Inbreeding and runs of homozygosity before and after genomic selection in North American Holstein cattle

Improved computation of genomic and pedigree inbreeding and relationships accounting for the X chromosome

Breeders for many decades used pedigrees to limit increases in inbreeding, but genomic measures of relationship and inbreeding provide more precise control. Previous calculations of pedigree inbreeding (Fped), genomic inbreeding (Fgen), pedigree expected future inbreeding (EFIped), and genomic expected future inbreeding (EFIgen) included the X chromosome but ignored its influence when estimating relationships. The X chromosome contributes to inbreeding in female progeny, for example, if parents with the same X chromosome are mated. Because the X-specific region has 3.0% of the 79,060 markers used in US genomic evaluation and those markers are coded as 100% homozygous in males, homozygosity of females appeared to be 3% less than for males. Allele frequency also affects the computation of Fgen. Programs to compute pedigree and genomic measures were revised to improve speed and memory use, as well as to better account for the X chromosome. Revised software reduced computational time from 33 h to 13 min (152 times faster) using 32 processors for Fped and EFIped with 88 million animals in the pedigree and from 19 h to 28 min (41 times faster) for Fgen and EFIgen for 3,280,753 genotyped animals of 5 breeds. Correlations were high between Fgen computed using either an allele frequency of 0.5 or a base population frequency for most breeds. Mean Fgen was higher for males than for females, but adjustments for the X chromosome made Fgen means more comparable across sexes. The X adjustments did not affect correlations within sex. After adjusting Fgen for the X chromosome using an allele frequency of 0.5, correlations across breeds and sex increased, and X-adjusted Fgen was more similar to Fped. Using an allele frequency of 0.5, mean correlation with Fped across breeds was 0.67 for Fgen, 0.67 for X-adjusted Fgen, and 0.54 for Fgen with base population allele frequency; corresponding EFI correlations were 0.83, 0.83, and 0.84. Breeds with smaller populations were more sensitive to the use of different allele frequencies. Mean correlation of haplotype-based inbreeding with Fped was 0.64. Revision of inbreeding software allowed simpler and more accurate comparison of genomic and pedigree relationships and much faster computation.

Enhanced Reliability of the Evaluation of Fertility Traits in Pura Raza Española Horses Using Single-Step Genomic Best Linear Unbiased Prediction

Background/Objectives: By simultaneously integrating both genotyped and non-genotyped animals into genetic evaluation, the single-step genomic BLUP method enhanced the accuracy of genetic assessments. This study aimed to compare the increase in prediction reliability (R2) between restricted maximum likelihood (REML) and single-step genomic REML (ssGREML) in the Pura Raza Española (PRE) horse breed. Methods: The dataset comprised reproductive records for seven fertility traits from 47,502 females, with a total of 57,316 animals represented in the pedigree. A total of 4009 animals were genotyped using the EQUIGENE 90K SNP array, and 71,322 SNPs were retained for analysis after quality control. Genetic parameters were estimated using a multivariate model with the BLUPF90+ v2.60 software. Results: Heritability estimates were similar between REML and ssGREML, ranging from 0.07 for IF12 to 0.349 for ALF. An increase in R2 was observed with ssGREML compared to REML across all traits, with overall gains ranging from 2.20% to 3.71%. Among genotyped animals, R2 values ranged from 17.81% to 24.04%, while significantly lower values (0.80% to 2.34%) were observed in non-genotyped animals. Notably, individuals with low initial R2 values under the REML approach exhibited the most significant gains using ssGREML. This improvement was particularly pronounced among stallions with fewer than 40 controlled foals. Conclusions: Our results demonstrated that incorporating genomic data improves the reliability of genetic evaluations for mare fertility in PRE horses.

Optimizing genetic diversity in Australian Holsteins and Jerseys: A comparative analysis of whole-genome and regional inbreeding depression effects

Homozygosity, which can arise from several genetic mechanisms including inbreeding, is frequently observed in the offspring of related parents. This inbreeding can lead to a reduced performance, owing to a phenomenon known as inbreeding depression. This study assessed inbreeding depression using whole-genome and regional approaches in first-lactation Australian Holsteins and Jerseys, involving ∼33,000 Holstein and 7,000 Jersey cows born between 2000 and 2017. These cows had phenotypic records (milk production, fertility, and survival), pedigree records, and genomic data available. We analyzed genome-wide inbreeding depression through a mixed animal model examining 4 measures of inbreeding: pedigree data, runs of homozygosity (ROH) of at least 1 Mb, ROH greater than 8 Mb, and ROH exceeding 16 Mb, which indicates more recent inbreeding. Additionally, unique ROH haplotypes, identified using a sliding-window approach, were incorporated as fixed effects in the model to estimate their effect on the traits of interest. Results indicated that a 1% increase in pedigree inbreeding led to reduced performance across all traits, with estimates of inbreeding depression ranging from 0.11% to 0.45% of the phenotypic mean. In Holsteins, genome-wide estimates (FROH) were significant and reasonably aligned with pedigree estimates, whereas more recent inbreeding (FROH >16 Mb) had between 2.6 and 3.3 times greater effect on inbreeding depression across all traits compared with smaller FROH (≥1 Mb). In Jerseys, more recent inbreeding had a 2.2 to 2.3 times greater reduction in the performance of milk and protein yields for a 1% increase in genomic inbreeding. For both fitness traits in Jerseys, the effects of inbreeding on fertility and survival were not significant. The most negative effects of ROH were also noted in specific traits: Jersey and Holstein cows with unfavorable ROH took significantly longer to recalve and showed marked reductions in production traits. Moreover, increased homozygosity in certain genomic regions, such as BTA25 in Jerseys, markedly reduced performance, highlighting the importance of genomic location in assessing the effects of homozygosity. These data inform next-generation mating programs, emphasizing avoiding inbreeding in genomic regions most susceptible to inbreeding depression, to enhance animal performance.

Impact of Implementing Female Genomic Selection and the Use of Sex-Selected Semen Technology on Genetic Gain in a Dairy Herd in New Zealand

Genomic selection (GS) has changed cattle breeding, but its use so far has been in selecting superior bulls for breeding. However, its farm-level impact, particularly on female selection, remains less explored. This study aimed to investigate the impact of implementing GS to identify superior cows and using artificial mating of those cows with sex-selected semen in a New Zealand Holstein-Friesian (HF) dairy herd (n = 1800 cows). Heifers (n = 2061) born over four consecutive years between 2021 and 2024 were genotyped and their genomic breeding values (GBVs) were estimated. These heifers were ranked based on the Balanced Performance Index (BPI; DataGene, Dairy Australia) Lower-performing cows producing less than 15 L/day (or 20 L/day for older cows) and those with severe mastitis were culled. Cows were mated with HF genetics based on production and udder breeding values, while lower-performing cows were mated to beef genetics. Milking adult cows were mated to bulls with similar BPI value. Annual genetic change was measured using Australian breeding values (ABVg) for milk fat production (FAT), protein production (PROT), fertility (FER), Mastitis Resistance (MAS), and BPI. The genetic merits of the heifers improved annually, with BPI increasing from 136 to 184 between 2021 and 2023, corresponding to a financial gain of NZD 17.53 per animal per year. The predicted BPI gain from 2023 to 2026 is expected to rise from 184 to 384, resulting in a financial gain of NZD 72.96 per animal per year. Using sex-selected semen on the top 50% of BPI-rated heifers in 2024 further accelerated genetic gain. Predicted BPI values for progeny born in 2025 and 2026 are 320 and 384, respectively. These findings revealed that the female GS, combined with sex-selected semen from genomically selected bulls, significantly accelerates genetic gain by improving the intensity and accuracy of selection. The approach achieves genetic progress equivalent to what traditionally would have required eight years of breeding without female GS, and has potential to improve dairy herd performance and profitability.

Comparative Analysis of Runs of Homozygosity Islands in Indigenous and Commercial Chickens Revealed Candidate Loci for Disease Resistance and Production Traits

Runs of homozygosity (ROH) are contiguous stretches of identical genomic regions inherited from both parents. Assessment of ROH in livestock species contributes significantly to our understanding of genetic health, population genetic structure, selective pressure and conservation efforts. In this study, whole genome re-sequencing data from 140 birds of 10 Iranian indigenous chicken ecotypes, 3 commercial chicken breeds and 1 red junglefowl (RJF) population were used to investigate their population genetic structure, ROH characteristics (length and frequency) and genomic inbreeding coefficients (FROH). Additionally, we examined ROH islands for selection footprints in the indigenous chicken populations. Our results revealed distinct genetic backgrounds, among which the White Leghorn breed exhibited the greatest genetic distance from other populations, while the gamecock populations formed a separate cluster. We observed significant differences in ROH characteristics, in which the commercial breeds showed a higher number of ROH compared to indigenous chickens and red junglefowls. Short ROH ranging from 0.1 to 1 Mb were dominant among the populations. The Arian line had the highest mean length of ROH, while the White Leghorn breed showed the highest number of ROH. Among indigenous chickens, the Lari-Afghani ecotype exhibited the highest FROH, but the Sari inherited the richest genetic diversity. Interestingly, GGA16 carried no ROH in the red junglefowls, whereas GGA22 had the highest FROH across all populations, except in the Isfahan ecotype. We also identified ROH islands associated with genetic adaptations in indigenous ecotypes. These islands harboured immune-related genes contributing to disease resistance (TLR2, TICAM1, IL22RA1, NOS2, CCL20 and IFNLR1), heat tolerance and oxidative stress response (NFKB1, HSF4, OSGIN1 and BDNF), and muscle development, lipid metabolism and reproduction (MEOX2, CEBPB, CDS2 and GnRH-I). Overall, this study highlights the genetic potential of indigenous chickens to survive and adapt to their respective environments.

