Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data

Genomic Insights and Conservation Priorities for Kongshan Cattle: A Whole-Genome Resequencing Approach

Kongshan Cattle, indigenous to Sichuan Province and recognized as China's 56th local cattle breed in 2024, exhibit unique adaptations including superior resistance to harsh conditions. Despite a declining population due to the influx of foreign breeds, there is a significant focus on preserving their genetic diversity through advanced genomic techniques. This study utilized whole-genome resequencing, a cost-effective and information-rich method, to perform a comprehensive genetic assessment of the Kongshan Cattle. High-quality resequencing data yielded an average of 17.5 billion clean bases per sample, with high proportions of Q20 and Q30 bases and a balanced GC content. SNP analysis revealed an average of 14 million SNPs per sample, with a notable transition-to-transversion ratio and a significant portion of heterozygosity. Further analysis of genomic and coding regions identified substantial insertions and deletions, particularly in coding sequences affecting gene functionality. A detailed examination of these genetic variations highlighted genes, including NEIL2 and PNKP, which are integral to stress resistance pathways, indicating potential adaptive advantages. This study not only underscores the genetic diversity of Kongshan Cattle but also contributes to broader efforts in germplasm conservation.

Genomic insights into adaptation and inbreeding among Sub-Saharan African cattle from pastoral and agropastoral systems

Background

In Sub-Saharan Africa (SSA), cattle are crucial for socioeconomic stability yet face numerous environmental stressors such as diseases, parasites, and extreme heat within pastoral and agropastoral systems. Despite their significance, gaps remain in understanding how genetic diversity and inbreeding influence traits essential for disease resistance and environmental adaptability. This study examines the genomic adaptations that enable SSA cattle to thrive under these conditions and assesses the impact of inbreeding on such adaptive traits.

Methods

We analyzed genomic data from 113 cattle across four breeds-Kuri, N'dama, Zebu-Fulani, and Zebu-Bororo-employing Runs of Homozygosity (ROH) and Integrated Haplotype Score (iHS) analyses to identify historical and recent genetic selections. Strict quality controls using PLINK software ensured accurate genomic pattern identification related to adaptation and inbreeding.

Results

ROH analysis revealed islands with genes such as RSAD2, CMPK2, and NOTCH1, which are involved in immune response and cellular stress management, highlighting regions of historical selection that have likely provided adaptive advantages in overcoming environmental and pathogenic stresses. In contrast, iHS analysis identified genes under recent selection like HIPK1, involved in stress response regulation, and EPHA5, which plays a crucial role in neural development and synaptic functions, potentially equipping these breeds with novel adaptations to ongoing and emergent environmental challenges.

Conclusion

This research confirms that selective pressures inherent in pastoral and agropastoral systems profoundly influence the genetic structure of SSA cattle. By delineating the genetic bases of key adaptive traits, our study offers crucial insights for targeted breeding programs to enhance cattle resilience and productivity. These findings provide a valuable framework for future genetic improvements and conservation strategies, crucial for sustainable livestock management and economic stability in SSA.

Identification of consensus homozygous regions and their associations with growth and feed efficiency traits in American mink

The recent chromosome-based genome assembly and the newly developed 70K single nucleotide polymorphism (SNP) array for American mink (Neogale vison) facilitate the identification of genetic variants underlying complex traits in this species. The objective of this study was to evaluate the association between consensus runs of homozygosity (ROH) with growth and feed efficiency traits in American mink. A subsample of two mink populations (n = 2,986) were genotyped using the Affymetrix Mink 70K SNP array. The identified ROH segments were included simultaneously, concatenated into consensus regions, and the ROH-based association studies were carried out with linear mixed models considering a genomic relationship matrix for 11 growth and feed efficiency traits implemented in ASReml-R version 4. In total, 298,313 ROH were identified across all individuals, with an average length and coverage of 4.16 Mb and 414.8 Mb, respectively. After merging ROH segments, 196 consensus ROH regions were detected and used for genome-wide ROH-based association analysis. Thirteen consensus ROH regions were significantly (P < 0.01) associated with growth and feed efficiency traits. Several candidate genes within the significant regions are known for their involvement in growth and body size development, including MEF2A, ADAMTS17, POU3F2, and TYRO3. In addition, we found ten consensus ROH regions, defined as ROH islands, with frequencies over 80% of the population. These islands harbored 12 annotated genes, some of which were related to immune system processes such as DTX3L, PARP9, PARP14, CD86, and HCLS1. This is the first study to explore the associations between homozygous regions with growth and feed efficiency traits in American mink. Our findings shed the light on the effects of homozygosity in the mink genome on growth and feed efficiency traits, that can be utilized in developing a sustainable breeding program for mink.

