Fine mapping of genomic regions associated with female fertility in Nellore beef cattle based on sequence variants from segregating sires

Abstract Background Impaired fertility in cattle limits the efficiency of livestock production systems. Unraveling the genetic architecture of fertility traits would facilitate their improvement by selection. In this study, we characterized SNP chip haplotypes at QTL blocks then used whole-genome sequencing to fine map genomic regions associated with reproduction in a population of Nellore (Bos indicus) heifers. Methods The dataset comprised of 1337 heifers genotyped using a GeneSeek® Genomic Profiler panel (74677 SNPs), representing the daughters from 78 sires. After performing marker quality control, 64800 SNPs were retained. Haplotypes carried by each sire at six previously identified QTL on BTAs 5, 14 and 18 for heifer pregnancy and BTAs 8, 11 and 22 for antral follicle count were constructed using findhap software. The significance of the contrasts between the effects of every two paternally-inherited haplotype alleles were used to identify sires that were heterozygous at each QTL. Whole-genome sequencing data localized to the haplotypes from six sires and 20 other ancestors were used to identify sequence variants that were concordant with the haplotype contrasts. Enrichment analyses were applied to these variants using KEGG and MeSH libraries. Results A total of six (BTA 5), six (BTA 14) and five (BTA 18) sires were heterozygous for heifer pregnancy QTL whereas six (BTA 8), fourteen (BTA 11), and five (BTA 22) sires were heterozygous for number of antral follicles’ QTL. Due to inadequate representation of many haplotype alleles in the sequenced animals, fine mapping analysis could only be reliably performed for the QTL on BTA 5 and 14, which had 641 and 3733 concordant candidate sequence variants, respectively. The KEGG “Circadian rhythm” and “Neurotrophin signaling pathway” were significantly associated with the genes in the QTL on BTA 5 whereas 32 MeSH terms were associated with the QTL on BTA 14. Among the concordant sequence variants, 0.2% and 0.3% were classified as missense variants for BTAs 5 and 14, respectively, highlighting the genes MTERF2, RTMB, ENSBTAG00000037306 (miRNA), ENSBTAG00000040351, PRKDC, and RGS20. The potential causal mutations found in the present study were associated with biological processes such as oocyte maturation, embryo development, placenta development and response to reproductive hormones. Conclusions The identification of heterozygous sires by positionally phasing SNP chip data and contrasting haplotype effects for previously detected QTL can be used for fine mapping to identify potential causal mutations and candidate genes. Genomic variants on genes MTERF2, RTBC, miRNA ENSBTAG00000037306, ENSBTAG00000040351, PRKDC, and RGS20, which are known to have influence on reproductive biological processes, were detected.

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

BMC Genomics ◽

10.1186/s12864-020-07340-0 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Xiaoting Xia ◽

Shunjin Zhang ◽

Huaju Zhang ◽

Zijing Zhang ◽

Ningbo Chen ◽

...

Keyword(s):

Population Structure ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Genomic Variation ◽

Genomic Diversity ◽

System Response ◽

Whole Genome ◽

Population Structure Analysis ◽

Native Cattle ◽

Genomic Regions

Abstract Background Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cattle breed, is reported to have originated from crossbreeding between taurine and indicine cattle; their history as a draft and meat animal dates back at least 30 years. Using whole-genome sequencing (WGS) data of 30 animals from the core breeding farm, we investigated the genetic diversity, population structure and genomic regions under selection of Jiaxian Red cattle. Furthermore, we used 131 published genomes of world-wide cattle to characterize the genomic variation of Jiaxian Red cattle. Results The population structure analysis revealed that Jiaxian Red cattle harboured the ancestry with East Asian taurine (0.493), Chinese indicine (0.379), European taurine (0.095) and Indian indicine (0.033). Three methods (nucleotide diversity, linkage disequilibrium decay and runs of homozygosity) implied the relatively high genomic diversity in Jiaxian Red cattle. We used θπ, CLR, FST and XP-EHH methods to look for the candidate signatures of positive selection in Jiaxian Red cattle. A total number of 171 (θπ and CLR) and 17 (FST and XP-EHH) shared genes were identified using different detection strategies. Functional annotation analysis revealed that these genes are potentially responsible for growth and feed efficiency (CCSER1), meat quality traits (ROCK2, PPP1R12A, CYB5R4, EYA3, PHACTR1), fertility (RFX4, SRD5A2) and immune system response (SLAMF1, CD84 and SLAMF6). Conclusion We provide a comprehensive overview of sequence variations in Jiaxian Red cattle genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Jiaxian Red cattle. We observed a high level of genomic diversity and low inbreeding in Jiaxian Red cattle. These results provide a basis for further resource protection and breeding improvement of this breed.

