orloff Mille Fleur, one egg-type Russian White subjected to artificial selection for cold tolerance, and one meat-type White Cornish. Signals of selective sweeps were determined in the studied breeds using three methods: (1) assessment of runs of homozygosity islands, (2) F_ST based population differential analysis, and (3) haplotype differentiation analysis. Genomic regions of true selection signatures were identified by two or more methods or in two or more breeds. In these regions, we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other studies. Amongst them, SOX5, ME3, ZNF536, WWP1, RIPK2, OSGIN2, DECR1, TPO, PPARGC1A, BDNF, MSTN, and beta-keratin genes can be especially mentioned as candidates for cold adaptation. Epigenetic factors may be involved in regulating some of these important genes (e.g., TPO and BDNF).

CONCLUSION

Based on a genome-wide scan, our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken breeds. These include genes representing the sine qua non for adaptation to harsh environments. Cold tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals, and this warrants further investigation.

PSXIV-26 Selection footprints in Russian red cattle identified by linkage disequilibrium blocks based on SNP data

Among the variety of cattle breeds in Russia, the Russian red dual-purpose cattle breeds have great importance because of their ability to produce high milk yields as well as to provide excellent milk quality. The low census size of the Russian red cattle breeds requires development of programs for conservation of their biodiversity. Our study aimed to investigate selection footprints in Russian red cattle breeds, using high values of linkage disequilibrium (LD) in SNP haplotype blocks as indicators. For finding such LD blocks, we used the genotypes (≈35K SNPs) of Red Gorbatov (RGB, n = 26), Bestuzhev (BST,n = 27), and Suksun (SKS,n = 17) breeds, as well as Red Holstein (RH,n = 16) as an outgroup. Quality control and LD calculations for different distances were performed in Plink 1.90. Top 0.01% SNP pairs by LD value (0.9≤r2< 1.0) were selected for further analysis. The effective population size derived from LD patterns was estimated using SNeP tool. Comparison of LD values for 70 kb interval between breeds and chromosomes by MANOVA pairwise testing significantly distinguished RH/RGB and BST/SKS breeds (P < 0.05-0.001). LD values among chromosomes were 0.195–0.287 for RH, 0.194–0.272 for RGB, 0.172–0.237 for BST, and 0.157–0.217 for SKS. The SKS and BST breeds had higher Ne values (84 and 113, respectively) compared to RH (63) and RGB (79). Selection footprints by LD blocks in Russian red cattle genome covered several relevant genes on BTA1 (EPHA6,DGKG), BTA2 (LRP1B,THSD7B,STAT1), BTA5 (CPM,BAIAP2L2), BTA9 (TRDN,UTRN), BTA10 (KCNN2,CAPN3), BTA11 (SH3RF3,RABGAP1,RALGPS1), BTA14 (ZNF16,ARHGAP39,TOX,DGAT1), and BTA19 (MYH10), BTA22 (FHIT). Detected genes were found to be responsible for milk fat and protein contents, fatty acid composition, somatic cells score, fertility, feet and legs, and udder conformation traits. Our results can be useful for developing the breeding and conservation programs of the Russian red cattle genetic resources. The study was funded by RFBR within project No. 20-516-00020

PSXV-10 Study of allelic pattern of PLAG1 gene in the historical and modern populations of two oldest Russian dairy cattle breeds

Increasing animal stature is one of the goals of modern breeding programs for many dairy cattle breeds, because stature related to higher milk yield. The PLAG1 gene was shown to be a strong candidate responsible for stature in different cattle breeds. The polymorphic SNP BovineHD1400007259, located within PLAG1 gene, is considered as a causal mutation responsible for stature. The aim of our work was to evaluate the effect of long selection for the increased body height on the alterations of the allele’s frequencies of the PLAG1 gene in the historical and modern populations of the Russian Yaroslavl and Kholmogor dairy cattle breeds. The historical specimens of Yaroslavl (n = 22) and Kholmogor (n = 12) cattle dated by the first quarter of the 20th century were derived from the craniological collection of the E.F. Liskun Museum for Animal Husbandry. The modern representatives of Yaroslavl (n = 31) and Kholmogor (n = 25) breeds were used for comparison. All works with historical samples were performed in dedicated facility of the L.K. Ernst Research Center for Animal Husbandry. The samples were genotyped using high-density DNA arrays (Illumina Inc., USA). The historical DNA was treated by USER enzyme before genotyping to avoid the misincoporated nucleotides occurred due to postmortem DNA damage. We observed significant differences in allele frequencies of PLAG1 genes between historical and modern populations of both breeds. The frequencies of G allele, which is associated with higher stature, were increased from 0.114 in historical Yaroslavl cattle and from 0.167 in historical Kholmogor cattle to 0.633 and 0.860 in the modern breeds’ representatives, respectively. Our data suggest that PLAG1 gene was affected by artificial selection in studied cattle breeds. The research results will be useful for elucidation of the history of these two oldest Russian dairy cattle breeds. The study was funded by the RSF No. 21-66-00007.