A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle

Presence-absence variations (PAVs) are important structural variations, wherein a genomic segment containing one or more genes is present in some individuals but absent in others. While PAVs have been extensively studied in plants, research in cattle remains limited. This study identified PAVs in 173 Holstein bulls using whole-genome sequencing data and assessed their associations with 46 economically important traits. Out of 28,772 cattle genes (from the longest transcripts), a total of 26,979 (93.77%) core genes were identified (present in all individuals), while variable genes included 928 softcore (present in 95-99% of individuals), 494 shell (present in 5-94%), and 371 cloud genes (present in <5%). Cloud genes were enriched in functions associated with hormonal and antimicrobial activities, while shell genes were enriched in immune functions. PAV-based genome-wide association studies identified associations between gene PAVs and 16 traits including milk, fat, and protein yields, as well as traits related to health and reproduction. Associations were found on multiple chromosomes, illustrating important associations on cattle chromosomes 7 and 15, involving olfactory receptor and immune-related genes, respectively. By examining the PAVs at the population level, the results of this research provided crucial insights into the genetic structures underlying the complex traits of Holstein cattle.

Runs of homozygosity and selection signature analyses reveal putative genomic regions for artificial selection in layer breeding

BACKGROUND

The breeding of layers emphasizes the continual selection of egg-related traits, such as egg production, egg quality and eggshell, which enhance their productivity and meet the demand of market. As the breeding process continued, the genomic homozygosity of layers gradually increased, resulting in the emergence of runs of homozygosity (ROH). Therefore, ROH analysis can be used in conjunction with other methods to detect selection signatures and identify candidate genes associated with various important traits in layer breeding.

RESULTS

In this study, we generated whole-genome sequencing data from 686 hens in a Rhode Island Red population that had undergone fifteen consecutive generations of intensive artificial selection. We performed a genome-wide ROH analysis and utilized multiple methods to detect signatures of selection. A total of 141,720 ROH segments were discovered in whole population, and most of them (97.35%) were less than 3 Mb in length. Twenty-three ROH islands were identified, and they overlapped with some regions bearing selection signatures, which were detected by the De-correlated composite of multiple signals methods (DCMS). Sixty genes were discovered and functional annotation analysis revealed the possible roles of them in growth, development, immunity and signaling in layers. Additionally, two-tailed analyses including DCMS and ROH for 44 phenotypes of layers were conducted to find out the genomic differences between subgroups of top and bottom 10% phenotype of individuals. Combining the results of GWAS, we observed that regions significantly associated with traits also exhibited selection signatures between the high and low subgroups. We identified a region significantly associated with egg weight near the 25 Mb region of GGA 1, which exhibited selection signatures and has higher genomic homozygosity in the low egg weight subpopulation. This suggests that the region may be play a role in the decline in egg weight.

CONCLUSIONS

In summary, through the combined analysis of ROH, selection signatures, and GWAS, we identified several genomic regions that associated with the production traits of layers, providing reference for the study of layer genome.

Identification of runs of homozygosity (ROHs) in Curraleiro Pé-Duro and Pantaneiro cattle breeds

This study aimed to identify and characterize runs of homozygosis (ROHs), genes involved in production characteristics and adaptation to tropical systems and to estimate the inbreeding coefficient of Curraleiro Pé-Duro (CPD) and Pantaneiro (PANT), two brazilian locally adapted cattle breeds. The results demonstrated that 79.25% and 54.29% of ROH segments were bigger than 8 Mb in CPD and PANT, respectively, indicating recent inbred matings in the studied population. Six homozygosis islands were identified simultaneously in both breeds, where 175 QTLs and 1072 genes previously described as associated with production traits are located. The inbreeding coefficient (FROH) estimated based on ROHs (FROH) showed that inbreeding is low (2 to 4%), which is different from expected for small populations such as locally adapted ones.

