Climate Adaptation of Tropical Cattle

Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation

BACKGROUND

Chinese indigenous sheep are valuable resources with unique features and characteristics. They are distributed across regions with different climates in mainland China; however, few reports have analyzed the environmental adaptability of sheep based on their genome. We examined the variants and signatures of selection involved in adaptation to extreme humidity, altitude, and temperature conditions in 173 sheep genomes from 41 phenotypically and geographically representative Chinese indigenous sheep breeds to characterize the genetic basis underlying environmental adaptation in these populations.

RESULTS

Based on the analysis of population structure, we inferred that Chinese indigenous sheep are divided into four groups: Kazakh (KAZ), Mongolian (MON), Tibetan (TIB), and Yunnan (YUN). We also detected a set of candidate genes that are relevant to adaptation to extreme environmental conditions, such as drought-prone regions (TBXT, TG, and HOXA1), high-altitude regions (DYSF, EPAS1, JAZF1, PDGFD, and NF1) and warm-temperature regions (TSHR, ABCD4, and TEX11). Among all these candidate genes, eight ABCD4, CNTN4, DOCK10, LOC105608545, LOC121816479, SEM3A, SVIL, and TSHR overlap between extreme environmental conditions. The TSHR gene shows a strong signature for positive selection in the warm-temperature group and harbors a single nucleotide polymorphism (SNP) missense mutation located between positions 90,600,001 and 90,650,001 on chromosome 7, which leads to a change in the protein structure of TSHR and influences its stability.

CONCLUSIONS

Analysis of the signatures of selection uncovered genes that are likely related to environmental adaptation and a SNP missense mutation in the TSHR gene that affects the protein structure and stability. It also provides information on the evolution of the phylogeographic structure of Chinese indigenous sheep populations. These results provide important genetic resources for future breeding studies and new perspectives on how animals can adapt to climate change.

Challenges and opportunities of using Bos indicus cattle to meet consumers' demand for quality beef

Beef consumption is expected to increase worldwide, which necessitates the use of Bos indicus cattle that are well-adapted to harsher climates, like the tropics. Yet, beef from these cattle is considered inferior to that of Bos taurus breeds, primarily due to lowered tenderness values and reduced intramuscular fat content. However, the benefits of using Bos indicus genetics are numerous and undeniable. Herein, we explore how decreases in meat quality in these cattle may be offset by increases in livability. Further, we review the knowledge surrounding beef tenderness and explore the processes occurring during the early events of the transformation of muscle to meat that are different in this biological type and may be altered by stress. Growth rate, calpastatin activity and mitochondrial function will be discussed as they relate to tenderness. The opportunities of using Bos indicus cattle are of great interest to the beef industry worldwide, especially given the pressures for enhancing the overall sustainability and carbon footprint of this sector. Delivering a consistently high-quality product for consumers by exploiting Bos indicus genetics in a more sustainable manner will be proposed. Information on novel factors that influence the conversion of muscle to meat is explored to provide insights into opportunities for maximizing beef tenderization and maturation across all cattle. Exploring the use of Bos indicus cattle in modern production schemes, while addressing the mechanisms undergirding meat tenderness should provide the industry with a path forward for building greater demand through producing higher quality beef.

Detection of genomic regions that differentiate Bos indicus from Bos taurus ancestral breeds for milk yield in Indian crossbred cows

Introduction: In India, crossbred cows incorporate the high production of B. taurus dairy breeds and the environmental adaptation of local B. indicus cattle. Adaptation to different environments and selection in milk production have shaped the genetic differences between B. indicus and B. taurus cattle. The aim of this paper was to detect, for milk yield of crossbred cows, quantitative trait loci (QTL) that differentiate B. indicus from B. taurus ancestry, as well as QTL that are segregating within the ancestral breeds. Methods: A total of 123,042 test-day milk records for 4,968 crossbred cows, genotyped with real and imputed 770 K SNP, were used. Breed origins were assigned to haplotypes of crossbred cows, and from that, were assigned to SNP alleles. Results: At a false discovery rate (FDR) of 30%, a large number of genomic regions showed significant effects of B. indicus versus B. taurus origin on milk yield, with positive effects coming from both ancestors. No significant regions were detected for Holstein Friesian (HF) versus Jersey effects on milk yield. Additionally, no regions for SNP alleles segregating within indigenous, within HF, and within Jersey were detected. The most significant effects, at FDR 5%, were found in a region on BTA5 (43.98-49.44 Mbp) that differentiates B. indicus from B. taurus, with an estimated difference between homozygotes of approximately 10% of average yield, in favour of B. indicus origin. Discussion: Our results indicate that evolutionary differences between B. indicus and B. taurus cattle for milk yield, as expressed in crossbred cows, occur at many causative loci across the genome. Although subject to the usual first estimation bias, some of the loci appear to have large effects that might make them useful for genomic selection in crossbreds, if confirmed in subsequent studies.

