scholarly journals Genome-Wide SNPs and InDels Characteristics of Three Chinese Cattle Breeds

Animals ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 596 ◽  
Author(s):  
Fengwei Zhang ◽  
Kaixing Qu ◽  
Ningbo Chen ◽  
Quratulain Hanif ◽  
Yutang Jia ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Genetic Characteristics ◽  
Cattle Breeds ◽  
Chinese Cattle ◽  
Genome Wide ◽  
Whole Genome Resequencing ◽  
Immune Related Genes ◽  
Go Terms ◽  
Subtropical Environment

We report genome characterization of three native Chinese cattle breeds discovering ~34.3 M SNPs and ~3.8 M InDels using whole genome resequencing. On average, 10.4 M SNPs were shared amongst the three cattle breeds, whereas, 3.0 M, 4.9 M and 5.8 M were specific to LQ, WN and WS breeds, respectively. Gene ontology (GO)analysis revealed four immune response-related GO terms were over represented in all samples, while two immune signaling pathways were significantly over-represented in WS cattle. Altogether, we found immune related genes (PGLYRP2, ROMO1, FYB2, CD46, TSC1) in the three cattle breeds. Our study provides insights into the genetic basis of Chinese indicine adaptation to the tropic and subtropical environment, and provides a valuable resource for further investigations of genetic characteristics of the three breeds.

scholarly journals Genomic Patterns of Homozygosity in Chinese Local Cattle

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Lingyang Xu ◽  
Guoyao Zhao ◽  
Liu Yang ◽  
Bo Zhu ◽  
Yan Chen ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Average Length ◽  
Nucleotide Polymorphism ◽  
Adaptive Traits ◽  
Single Nucleotide ◽  
Cattle Breeds ◽  
Chinese Cattle ◽  
Genome Wide ◽  
Average Proportion ◽  
Genomic Patterns

AbstractGenome-wide single nucleotide polymorphism (SNP) arrays can be used to explore homozygosity segments, where two haplotypes inherited from the parents are identical. In this study, we identified a total of 27,358 runs of homozygosity (ROH) with an average of 153 ROH events per animal in Chinese local cattle. The sizes of ROH events varied considerably ranging from 0.5 to 66 Mb, with an average length of 1.22 Mb. The highest average proportion of the genome covered by ROH (~11.54% of the cattle genome) was found in Nanda cattle (NDC) from South China, whereas the lowest average proportion (~3.1%) was observed in Yanhuang cattle (YHC). The average estimated FROH ranged from 0.03 in YHC to 0.12 in NDC. For each of three ROH classes with different sizes (Small 0.5–1 Mb, Medium 1–5 Mb and Large >5 Mb), the numbers and total lengths of ROH per individual showed considerable differences across breeds. Moreover, we obtained 993 to 3603 ROH hotspots (which were defined where ROH frequency at a SNP within each breed exceeded the 1% threshold) among eight cattle breeds. Our results also revealed several candidate genes embedded with ROH hotspots which may be related to environmental conditions and local adaptation. In conclusion, we generated baselines for homozygosity patterns in diverse Chinese cattle breeds. Our results suggested that selection has, at least partially, played a role with other factors in shaping the genomic patterns of ROH in Chinese local cattle and might provide valuable insights for understanding the genetic basis of economic and adaptive traits.

scholarly journals Genome-wide prediction and functional characterization of the genetic basis of autism spectrum disorder

2016 ◽  
Vol 19 (11) ◽  
pp. 1454-1462 ◽  
Author(s):  
Arjun Krishnan ◽  
Ran Zhang ◽  
Victoria Yao ◽  
Chandra L Theesfeld ◽  
Aaron K Wong ◽  
...  
Keyword(s):  
Autism Spectrum Disorder ◽  
Genetic Basis ◽  
Functional Characterization ◽  
Autism Spectrum ◽  
Spectrum Disorder ◽  
Genome Wide

scholarly journals Genome-wide Association Study Reveals the IBSP Locus Affect Ear Size in Cattle