Performance, body development and ingestive behavior of Nelore and crossbred heifers finished in a grazing system

The aim of this experiment was to evaluate growth, body development and ingestive behavior of Nelore and crossbred heifers. Twenty-two contemporary heifers (eight Nelore, seven Nelore × Angus (½ Angus) and seven Nelore × Pantaneiro (½ Pantaneiro) crosses) were evaluated. The variables evaluated were weight, subcutaneous fat thickness [assessed by ultrasound in the longissimus dorsi (SFT) and biceps femoris (SFTP8)] morphometric measures and ingestive behavior (determined between 7 am and 5 pm). The daily gain differed between the breeds (P < 0.05), being greater for the ½ Pantaneiro than Nelore and equal to ½ Angus at the end of the study. The ½ Angus heifers differed (P < 0.01) from the other breeds for SFT (4.36 mm), with no difference between Nelore (2.77 mm) and ½ Pantaneiro (3.38 mm). The SFTP8 was greater (P < 0.01) (5.36 mm) in ½ Angus heifers than t others crossbreed, and greater in ½ Pantaneiro than in Nelore (4.28 vs 3.29 mm). The heart girth and rump width between the ilia were larger (P < 0.01) for the ½ Angus than ½ Pantaneiro and Nelore (169 cm; 41.6 cm, respectively). Substernal height was greatest (P < 0.01) for the Nelore (69.1 cm), reflecting the greater anterior and posterior height. The ½ Angus spent the longest time (P < 0.05) walking and less time grazing. Idleness also differed (P < 0.05) throughout the day. Crossbred heifers exhibited better performance and development than Nelore. The grazing pattern of ½ Pantaneiro heifers was identical to Nelore, but walked less, gained more weight, and exhibited better carcass finishing.

Phenotypic variation in milk fatty acid composition and its association with stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in Gir cows

Individual variation in milk fatty acid (FA) composition has been partially attributed to stearoyl-CoA desaturase 1 (SCD1) gene polymorphisms in taurine breeds, but much less is known for Zebu breeds. This study investigated the phenotypic variation in milk FA composition, and the influence of SCD1 variants on this trait and on milk fat desaturase indices (DI) in Gir cows. The functional impact of SCD1 variants was predicted using bioinformatics tools. Milk and blood samples were collected from 312 cows distributed in 10 herds from five states of Brazil. SCD1 variants were identified through target sequencing, and milk FA composition was determined by gas chromatography. Phenotypic variation in milk FA composition fell within the range reported for taurine breeds, with SCD18 index showing the lowest variation among the DI. Fourteen SCD1 variants were identified, six of which not previously described. Regarding the A293V polymorphism, all cows were homozygous for the C allele (coding for alanine), whereas all genotypes were detected for the second SNP affecting the 293 codon (G > A), with compelling evidence for functional effects. Significant associations (based on raw p-values) were found between this SNP and C12:0, cis-9, trans-11 CLA and short-chain FA, and between another SNP (rs523411937) and C15:0 and odd-chain linear FA. A new SNP on Chr26:21277069 was associated with trans-11 C18:1, cis-9, trans-11 CLA, C18:3 n-3 and n-3 FA. These findings indicate that SCD1 polymorphisms also contributes to the phenotypic variation in milk FA composition of Gir cows, with potential use in their breeding programmes.

Analysis of runs of homozygosity of cattle living in different climate zones

Aim of this study was to analyze the distribution and characteristics of runs of homozygosity in Bos taurus taurus and Bos taurus indicus breeds, as well as their crosses, farmed all around the world. With this aim in view, we used single-nucleotide polymorphisms (SNP) genotypes for 3,263 cattle belonging to 204 different breeds. After quality control, 23,311 SNPs were retained for the analysis. Animals were divided into seven different groups: 1) continental taurus, 2) temperate taurus, 3) temperate indicus, 4) temperate composite, 5) tropical taurus, 6) tropical indicus, and 7) tropical composite. The climatic zones were created according to the latitude of the breeds' country of origin: i) continental, latitude ≥ 45°; ii) temperate, 45°< Latitude >23.26°; iii) tropics, latitude ≤ 23.26°. Runs of homozygosity were computed as 15 SNPs spanning in at least 2 Mb; number of ROH per animal (nROH), average ROH length (meanMb), and ROH-based inbreeding coefficients (FROH) were also computed. Temperate indicus showed the largest nROH, whereas Temperate taurus the lowest value. Moreover, the largest meanMb was observed for Temperate taurus, whereas the lowest value for Tropics indicus. Temperate indicus breeds showed the largest FROH values. Genes mapped in the identified ROH were reported to be associated with the environmental adaptation, disease resistance, coat color determinism, and production traits. Results of the present study confirmed that runs of homozygosity could be used to identify genomic signatures due to both artificial and natural selection.