PSI-B-23 Assessment of genomic inbreeding in Russian local and commercial dairy breeds of cattle

Drastic decline of population size of Russian local cattle breeds observed during last three decades has led to the decrease of genetic diversity. Due to the limited number of bulls used for artificial insemination, inbreeding in herds can be increased, which can lead to the decrease of reproduction capacity and adaptability of animals. Our aim was to assess genomic inbreeding in two Russian local cattle breeds, including Kholmogor (n = 26) and Istoben (n = 21). Two transboundary cattle breeds used for milk production in Russia including Holstein (n = 49) and Simmental (n = 38) were chosen for comparison. SNP genotyping was performed using the Bovine GGP 150K BeadArray (Illumina, CA, USA). After the quality control, 117591 autosomal SNPs were selected for analyzes. The degree of genomic inbreeding was assessed by calculations of inbreeding coefficient based on run of homozygosity (F(ROH)) and multilocus heterozygosity (sMLH). We found the strong negative correlations between the F(ROH) and sMLH values in animals of all of studied breeds (r2 = -0.805). The average F(ROH) values were 0.065 < mo >±< /mo >< /math >“>±± 0.003 for Kholmogor, 0.048 < mo >±< /mo >< /math >“>±± 0.006 for Istoben, 0.129 < mo >±< /mo >< /math >“>±± 0.007 for Holstein, and 0.102 < mo >±< /mo >< /math >“>±± 0.007 for Simmental breed. The sMLH values in Kholmogor, Istoben, Holstein and Simmental breeds varied from 0,99 to 1,076, from 0,829 to 1,102, from 0,890 to 1,069 and from 0,866 to 1,041, and averaged to 1.030, 1.013, 1.000, and 0.974, respectively. According to our research results, two studied Russian cattle breeds are characterized by lower levels of genomic inbreeding compared to transboundary cattle breeds. Our results will be helpful for developing the conservation programs for Russian Kholmogor and Istoben cattle breeds. The study was funded by the Russian Ministry of Science and Higher Education within theme No. 0445-2019-0024 and RFBR within project 19-316-90017 (the study of Kholmogor cattle).

PSI-B-25 Assessment of the genetic resources of Russian local cattle breeds by genome-wide SNP analysis

Russia is reach by local cattle genetic resources, which are well adapted to the different environment. However, the modern cattle husbandry tends to the replacing the local cattle breeds by highly productive commercial breeds, which can lead to the decline of genetic diversity. The aim of our work was to estimate the genetic identity of five Russian local cattle breeds, including Yaroslavl (n = 52), Kholmogor (n = 26), Istoben (n = 21), Tagil (n = 26), and Black-and-White (n = 44). The Holstein breed (n = 49), which is actively used for improvement of above breeds was included in the study for comparison. The genotyping was performed using GGP Bovine 150K Array (Illumina, San Diego, CA, USA) and more than 112000 autosomal SNPs passed through the quality control and were selected for the analysis. We observed the significant excess of heterozygotes in four studied breeds (the values of unbiased inbreeding coefficient were varied from -0.009 to -0.022), except for Black-and-White breed. The effective population size (Ne) for Istoben, Tagil and Kholmogor breeds was declined until present, while Holstein and Black-and-White breeds showed the increase of Ne values starting at 5 generations ago. The Black-and-White breed was the closest to the Holsteins (Fst=0.014), while the Yaroslavl breed was the most distant (Fst=0.115). The highest ratio of Holstein specific genomic components was shown for Tagil (18.79%) and Black-and-White (59.73%) breeds. Our results indicated replacing the part of aboriginal genomic components in several Russian local cattle breeds by Holstein specific components. The comprehensive strategies for conservation of the Russian local cattle breeds are needed to avoid the further decline of genetic diversity of these valuable national animal genetic resources. The study was funded by the Ministry of Science and Higher Education of the Russian Federation within theme 0445-2019-0024.