2020 ◽  
Author(s):  
Jiafei Shen ◽  
Xiaoting Xia ◽  
Qiuming Chen ◽  
Fengwei Zhang ◽  
Bizhi Huang ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Genome Wide Association Study ◽  
Bos Taurus ◽  
Classical Model ◽  
3D Structure ◽  
Three Dimensional ◽  
Allele Distribution ◽  
Cattle Breeds ◽  
Hot Climate ◽  
Genome Wide

Abstract BackgroundEar size is a classical model for hot climate adaptation following evolution, however, the genetic basis of the traits associated with the ear size remains to be elucidated.ResultsIn the current study, we performed GWAS on 158 cattle individuals to to explain the genetic mechanism of ear size. The results suggested significant association of IBSP locus with ear size. A missense mutation (Threonine-250→Isoleucine) on the seventh exon of IBSP was observed, which occurred at a quite conserved site and changed the three-dimensional (3D) structure simulations. In addition to GWAS, 14 cattle breeds were screened for the selection signals associating with the ear size using Fst and SweepD. The selective sweep analysis also suggested that IBSP was under positive selection amongst 4 breeds with relatively large ear size. The allele distribution of this mutation was validated among 394 samples from 21 worldwide cattle breeds, which strongly implied the origin of the A allele mutation to be from the Bos taurus.ConclusionsThese findings not only have important theoretical significance for the exploration of major genes associated with the ear size but also provide important molecular markers for the identification of cattle germplasm resources.

scholarly journals Characterization of a major QTL and Genome-Wide Epistatic Interactions for the Transformation of Single Spikelet in Teosinte Ears into Paired Spikelets in Maize Ears During Maize Domestication

2021 ◽  
Author(s):  
Zhengjie Chen ◽  
Kun Hu ◽  
Yong Yin ◽  
Dengguo Tang ◽  
Jixing Ni ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Interval Mapping ◽  
Phenotypic Variance ◽  
Epistatic Interactions ◽  
Genome Wide ◽  
Qtl Fine Mapping ◽  
Inclusive Composite Interval Mapping ◽  
Maize Domestication ◽  
Maize Ear

Abstract Maize ear carries paired spikelets, whereas the ear of its wild ancestor, teosinte, bears single spikelets. However, little is known about the genetic basis of the processes of transformation of single spikelets in teosinte ear to paired spikelets in maize ear. In this study, a two-ranked, paired-spikelets primitive maize and a two-ranked, single-spikelet teosinte were utilized to develop an F2 population, and QTL mapping for single vs. paired spikelets (PEDS) was performed. Two QTL (qPEDS1.1 and qPEDS3.1) for PEDS located on chromosomes 1L and 3S were identified in the 162 F2 plants using the inclusive composite interval mapping of additive (ICIM-ADD) module, explaining 1.93% and 23.79% of the phenotypic variance, respectively. Out of the 409 F2 plants, 43 plants with PEDS = 0% and 43 plants with PEDS > 20% were selected for selective genotyping; the QTL (qPEDS3.1) accounting for 64.01% of the phenotypic variance for PEDS was also detected. Moreover, the QTL (qPEDS3.1) was validated in three environments, which explained 31.05%, 38.94% and 23.16% of the phenotypic variance, respectively. In addition, 50 epistatic QTLs were detected in 162 F2 plants using the two-locus epistatic QTL (ICIM-EPI) module; they were distributed on all 10 chromosomes and explained 94.40% of the total phenotypic variance. The results contribute to a better understanding of the genetic basis of domestication of paired spikelets and provide a genetic resource for future map-based cloning; in addition, the systematic dissection of epistatic interactions underlies a theoretical framework for overcoming epistatic effects on QTL fine mapping.