Assessing genomic diversity and signatures of selection in Pinan cattle using whole-genome sequencing data

BACKGROUND

Crossbreeding is an important way to improve production beef cattle performance. Pinan cattle is a new hybrid cattle obtained from crossing Piedmontese bulls with Nanyang cows. After more than 30 years of cross-breeding, Pinan cattle show a variety of excellent characteristics, including fast growth, early onset of puberty, and good meat quality. In this study, we analyzed the genetic diversity, population structure, and genomic region under the selection of Pinan cattle based on whole-genome sequencing data of 30 Pinan cattle and 169 published cattle genomic data worldwide.  RESULTS: Estimating ancestry composition analysis showed that the composition proportions for our Pinan cattle were mainly Piedmontese and a small amount of Nanyang cattle. The analyses of nucleotide diversity and linkage disequilibrium decay indicated that the genomic diversity of Pinan cattle was higher than that of European cattle and lower than that of Chinese indigenous cattle. De-correlated composite of multiple selection signals, which combines four different statistics including θπ, CLR, F_ST, and XP-EHH, was computed to detect the signatures of selection in the Pinan cattle genome. A total of 83 genes were identified, affecting many economically important traits. Functional annotation revealed that these selected genes were related to immune (BOLA-DQA2, BOLA-DQB, LSM14A, SEC13, and NAALADL2), growth traits (CYP4A11, RPL26, and MYH10), embryo development (REV3L, NT5E, CDX2, KDM6B, and ADAMTS9), hornless traits (C1H21orf62), and climate adaptation (ANTXR2).

CONCLUSION

In this paper, we elucidated the genomic characteristics, ancestry composition, and selective signals related to important economic traits in Pinan cattle. These results will provide the basis for further genetic improvement of Pinan cattle and reference for other hybrid cattle related studies.

Identification of selection signatures in Iranian dromedary and Bactrian camels using whole genome sequencing data

The Old World camels play an important role as one of the main food sources in large parts of Asia and Africa. Natural selection combined with artificial selection by human has affected parts of the domestic animal genome for adapting them to their habitats and meeting human needs. Here, we used whole genome sequencing data of 34 camels (including 14 dromedaries and 20 Bactrian camels) to identify the genomic signature of selection in the Iranian dromedary (ID) and Bactrian camels (IB). To detect the mentioned regions, we used two methods including population differentiation index (Fst) and cross-population extended haplotype homozygosity (XP-EHH) with 50 kb sliding window and 25 kb step size. Based on gene ontology analysis on the candidate genes identified for IB camels, we found GO terms associated with lung development, nervous system development, immune system and behavior. Also, we identified several genes related to body thermoregulation (ZNF516), meat quality (ANK1 and HSPA13), and high-altitude adaptation (OPA1) for IB camels. In the list of detected candidate genes under selection in ID camels, the genes related to energy metabolism (BDH1), reproduction (DLG1, IMMP2L and FRASI), long-term memory (GRIA1), kidney (SLC12A1), lung development (EMILIN2 and FBN1) and immunity (SOCS2, JAK1, NRROS and SENP1) were found. Our findings, along with further studies in this field, will strengthen our knowledge about the effect of selection on the camelid genome under different geographical, climatic and even cultural conditions.

Elucidation of the mechanism of NEFA-induced PERK-eIF2α signaling pathway regulation of lipid metabolism in bovine hepatocytes