Selection signatures associated with adaptation in South African Drakensberger, Nguni, and Tuli beef breeds

In the present study 1,709 cattle, including 1,118 Drakensberger (DRB), 377 Nguni (NGI), and 214 Tuli (TUL), were genotyped using the GeneSeek® Genomic Profiler™ 150 K bovine SNP panel. A genomic data set of 122,632 quality-filtered single nucleotide polymorphisms (SNPs) were used to identify selection signatures within breeds based on conserved runs of homozygosity (ROH) and heterozygosity (ROHet) estimated with the detectRUNS R package. The mean number of ROH per animal varied across breeds ranging from 36.09 ± 12.82 (NGI) to 51.82 ± 21.01 (DRB), and the mean ROH length per breed ranged between 2.31 Mb (NGI) and 3.90 Mb (DRB). The smallest length categories i.e., ROH < 4 Mb were most frequent, indicating historic inbreeding effects for all breeds. The ROH based inbreeding coefficients (FROH) ranged between 0.033 ± 0.024 (NGI) and 0.081 ± 0.046 (DRB). Genes mapped to candidate regions were associated with immunity (ADAMTS12, LY96, WDPCP) and adaptation (FKBP4, CBFA2T3, TUBB3) in cattle and genes previously only reported for immunity in mice and human (EXOC3L1, MYO1G). The present study contributes to the understanding of the genetic mechanisms of adaptation, providing information for potential molecular application in genetic evaluation and selection programs.

Efficient large-scale genomic prediction in approximate genome-based kernel model

KEY MESSAGE

Three computationally efficient algorithms of GP including RHBK, RHDK, and RHPK were developed in approximate genome-based kernel model. The drastically growing amount of genomic information contributes to increasing computational burden of genomic prediction (GP). In this study, we developed three computationally efficient algorithms of GP including RHBK, RHDK, and RHPK in approximate genome-based kernel model, which reduces dimension of genomic data via Nyström approximation and decreases the computational cost significantly thereby. According to the simulation study and real datasets, our three methods demonstrated predictive accuracy similar to or better than RHAPY, GBLUP, and rrBLUP in most cases. They also demonstrated a substantial reduction in computational time compared to GBLUP and rrBLUP in simulation. Due to their advanced computing efficiency, our three methods can be used in a wide range of application scenarios in the future.

Analysis of genetic structure and identification of important genes associated with muscle growth in Fujian Muscovy duck

Fujian Muscovy duck is a well-known meat waterfowl in Fujian Province due to its high meat production, superior breeding potential, and strong resistance. To fully explore the genetic characteristics of these advantages, Fujian black Muscovy duck and white Muscovy duck were used for whole-genome re-sequencing and transcriptome analyses. Population structure analysis showed significant differentiation between the two feather strains. Runs of homozygosity analysis indicated a stronger artificial influence on the black-feathered strain, with ROH island genes notably enriched in muscle tissue-related terms and pathways. Selective sweep and transcriptome analysis revealed a significant enrichment of genes linked to muscle tissue and muscle fiber-related terms and pathways. Key candidate genes identified, such as MEF2C, MYOZ2, and METTL21C, are believed to play crucial roles in meat production in Fujian Muscovy duck. This study offers a new perspective on improving meat production in Fujian Muscovy duck, which can benefit breeding strategies and production management.

Evaluation of genomic mating approach based on genetic algorithms for long-term selection in Huaxi cattle

BACKGROUND

Genomic mating (GM) can effectively control the growth rate of inbreeding in population and achieve long-term sustainable genetic progress. However, the design of GM method and assessment of its effects during long-term selection have not been fully explored in beef cattle breeding.

RESULTS

In this study, we constructed a simulated population based on the real genotypes of Huaxi cattle, where five generations of simulated breeding were carried out using the genomic optimal contribution selection (GOCS), genetic algorithms strategy and three traditional mating strategies. During the breeding process, genetic parameters including average genomic estimated breeding value (GEBV), genetic gain values ( Δ G ), the rate of inbreeding values ( Δ F ) were calculated and compared across generations. Our results showed that the GM method could significantly improve the genetic gain while effectively controlling the inbreeding accumulation within the population. When using the GM method, there was an increase in genetic gain for Huaxi cattle ranging from 1.1% to 25.6% compared to traditional mating strategy, with inbreeding decreasing in the range of 5.8% to 36.2%. Validation using the real dataset from Huaxi cattle further confirmed our findings from the simulated study, offspring populations using the GM strategy exhibited a 7.3% increase in genetic gain compared to positive assortative mating.

CONCLUSIONS

These findings suggest that the GM method shows potential for achieving sustainable genetic gain and could be utilized during long-term selection in beef cattle breeding.

Selection signatures for high altitude adaptation in livestock: A review

High altitude adapted livestock species (cattle, yak, goat, sheep, and horse) has critical role in the human socioeconomic sphere and acts as good source of animal source products including milk, meat, and leather, among other things. These species sustain production and reproduction even in harsh environments on account of adaptation resulting from continued evolution of beneficial traits. Selection pressure leads to various adaptive strategies in livestock whose footprints are evident at the different genomic sites as the "Selection Signature". Scrutiny of these signatures provides us crucial insight into the evolutionary process and domestication of livestock adapted to diverse climatic conditions. These signatures have the potential to change the sphere of animal breeding and further usher the selection programmes in right direction. Technological revolution and recent strides made in genomic studies has opened the routes for the identification of selection signatures. Numerous statistical approaches and bioinformatics tools have been developed to detect the selection signature. Consequently, studies across years have identified candidate genes under selection region found associated with numerous traits which have a say in adaptation to high-altitude environment. This makes it pertinent to have a better understanding about the selection signature, the ways to identify and how to utilize them for betterment of livestock populations as well as farmers. This review takes a closer look into the general concept, various methodologies, and bioinformatics tools commonly employed in selection signature studies and summarize the results of recent selection signature studies related to high-altitude adaptation in various livestock species. This review will serve as an informative and useful insight for researchers and students in the field of animal breeding and evolutionary biology.

Inference of Genetic Diversity, Population Structure, and Selection Signatures in Xiangxi White Buffalo of China Through Whole-Genome Resequencing

(1) Background: Buffaloes are crucial livestock species for food and service in tropical and subtropical regions. Buffalo genetics, particularly in indigenous Chinese breeds such as the Xiangxi white buffalo (XWB), remains an intriguing area of study due to its unique traits and regional significance. (2) Methods: This investigation utilized the whole-genome sequences of twenty XWBs (newly sequenced), along with eighty published whole-genome sequences of other buffalo breeds (including Guizhou white buffalo, river buffalo, and Chinese buffalo in the Yangtze River). Using whole-genome sequencing analysis technology, the population structure, genomic diversity, and selection signatures of XWB were determined. (3) Results: This study revealed that the XWB, being phylogenetically positioned in the middle and lower reaches of the Yangtze River, exhibited substantial genomic diversity. Employing four selection sweep detection methods (CLR, iHS, π-ratio, and FST), several genes were positively identified for adaptive traits in the XWB, including coat color phenotypes (ASIP, KIT), the nervous system (GRIK2), reproduction (KCNIP4), growth and development (IFNAR1, BMP6, HDAC9, MGAT4C, and SLC30A9), the body (LINGO2, LYN, and FLI1), immunity (IRAK3 and MZB1), and lactation (TP63, LPIN1, SAE1). (4) Conclusions: In conclusion, this study enhances our understanding of the genetic distinctiveness and adaptive traits of XWB, highlighting selection signatures crucial for future breeding and conservation and ensuring sustainable use of this vital livestock resource.

Assessment of inbreeding coefficients and inbreeding depression on complex traits from genomic and pedigree data in Nelore cattle

BACKGROUND

Nelore cattle play a key role in tropical production systems due to their resilience to harsh conditions, such as heat stress and seasonally poor nutrition. Monitoring their genetic diversity is essential to manage the negative impacts of inbreeding. Traditionally, inbreeding and inbreeding depression are assessed by pedigree-based coefficients (F), but recently, genetic markers have been preferred for their precision in capturing the inbreeding level and identifying animals at risk of reduced productive and reproductive performance. Hence, we compared the inbreeding and inbreeding depression for productive and reproductive performance traits in Nelore cattle using different inbreeding coefficient estimation methods from pedigree information (FPed), the genomic relationship matrix (FGRM), runs of homozygosity (FROH) of different lengths (> 1 Mb (genome), between 1 and 2 Mb - FROH 1-2; 2-4 Mb FROH 2-4 or > 8 Mb FROH >8) and excess homozygosity (FSNP).

RESULTS

The correlation between FPed and FROH was lower when the latter was based on shorter segments (r = 0.15 with FROH 1-2, r = 0.20 with FROH 2-4 and r = 0.28 with FROH 4-8). Meanwhile, the FPed had a moderate correlation with FSNP (r = 0.47) and high correlation with FROH >8 (r = 0.58) and FROH-genome (r = 0.60). The FROH-genome was highly correlated with inbreeding based on FROH>8 (r = 0.93) and FSNP (r = 0.88). The FGRM exhibited a high correlation with FROH-genome (r = 0.55) and FROH >8 (r = 0.51) and a lower correlation with other inbreeding estimators varying from 0.30 for FROH 2-4 to 0.37 for FROH 1-2. Increased levels of inbreeding had a negative impact on the productive and reproductive performance of Nelore cattle. The unfavorable inbreeding effect on productive and reproductive traits ranged from 0.12 to 0.51 for FPed, 0.19-0.59 for FGRM, 0.21-0.58 for FROH-genome, and 0.19-0.54 for FSNP per 1% of inbreeding scaled on the percentage of the mean. When scaling the linear regression coefficients on the standard deviation, the unfavorable inbreeding effect varied from 0.43 to 1.56% for FPed, 0.49-1.97% for FGRM, 0.34-2.2% for FROH-genome, and 0.50-1.62% for FSNP per 1% of inbreeding. The impact of the homozygous segments on reproductive and performance traits varied based on the chromosomes. This shows that specific homozygous chromosome segments can be signs of positive selection due to their beneficial effects on the traits.

CONCLUSIONS

The low correlation observed between FPed and genomic-based inbreeding estimates suggests that the presence of animals with one unknown parent (sire or dam) in the pedigree does not account for ancient inbreeding. The ROH hotspots surround genes related to reproduction, growth, meat quality, and adaptation to environmental stress. Inbreeding depression has adverse effects on productive and reproductive traits in Nelore cattle, particularly on age at puberty in young bulls and heifer calving at 30 months, as well as on scrotal circumference and body weight when scaled on the standard deviation of the trait.