PSXVI-17 Estimation of inbreeding in local sheep breeds of west Asian and central Asian origin based on high-density SNP-genotypes

Maintaining high levels of genetic diversity is a key factor of successful breeding of resilient, resistant to diseases and productive sheep. Prevention of inbreeding is of special importance in the mountainous hard-to-get habitats where gene flow is limited or absent. An assessment of inbreeding coefficients based only on pedigree information is not always correct. In addition, pedigree information is often missing for flocks of native sheep. In this regard, we performed a genomic assessment of inbreeding in 15 local sheep breeds inhabiting severe environments of Russia and neighboring Asian countries based on estimations of standardized multilocus heterozygosity (sMLH) and runs of homozygosity [F(ROH)]. For this study, we used SNP genotypes of twelve Russian local breeds (n = 316) and three Kyrgyz local breeds (n = 68), which were generated using Ovine Infinium® HD SNP BeadChip (Illumina, CA, USA). The sMLH values were calculated using R package inbreedR and visualized in R package ggplot2. The F(ROH) values were calculated using the R package detectRUNS by applying the consecutive runs method. Mean sMLH values were varied from 0.962 ± 0.006 in the Andean breed to 1.031 ± 0.002 in the Buryat breed and averaged to 1.001± 0.004. The least mean F(ROH) value was detected in the Mongolian breed (0.0043 ± 0.0009) while the greatest ones were observed in the Alai and Andean breeds (0.0364 ± 0.0049 and 0.0357 ± 0.0061, respectively). The strong negative correlations between sMLH and F(ROH) were detected for all of studied breeds (r2 = –0.8496, CI = –0.8752… –0.8192). The obtained data is relevant for control of inbreeding level in the populations and for future sustainable management of native fat-tailed sheep breeds. The study was funded by RSF No. 19-16-00070.

Unveiling Comparative Genomic Trajectories of Selection and Key Candidate Genes in Egg-Type Russian White and Meat-Type White Cornish Chickens

Comparison of genomic footprints in chicken breeds with different selection history is a powerful tool in elucidating genomic regions that have been targeted by recent and more ancient selection. In the present work, we aimed at examining and comparing the trajectories of artificial selection in the genomes of the native egg-type Russian White (RW) and meat-type White Cornish (WC) breeds. Combining three different statistics (top 0.1% SNP by F_ST value at pairwise breed comparison, hapFLK analysis, and identification of ROH island shared by more than 50% of individuals), we detected 45 genomic regions under putative selection including 11 selective sweep regions, which were detected by at least two different methods. Four of such regions were breed-specific for each of RW breed (on GGA1, GGA5, GGA8, and GGA9) and WC breed (on GGA1, GGA5, GGA8, and GGA28), while three remaining regions on GGA2 (two sweeps) and GGA3 were common for both breeds. Most of identified genomic regions overlapped with known QTLs and/or candidate genes including those for body temperatures, egg productivity, and feed intake in RW chickens and those for growth, meat and carcass traits, and feed efficiency in WC chickens. These findings were concordant with the breed origin and history of their artificial selection. We determined a set of 188 prioritized candidate genes retrieved from the 11 overlapped regions of putative selection and reviewed their functions relative to phenotypic traits of interest in the two breeds. One of the RW-specific sweep regions harbored the known domestication gene, TSHR. Gene ontology and functional annotation analysis provided additional insight into a functional coherence of genes in the sweep regions. We also showed a greater candidate gene richness on microchromosomes relative to macrochromosomes in these genomic areas. Our results on the selection history of RW and WC chickens and their key candidate genes under selection serve as a profound information for further conservation of their genomic diversity and efficient breeding.

Genome-wide SNP analysis clearly distinguished the Belarusian Red cattle from other European cattle breeds

Local breeds can serve as an important source of genetic variability in domestic animal species. This study aimed to assess the genetic diversity and population structure of Belarusian Red cattle and their differentiation from other European cattle populations based on genome-wide SNP genotypes. Twenty pedigree-recorded non-closely related cows of Belarusian Red cattle were genotyped using the Illumina BovineHD BeadChip. Genotypes of 22 other European cattle breeds were included in the study for comparison. A total of 28 562 SNPs passed through the quality control checks and were selected for analysis. The Belarusian Red cattle displayed a moderate level of genetic variability (_U H_E  = 0.341, H_O  = 0.368), and the highest heterozygote excess (_U F_IS  = -0.066), among the studied breeds; this reflects the contribution of multiple breeds to their formation. The principal component analysis, F_ST -based Neighbor-Net tree and Admixture clustering, clearly distinguished the Belarusian Red cattle from the other European cattle breeds. Moreover, the presence of ancestral genomic components of Danish Red and Brown Swiss breeds were clearly visible, which agrees with the breed's history and its recent development. Our study highlights the importance of maintaining the specific genomic components, which makes a significant contribution to the global genetic diversity in the modern population of Belarusian Red cattle, allowing us to consider them a valuable national genetic resource. Our research results will be useful for the development of conservation programs for this local cattle breed.