During the periparturient transition period, negative energy balance (NEB) characterized by high concentrations of non-esterified fatty acids (NEFA) may cause fatty liver and ketosis in dairy cows. Previous studies have shown that the protein kinase R-like endoplasmic reticulum kinase (PERK) branch of the endoplasmic reticulum stress (ERS) response plays an important role in lipid metabolism in hepatocytes. This study, therefore, investigated the role of the PERK-branch in NEFA-induced fatty liver. Different concentrations of NEFA or GSK2656157 (a novel catalytic inhibitor of PERK) were used to treat hepatocytes isolated from calves. The NEFA treatment significantly increased the triacylglycerol (TG) content, the phosphorylation level of PERK and eukaryotic initiation factor 2α (eIF2α), and the abundance of glucose-regulated protein 78 (Grp78), C/EBP homologous protein (CHOP), sterol regulatory element-binding protein 1c (SREBP-1c), fatty acid synthase (FASN), peroxisome proliferator-activated receptor-α (PPARα), carnitine palmitoyltransferase 1A (CPT1A), apolipoprotein B (APOB), and the low-density lipoprotein receptor (LDLR). Compared with the 1.2 mM NEFA group, inhibition of PERK activity further increased the TG content in hepatocytes, the very-low-density lipoprotein (VLDL) content in the supernatant and the protein abundance of APOB while reducing the expression and nuclear levels of SREBP-1c and PPARα, as well as the expression of CPT1A and CPT2. In conclusion, the results showed that the NEFA-induced PERK-eIF2α signaling pathway promotes lipid synthesis, lipid oxidation, but inhibits the assembly and secretion of VLDL. Therefore, during the transition period, the activation of the PERK-eIF2α signaling pathway in the liver of dairy cows could defeat the acid-induced lipotoxicity and provide energy to alleviate NEB.

How imputation can mitigate SNP ascertainment Bias

Background

Population genetic studies based on genotyped single nucleotide polymorphisms (SNPs) are influenced by a non-random selection of the SNPs included in the used genotyping arrays. The resulting bias in the estimation of allele frequency spectra and population genetics parameters like heterozygosity and genetic distances relative to whole genome sequencing (WGS) data is known as SNP ascertainment bias. Full correction for this bias requires detailed knowledge of the array design process, which is often not available in practice. This study suggests an alternative approach to mitigate ascertainment bias of a large set of genotyped individuals by using information of a small set of sequenced individuals via imputation without the need for prior knowledge on the array design.

Results

The strategy was first tested by simulating additional ascertainment bias with a set of 1566 chickens from 74 populations that were genotyped for the positions of the Affymetrix Axiom™ 580 k Genome-Wide Chicken Array. Imputation accuracy was shown to be consistently higher for populations used for SNP discovery during the simulated array design process. Reference sets of at least one individual per population in the study set led to a strong correction of ascertainment bias for estimates of expected and observed heterozygosity, Wright’s Fixation Index and Nei’s Standard Genetic Distance. In contrast, unbalanced reference sets (overrepresentation of populations compared to the study set) introduced a new bias towards the reference populations. Finally, the array genotypes were imputed to WGS by utilization of reference sets of 74 individuals (one per population) to 98 individuals (additional commercial chickens) and compared with a mixture of individually and pooled sequenced populations. The imputation reduced the slope between heterozygosity estimates of array data and WGS data from 1.94 to 1.26 when using the smaller balanced reference panel and to 1.44 when using the larger but unbalanced reference panel. This generally supported the results from simulation but was less favorable, advocating for a larger reference panel when imputing to WGS.

Conclusions

The results highlight the potential of using imputation for mitigation of SNP ascertainment bias but also underline the need for unbiased reference sets.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07663-6.

The distribution of runs of homozygosity in the genome of river and swamp buffaloes reveals a history of adaptation, migration and crossbred events

Background

Water buffalo is one of the most important livestock species in the world. Two types of water buffalo exist: river buffalo (Bubalus bubalis bubalis) and swamp buffalo (Bubalus bubalis carabanensis). The buffalo genome has been recently sequenced, and thus a new 90 K single nucleotide polymorphism (SNP) bead chip has been developed. In this study, we investigated the genomic population structure and the level of inbreeding of 185 river and 153 swamp buffaloes using runs of homozygosity (ROH). Analyses were carried out jointly and separately for the two buffalo types.

Results

The SNP bead chip detected in swamp about one-third of the SNPs identified in the river type. In total, 18,116 ROH were detected in the combined data set (17,784 SNPs), and 16,251 of these were unique. ROH were present in both buffalo types mostly detected (~ 59%) in swamp buffalo. The number of ROH per animal was larger and genomic inbreeding was higher in swamp than river buffalo. In the separated datasets (46,891 and 17,690 SNPs for river and swamp type, respectively), 19,760 and 10,581 ROH were found in river and swamp, respectively. The genes that map to the ROH islands are associated with the adaptation to the environment, fitness traits and reproduction.

Conclusions

Analysis of ROH features in the genome of the two water buffalo types allowed their genomic characterization and highlighted differences between buffalo types and between breeds. A large ROH island on chromosome 2 was shared between river and swamp buffaloes and contained genes that are involved in environmental adaptation and reproduction.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12711-021-00616-3.