scholarly journals Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes in Three Pig Breeds

Animals ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 518 ◽  
Author(s):  
Xie ◽  
Shi ◽  
Liu ◽  
Deng ◽  
Wang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Target Genes ◽  
Average Length ◽  
Reproductive Traits ◽  
Genomic Region ◽  
Inbreeding Coefficient ◽  
Runs Of Homozygosity ◽  
Pig Breeds ◽  
Yorkshire Pigs ◽  
The Difference

Runs of homozygosity (ROH) are contiguous homozygous genotype segments in the genome that are present in an individual since the identical haplotypes are inherited from each parent. The aim of this study was to investigate the frequency and distribution of ROH in the genomes of Landrace, Songliao black and Yorkshire pigs. We calculated two types of genome inbreeding coefficients and their correlation, including the inbreeding coefficient based on ROH (FROH) and the inbreeding coefficient based on the difference between the observed and expected number of homozygous genotypes (FHOM). Furthermore, we identified candidate genes in the genomic region most associated with ROH. We identified 21,312 ROH in total. The average number of ROH per individual was 32.99 ± 0.38 and the average length of ROH was 6.40 ± 0.070 Mb in the three breeds. The FROH results showed that Yorkshire pigs exhibited the highest level of inbreeding (0.092 ± 0.0015) and that Landrace pigs exhibited the lowest level of inbreeding (0.073 ± 0.0047). The average correlation between FROH and FHOM was high (0.94) within three breeds. The length of ROH provides insight into the inbreeding history of these three pig breeds. In this study, Songliao black pigs presented a higher frequency and average length of long ROH (>40 Mb) compared with those of Landrace and Yorkshire pigs, which indicated greater inbreeding in recent times. Genes related to reproductive traits (GATM, SPATA46, HSD17B7, VANGL2, DAXX, CPEB1), meat quality traits (NR1I3, APOA2, USF1) and energy conversion (NDUFS2) were identified within genomic regions with a high frequency of ROH. These genes could be used as target genes for further marker-assisted selection and genome selection.

scholarly journals Runs of homozygosity analysis reveals consensus homozygous regions affecting production traits in Chinese Simmental beef cattle

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guoyao Zhao ◽  
Yuqiang Liu ◽  
Qunhao Niu ◽  
Xu Zheng ◽  
Tianliu Zhang ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Average Length ◽  
Snp Array ◽  
Reproductive Traits ◽  
Farm Animals ◽  
Production Traits ◽  
Runs Of Homozygosity ◽  
Exact Test ◽  
Genomic Regions

Abstract Background Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle. Results We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher’s exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle. Conclusions Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.

scholarly journals Genome-Wide Scan for Runs of Homozygosity Identifies Candidate Genes Related to Economically Important Traits in Chinese Merino

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 524 ◽  
Author(s):  
Sangang He ◽  
Jiang Di ◽  
Bing Han ◽  
Lei Chen ◽  
Mingjun Liu ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Average Length ◽  
Inbreeding Coefficient ◽  
Whole Genome ◽  
Runs Of Homozygosity ◽  
Genotyping Array ◽  
Genome Region ◽  
Genome Wide ◽  
Genomic Regions ◽  
Genome Wide Scan

In this study, we estimated the number, length, and frequency of runs of homozygosity (ROH) in 635 Chinese Merino and identified genomic regions with high ROH frequency using the OvineSNP50 whole-genome genotyping array. A total of 6039 ROH exceeding 1 Mb were detected in 634 animals. The average number of ROH in each animal was 9.23 and the average length was 5.87 Mb. Most of the ROH were less than 10 Mb, accounting for 88.77% of the total number of detected ROH. In addition, Ovies aries chromosome (OAR) 21 and OAR3 exhibited the highest and lowest coverage of chromosomes by ROH, respectively. OAR1 displayed the highest number of ROH, while the lowest number of ROH was found on OAR24. An inbreeding coefficient of 0.023 was calculated from ROH greater than 1 Mb. Thirteen regions on chromosomes 1, 2, 3, 5, 6, 10, 11, and 16 were found to contain ROH hotspots. Within the genome regions of OAR6 and OAR11, NCAPG/LCORL, FGF11 and TP53 were identified as the candidate genes related to body size, while the genome region of OAR10 harbored RXFP2 gene responsible for the horn trait. These findings indicate the adaptive to directional trait selection in Chinese Merino.