Integration of ssGWAS and ROH analyses for uncovering genetic variants associated with reproduction traits in Large White pigs

The low heritability of reproduction traits such as total number born (TNB), number born alive (NBA) and adjusted litter weight until 21 days at weaning (ALW) poses a challenge for genetic improvement. In this study, we aimed to identify genetic variants that influence these traits and evaluate the accuracy of genomic selection (GS) using these variants as genomic features. We performed single-step genome-wide association studies (ssGWAS) on 17 823 Large White (LW) pigs, of which 2770 were genotyped by 50K single nucleotide polymorphism (SNP) chips. Additionally, we analyzed runs of homozygosity (ROH) in the population and tested their effects on the traits. The genomic feature best linear unbiased prediction (GFBLUP) was then carried out in an independent population of 350 LW pigs using identified trait-related SNP subsets as genomic features. As a result, our findings identified five, one and four SNP windows that explaining more than 1% of genetic variance for ALW, TNB, and NBA, respectively and discovered 358 hotspots and nine ROH islands. The ROH SSC1:21814570-27186456 and SSC11:7220366-14276394 were found to be significantly associated with ALW and NBA, respectively. We assessed the genomic estimated breeding value accuracy through 20 replicates of five-fold cross-validation. Our findings demonstrate that GFBLUP, incorporating SNPs located in effective ROH (p-value < 0.05) as genomic features, might enhance GS accuracy for ALW compared with GBLUP. Additionally, using SNPs explaining more than 0.1% of the genetic variance in ssGWAS for NBA as genomic features might improve the GS accuracy, too. However, it is important to note that the incorporation of inappropriate genomic features can significantly reduce GS accuracy. In conclusion, our findings provide valuable insights into the genetic mechanisms of reproductive traits in pigs and suggest that the ssGWAS and ROH have the potential to enhance the accuracy of GS for reproductive traits in LW pigs.

Detectability of runs of homozygosity is influenced by analysis parameters and population-specific demographic history

Wild populations are increasingly threatened by human-mediated climate change and land use changes. As populations decline, the probability of inbreeding increases, along with the potential for negative effects on individual fitness. Detecting and characterizing runs of homozygosity (ROHs) is a popular strategy for assessing the extent of individual inbreeding present in a population and can also shed light on the genetic mechanisms contributing to inbreeding depression. Here, we analyze simulated and empirical datasets to demonstrate the downstream effects of program selection and long-term demographic history on ROH inference, leading to context-dependent biases in the results. Through a sensitivity analysis we evaluate how various parameter values impact ROH-calling results, highlighting its utility as a tool for parameter exploration. Our results indicate that ROH inferences are sensitive to factors such as sequencing depth and ROH length distribution, with bias direction and magnitude varying with demographic history and the programs used. Estimation biases are particularly pronounced at lower sequencing depths, potentially leading to either underestimation or overestimation of inbreeding. These results are particularly important for the management of endangered species, as underestimating inbreeding signals in the genome can substantially undermine conservation initiatives. We also found that small true ROHs can be incorrectly lumped together and called as longer ROHs, leading to erroneous inference of recent inbreeding. To address these challenges, we suggest using a combination of ROH detection tools and ROH length-specific inferences, along with sensitivity analysis, to generate robust and context-appropriate population inferences regarding inbreeding history. We outline these recommendations for ROH estimation at multiple levels of sequencing effort, which are typical of conservation genomics studies.

Assessment of genetic diversity, inbreeding and collection completeness of Jersey bulls in the US National Animal Germplasm Program

Genomic selection and extensive use of a few elite bulls through artificial insemination are leading to reduced genetic diversity in Jersey cattle. Conservation of genetic diversity through gene banks can protect a breed's genetic diversity and genetic gain, ensuring continued genetic advancement in the future. The availability of genomic information in the US National Animal Germplasm Program (NAGP) facilitates characterization of Jersey bulls in the germplasm collection. Therefore, in this study, we compared the genetic diversity and inbreeding between Jersey bulls in the NAGP and the national cooperator database (NCD). The NCD is maintained and curated by the Council on Dairy Cattle Breeding (CDCB). We found the genetic diversity to be marginally higher in NAGP (Ho = 0.34 ± 0.17) relative to the NCD population (Ho = 0.33 ± 0.16). The average pedigree and genomic inbreeding (FPED, FGRM, FROH > 2Mb) were similar between the groups, with estimates of 7.6% with FPED, 11.07% with FGRM and 20.13% with FROH > 2Mb. An increasing trend in inbreeding was detected, and a significantly higher level of inbreeding was estimated among the older bulls in the NAGP collection, suggesting an overrepresentation of the genetics from elite bulls. Results from principal component analyses (PCA) provided evidence that the NAGP collection is representative of the genetic variation found in the NCD population and a broad majority of the loci segregating (98.2%) in the NCD population were also segregating in the NAGP. Ward's clustering was used to assess collection completeness of Jerseys in the NAGP by comparison with top 1000 sires of bulls, top 1000 sires of cow, and bulls with high Lifetime Net Merit (NM$). All the clusters were represented in the NAGP suggesting that most of the genetic diversity in the US Jersey population is represented in the NAGP and confirmed the PCA results. The decade of birth was the major driver grouping bulls into clusters, suggesting the importance of selection over time. Selection signature analysis between the historic bulls in the NAGP with the newer bulls, born in the decade after implementation of genomic selection, identified selection for milk production, fat and protein yield, fertility, health, and reproductive traits. Cluster analysis revealed that the NAGP has captured allele frequency changes over time associated with selection, validating the strategy of repeated sampling and suggests that the continuation of a repeated sampling policy is essential for the germplasm collection to maintain its future utility. While NAGP should continue to collect bulls that have large influence on the population due to selection, care should be taken to include the entire breadth of bulls, including low merit bulls.

Analyzing Runs of Homozygosity Reveals Patterns of Selection in German Brown Cattle

An increasing trend in ancestral and classical inbreeding coefficients as well as inbreeding depression for longevity were found in the German Brown population. In addition, the proportion of US Brown Swiss genes is steadily increasing in German Browns. Therefore, the aim of the present study was to analyze the presence and genomic localization of runs of homozygosity (ROH) in order to evaluate their associations with the proportion of US Brown Swiss genes and survival rates of cows to higher lactations. Genotype data were sampled in 2364 German Browns from 258 herds. The final data set included 49,693 autosomal SNPs. We identified on average 35.996 ± 7.498 ROH per individual with a mean length of 8.323 ± 1.181 Mb. The genomic inbreeding coefficient FROH was 0.122 ± 0.032 and it decreased to 0.074, 0.031 and 0.006, when genomic homozygous segments > 8 Mb (FROH>8), >16 Mb (FROH>16) and >32 Mb (FROH>32) were considered. New inbreeding showed the highest correlation with FROH>32, whereas ancestral inbreeding coefficients had the lowest correlations with FROH>32. The correlation between the classical inbreeding coefficient and FROH was 0.572. We found significantly lower FROH, FROH>4, FROH>8 and FIS for US Brown Swiss proportions <60% compared to >80%. Cows surviving to the 2nd, 4th, 6th, 8th, and 10th lactation had lower genomic inbreeding for FROH and up to FROH>32, which was due to a lower number of ROH and a shorter average length of ROH. The strongest ROH island and consensus ROH shared by 50% of the animals was found on BTA 6 at 85-88 Mb. The genes located in this genomic region were associated with longevity (NPFFR2 and ADAMTS3), udder health and morphology (SLC4A4, NPFFR2, GC and RASSF6), milk production, milk protein percentage, coagulation properties of milk and milking speed (CSN3). On BTA 2, a ROH island was detected only in animals with <60% US Brown Swiss genes. Genes within this region are predominantly important for dual-purpose cattle breeds including Original Browns. For cows reaching more than 9 lactations, an exclusive ROH island was identified on BTA 7 with genes assumed to be associated with longevity. The analysis indicated that genomic homozygous regions important for Original Browns are still present and also ROH containing genes affecting longevity may have been identified. The breeding of German Browns should prevent any further increase in genomic inbreeding and run a breeding program with balanced weights on production, robustness and longevity.

Development and optimization of expected cross value for mate selection problems

In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic characteristics are selected to cross in order to maximize the likelihood of the inheritance of desirable genetic materials to the progeny. Unlike approaches that use phenotypic values for parental selection and evaluate individuals separately, we use a criterion that relies on the genetic architecture of traits and evaluates combinations of genomic information of the pairs of individuals. We introduce the expected cross value (ECV) criterion that measures the expected number of desirable alleles for gametes produced by pairs of individuals sampled from a population of potential parents. We use the ECV criterion to develop an integer linear programming formulation for the parental selection problem. The formulation is capable of controlling the inbreeding level between selected mates. We evaluate the approach or two applications: (i) improving multiple target traits simultaneously, and (ii) finding a multi-parental solution to design crossing blocks. We evaluate the performance of the ECV criterion using a simulation study. Finally, we discuss how the ECV criterion and the proposed integer linear programming techniques can be applied to improve breeding efficiency while maintaining genetic diversity in a breeding program.