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QTG-Seq Accelerates QTL Fine Mapping through QTL Partitioning and Whole-Genome Sequencing of Bulked Segregant Samples

Molecular Plant ◽

10.1016/j.molp.2018.12.018 ◽

2019 ◽

Vol 12 (3) ◽

pp. 426-437 ◽

Cited By ~ 14

Author(s):

Hongwei Zhang ◽

Xi Wang ◽

Qingchun Pan ◽

Pei Li ◽

Yunjun Liu ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Fine Mapping ◽

Whole Genome ◽

Qtl Fine Mapping

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Detection of quantitative trait loci and putative causal variants affecting somatic cell score in dairy sheep by using a 50K SNP chip and whole-genome sequencing

Journal of Dairy Science ◽

10.3168/jds.2018-14736 ◽

2018 ◽

Vol 101 (10) ◽

pp. 9072-9088 ◽

Cited By ~ 4

Author(s):

B. Gutiérrez-Gil ◽

C. Esteban-Blanco ◽

A. Suarez-Vega ◽

J.J. Arranz

Keyword(s):

Quantitative Trait Loci ◽

Somatic Cell ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Quantitative Trait ◽

Somatic Cell Score ◽

Whole Genome ◽

Dairy Sheep ◽

Snp Chip ◽

Causal Variants

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

10.1101/703439 ◽

2019 ◽

Cited By ~ 1

Author(s):

Meenu Bhati ◽

Naveen Kumar Kadri ◽

Danang Crysnanto ◽

Hubert Pausch

Keyword(s):

Whole Genome Sequencing ◽

Meat Quality ◽

Genome Sequencing ◽

Genomic Diversity ◽

Whole Genome ◽

Runs Of Homozygosity ◽

Cattle Breeds ◽

Signatures Of Selection ◽

Genomic Inbreeding ◽

Genomic Regions

AbstractBackgroundAutochthonous cattle breeds represent an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution.ResultsWe annotated 15,722,811 million SNPs and 1,580,878 million Indels including 10,738 and 2,763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10-3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding quantified using runs of homozygosity (ROH) was relatively low (FROH=0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in more recent generations of OB cattle (FROH=0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus.ConclusionsWe provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation and adoption of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

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Whole Genome Sequencing Assembly and Annotation of Halobacillus Trueperi S61 Isolated From the Qarhan Salt Lake

10.21203/rs.3.rs-1188620/v1 ◽

2022 ◽

Author(s):

Wei Li ◽

Shuo Shen ◽

Jian Wang

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Protein Function ◽

Salt Lake ◽

Gc Content ◽

Whole Genome ◽

Biological Processes ◽

Circular Chromosome ◽

Advanced Analysis ◽

Qarhan Salt Lake

Abstract Background: Halophilic microbial as prospective resources of biotechnology due to the advantages of flexible survivability. Qarhan Salt Lake is the second largest Salt Lake in the world which contains rich-unique extremophiles and deserved in-depth exploration. Results: Present study first time isolated novel strain Halobacillus trueperi S61 from Qarhan Salt Lake and performed whole-genome sequencing through combined third-generation PacBio and second-generation Illumina technology. The whole genome of Halobacillus trueperi S61 identified 57549 total reads and consists a complete circular chromosome of 4047887 bp with 43.86% GC content without gaps. Total number of 139 non-coding RNA (included 86 tRNA, 30 rRNA and 23 sRNA), 16 gene islands with 260275 bp and two prophages (with 82682 length) were predicted. In addition, the whole genome of Halobacillus trueperi S61 summarized basic annotation for 3982 protein-coding genes, 3980, 3667, 2998 and 2303 unigenes were annotated with Nr, Swissport, KOG and KEGG database. Combined with advanced analysis, 561 carbohydrate enzymes and 4416 pathogen host interactions related genes were identified. The protein function of Halobacillus trueperi S61 was mainly focus on biological processes, and the protein function was mainly distributed in gene transcription and amino acids, and carbohydrates metabolism. Conclusions: The complete whole genome sequence assembly and annotation of novel strain Halobacillus trueperi S61 isolated from Qarhan Salt Lake mainly focus on protein biological processes and antibiotic resistance, provides a potential resource for biotechnology.

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Genomic Diversity of the Ostreid Herpesvirus Type 1 Across Time and Location and Among Host Species

Frontiers in Microbiology ◽

10.3389/fmicb.2021.711377 ◽

2021 ◽

Vol 12 ◽

Author(s):

Benjamin Morga ◽

Maude Jacquot ◽

Camille Pelletier ◽

Germain Chevignon ◽

Lionel Dégremont ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Phylogenetic Analyses ◽