Genomics, Origin and Selection Signals of Loudi Cattle in Central Hunan

Due to the geographical, cultural and environmental variability in Xiangxi, China, distinctive indigenous cattle populations have formed. Among them, Loudi cattle and Xiangxi cattle are the local cattle in Hunan, and the environment in Loudi is relatively more enclosed and humid than that in Xiangxi. To study the genome and origin of Loudi cattle in hot and humid environments, 29 individuals were collected and sequenced by whole-genome resequencing. In addition, genomic data were obtained from public databases for 96 individuals representing different cattle breeds worldwide, including 23 Xiangxi cattle from western Hunan. Genetic analysis indicated that the genetic diversity of Loudi cattle was close to that of Chinese cattle and higher than that of other breeds. Population structure and ancestral origin analysis indicated the relationship between Loudi cattle and other breeds. Loudi has four distinctive seasons, with a stereoscopic climate and extremely rich water resources. Selective sweep analysis revealed candidate genes and pathways associated with environmental adaptation and homeostasis. Our findings provide a valuable source of information on the genetic diversity of Loudi cattle and ideas for population conservation and genome-associated breeding of local cattle in today's extreme climate environment.

Effect of in utero exposure to hyperthermia on postnatal hair length, skin morphology, and thermoregulatory responses

Skin and hair coat play important functions in maintaining homeostasis and thermoregulation for cattle, which can affect all modes of heat loss. Our objective was to investigate the effect of hyperthermia experienced in utero during late gestation on postnatal hair length, skin properties, and thermoregulation. Pregnant dams were heat stressed (n = 41) or actively cooled (n = 41) for the last ∼56 d of gestation and gave birth to heifers that were in utero heat stressed (IUHT) or in utero cooled (IUCL), respectively. Hair samples and skin tissue biopsies were collected from neck and rump locations at birth (d 0), 1 wk after weaning (d 63), and at 12 mo. Hair samples were also obtained at 4 and 8 mo. Skin tissue was stained with hematoxylin and eosin to visualize morphology. Hair length (short and long hairs, undercoat and topcoat, respectively), stratum corneum (SC) area, SC thickness, epidermis thickness, sweat gland (SWT) number, SWT cross-sectional area, SWT average size, sebaceous gland (SEB) number, SEB cross-sectional area, SEB average size, and sweat gland depth were assessed. Respiration rate, skin temperature, sweating rate, and rectal temperature was measured weekly from d 7 to 63. Additionally, thermoregulatory patterns were measured every 4 h over a 36-h interval beginning 4 d after weaning. Data were analyzed using PROC MIXED in SAS with a main effect of in utero treatment with location and time points analyzed separately. No difference in hair parameters were detected at d 0 or 12 mo. At d 63, IUHT heifers had longer average hair length (14.8 vs. 13.8 ± 0.2 mm, standard error), shorter undercoats (9.3 vs. 10.4 ± 0.3 mm), longer topcoats (19.6 vs. 17.1 ± 0.3 mm), and a greater difference between topcoat and undercoat (10.1 vs. 7.0 ± 0.4 mm). At 4 mo, IUHT heifers had longer average hair lengths (26.1 vs. 22.2 ± 1.0 mm) and longer topcoats (36.9 vs. 33.9 ± 1.1 mm), and at 8 mo, IUHT had longer average hair lengths (17.9 vs. 16.2 ± 0.6 mm), relative to IUCL. At d 0, IUHT heifers had more (13 vs. 9 ± 2 glands) but smaller average sized SEB (neck: 1,636 vs. 2,238 ± 243 µm²; rump: 2,100 vs. 3,352 ± 379 µm²) and reduced SC area (79,243 vs. 169,419 ± 13,071 µm²). At d 63, IUHT had fewer SEB (11 vs. 15 ± 2 glands), smaller SWT (0.16 vs. 0.23 ± 0.02 mm²), fewer SWT (16 vs. 23 ± 4 glands), and deeper SWT (0.5 vs. 0.4 ± 0.03 mm). At 12 mo, IUHT had greater distance from the skin surface to the most superficial SWT (0.016 vs. 0.015 ± 0.0004 mm), shorter distance to the deepest SWT (0.031 vs. 0.033 ± 0.001 mm), and smaller SWT (81.1 vs. 108.9 ± 10.8 µm²), relative to IUCL. When measured both weekly and hourly, IUHT heifers had higher rectal temperature and sweating rate. Overall, in utero hyperthermia triggers long-lasting hair and skin adaptations, possibly leading to differences in postnatal thermoregulation.