Genomic analysis of inbreeding and coancestry in Nordic Jersey and Holstein dairy cattle populations

In recent years, genomic selection (GS) has accelerated genetic gain in dairy cattle breeds worldwide. Despite the evident genetic progress, several dairy populations have also encountered challenges such as heightened inbreeding rates and reduced effective population sizes. The challenge has been to find a balance between achieving substantial genetic gain while managing genetic diversity within the population, thereby mitigating the negative effects of inbreeding depression. This study aims to elucidate the impact of GS on pedigree and genomic rates of inbreeding (ΔF) and coancestry (ΔC) in Nordic Jersey (NJ) and Holstein (NH) cattle populations. Furthermore, key genetic metrics, including the generation interval (L), effective population size (Ne), and future effective population size (FNe) were assessed between 2 time periods, before and after GS, and across distinct animal cohorts in both breeds: females, bulls, and approved semen-producing bulls (AI-sires). Analysis of ΔF and ΔC revealed distinct trends across the studied periods and animal groups. Notably, there was a consistent increase in yearly ΔF for most animal groups in both breeds. An exception was observed in NH AI-sires, which demonstrated a slight decrease in yearly ΔF. Moreover, NJ displayed minimal changes in yearly ΔC between the periods, whereas NH exhibited elevated ΔC values across all animal groups. Particularly striking was the substantial increase in yearly ΔC within the NH female population, surging from 0.02% to 0.39% between the periods. Implementation of GS resulted in a reduction of the generation interval across all animal cohorts in both NJ and NH breeds. However, the extent of reduction was more pronounced in males compared with females. This reduction in generation interval influenced generational changes in ΔF and ΔC. Bulls and AI-sires of both breeds exhibited reduced generational ΔF between periods, in contrast to females that demonstrated an opposing pattern. Between the periods, NJ maintained a relatively stable Ne (29.4 before and 30.3 after GS), whereas NH experienced a notable decline from 54.3 to 42.8. Female groups in both breeds displayed a negative Ne trend, whereas males demonstrated either neutral or positive Ne developments. Regarding FNe, NJ exhibited positive FNe development with an increase from 40.7 to 57.2. The opposite was observed in NH, where FNe decreased from 198.8 to 42.7. In summary, it was evident that the genomic methods could detect differences between the populations and changes in ΔF and ΔC more efficiently than pedigree methods. Implementation of GS yielded positive outcomes within the NJ population regarding the rate of coancestry but the opposite was observed with NH. Moreover, analysis of ΔC data hints at the potential to decrease future ΔF through informed mating strategies. Conversely, NH faces more pressing concerns, even though ΔF remains comparatively modest in contrast to what has been observed in other Holstein populations. These findings underscore the necessity of genomic control of inbreeding and coancestry with strategic changes in the Nordic breeding schemes for dairy to ensure long-term sustainability in the forthcoming years.

Assessing different metrics of pedigree and genomic inbreeding and inbreeding effect on growth, fertility, and feed efficiency traits in a closed-herd Nellore cattle population

BACKGROUND

The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1-2 Mb), FROH2 (2-4 Mb), FROH3 (4-8 Mb), FROH4 (8-16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits.

RESULTS

The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits.

CONCLUSIONS

Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.

Detection and evaluation of parameters influencing the identification of heterozygous-enriched regions in Holstein cattle based on SNP chip or whole-genome sequence data

BACKGROUND

A heterozygous-enriched region (HER) is a genomic region with high variability generated by factors such as balancing selection, introgression, and admixture processes. In this study, we evaluated the genomic background of HERs and the impact of different parameters (i.e., minimum number of SNPs in a HER, maximum distance between two consecutive SNPs, minimum length of a HER, maximum number of homozygous allowed in a HER) and scenarios [i.e., different SNP panel densities and whole-genome sequence (WGS)] on the detection of HERs. We also compared HERs characterized in Holstein cattle with those identified in Angus, Jersey, and Norwegian Red cattle using WGS data.

RESULTS

The parameters used for the identification of HERs significantly impact their detection. The maximum distance between two consecutive SNPs did not impact HERs detection as the same average of HERs (269.31 ± 787.00) was observed across scenarios. However, the minimum number of markers, maximum homozygous markers allowed inside a HER, and the minimum length size impacted HERs detection. For the minimum length size, the 10 Kb scenario showed the highest average number of HERs (1,364.69 ± 1,483.64). The number of HERs decreased as the minimum number of markers increased (621.31 ± 1,271.83 to 6.08 ± 21.94), and an opposite pattern was observed for the maximum homozygous markers allowed inside a HER (54.47 ± 195.51 to 494.89 ± 1,169.35). Forty-five HER islands located in 23 chromosomes with high Tajima's D values and differential among the observed and estimated heterozygosity were detected in all evaluated scenarios, indicating their ability to potentially detect regions under balancing selection. In total, 3,440 markers and 28 genes previously related to fertility (e.g., TP63, ZSCAN23, NEK5, ARHGAP44), immunity (e.g., TP63, IGC, ARHGAP44), residual feed intake (e.g., MAYO9A), stress sensitivity (e.g., SERPINA6), and milk fat percentage (e.g., NOL4) were identified. When comparing HER islands among breeds, there were substantial overlaps between Holstein with Angus (95.3%), Jersey (94.3%), and Norwegian Red cattle (97.1%), indicating conserved HER across taurine breeds.

CONCLUSIONS

The detection of HERs varied according to the parameters used, but some HERs were consistently identified across all scenarios. Heterozygous genotypes observed across generations and breeds appear to be conserved in HERs. The results presented could serve as a guide for defining HERs detection parameters and further investigating their biological roles in future studies.

Signatures of positive selection after the introduction of genomic selection in the Finnish Ayrshire population

The Finnish Ayrshire (FAY) belongs to the Nordic Red breeds and is characterized by high milk yield, high milk components, good fertility, and functional conformation. The FAY breeding program is based on genomic selection. Despite the benefits of selection on breeding values, autozygosity in the genome may increase due to selection, and increased autozygosity may cause inbreeding depression in selected traits. However, there is lack of studies concerning selection signatures in the FAY after genomic selection introduction. The aim of this study was to identify signatures of selection in FAY after the introduction of genomic selection. Genomic data included 45,834 SNPs. The genotyped animals were divided into 2 groups: animals born before genomic selection introduction (6,108 cows) and animals born after genomic selection introduction (47,361 cows). We identified the selection signatures using 3 complementary methods: 2 based on identification of selection signatures from runs of homozygosity (ROH) islands and one based on the decay of site-specific extended haplotype between populations at SNP sites (Rsb). In total, we identified 34 ROH islands on chromosomes 1, 3, 6, 8, 12-15, 17, 19, 22, and 26 in FAY animals born before genomic selection (between 1980 and 2011) and 30 ROH islands on chromosomes 1-3, 13-17, 22, and 25-26 in FAY animals born after genomic selection introduction (between 2015 and 2020). We additionally detected 22 ΔROH islands on chromosomes 2-3, 11, 13, 14, 16, 18, 20, and 25-26. Finally, a total of 31 Rsb regions on chromosomes 2, 3, 14, 18, 20, and 25 were identified. Based on the results, genomic selection has favored certain alleles and haplotypes on genomic regions related to traits relevant in the FAY breeding program: milk production, fertility, growth, beef production traits, and feed efficiency. Several genes related to these traits (e.g., PLA2G4A, MECR, CHUK, COX15, RICTOR, SHISA9, and SEMA4G) overlapped or partially overlapped the observed selection signature regions. The association of genotypes within these regions and their effects on traits relevant in the FAY breeding program should be studied and genetic regions undergoing selection monitored in the FAY population.

Impact of inbreeding on production, fertility, and health traits in German Holstein dairy cattle utilizing various inbreeding estimators

In dairy cattle production, it is important to understand how inbreeding affects production, fertility, and health traits. However, there is still limited use of genomic information to estimate inbreeding, despite advancements in genotyping technologies. To address this gap, we investigated the effect of inbreeding on German Holstein dairy cattle using both pedigree-based and genomic-based inbreeding estimators. We employed one method based on pedigree information (Fped) together with 6 genomic-based methods, including 3 genome-wide complex trait analysis software estimators (Fhat1, Fhat2, Fhat3), VanRaden's first method (FVR1, with observed allele frequencies, and FVR0.5, when allele frequencies are set to 0.5), and one based on runs of homozygosity (Froh). Data from 24,489 cows with both phenotypes and genotypes were used, with a pedigree including 232,780 animals born between 1970 and 2018. We analyzed the effects of inbreeding depression on production, fertility, and health traits separately, using single-trait linear animal models as well as threshold models to account for the binary nature of the health traits. For the health traits, we transformed solutions from the liability scale to a probability scale for easier interpretation. Our results showed that the mean inbreeding coefficients from all estimators ranged from -0.003 to 0.243, with negative values observed for most genomic-based methods. We found out that a 1% increase in inbreeding caused a depression ranging from 25.94 kg (Fhat1) to 40.62 kg (Fhat3), 1.18 kg (Fhat2) to 1.70 kg (Fhat3), 0.90 kg (Fhat2) to 1.45 kg (Froh and Fhat3), 0.19 (Fped) to 0.34 d (Fhat3) for 305-d milk yield, fat, protein, and calving interval, respectively. The health traits showed very slight gradual changes when inbreeding was increased steadily from 0% to 50%, with digital dermatitis showing a rather contrasting trend to that of mastitis, which increased the more an animal was inbred. Overall, our study highlights the importance of considering both pedigree-based and genomic-based inbreeding estimators when assessing the impact on inbreeding, emphasizing that not all inbreeding is harmful.

Genetic assessment and candidate genes identification for breed-specific characteristics of Qingyuan partridge chicken based on runs of homozygosity

BACKGROUND

Several core breeding and supporting lines of the Qingyuan partridge chicken, a representative local chicken breed in China, have been developed over 20 years. Consequently, its economic traits related to growth and reproduction have been significantly improved by breeding selection and commercial utilization, but some characteristic traits, such as partridge feathers, high meat quality and sufficient flavor, have always been retained. However, effective methods for genetic assessment and functional gene exploration of similar trait groups are lacking. The presence of identical haplotype fragments transmitted from parent to offspring results in runs of homozygosity (ROH), which offer an efficient solution. In this study, genomes of 134 Qingyuan partridge chickens representing two breeding populations and one preserved population were re-sequenced to evaluate the genetic diversity and explore functional genes by analyzing the diversity, distribution, and frequency of ROH.

RESULTS

The results showed a low level of genomic linkage and degree of inbreeding within both the bred and preserved populations, suggesting abundant genetic diversity and an adequate genetic potential of the Qingyuan partridge chicken. Throughout the long-term selection process, 21 genes, including GLI3, ANO5, BLVRA, EFNB2, SLC5A12, and SVIP, associated with breed-specific characteristics were accumulated within three ROH islands, whereas another 21 genes associated with growth traits including IRX1, IRX2, EGFR, TPK1, NOVA1, BDNF and so on were accumulated within five ROH islands.

CONCLUSIONS

These findings provide new insights into the genetic assessment and identification of genes with breed-specific and selective characteristics, offering a solid genetic basis for breeding and protection of Qingyuan partridge chickens.