scholarly journals Genome-Wide Assessment of Runs of Homozygosity in Chinese Wagyu Beef Cattle

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1425 ◽  
Author(s):  
Guoyao Zhao ◽  
Tianliu Zhang ◽  
Yuqiang Liu ◽  
Zezhao Wang ◽  
Lei Xu ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Candidate Genes ◽  
Complex Traits ◽  
Average Length ◽  
Body Height ◽  
Reproductive Traits ◽  
Valuable Insight ◽  
Runs Of Homozygosity ◽  
Genome Wide ◽  
Candidate Regions

Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of ROH leading to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with important traits in Chinese Wagyu beef cattle. We identified a total of 29,271 ROH segments from 462 animals. Within each animal, an average number of ROH was 63.36 while an average length was 62.19 Mb. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events across all individuals. Of these, nine regions containing 154 candidate genes, were significantly associated with six traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, and carcass length; p < 0.01). Moreover, we found 26 consensus ROH regions with frequencies exceeding 10%, and several regions overlapped with QTLs, which are associated with body weight, calving ease, and stillbirth. Among them, we observed 41 candidate genes, including BCKDHB, MAB21L1, SLC2A13, FGFR3, FGFRL1, CPLX1, CTNNA1, CORT, CTNNBIP1, and NMNAT1, which have been previously reported to be related to body conformation, meat quality, susceptibility, and reproductive traits. In summary, we assessed genome-wide autozygosity patterns and inbreeding levels in Chinese Wagyu beef cattle. Our study identified many candidate regions and genes overlapped with ROH for several important traits, which could be unitized to assist the design of a selection mating strategy in beef cattle.

scholarly journals Decoding the molecular mechanism of parthenocarpy in Musa spp. through protein–protein interaction network

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Suthanthiram Backiyarani ◽  
Rajendran Sasikala ◽  
Simeon Sharmiladevi ◽  
Subbaraya Uma
Keyword(s):  
Candidate Genes ◽  
Protein Interaction ◽  
Target Genes ◽  
Interaction Network ◽  
Enrichment Analysis ◽  
Auxin Signaling ◽  
Pathway Enrichment Analysis ◽  
Ppi Network ◽  
Protein Protein Interaction ◽  
The Difference

AbstractBanana, one of the most important staple fruit among global consumers is highly sterile owing to natural parthenocarpy. Identification of genetic factors responsible for parthenocarpy would facilitate the conventional breeders to improve the seeded accessions. We have constructed Protein–protein interaction (PPI) network through mining differentially expressed genes and the genes used for transgenic studies with respect to parthenocarpy. Based on the topological and pathway enrichment analysis of proteins in PPI network, 12 candidate genes were shortlisted. By further validating these candidate genes in seeded and seedless accession of Musa spp. we put forward MaAGL8, MaMADS16, MaGH3.8, MaMADS29, MaRGA1, MaEXPA1, MaGID1C, MaHK2 and MaBAM1 as possible target genes in the study of natural parthenocarpy. In contrary, expression profile of MaACLB-2 and MaZEP is anticipated to highlight the difference in artificially induced and natural parthenocarpy. By exploring the PPI of validated genes from the network, we postulated a putative pathway that bring insights into the significance of cytokinin mediated CLAVATA(CLV)–WUSHEL(WUS) signaling pathway in addition to gibberellin mediated auxin signaling in parthenocarpy. Our analysis is the first attempt to identify candidate genes and to hypothesize a putative mechanism that bridges the gaps in understanding natural parthenocarpy through PPI network.

scholarly journals Transcriptome Analysis Reveals Long Intergenic Non-Coding RNAs Contributed to Intramuscular Fat Content Differences between Yorkshire and Wei Pigs