Whole-Genome Analyses Reveal Genomic Characteristics and Selection Signatures of Lincang Humped Cattle at the China-Myanmar Border

The location on the Yunnan border with Myanmar and its unique cultural landscape has shaped Lincang humped cattle over time. In the current study, we investigated the genetic characteristics of 22 Lincang humped cattle using whole-genome resequencing data. We found that Lincang humped cattle derived from both Indian indicine and Chinese indicine cattle depicted higher levels of genomic diversity. Based on genome-wide scans, candidate genomic regions were identified that were potentially involved in local thermal and humid environmental adaptions, including genes associated with the body size (TCF12, SENP2, KIF1C, and PFN1), immunity (LIPH, IRAK3, GZMM, and ELANE), and heat tolerance (MED16, DNAJC8, HSPA4, FILIP1L, HELB, BCL2L1, and TPX2). Missense mutations were detected in candidate genes IRAK3, HSPA4, and HELB. Interestingly, eight missense mutations observed in the HELB gene were specific to the indicine cattle pedigree. These mutations may reveal differences between indicine and taurine cattle adapted to variable climatic conditions. Our research provides new insights into the genetic characteristics of Lincang humped cattle representing Lincang and Pu'er areas as an important channel for the migration of Indian indicine from domestication centers toward southwestern China.

Climate Change and Livestock Production: A Literature Review

Globally, the climate is changing, and this has implications for livestock. Climate affects livestock growth rates, milk and egg production, reproductive performance, morbidity, and mortality, along with feed supply. Simultaneously, livestock is a climate change driver, generating 14.5% of total anthropogenic Greenhouse Gas (GHG) emissions. Herein, we review the literature addressing climate change and livestock, covering impacts, emissions, adaptation possibilities, and mitigation strategies. While the existing literature principally focuses on ruminants, we extended the scope to include non-ruminants. We found that livestock are affected by climate change and do enhance climate change through emissions but that there are adaptation and mitigation actions that can limit the effects of climate change. We also suggest some research directions and especially find the need for work in developing country settings. In the context of climate change, adaptation measures are pivotal to sustaining the growing demand for livestock products, but often their relevance depends on local conditions. Furthermore, mitigation is key to limiting the future extent of climate change and there are a number of possible strategies.

Increasing importance of heat stress for cattle farming under future global climate scenarios

In the last decades, livestock species have been severely affected by heat stress because of increasing temperatures, which has threatened animal welfare and decreased production. Based on thermal comfort indices and ensemble climate projections, we analyzed the current and future global spatiotemporal patterns of the heat exposure of cattle in 10 agroclimatic zones. The results show that ~7% of the global cattle population is currently exposed to dangerous heat conditions. This percentage is projected to increase to ~48% before 2100 under a scenario of growing emissions. Tropical agroclimatic zones are expected to face an early increase in the exposure to intense heat before 2050. Heat exposure was negatively correlated with the socioeconomic variables, showing that poor and livestock-dependent tropical countries are the most affected. Our results demonstrate the near-future consequences of heat stress on livestock, emphasizing the limited time available to implement effective abatement strategies.

Characteristics and trait preferences of West African Dwarf goat keepers in Ghana

A study was conducted to evaluate the characteristics of West African Dwarf (WAD) goat keepers and their trait preferences as part of a broader phenotypic characterisation work with the aim of providing information for improving the household management, conservation and productivity of the breed in Ghana. A total of 384 respondent households were selected from four agro-ecological zones in the middle belt and southern part of the country for questionnaire administration and direct observation of animals under field conditions. The results showed that there are slightly more women (54.2%) keeping WAD goats than men (45.8%) and fall within the economically active population of youthful and middle age categories (53.9%). A majority of these goat keepers were married (73.8%) and educated (87.3%) in one way or the other. They obtained their starter or foundation stock mainly from neighbours (80.5%) and the open market (16.0%). The average flock size from the households sampled was 7.9 ± 1.5, whereas the flock structure constituted 56.1% adult females, 27.5% adult intact males, 1.2% castrates and 15.2% kids of both sexes. Survivability, fast growth rate and larger litter size were the farmers' most preferred quantitative traits, whereas most of these respondents preferred to keep WAD goats which do not have qualitative traits such as horn, wattle and beard. From the findings of the research, it was concluded that the favourable socio-economic characteristics of WAD goat keepers could sustain intensification and increase the productivity of the breed when given the necessary input assistance along the goat value chain. The primary objective of WAD goat farmers is to produce matured animals for various purposes and the breeding goal for a WAD goat breeding programme would be to increase survival, growth rate and litter size of light coat (white, grey and light brown) goats. Finally, most farmers lack knowledge on the significance of tropically beneficial qualitative traits such as horn, wattle, beard and light coat colouration on the survivability, climate adaptability or resilience and productivity of their goats. Educating farmers on the importance of conserving and inclusion of animals possessing such traits in their selection practices under the Government's Rearing for Food and Jobs Initiative is therefore suggested.