Unraveling inbreeding patterns and selection signals in Alpine Grey cattle

Inbreeding plays a crucial role in livestock breeding, influencing genetic diversity and phenotypic traits. Genomic data have helped address limitations posed by incomplete pedigrees, providing deeper insights into breed genetic diversity. This study assesses inbreeding levels via pedigree and genomic approaches and analyzes old and recent inbreeding using runs of homozygosity (ROH), and selection signals in Alpine Grey cattle. Pedigree data from 165 575 individuals, analyzed with INBUPGF90 software, computed inbreeding coefficients. Genomic-based coefficients derived from PLINK v1.9. or DetectRUNS R package analyses of 1 180 individuals' genotypes. Common single nucleotide polymorphisms within ROH pinpointed genomic regions, aggregating into "ROH islands" indicative of selection pressure. Overlaps with USCS Genome Browser unveiled gene presence. Moderate correlations (0.20-0.54) existed between pedigree and genomic coefficients, with most genomic estimators having higher (>0.8) correlation values. Inbreeding averaged 0.04 in < 8 Mb ROH segments, and 0.03 in > 16 Mb segments; > 90% of ROHs were < 8 Mb, indicating ancient inbreeding prevalence. Recent inbreeding proved less detrimental than in cosmopolitan breeds. Two major ROH islands on chromosomes 6 and 7 harbored genes linked to immune response, disease resistance (PYURF, HERC3), and fertility (EIF4EBP3, SRA1). This study underscores the need for detailed inbreeding analyses to understand genetic characteristics and historical changes in local breeds like Alpine Grey cattle. Genomic insights, especially from ROH, facilitated overcoming pedigree limitations, illuminating breed genetic diversity. Our findings reveal ancient inbreeding's enduring genetic impact and ROH islands potential for selective sweeps, elucidating traits in Alpine Grey cattle.

Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat

Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.

Genetic Variation and Composition of Two Commercial Estonian Dairy Cattle Breeds Assessed by SNP Data

The aims of this study were to assess the genomic relatedness of Estonian and selected European dairy cattle breeds and to examine the within-breed diversity of two Estonian dairy breeds using genome-wide SNP data. This study was based on a genotyped heifer population of the Estonian Red (ER) and Estonian Holstein (EH) breeds, including about 10% of all female cattle born in 2017-2020 (sample sizes n = 215 and n = 2265, respectively). The within-breed variation study focused on the level of inbreeding using the ROH-based inbreeding coefficient. The genomic relatedness analyses were carried out among two Estonian and nine European breeds from the WIDDE database. Admixture analysis revealed the heterogeneity of ER cattle with a mixed pattern showing several ancestral populations containing a relatively low proportion (1.5-37.0%) of each of the reference populations used. There was a higher FROH in EH (FROH = 0.115) than in ER (FROH = 0.044). Compared to ER, the long ROHs of EH indicated more closely related parents. The paternal origin of the genetic material used in breeding had a low effect on the inbreeding level. However, among EH, the highest genomic inbreeding was estimated in daughters of USA-born sires.

Genome-Wide Analysis of Milk Production Traits and Selection Signatures in Serbian Holstein-Friesian Cattle

To improve the genomic evaluation of milk-related traits in Holstein-Friesian (HF) cattle it is essential to identify the associated candidate genes. Novel SNP-based analyses, such as the genetic mapping of inherited diseases, GWAS, and genomic selection, have led to a new era of research. The aim of this study was to analyze the association of each individual SNP in Serbian HF cattle with milk production traits and inbreeding levels. The SNP 60 K chip Axiom Bovine BovMDv3 was deployed for the genotyping of 334 HF cows. The obtained genomic results, together with the collected phenotypic data, were used for a GWAS. Moreover, the identification of ROH segments was performed and served for inbreeding coefficient evaluation and ROH island detection. Using a GWAS, a polymorphism, rs110619097 (located in the intron of the CTNNA3 gene), was detected to be significantly (p < 0.01) associated with the milk protein concentration in the first lactation (adjusted to 305 days). The average genomic inbreeding value (FROH) was 0.079. ROH islands were discovered in proximity to genes associated with milk production traits and genomic regions under selection pressure for other economically important traits of dairy cattle. The findings of this pilot study provide useful information for a better understanding of the genetic architecture of milk production traits in Serbian HF dairy cows and can be used to improve lactation performances in Serbian HF cattle breeding programs.

Genome-Wide Detection for Runs of Homozygosity in Baoshan Pigs Using Whole Genome Resequencing

Baoshan pigs (BS) are a local breed in Yunnan Province that may face inbreeding owing to its limited population size. To accurately evaluate the inbreeding level of the BS pig population, we used whole-genome resequencing to identify runs of homozygosity (ROH) regions in BS pigs, calculated the inbreeding coefficient based on pedigree and ROH, and screened candidate genes with important economic traits from ROH islands. A total of 22,633,391 SNPS were obtained from the whole genome of BS pigs, and 201 ROHs were detected from 532,450 SNPS after quality control. The number of medium-length ROH (1-5 Mb) was the highest (98.43%), the number of long ROH (>5 Mb) was the lowest (1.57%), and the inbreeding of BS pigs mainly occurred in distant generations. The inbreeding coefficient FROH, calculated based on ROH, was 0.018 ± 0.016, and the FPED, calculated based on the pedigree, was 0.027 ± 0.028, which were positively correlated. Forty ROH islands were identified, containing 507 genes and 891 QTLs. Several genes were associated with growth and development (IGFALS, PTN, DLX5, DKK1, WNT2), meat quality traits (MC3R, ACSM3, ECI1, CD36, ROCK1, CACNA2D1), and reproductive traits (NPW, TSHR, BMP7). This study provides a reference for the protection and utilization of BS pigs.

Dissecting the genomic regions of selection on the X chromosome in different cattle breeds

Mammalian X and Y chromosomes independently evolved from various autosomes approximately 300 million years ago (MYA). To fully understand the relationship between genomic composition and phenotypic diversity arising due to the course of evolution, we have scanned regions of selection signatures on the X chromosome in different cattle breeds. In this study, we have prepared the datasets of 184 individuals of different cattle breeds and explored the complete X chromosome by utilizing four within-population and two between-population methods. There were 23, 25, 30, 17, 17, and 12 outlier regions identified in Tajima's D, CLR, iHS, ROH, FST, and XP-EHH. Bioinformatics analysis showed that these regions harbor important candidate genes like AKAP4 for reproduction in Brown Swiss, MBTS2 for production traits in Brown Swiss and Guernsey, CXCR3 and CITED1 for health traits in Jersey and Nelore, and BMX and CD40LG for regulation of X chromosome inactivation in Nelore and Gir. We identified genes shared among multiple methods, such as TRNAC-GCA and IL1RAPL1, which appeared in Tajima's D, ROH, and iHS analyses. The gene TRNAW-CCA was found in ROH, CLR and iHS analyses. The X chromosome exhibits a distinctive interaction between demographic factors and genetic variations, and these findings may provide new insight into the X-linked selection in different cattle breeds.

Characterization of runs of Homozygosity revealed genomic inbreeding and patterns of selection in indigenous sahiwal cattle

Runs of homozygosity (ROH) are contiguous genomic regions, homozygous across all sites which arise in an individual due to the parents transmitting identical haplotypes to their offspring. The genetic improvement program of Sahiwal cattle after decades of selection needs re-assessment of breeding strategy and population phenomena. Hence, the present study was carried out to optimize input parameters in PLINK for ROH estimates, to explore ROH islands and assessment of pedigree and genome-based inbreeding in Sahiwal cattle. The sliding window approach with parameters standardized to define ROH for the specific population under study was used for the identification of runs. The optimum maximum gap, density, window-snp and window-threshold were 250 Kb, 120 Kb/SNP, 10, 0.05 respectively and ROH patterns were also characterized. ROH islands were defined as the short homozygous genomic regions shared by a large proportion of individuals in a population, containing significantly higher occurrences of ROH than the population specific threshold level. These were identified using the -homozyg-group function of the PLINK v1.9 program. Our results indicated that the Islands of ROH harbor a few candidate genes, ACAD11, RFX4, BANP, UBA5 that are associated with major economic traits. The average FPED (Pedigree based inbreeding coefficient), FROH (Genomic inbreeding coefficient), FHOM (Inbreeding estimated as the ratio of observed and expected homozygous genotypes), FGRM (Inbreeding estimated on genomic relationship method) and FGRM0.5 (Inbreeding estimated from the diagonal of a GRM with allele frequencies near to 0.5) were 0.009, 0.091, 0.035, -0.104 and -0.009, respectively. Our study revealed the optimum parameter setting in PLINK viz. maximal gaps between two SNPs, minimal density of SNPs in a segment (in kb/SNP) and scanning window size to identify ROH segments, which will enable ROH estimation more efficient and comparable across various SNP genotyping-based studies. The result further emphasized the significant role of genomics in unraveling population diversity, selection signatures and inbreeding in the ongoing Sahiwal breed improvement programs.

Effect of genotyping density on the detection of runs of homozygosity and heterozygosity in cattle

Runs of homozygosity (ROHom) are contiguous stretches of homozygous regions of the genome. In contrast, runs of heterozygosity (ROHet) are heterozygosity-rich regions. The detection of these two types of genomic regions (ROHom and ROHet) is influenced by the parameters involved in their identification and the number of available single-nucleotide polymorphisms (SNPs). The present study aimed to test the effect of chip density in detecting ROHom and ROHet in the Italian Simmental cattle breed. A sample of 897 animals were genotyped at low density (50k SNP; 397 individuals), medium density (140k SNP; 348 individuals), or high density (800k SNP; 152 individuals). The number of ROHom and ROHet per animal (nROHom and nROHet, respectively) and their average length were calculated. ROHom or ROHet shared by more than one animal and the number of times a particular SNP was inside a run were also computed (SNPROHom and SNPROHet). As the chip density increased, the nROHom increased, whereas their average length decreased. In contrast, the nROHet decreased and the average length increased as the chip density increased. The most repeated ROHom harbored no genes, whereas in the most repeated ROHet four genes (SNRPN, SNURF, UBE3A, and ATP10A) previously associated with reproductive traits were found. Across the 3 datasets, 31 SNP, located on Bos taurus autosome (BTA) 6, and 37 SNP (located on BTA21) exceeded the 99th percentile in the distribution of the SNPROHom and SNPROHet, respectively. The genomic region on BTA6 mapped the SLIT2, PACRGL, and KCNIP4 genes, whereas 19 and 18 genes were mapped on BTA16 and BTA21, respectively. Interestingly, most of genes found through the ROHet analysis were previously reported to be related to health, reproduction, and fitness traits. The results of the present study confirm that the detection of ROHom is more reliable when the chip density increases, whereas the ROHet trend seems to be the opposite. Genes and quantitative trait loci (QTL) mapped in the highlighted regions confirm that ROHet can be due to balancing selection, thus related to fitness traits, health, and reproduction, whereas ROHom are mainly involved in production traits. The results of the present study strengthened the usefulness of these parameters in analyzing the genomes of livestock and their biological meaning.