Inherited skin disease

2020 ◽  
pp. 5602-5611
Author(s):  
Thiviyani Maruthappu ◽  
David P. Kelsell
Keyword(s):  
Genetic Basis ◽  
High Throughput Sequencing ◽  
Skin Diseases ◽  
Association Studies ◽  
Sequencing Technologies ◽  
Ectodermal Dysplasias ◽  
Genome Wide ◽  
Whole Exome ◽  
Common Skin ◽  
Immune Related Genes

Considerable advances in our understanding of inherited skin diseases have been made over the last decade as a result of high throughput sequencing technologies, including next generation sequencing and whole exome sequencing. The genetic basis of a myriad of monogenic epidermal disorders and syndromes including blistering diseases, ichthyoses, palmoplantar keratodermas, and the ectodermal dysplasias have now been elucidated. However, most patients referred from primary care to the dermatology clinic will be seeking treatment for a few common skin disorders such as psoriasis, eczema, and acne. The genetic basis of these disorders is rather more complex, but progress has been made through genome-wide association studies, which, for example, have linked susceptibility variants in the gene for filaggrin (FLG) and SPINK5 to atopic eczema, and IL23R and many other immune-related genes to psoriasis.

scholarly journals Characterization of recombination features and the genetic basis in multiple cattle breeds

BMC Genomics ◽  
2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Botong Shen ◽  
Jicai Jiang ◽  
Eyal Seroussi ◽  
George E. Liu ◽  
Li Ma
Keyword(s):  
Genetic Basis ◽  
Cattle Breeds

scholarly journals Genome-wide identification and characterisation of long non-coding RNAs in two Chinese cattle breeds

2020 ◽  
Vol 19 (1) ◽  
pp. 383-391
Author(s):  
Xianbo Jia ◽  
Yang He ◽  
Shi-Yi Chen ◽  
Jie Wang ◽  
Shenqiang Hu ◽  
...  
Keyword(s):  
Cattle Breeds ◽  
Chinese Cattle ◽  
Genome Wide ◽  
Non Coding Rnas

scholarly journals Genetic Basis of Transcriptome Diversity in Drosophila melanogaster

2015 ◽  
Author(s):  
Wen Huang ◽  
Mary Anna Carbone ◽  
Michael Magwire ◽  
Jason Peiffer ◽  
Richard Lyman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Drosophila Melanogaster ◽  
Quantitative Trait ◽  
Genetic Basis ◽  
Trait Variation ◽  
Regulatory Variants ◽  
Genome Wide ◽  
Mean And Variance ◽  
The Mean

Understanding how DNA sequence variation is translated into variation for complex phenotypes has remained elusive, but is essential for predicting adaptive evolution, selecting agriculturally important animals and crops, and personalized medicine. Here, we quantified genome-wide variation in gene expression in the sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel (DGRP). We found that a substantial fraction of the Drosophila transcriptome is genetically variable and organized into modules of genetically correlated transcripts, which provide functional context for newly identified transcribed regions. We identified regulatory variants for the mean and variance of gene expression, the latter of which could often be explained by an epistatic model. Expression quantitative trait loci for the mean, but not the variance, of gene expression were concentrated near genes. This comprehensive characterization of population scale diversity of transcriptomes and its genetic basis in the DGRP is critically important for a systems understanding of quantitative trait variation.

scholarly journals Neurocognitive phenomics: examining the genetic basis of cognitive abilities

2012 ◽  
Vol 43 (10) ◽  
pp. 2027-2036 ◽  
Author(s):  
G. Donohoe ◽  
I. J. Deary ◽  
D. C. Glahn ◽  
A. K. Malhotra ◽  
K. E. Burdick
Keyword(s):  
Psychiatric Disorders ◽  
Cognitive Deficits ◽  
Genetic Variants ◽  
Cognitive Abilities ◽  
Genetic Basis ◽  
Phenotypic Characterization ◽  
Cognitive Studies ◽  
Risk Variants ◽  
Genome Wide

Cognitive deficits are core to the disability associated with many psychiatric disorders. Both variation in cognition and psychiatric risk show substantial heritability, with overlapping genetic variants contributing to both. Unsurprisingly, therefore, these fields have been mutually beneficial: just as cognitive studies of psychiatric risk variants may identify genes involved in cognition, so too can genome-wide studies based on cognitive phenotypes lead to genes relevant to psychiatric aetiology. The purpose of this review is to consider the main issues involved in the phenotypic characterization of cognition, and to describe the challenges associated with the transition to genome-wide approaches. We conclude by describing the approaches currently being taken by the international consortia involving many investigators in the field internationally (e.g. Cognitive Genomics Consortium; COGENT) to overcome these challenges.

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