Tropical Beef: Is There an Axiomatic Basis to Define the Concept?

Cattle production in tropical regions has been estimated to account for just over half of cattle worldwide, yet it has not been demonstrated that sufficient similarities in the cattle exist to describe tropical cattle and, even less so, to characterize the meat from these animals. The aim of this review is to investigate the quality and nutrient composition of meat from cattle raised in the Tropics to determine if there is an axiomatic basis that would allow the definition of a concept of “tropical beef”. Tropical beef is the meat obtained from cattle raised in tropical environments, the population of which remains largely uncharacterized. Production systems in the Tropics are highly diverse but converge on the use of indigenous and Bos indicus breeds or Bos indicus-influenced crossbreeds under pasture feeding regimes. While some systems allow cattle to be slaughtered at ≤2 years of age, most often animals are ≥3 years. These production systems generally produce lean, low-yielding carcasses and tough (>46 N), lean (≤3.6% intramuscular fat) meat with a macronutrient composition otherwise similar to beef from animals raised elsewhere (72–74% moisture and 20–24% protein). Fatty acid profiles depend on the breed and production systems, while mineral content is influenced by the environment. Although lean and tough, tropical beef is highly acceptable to the consumers it serves, is culturally and traditionally relevant and, in many countries, contributes to food security. Consolidating the findings from animal and meat science studies in the Tropics has allowed the demonstration of an axiomatic basis defining “tropical beef” as a concept.

A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits

BACKGROUND

Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits.

RESULTS

SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117).

CONCLUSIONS

Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.

Selection signatures in tropical cattle are enriched for promoter and coding regions and reveal missense mutations in the damage response gene HELB

Background

Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome.

Results

We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB, IRAK3, ENSBTAG00000026993, GRIP1 and part of HMGA2. Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B (HELB) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N’Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2-CNV, which is located in the same region.

Conclusions

Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultra-violet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.

Prospects for gene introgression or gene editing as a strategy for reduction of the impact of heat stress on production and reproduction in cattle

In cattle, genetic variation exists in regulation of body temperature and stabilization of cellular function during heat stress. There are opportunities to reduce the impact of heat stress on cattle production by identifying the causative mutations responsible for genetic variation in thermotolerance and transferring specific alleles that confer thermotolerance to breeds not adapted to hot climates. An example of a mutation conferring superior ability to regulate body temperature is the group of frame-sift mutations in the prolactin receptor gene (PRLR) that lead to a truncated receptor and development of cattle with a short, sleek hair coat. Slick mutations in PRLR have been found in several extant breeds derived from criollo cattle. The slick mutation in Senepol cattle has been introgressed into dairy cattle in Puerto Rico, Florida and New Zealand. An example of a mutation that confers cellular protection against elevated body temperature is a deletion mutation in the promoter region of a heat shock protein 70 gene called HSPA1L. Inheritance of the mutation results in amplification of the transcriptional response of HSPA1L to heat shock and increased cell survival. The case of PRLR provides a promising example of the efficacy of the genetic approach outlined in this paper. Identification of other mutations conferring thermotolerance at the whole-animal or cellular level will lead to additional opportunities for using genetic solutions to reduce the impact of heat stress.