Genomic Diversity ◽

Microbial Pathogens ◽

Whole Genome ◽

Site Mutation ◽

Herpesvirus Type ◽

New Variant ◽

Genomic Regions

The mechanisms underlying virus emergence are rarely well understood, making the appearance of outbreaks largely unpredictable. This is particularly true for pathogens with low per-site mutation rates, such as DNA viruses, that do not exhibit a large amount of evolutionary change among genetic sequences sampled at different time points. However, whole-genome sequencing can reveal the accumulation of novel genetic variation between samples, promising to render most, if not all, microbial pathogens measurably evolving and suitable for analytical techniques derived from population genetic theory. Here, we aim to assess the measurability of evolution on epidemiological time scales of the Ostreid herpesvirus 1 (OsHV-1), a double stranded DNA virus of which a new variant, OsHV-1 μVar, emerged in France in 2008, spreading across Europe and causing dramatic economic and ecological damage. We performed phylogenetic analyses of heterochronous (n = 21) OsHV-1 genomes sampled worldwide. Results show sufficient temporal signal in the viral sequences to proceed with phylogenetic molecular clock analyses and they indicate that the genetic diversity seen in these OsHV-1 isolates has arisen within the past three decades. OsHV-1 samples from France and New Zealand did not cluster together suggesting a spatial structuration of the viral populations. The genome-wide study of simple and complex polymorphisms shows that specific genomic regions are deleted in several isolates or accumulate a high number of substitutions. These contrasting and non-random patterns of polymorphism suggest that some genomic regions are affected by strong selective pressures. Interestingly, we also found variant genotypes within all infected individuals. Altogether, these results provide baseline evidence that whole genome sequencing could be used to study population dynamic processes of OsHV-1, and more broadly herpesviruses.

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Whole genome sequencing of canids reveals genomic regions under selection and variants influencing morphology

Nature Communications ◽

10.1038/s41467-019-09373-w ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 41

Author(s):

Jocelyn Plassais ◽

Jaemin Kim ◽

Brian W. Davis ◽

Danielle M. Karyadi ◽

Andrew N. Hogan ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Genomic Regions

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Sequence variants from whole genome sequencing a large group of Icelanders

Scientific Data ◽

10.1038/sdata.2015.11 ◽

2015 ◽

Vol 2 (1) ◽

Cited By ~ 36

Author(s):

Daniel F Gudbjartsson ◽

Patrick Sulem ◽

Hannes Helgason ◽

Arnaldur Gylfason ◽

Sigurjon A Gudjonsson ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Sequence Variants ◽

Whole Genome ◽

Large Group

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

BMC Genomics ◽

10.1186/s12864-020-6446-y ◽

2020 ◽

Vol 21 (1) ◽

Cited By ~ 8

Author(s):

Meenu Bhati ◽

Naveen Kumar Kadri ◽

Danang Crysnanto ◽

Hubert Pausch

Keyword(s):

Whole Genome Sequencing ◽

Meat Quality ◽

Genome Sequencing ◽

Genomic Diversity ◽

Whole Genome ◽

Runs Of Homozygosity ◽

Cattle Breeds ◽

Signatures Of Selection ◽

Genomic Inbreeding ◽

Genomic Regions

Abstract Background Autochthonous cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and food conditions. Original Braunvieh (OB) is a local cattle breed of Switzerland used for beef and milk production in alpine areas. Using whole-genome sequencing (WGS) data of 49 key ancestors, we characterize genomic diversity, genomic inbreeding, and signatures of selection in Swiss OB cattle at nucleotide resolution. Results We annotated 15,722,811 SNPs and 1,580,878 Indels including 10,738 and 2763 missense deleterious and high impact variants, respectively, that were discovered in 49 OB key ancestors. Six Mendelian trait-associated variants that were previously detected in breeds other than OB, segregated in the sequenced key ancestors including variants causal for recessive xanthinuria and albinism. The average nucleotide diversity (1.6 × 10− 3) was higher in OB than many mainstream European cattle breeds. Accordingly, the average genomic inbreeding derived from runs of homozygosity (ROH) was relatively low (FROH = 0.14) in the 49 OB key ancestor animals. However, genomic inbreeding was higher in OB cattle of more recent generations (FROH = 0.16) due to a higher number of long (> 1 Mb) runs of homozygosity. Using two complementary approaches, composite likelihood ratio test and integrated haplotype score, we identified 95 and 162 genomic regions encompassing 136 and 157 protein-coding genes, respectively, that showed evidence (P < 0.005) of past and ongoing selection. These selection signals were enriched for quantitative trait loci related to beef traits including meat quality, feed efficiency and body weight and pathways related to blood coagulation, nervous and sensory stimulus. Conclusions We provide a comprehensive overview of sequence variation in Swiss OB cattle genomes. With WGS data, we observe higher genomic diversity and less inbreeding in OB than many European mainstream cattle breeds. Footprints of selection were detected in genomic regions that are possibly relevant for meat quality and adaptation to local environmental conditions. Considering that the population size is low and genomic inbreeding increased in the past generations, the implementation of optimal mating strategies seems warranted to maintain genetic diversity in the Swiss OB cattle population.

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