2020 ◽  
Vol 21 (5) ◽  
pp. 1732 ◽  
Author(s):  
Qianqian Li ◽  
Ziying Huang ◽  
Wenjuan Zhao ◽  
Mengxun Li ◽  
Changchun Li
Keyword(s):  
Target Genes ◽  
Intramuscular Fat ◽  
Differentially Expressed ◽  
Published Data ◽  
Pig Breeds ◽  
Longissimus Dorsi Muscle ◽  
Yorkshire Pigs ◽  
Non Coding Rnas ◽  
Trans Regulation ◽  
Imf Content

Intramuscular fat (IMF) content is closely related to various meat traits, such as tenderness, juiciness, and flavor. The IMF content varies considerably among pig breeds with different genetic backgrounds. Long intergenic non-coding RNAs (lincRNAs) have been widely identified in many species and found to be an important class of regulators that can participate in multiple biological processes. However, the mechanism behind lincRNAs regulation of pig IMF content remains unknown and requires further study. In our study, we identified a total of 156 lincRNAs in the longissimus dorsi muscle of Wei (fat-type) and Yorkshire (lean-type) pigs using previously published data. These identified lincRNAs have shorter transcript length, longer exon length, lower exon number, and lower expression level as compared with protein-coding transcripts. We predicted potential target genes (PTGs) that are potentially regulated by lincRNAs in cis or trans regulation. Gene ontology and pathway analyses indicated that many potential lincRNAs target genes are involved in IMF-related processes or pathways, such as fatty acid catabolic process and adipocytokine signaling pathway. In addition, we analyzed quantitative trait locus (QTL) sites that differentially expressed lincRNAs (DE lincRNAs) between Wei and Yorkshire pigs co-localized. The QTL sites where DE lincRNAs co-localize are mostly related to IMF content. Furthermore, we constructed a co-expressed network between DE lincRNAs and their differentially expressed PTGs (DEPTGs). On the basis of their expression levels, we suggest that many DE lincRNAs can affect IMF development by positively or negatively regulating their PTGs. This study identified and analyzed some lincRNAs- and PTGs-related IMF development of the two pig breeds and provided new insight into research on the roles of lincRNAs in the two types of breeds.

scholarly journals Title: Meta-Analysis of Heifer Traits Identified Reproductive Pathways in Bos indicus Cattle

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 768
Author(s):  
Muhammad S. Tahir ◽  
Laercio R. Porto-Neto ◽  
Cedric Gondro ◽  
Olasege B. Shittu ◽  
Kimberley Wockner ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Molecular Mechanisms ◽  
Meta Analysis ◽  
Reproductive Traits ◽  
Significant Snps ◽  
Genomic Region ◽  
Chromosome 8 ◽  
Positional Candidate ◽  
Brahman Cattle ◽  
Genomic Regions

Fertility traits measured early in life define the reproductive potential of heifers. Knowledge of genetics and biology can help devise genomic selection methods to improve heifer fertility. In this study, we used ~2400 Brahman cattle to perform GWAS and multi-trait meta-analysis to determine genomic regions associated with heifer fertility. Heifer traits measured were pregnancy at first mating opportunity (PREG1, a binary trait), first conception score (FCS, score 1 to 3) and rebreeding score (REB, score 1 to 3.5). The heritability estimates were 0.17 (0.03) for PREG1, 0.11 (0.05) for FCS and 0.28 (0.05) for REB. The three traits were highly genetically correlated (0.75–0.83) as expected. Meta-analysis was performed using SNP effects estimated for each of the three traits, adjusted for standard error. We identified 1359 significant SNPs (p-value < 9.9 × 10−6 at FDR < 0.0001) in the multi-trait meta-analysis. Genomic regions of 0.5 Mb around each significant SNP from the meta-analysis were annotated to create a list of 2560 positional candidate genes. The most significant SNP was in the vicinity of a genomic region on chromosome 8, encompassing the genes SLC44A1, FSD1L, FKTN, TAL2 and TMEM38B. The genomic region in humans that contains homologs of these genes is associated with age at puberty in girls. Top significant SNPs pointed to additional fertility-related genes, again within a 0.5 Mb region, including ESR2, ITPR1, GNG2, RGS9BP, ANKRD27, TDRD12, GRM1, MTHFD1, PTGDR and NTNG1. Functional pathway enrichment analysis resulted in many positional candidate genes relating to known fertility pathways, including GnRH signaling, estrogen signaling, progesterone mediated oocyte maturation, cAMP signaling, calcium signaling, glutamatergic signaling, focal adhesion, PI3K-AKT signaling and ovarian steroidogenesis pathway. The comparison of results from this study with previous transcriptomics and proteomics studies on puberty of the same cattle breed (Brahman) but in a different population identified 392 genes in common from which some genes—BRAF, GABRA2, GABR1B, GAD1, FSHR, CNGA3, PDE10A, SNAP25, ESR2, GRIA2, ORAI1, EGFR, CHRNA5, VDAC2, ACVR2B, ORAI3, CYP11A1, GRIN2A, ATP2B3, CAMK2A, PLA2G, CAMK2D and MAPK3—are also part of the above-mentioned pathways. The biological functions of the positional candidate genes and their annotation to known pathways allowed integrating the results into a bigger picture of molecular mechanisms related to puberty in the hypothalamus–pituitary–ovarian axis. A reasonable number of genes, common between previous puberty studies and this study on early reproductive traits, corroborates the proposed molecular mechanisms. This study identified the polymorphism associated with early reproductive traits, and candidate genes that provided a visualization of the proposed mechanisms, coordinating the hypothalamic, pituitary, and ovarian functions for reproductive performance in Brahman cattle.