Evidence for selective sweeps in the MHC gene repertoire of various cattle breeds

Major Histocompatibility Complex (MHC) genes are among the immune genes that have been extensively studied in vertebrates and are necessary for adaptive immunity. In the immunological response to infectious diseases, they play several significant roles. This research paper provides the selection signatures in the MHC region of the bovine genome as well as how certain genes related to innate immunity are undergoing a positive selective sweep. Here, we investigated signatures of historical selection on MHC genes in 15 different cattle populations and a total of 427 individuals. To identify the selection signatures, we have used three separate summary statistics. The findings show potential selection signatures in cattle from whom we isolated genes involved in the MHC. The most significant regions related to the bovine MHC are BOLA, non-classical MHC class I antigen (BOLA-NC1), Microneme protein 1 (MIC1) , Cluster of Differentiation 244 (CD244), Gap Junction Alpha-5 Protein (GJA5). It will be possible to gain new insight into immune system evolution by understanding the distinctive characteristics of MHC in cattle.

Whole-genome SNP markers reveal runs of homozygosity in indigenous cattle breeds of Pakistan

The runs of homozygosity (ROH) were identified in 14 Pakistani cattle breeds (n = 105) by genotyping with the Illumina 50 K SNP BeadChip. These breeds were categorized into Dairy, Dual, and Draft breeds based on their utility and production performance. We identified a total of 10,936 ROHs which mainly consisted of a high number of shorter segments (1-4 Mb). Dairy group exhibited the highest level of inbreeding (FROH: 0.078 ± 0.028) while the lowest (FROH: 0.002 ± 0.008) was observed in Dual group. In 48 genomic regions identified with a high frequency of ROH, 207 genes were detected in the three breed groups. A substantially higher number of ROH islands detected in dairy breeds indicated the impact of the positive selection pressure over the years. Important candidate genes and QTL were detected in the ROH islands associated with economic traits like milk production, reproduction, meat, carcass, and health traits in dairy cattle.

Distribution of Runs of Homozygosity and Their Relationship with Candidate Genes for Productivity in Kazakh Meat-Wool Sheep Breed

Increasing the fertility of sheep remains one of the crucial issues of modern sheep breeding. The Kazakh meat-wool sheep is an excellent breed with high meat and wool productivity and well adapted to harsh conditions. Nowadays, runs of homozygosity (ROHs) are considered a suitable approach for studying the genetic characteristics of farm animals. The aims of the study were to analyze the distribution of ROHs, describe autozygosity, and detect genomic regions with high ROH islands. In this study, we genotyped a total of 281 Kazakh meat-wool sheep using the Illumina iScan® system (EquipNet, Canton, MA, USA) via Ovine SNP50 BeadChip array. As a results, a total of 15,069 ROHs were found in the three Kazakh meat-wool sheep populations. The mean number of ROH per animal across populations varied from 40.3 (POP1) to 42.2 (POP2) in the category 1+ Mb. Furthermore, the number of ROH per animal in ROH1-2 Mb were much higher than ROH2-4 Mb and ROH8-16 Mb in the three sheep populations. Most of individuals had small number of ROH>16 Mb. The highest and lowest genomic inbreeding coefficient values were observed in POP2 and POP3, respectively. The estimated FROH presented the impact that recent inbreeding has had in all sheep populations. Furthermore, a set of interesting candidate genes (BMP2, BMPR2, BMPRIB, CLOCK, KDM2B, TIAM1, TASP1, MYBPC1, MYOM1, and CACNA2D1), which are related to the productive traits, were found. Collectively, these findings will contribute to the breeding and conservation strategies of the Kazakh meat-wool sheep breed.

Genome-wide landscape of runs of homozygosity and differentiation across Egyptian goat breeds

Understanding the genomic features of livestock is essential for successful breeding programs and conservation. This information is scarce for local goat breeds in Egypt. In the current study, genomic regions with selection signatures were identified as well as runs of homozygosity (ROH), genomic inbreeding coefficients (FROH) and fixation index (FST) were detected in Egyptian Nubian, Damascus, Barki and Boer goat breeds. A total of 46,268 SNP markers and 337 animals were available for the genomic analyses. On average, 145.44, 42.02, 87.90 and 126.95 ROHs were detected per individual in the autosomal genome of the respective breeds. The mean accumulative ROH lengths ranged from 46.5 Mb in Damascus to 360 Mb in Egyptian Nubian. The short ROH segments (< 2 Mb) were most frequent in all breeds, while the longest ROH segments (> 16 Mb) were exclusively found in the Egyptian Nubian. The highest average FROH was observed in Egyptian Nubian (~ 0.12) followed by Boer (~ 0.11), while the lowest FROH was found in Damascus (~ 0.05) and Barki breed (~ 0.03). The estimated mean FST was 0.14 (Egyptian Nubian and Boer), 0.077 (Egyptian Nubian and Barki), 0.075 (Egyptian Nubian and Damascus), 0.071 (Barki and Boer), 0.064 (Damascus and Boer), and 0.015 (Damascus and Barki), for each pair of breeds. Interestingly, multiple SNPs that accounted for high FST values were observed on chromosome 6 in regions harboring ALPK1 and KCNIP4. Genomic regions overlapping both FST and ROH harbor genes related to immunity (IL4R, PHF23, GABARAP, GPS2, and CD68), reproduction (SPATA2L, TNFSF12, TMEM95, and RNF17), embryonic development (TCF25 and SOX15) and adaptation (MC1R, KDR, and KIT), suggesting potential genetic adaptations to local environmental conditions. Our results contribute to the understanding of the genetic architecture of different goat breeds and may provide valuable information for effective preservation and breeding programs of local goat breeds in Egypt.

Identification of homozygosity-rich regions in the Holstein genome

In this study, 371 Holstein cows from six herds and 26 Holstein bulls, which were used in these herds, were genotyped by the Illumina BovineSNP50 array. For runs of homozygosity (ROH) identification, consecutive and sliding runs were performed by the detectRUNS and Plink software. The missing calls did not significantly affect the ROH data. The mean number of ROH identified by consecutive runs was 95.4 ± 2.7, and that by sliding runs was 86.0 ± 2.6 in cows, while this number for Holstein bulls was lower 58.9 ± 1.9. The length of the ROH segments varied from 1 Mb to over 16 Mb, with the largest number of ROH having a length of 1-2 Mb. Of the 29 chromosomes, BTA 14, BTA 16, and BTA 7 were the most covered by ROH. The mean coefficient of inbreeding across the herds was 0.111 ± 0.003 and 0.104 ± 0.004 based on consecutive and sliding runs, respectively, and 0.078 ± 0.005 for bulls based on consecutive runs. These values do not exceed those for Holstein cattle in North America. The results of this study confirmed the more accurate identification of ROH by consecutive runs, and also that the number of allowed heterozygous SNPs may have a significant effect on ROH data.

Evaluation of Linear Programming and Optimal Contribution Selection Approaches for Long-Term Selection on Beef Cattle Breeding

The optimized selection method can maximize the genetic gain in offspring under the premise of controlling the inbreeding level of the population. At present, genetic gain has been largely improved by using genomic selection in multiple farm animals. However, the design of the optimal selection method and assessment of its effects during long-term selection in beef cattle breeding are yet to be fully explored. In this study, a simulated beef cattle population was constructed, and 15 generations of simulated breeding were carried out using the linear programming breeding strategy (LP) and optimal contribution selection strategy (OCS), respectively. The truncation selection strategy (TS-I and TS-II) was used as the control. During the breeding process, genetic parameters including genetic gain, average kinship coefficient, QTL effect variance, and average observed heterozygosity were calculated and compared across generations. Our results showed that the LP method can significantly improve the genetic gain in the population, especially the genetic performance of the traits with high heritability and the traits with high weight in the breeding process, but the inbreeding level of the population is higher under LP strategy. Although the genetic gain in the population under the OCS strategy is lower than the TS-II strategy, this method can effectively control the inbreeding level of the population. Our findings also suggest that the LP and OCS method can be used as an effective means to improve genetic gain, while the OCS method is a more ideal method to obtain sustainable genetic gain during long-term selection.

Genetic diversity, population structure, and genome-wide association analysis of ginkgo cultivars

Ginkgo biloba is an economically valuable tree worldwide. The species has nearly become extinct during the Quaternary, which has likely resulted in reduction of its genetic variability. The genetic variability is now conserved in few natural populations in China and a number of cultivars that are, however, derived from a few ancient trees, helping the species survive in China through medieval times. Despite the recent interest in ginkgo, however, detailed knowledge of its genetic diversity, conserved in cultivated trees and cultivars, has remained poor. This limits efficient conservation of its diversity as well as efficient use of the existing germplasm resources. Here we performed genotyping-by-sequencing (GBS) on 102 cultivated germplasms of ginkgo collected to explore their genetic structure, kinship, and inbreeding prediction. For the first time in ginkgo, a genome-wide association analysis study (GWAS) was used to attempt gene mapping of seed traits. The results showed that most of the germplasms did not show any obvious genetic relationship. The size of the ginkgo germplasm population expanded significantly around 1500 years ago during the Sui and Tang dynasties. Classification of seed cultivars based on a phylogenetic perspective does not support the current classification criteria based on phenotype. Twenty-four candidate genes were localized after performing GWAS on the seed traits. Overall, this study reveals the genetic basis of ginkgo seed traits and provides insights into its cultivation history. These findings will facilitate the conservation and utilization of the domesticated germplasms of this living fossil plant.