Genetic parameters for hair characteristics and core body temperature in a multibreed Brahman-Angus herd1

Thermal stress in hot humid conditions limits cattle production. The objectives for this study were to estimate genetic parameters for hair characteristics and core body temperature under low and high temperature humidity index (THI) conditions. Hair samples were collected and measured for length and diameter. Core body temperature was measured as vaginal temperature every 15 min over a 5-d period using an iButton temperature measuring device implanted in a blank CIDR in 336 heifers from the University of Florida multibreed herd (ranging from 100% Angus to 100% Brahman). Restricted maximum likelihood procedures were used to estimate heritabilities from multiple bivariate animal models using the WOMBAT program. Estimates of heritability for hair diameter, undercoat length, topcoat length, body temperature under low THI conditions, and body temperature under high THI conditions were 0.50, 0.67, 0.42, 0.32, and 0.26, respectively. The genetic parameters estimated in this study indicate a large, exploitable genetic variance which can be selected upon to improve tolerance in cattle. Breed effects for differing compositions of Brahman and Angus were also estimated. As Brahman breed composition increased by 25% undercoat length, topcoat length, body temperature under low THI conditions, and body temperature under high THI conditions decreased by 1.32 mm, 2.94 mm, 0.11 °C, and 0.14 °C, respectively. Under both low and high THI conditions, cattle with 25% Brahman breed composition or greater maintained a significantly lower body temperature than the 100% Angus breed group. The incorporation of Brahman germplasm is recommended for herds that often experience heat stress conditions in order to increase resilience to heat stress.

Can Bos indicus cattle breeds be discriminated by differences in the changes of their sweat gland traits across summer and winter seasons?

This study addresses the hypothesis that Bos indicus cattle breeds can be discriminated by the changes that occur in their sweat gland traits between summer and winter seasons in tropical conditions. Samples of the skin were taken from six Bos indicus cattle breeds (eight subjects per breed), including Nellore, Cangaian, Gyr, Guzerat, Punganur, and Sindhi in winter and summer. The sweat gland epithelium (μm), glandular portion length (μm), sweat gland duct length (μm), gland depth (μm), and sweat gland density (cm²) were determined. Principal component analyses were performed to address the overall structure of breed's group, together with confirmatory analyses by the least squares procedures. Exploratory analysis showed that cattle breeds presented patterns of dissimilarity in the changes in their skin and sweat glands traits between winter and summer seasons. Breeds were separated into three groups under the two principal components, which represented 77.26% of the total variance. The first group was composed of Sindh and Guzerat cattle, which did not present modifications in the parameters assessed between seasons. The most visible alterations were observed in Gyr cattle (third group). In fact, confirmatory analyses showed that glandular portion length, sweat gland duct length, gland depth, and sweat gland density of the Gyr cattle increased (P < 0.05) during the summer season. In conclusion, the results of this investigation demonstrated that morphological traits of the skin and sweat glands associated with seasonal changes in tropical conditions were able to discriminate among Bos indicus cattle breeds.

Genetic basis of voluntary water consumption in two divergently selected strains of inbred mice

Background

Inbred mouse strains with normal renal function show a substantial difference in daily water consumption across strains. This study uses two strains of inbred mice C57BR/CDJ (BR), which are high consumers, and C57BL/10J (BL), which are low consumers, their reciprocal F₁ crosses, inter se bred F₂s and backcrosses produced by breeding high consuming F₂ animals to the low consumer parent strain and low consuming F₂ animals to the high consuming parent strain. Consumption was corrected for body weight prior to analysis.

Methods

The effective number of genes controlling water consumption was estimated using the Castle–Wright estimator. Additive and dominance genotypic values as well as the degree of dominance were calculated using estimated strain means.

Results

According to Castle–Wright, a minimum of 10 factors were estimated to affect the difference in consumption across the two strains. Between seven and eight are expected to be high effect factors. Using the Zeng adjustment, it was determined that 30–40 factors potentially affect the difference in consumption.

Conclusions

These numbers were surprising but may be related to several sources of variation present in the BR strain. A negative degree of dominance indicated the BL strain has more dominant factors.

Scans for signatures of selection in Russian cattle breed genomes reveal new candidate genes for environmental adaptation and acclimation

Domestication and selective breeding has resulted in over 1000 extant cattle breeds. Many of these breeds do not excel in important traits but are adapted to local environments. These adaptations are a valuable source of genetic material for efforts to improve commercial breeds. As a step toward this goal we identified candidate regions to be under selection in genomes of nine Russian native cattle breeds adapted to survive in harsh climates. After comparing our data to other breeds of European and Asian origins we found known and novel candidate genes that could potentially be related to domestication, economically important traits and environmental adaptations in cattle. The Russian cattle breed genomes contained regions under putative selection with genes that may be related to adaptations to harsh environments (e.g., AQP5, RAD50, and RETREG1). We found genomic signatures of selective sweeps near key genes related to economically important traits, such as the milk production (e.g., DGAT1, ABCG2), growth (e.g., XKR4), and reproduction (e.g., CSF2). Our data point to candidate genes which should be included in future studies attempting to identify genes to improve the extant breeds and facilitate generation of commercial breeds that fit better into the environments of Russia and other countries with similar climates.