scholarly journals Emerging role of PLAG1 as a regulator of growth and reproduction

2015 ◽  
Vol 228 (2) ◽  
pp. R45-R56 ◽  
Author(s):  
Almas R Juma ◽  
Pauliina E Damdimopoulou ◽  
Sylvia V H Grommen ◽  
Wim J M Van de Ven ◽  
Bert De Groef
Keyword(s):  
Target Genes ◽  
Association Studies ◽  
Reproductive Traits ◽  
Postnatal Growth ◽  
Genomic Region ◽  
Current Evidence ◽  
Genome Wide Association Studies ◽  
Genome Wide ◽  
Growth And Reproduction

Pleomorphic adenoma gene 1 (PLAG1) belongs to the PLAG family of zinc finger transcription factors along with PLAG-like 1 and PLAG-like 2. The PLAG1 gene is best known as an oncogene associated with certain types of cancer, most notably pleomorphic adenomas of the salivary gland. While the mechanisms of PLAG1-induced tumorigenesis are reasonably well understood, the role of PLAG1 in normal physiology is less clear. It is known that PLAG1 is involved in cell proliferation by directly regulating a wide array of target genes, including a number of growth factors such as insulin-like growth factor 2. This is likely to be a central mode of action for PLAG1 both in embryonic development and in cancer. The phenotype of Plag1 knockout mice suggests an important role for PLAG1 also in postnatal growth and reproduction, as PLAG1 deficiency causes growth retardation and reduced fertility. A role for PLAG1 in growth and reproduction is further corroborated by genome-wide association studies in humans and domestic animals in which polymorphisms in the PLAG1 genomic region are associated with body growth and reproductive traits. Here we review the current evidence for PLAG1 as a regulator of growth and fertility and discuss possible endocrine mechanisms involved.

Genetic rescue by augmenting gene flow

2017 ◽  
Author(s):  
Richard Frankham ◽  
Jonathan D. Ballou ◽  
Katherine Ralls ◽  
Mark D. B. Eldridge ◽  
Michele R. Dudash ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
Inbreeding Coefficient ◽  
Outbreeding Depression ◽  
Genetic Rescue ◽  
Evolutionary Potential ◽  
Beneficial Effects ◽  
The Difference ◽  
Inbred Populations ◽  
Harmful Effects

Inbreeding is reduced and genetic diversity enhanced when a small isolated inbred population is crossed to another unrelated population. Crossing can have beneficial or harmful effects on fitness, but beneficial effects predominate, and the risks of harmful ones (outbreeding depression) can be predicted and avoided. For crosses with a low risk of outbreeding depression, there are large and consistent benefits on fitness that persist across generations in outbreeding species. Benefits are greater in species that naturally outbreed than those that inbreed, and increase with the difference in inbreeding coefficient between crossed and inbred populations in mothers and zygotes. However, benefits are similar across invertebrates, vertebrates and plants. There are also important benefits for evolutionary potential of crossing between populations.