Runs of homozygosity and cross-generational inbreeding of Iranian fat-tailed sheep

The Lori-Bakhtiari fat-tailed sheep is one of the most important heavyweight native breeds of Iran. The breed is robust and well-adapted to semi-arid regions and an important resource for smallholder farms. An established nucleus-based breeding scheme is used to improve their production traits but there is an indication of inbreeding depression and loss of genetic diversity due to selection. Here, we estimated the inbreeding levels and the distribution of runs of homozygosity (ROH) islands in 122 multi-generational female Lori-Bakhtiari from different half-sib families selected from a breeding station that were genotyped on the 50k array. A total of 2404 ROH islands were identified. On average, there were 19.70 ± 1.4 ROH per individual ranging between 6 and 41. The mean length of the ROH was 4.1 ± 0.14 Mb. There were 1999 short ROH of length 1-6 Mb and another 300 in the 6-12 Mb range. Additionally long ROH indicative of inbreeding were found in the ranges of 12-24 Mb (95) and 24-48 Mb (10). The average inbreeding coefficient (FROH) was 0.031 ± 0.003 with estimates varying from 0.006 to 0.083. Across generations, FROH increased from 0.019 ± 0.012 to 0.036 ± 0.007. Signatures of selection were identified on chromosomes 2, 6, and 10, encompassing 55 genes and 23 QTL associated with production traits. Inbreeding coefficients are currently within acceptable levels but across generations, inbreeding is increasing due to selection. The breeding program needs to actively monitor future inbreeding rates and ensure that the breed maintains or improves on its current levels of environmental adaptation.

Characterization of the genetic pool of the Canadienne dairy cattle breed

BACKGROUND

Canadienne cattle are the oldest breed of dairy cattle in North America. The Canadienne breed originates from cattle that were brought to America by the mid-seventeenth century French settlers. The herd book was established in 1886 and the current breed characteristics include dark coat color, small size compared to the modern Holstein breed, and overall rusticity shaped by the harsh environmental conditions that were prevalent during the settlement of North America. The Canadienne breed is an invaluable genetic resource due to its high resilience, longevity and fertility. However, it is heavily threatened with a current herd limited to an estimated 1200 registered animals, of which less than 300 are fullblood. To date, no effort has been made to document the genetic pool of this heritage breed in order to preserve it.

RESULTS

In this project, we used genomic data, which allow a precise description of the genetic makeup of a population, to provide valuable information on the genetic diversity of this heritage breed and suggest management options for its long-term viability. Using a panel that includes 640,000 single nucleotide polymorphisms (SNPs), we genotyped 190 animals grouped into six purity ranges. Unsupervised clustering analyses revealed three genetically distinct groups among those with the higher levels of purity. The observed heterozygosity was higher than expected even in the 100% purebreds. Comparison with Holstein genotypes showed significantly shorter runs of homozygosity for the Canadienne breed, which was unexpected due to the high inbreeding value calculated from pedigree data.

CONCLUSIONS

Overall, our data indicate that the fullblood gene pool of the Canadienne breed is more diversified than expected and that bloodline management could promote breed sustainability. In its current state, the Canadienne is not a dead-end breed but remains highly vulnerable due to its small population size.

Mating allocations in Holstein combining genomic information and linear programming optimization at the herd level

In this study, we explored mating allocation in Holstein using genomic information for 24,333 Holstein females born in Denmark, Finland, and Sweden. We used 2 data sets of bulls: the top 50 genotyped bulls and the top 25 polled genotyped bulls on the Nordic total merit scale. We used linear programming to optimize economic scores within each herd, considering genetic level, genetic relationship, semen cost, the economic impact of genetic defects, polledness, and β-casein. We found that it was possible to reduce genetic relationships and eliminate expression of genetic defects with minimal effect on the genetic level in total merit index. Compared with maximizing only Nordic total merit index, the relative frequency of polled offspring increased from 13.5 to 22.5%, and that of offspring homozygous for β-casein (A2A2) from 66.7 to 75.0% in one generation, without any substantial negative impact on other comparison criteria. Using only semen from polled bulls, which might become necessary if dehorning is banned, considerably reduced the genetic level. We also found that animals carrying the polled allele were less likely to be homozygous for β-casein (A2A2) and more likely to be carriers of the genetic defect HH1. Hence, adding economic value to a monogenic trait in the economic score used for mating allocation sometimes negatively affected another monogenetic trait. We recommend that the comparison criteria used in this study be monitored in a modern genomic mating program.

Estimates of genomic inbreeding and identification of candidate regions in Beijing-You chicken populations

Runs of homozygosity (ROHs) has become an effective method for analysing inbreeding in livestock populations. Moreover, ROHs is well-suited to detect signatures of selection via ROH islands. This study aimed to investigate the occurrence and distribution of ROHs, compare the genomic inbreeding coefficients and identify the genomic regions with high ROH frequencies in different Beijing-You chicken (BY) populations, including a random conservation population (BY_R), a pedigree conservation population (BY_P), and a commercial population obtained from the market (BY_C). Among them, BY_R in 2010 and 2019 were BY_R1 and BY_R2 respectively. A total of 27 916 ROHs were identified. The average number of ROHs per individual across the three BY populations ranged from 213 (BY_P) to 161 (BY_C), and the average length of ROHs ranged from 0.432 Mb (BY_R2) to 0.451 Mb (BY_P). The highest inbreeding coefficient calculated based on ROHs (F_ROH ) was 0.1 in BY_P, whereas the lowest F_ROH was 0.0743 in BY_C. In addition, the inbreeding coefficient of BY_R2 (F_ROH  = 0.0798) was higher than that of BY_R1 (F_ROH  = 0.0579). Furthermore, the highest proportion of long ROH fragments (>4 Mb) was observed in BY_P and BY_C. This study showed the top 10 ROH islands of each population, and these ROH islands harboured 53 genes, some of which were related to limb development, body size and immune response. These findings contribute to the understanding of genetic diversity and population demography, and might help improve breeding and conservation strategies for BY populations.

Pedigree and genome-based patterns of homozygosity in the South African Ayrshire, Holstein, and Jersey breeds

The erosion of genetic diversity limits long-term genetic gain and impedes the sustainability of livestock production. In the South African (SA) dairy industry, the major commercial dairy breeds have been applying estimated breeding values (EBVs) and/or have been participating in Multiple Across Country Evaluations (MACE). The transition to genomic estimated breeding values (GEBVs) in selection strategies requires monitoring of the genetic diversity and inbreeding of current genotyped animals, especially considering the comparatively small population sizes of global dairy breeds in SA. This study aimed to perform a homozygosity-based evaluation of the SA Ayrshire (AYR), Holstein (HST), and Jersey (JER) dairy cattle breeds. Three sources of information, namely 1) single nucleotide polymorphism (SNP) genotypes (3,199 animals genotyped for 35,572 SNPs) 2) pedigree records (7,885 AYR; 28,391 HST; 18,755 JER), and 3) identified runs of homozygosity (ROH) segments were used to quantify inbreeding related parameters. The lowest pedigree completeness was for the HST population reducing from a value of 0.990 to 0.186 for generation depths of one to six. Across all breeds, 46.7% of the detected ROH were between 4 megabase pairs (Mb) and 8 Mb in length. Two conserved homozygous haplotypes were identified in more than 70% of the JER population on Bos taurus autosome (BTA) 7. The JER breed displayed the highest level of inbreeding across all inbreeding coefficients. The mean (± standard deviation) pedigree-based inbreeding coefficient (FPED) ranged from 0.051 (±0.020) for AYR to 0.062 (±0.027) for JER, whereas SNP-based inbreeding coefficients (FSNP) ranged from 0.020 (HST) to 0.190 (JER) and ROH-based inbreeding coefficients, considering all ROH segment coverage (FROH), ranged from 0.053 (AYR) to 0.085 (JER). Within-breed Spearman correlations between pedigree-based and genome-based estimates ranged from weak (AYR: 0.132 between FPED and FROH calculated for ROH <4Mb in size) to moderate (HST: 0.584 between FPED and FSNP). Correlations strengthened between FPED and FROH as the ROH length category was considered lengthened, suggesting a dependency on breed-specific pedigree depth. The genomic homozygosity-based parameters studied proved useful in investigating the current inbreeding status of reference populations genotyped to implement genomic selection in the three most prominent South African dairy cattle breeds.

Estimating inbreeding rate and effective population size in the Finnish Ayrshire population in the era of genomic selection

Genomic selection has been applied in dairy cattle breeding over the last decade. Using genomic information may speed up genetic gain as breeding values can be predicted reasonably accurately directly after birth. However, genetic diversity may decrease if the inbreeding rate per generation increases and the effective population size decreases. Despite many positive qualities of the Finnish Ayrshire, for example, high average protein yield and fertility, over time the breed has lost its place as the most common dairy breed in Finland. Thus, maintaining the genetic variability of the breed is becoming more important. The aim of our research was to estimate the impact of genomic selection on inbreeding rate and effective population size using both pedigree and genomic data. The genomic data included 46,914 imputed single nucleotide polymorphism (SNP) variants from 75,038 individuals, and the pedigree data included 2,770,025 individuals. All animals in the data were born between 2000 and 2020. Genomic inbreeding coefficients were estimated as the proportion of SNPs in runs of homozygosity (ROH) out of the total number of SNPs. The inbreeding rate was estimated by regressing the mean genomic inbreeding coefficients on birth years. Effective population size was then estimated based on the inbreeding rate. Additionally, effective population size was estimated from the mean increase in individual inbreeding using pedigree data. Introduction of genomic selection was assumed to have taken place gradually; years 2012-2014 were treated as a transition period from the traditional phenotype-based breeding value estimation to genomic-based estimation. The median length of the identified homozygous segments was 5.5 Mbp, and a slight increase in the proportion of segments over 10 Mbp was observed after 2010. The inbreeding rate decreased from 2000 to 2011 and subsequently increased slightly. The pedigree- and genomic-based estimates of inbreeding rate were similar to each other. The estimates of effective population size based on the regression method were very sensitive to the number of years considered; thus, the estimates were not very reliable. The effective population size estimated from the mean increase in individual inbreeding reached its highest value of 160 in 2011 and decreased to 150 after that. In addition, the generation interval in the sire path has decreased from 5.5 years to 3.5 years after genomic selection was implemented. Based on our results, after the implementation of genomic selection, the proportion of long ROH stretches has increased, the generation interval in the sire path has decreased, the inbreeding rate has increased and the effective population size has decreased. However, the effective population size is still at a good level, allowing for an efficient selection scheme in the Finnish Ayrshire breed.