scholarly journals Transcriptomic Profiling of Skeletal Muscle Reveals Candidate Genes Influencing Muscle Growth and Associated Lipid Composition in Portuguese Local Pig Breeds

Animals ◽  
2021 ◽  
Vol 11 (5) ◽  
pp. 1423
Author(s):  
André Albuquerque ◽  
Cristina Óvilo ◽  
Yolanda Núñez ◽  
Rita Benítez ◽  
Adrián López-Garcia ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Muscle Growth ◽  
Rna Seq ◽  
Next Generation Sequencing Technology ◽  
Pig Breeds ◽  
Nfkb Activation ◽  
Main Gene ◽  
Slow Type ◽  
Longissimus Lumborum ◽  
Generation Sequencing

Gene expression is one of the main factors to influence meat quality by modulating fatty acid metabolism, composition, and deposition rates in muscle tissue. This study aimed to explore the transcriptomics of the Longissimus lumborum muscle in two local pig breeds with distinct genetic background using next-generation sequencing technology and Real-Time qPCR. RNA-seq yielded 49 differentially expressed genes between breeds, 34 overexpressed in the Alentejano (AL) and 15 in the Bísaro (BI) breed. Specific slow type myosin heavy chain components were associated with AL (MYH7) and BI (MYH3) pigs, while an overexpression of MAP3K14 in AL may be associated with their lower loin proportion, induced insulin resistance, and increased inflammatory response via NFkB activation. Overexpression of RUFY1 in AL pigs may explain the higher intramuscular (IMF) content via higher GLUT4 recruitment and consequently higher glucose uptake that can be stored as fat. Several candidate genes for lipid metabolism, excluded in the RNA-seq analysis due to low counts, such as ACLY, ADIPOQ, ELOVL6, LEP and ME1 were identified by qPCR as main gene factors defining the processes that influence meat composition and quality. These results agree with the fatter profile of the AL pig breed and adiponectin resistance can be postulated as responsible for the overexpression of MAP3K14′s coding product NIK, failing to restore insulin sensitivity.

white+ Transgene Insertions Presenting a Dorsal/Ventral Pattern Define a Single Cluster of Homeobox Genes That Is Silenced by the Polycomb-group Proteins in Drosophila melanogaster

Genetics ◽  
1998 ◽  
Vol 149 (1) ◽  
pp. 257-275 ◽  
Author(s):  
Sophie Netter ◽  
Marie-Odile Fauvarque ◽  
Ruth Diez del Corral ◽  
Jean-Maurice Dura ◽  
Dario Coen
Keyword(s):  
Chromatin Structure ◽  
Target Genes ◽  
Position Effect ◽  
Phenotypic Expression ◽  
Positional Information ◽  
Genomic Region ◽  
Polycomb Group ◽  
Position Effect Variegation ◽  
Trithorax Group ◽  
Clear Cut

AbstractWe used the white gene as an enhancer trap and reporter of chromatin structure. We collected white+ transgene insertions presenting a peculiar pigmentation pattern in the eye: white expression is restricted to the dorsal half of the eye, with a clear-cut dorsal/ventral (D/V) border. This D/V pattern is stable and heritable, indicating that phenotypic expression of the white reporter reflects positional information in the developing eye. Localization of these transgenes led us to identify a unique genomic region encompassing 140 kb in 69D1–3 subject to this D/V effect. This region contains at least three closely related homeobox-containing genes that are constituents of the iroquois complex (IRO-C). IRO-C genes are coordinately regulated and implicated in similar developmental processes. Expression of these genes in the eye is regulated by the products of the Polycomb -group (Pc-G) and trithorax-group (trx-G) genes but is not modified by classical modifiers of position-effect variegation. Our results, together with the report of a Pc -G binding site in 69D, suggest that we have identified a novel cluster of target genes for the Pc-G and trx-G products. We thus propose that ventral silencing of the whole IRO-C in the eye occurs at the level of chromatin structure in a manner similar to that of the homeotic gene complexes, perhaps by local compaction of the region into a heterochromatin-like structure involving the Pc-G products.

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