The coefficients of inbreeding revealed by ROH study among inbred individuals belonging to each type of the first cousin marriage: A preliminary report from North India

BACKGROUND

Genome-wide runs of homozygosity (ROH) are appropriate to estimate genomic inbreeding, determine population history, unravel the genetic architecture of complex traits and disorders.

OBJECTIVE

The study sought to investigate and compare the actual proportion of homozygosity or autozygosity in the genomes of progeny of four subtypes of first cousin mating in humans, using both pedigree and genomic measures for autosomes and sex chromosomes.

METHODS

For this purpose, Illumina Global Screening Array-24 v1.0 BeadChip followed by cyto-ROH analysis through Illumina Genome Studio was used to characterise the homozygosity in five participants from North Indian state (Uttar Pradesh). PLINK v.1.9 software was used to estimate the genomic inbreeding coefficients viz. ROH-based inbreeding estimate (F_ROH) and homozygous loci-based inbreeding estimate (F_HOM).

RESULTS

A total of 133 ROH segments were detected with maximum number and genomic coverage in Matrilateral Parallel (MP) type and minimum in outbred individual. ROH pattern revealed that MP type has a higher degree of homozygosity than other subtypes. The comparison of F_ROH, F_HOM, and pedigree-based inbreeding estimate (F_PED) showed some difference in theoretical and realised proportion of homozygosity for sex-chromosomal loci but not for autosome for each type of consanguinity.

CONCLUSIONS

This is the very first study to compare and estimate the pattern of homozygosity among the kindreds of first cousin unions. However, a greater number of individuals from each type of marriage is required for statistical inference of no difference between theoretical and realized homozygosity among different degrees of inbreeding prevalent in humans worldwide.

Weighted kernels improve multi-environment genomic prediction

Crucial to variety improvement programs is the reliable and accurate prediction of genotype's performance across environments. However, due to the impactful presence of genotype by environment (G×E) interaction that dictates how changes in expression and function of genes influence target traits in different environments, prediction performance of genomic selection (GS) using single-environment models often falls short. Furthermore, despite the successes of genome-wide association studies (GWAS), the genetic insights derived from genome-to-phenome mapping have not yet been incorporated in predictive analytics, making GS models that use Gaussian kernel primarily an estimator of genomic similarity, instead of the underlying genetics characteristics of the populations. Here, we developed a GS framework that, in addition to capturing the overall genomic relationship, can capitalize on the signal of genetic associations of the phenotypic variation as well as the genetic characteristics of the populations. The capacity of predicting the performance of populations across environments was demonstrated by an overall gain in predictability up to 31% for the winter wheat DH population. Compared to Gaussian kernels, we showed that our multi-environment weighted kernels could better leverage the significance of genetic associations and yielded a marked improvement of 4-33% in prediction accuracy for half-sib families. Furthermore, the flexibility incorporated in our Bayesian implementation provides the generalizable capacity required for predicting multiple highly genetic heterogeneous populations across environments, allowing reliable GS for genetic improvement programs that have no access to genetically uniform material.

Analysis of genetic diversity and selection characteristics using the whole genome sequencing data of five buffaloes, including Xilin buffalo, in Guangxi, China

Buffalo is an economically important livestock that renders useful services to manhood in terms of meat, milk, leather, and draught. The Xilin buffalo is among the native buffalo breeds of China. In the present study, the genetic architecture and selection signature signals of Xilin buffalo have been explored. Correlation analysis of the population structure of Xilin buffalo was conducted by constructing NJ tree, PCA, ADMIXTURE and other methods. A total of twenty-five (n = 25) Xilin buffalo whole genome data and data of forty-six (n = 46) buffaloes published data were used. The population structure analysis showed that the Xilin buffalo belong to the Middle-Lower Yangtze. The genome diversity of Xilin buffalo was relatively high. The CLR, π ratio, F _ST, and XP-EHH were used to detect the candidate genes characteristics of positive selection in Xilin buffalo. Among the identified genes, most of the enriched signal pathways were related to the nervous system and metabolism. The mainly reported genes were related to the nervous system (GRM5, GRIK2, GRIA4), reproductive genes (CSNK1G2, KCNIP4), and lactation (TP63). The results of this study are of great significance for understanding the molecular basis of phenotypic variation of related traits of Xilin buffalo. We provide a comprehensive overview of sequence variations in Xilin buffalo genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Xilin buffalo and help in future breeding and conservation programs of this important livestock genetic resource.

Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing

German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (F_ST), phylogenetic, and admixture analyses were performed between DSN and 68 other breeds from the 1000 Bull Genomes Project. Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. Inbreeding was measured as excess of homozygosity (F_Hom) and genomic inbreeding (F_RoH) through runs of homozygosity (RoHs). Region-wide F_ST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. DSN showed a close genetic relationship with breeds from the Netherlands, Belgium, Northern Germany, and Scandinavia, such as Dutch Friesian Red, Dutch Improved Red, Belgian Red White Campine, Red White Dual Purpose, Modern Angler, Modern Danish Red, and Holstein. The nucleotide diversity in DSN (0.151%) was higher than in Holstein (0.147%) and other breeds, e.g., Norwegian Red (0.149%), Red White Dual Purpose (0.149%), Swedish Red (0.149%), Hereford (0.145%), Angus (0.143%), and Jersey (0.136%). The F_Hom and F_RoH values in DSN were among the lowest. Regions with high F_ST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. The selection signatures between DSN and Holstein provide evidence of regions responsible for the dual-purpose properties of DSN and the milk type of Holstein. Despite the small population size, DSN has a high level of diversity and low inbreeding. F_ST supports its relatedness to breeds from the same geographic origin and provides information on potential gene pools that could be used to maintain diversity in DSN.

The role of inbreeding depression on productive performance in the Italian Holstein breed

Inbreeding depression has become an urgent issue in cosmopolitan breeds where the massive genetic progress achieved in the latest generations is counterbalanced by a dramatic loss of genetic diversity causing increased health issues. Thus, the aim of this study was to estimate inbreeding depression on productive traits in Holstein dairy cattle. More precisely, we aimed to i) determine the level of inbreeding in 27,735 Italian Holstein dairy cows using pedigree and genotype data, ii) quantify the effect of inbreeding on 305-d in milk yield (MY; kg), fat yield (FY; kg), and protein yield (PY; kg) based on different statistical approaches, iii) determine if recent inbreeding has a more harmful impact than ancestral ones, and iv) quantify chromosomal homozygosity effect on productive traits. Quality control was performed on the autosomal chromosomes resulting in a final dataset of 84,443 single nucleotide polymorphisms. Four statistical models were used to evaluate the presence of inbreeding depression, which included linear regression analysis and division of FPED and FROH into percentile classes. Moreover, FROH was partitioned into i) length classes to assess the role of recent and ancestral inbreeding and ii) chromosome-specific contributions (FROH-CHR). Results evidenced that inbreeding negatively impacted the productive performance of Italian Holstein Friesian cows. However, differences between the estimated FPED and FROH coefficients resulted in different estimates of inbreeding depression. For instance, a 1% increase in FPED and FROH was associated with a decrease in MY of about 44 and 61 kg (P < 0.01). Further, when considering the extreme inbreeding percentile classes moving from the 5th lowest to the 95th highest, there was a reduction of -263 kg and -561 kg per lactation for FPED and FROH. Increased inbreeding, estimated by FPED and FROH, had also a negative effect on PY and FY, either fit as a regressor or percentile classes. When evaluating the impact of inbreeding based on runs of homozygosity (ROH) length classes, longer ROH (over 8 Mb) had a negative effect in all traits, indicating that recent inbreeding might be more harmful than the ancestral one. Finally, results within chromosome homozygosity highlighted specific chromosomes with a more deleterious effect on productive traits.

A comparison of marker-based estimators of inbreeding and inbreeding depression

BACKGROUND

The availability of genome-wide marker data allows estimation of inbreeding coefficients (F, the probability of identity-by-descent, IBD) and, in turn, estimation of the rate of inbreeding depression (ΔID). We investigated, by computer simulations, the accuracy of the most popular estimators of inbreeding based on molecular markers when computing F and ΔID in populations under random mating, equalization of parental contributions, and artificially selected populations. We assessed estimators described by Li and Horvitz (F_LH1 and F_LH2), VanRaden (F_VR1 and F_VR2), Yang and colleagues (F_YA1 and F_YA2), marker homozygosity (F_HOM), runs of homozygosity (F_ROH) and estimates based on pedigree (F_PED) in comparison with estimates obtained from IBD measures (F_IBD).

RESULTS

If the allele frequencies of a base population taken as a reference for the computation of inbreeding are known, all estimators based on marker allele frequencies are highly correlated with F_IBD and provide accurate estimates of the mean ΔID. If base population allele frequencies are unknown and current frequencies are used in the estimations, the largest correlation with F_IBD is generally obtained by F_LH1 and the best estimator of ΔID is F_YA2. The estimators F_VR2 and F_LH2 have the poorest performance in most scenarios. The assumption that base population allele frequencies are equal to 0.5 results in very biased estimates of the average inbreeding coefficient but they are highly correlated with F_IBD and give relatively good estimates of ΔID. Estimates obtained directly from marker homozygosity (F_HOM) substantially overestimated ΔID. Estimates based on runs of homozygosity (F_ROH) provide accurate estimates of inbreeding and ΔID. Finally, estimates based on pedigree (F_PED) show a lower correlation with F_IBD than molecular estimators but provide rather accurate estimates of ΔID. An analysis of data from a pig population supports the main findings of the simulations.

CONCLUSIONS

When base population allele frequencies are known, all marker-allele frequency-based estimators of inbreeding coefficients generally show a high correlation with F_IBD and provide good estimates of ΔID. When base population allele frequencies are unknown, F_LH1 is the marker frequency-based estimator that is most correlated with F_IBD, and F_YA2 provides the most accurate estimates of ΔID. Estimates from F_ROH are also very precise in most scenarios. The estimators F_VR2 and F_LH2 have the poorest performances.