Phylogenomics provides new insight into evolutionary relationships and genealogical discordance in the reef-building coral genus
            Acropora

Understanding the genetic basis of reproductive isolation is a long-standing goal of speciation research. In recently diverged populations, genealogical discordance may reveal genes and genomic regions that contribute to the speciation process. Previous work has shown that conspecific colonies of Acropora that spawn in different seasons (spring and autumn) are associated with highly diverged lineages of the phylogenetic marker PaxC . Here, we used 10 034 single-nucleotide polymorphisms to generate a genome-wide phylogeny and compared it with gene genealogies from the PaxC intron and the mtDNA Control Region in 20 species of Acropora , including three species with spring- and autumn-spawning cohorts. The PaxC phylogeny separated conspecific autumn and spring spawners into different genetic clusters in all three species; however, this pattern was not supported in two of the three species at the genome level, suggesting a selective connection between PaxC and reproductive timing in Acropora corals. This genome-wide phylogeny provides an improved foundation for resolving phylogenetic relationships in Acropora and, combined with PaxC , provides a fascinating platform for future research into regions of the genome that influence reproductive isolation and speciation in corals.

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Genome-Wide Association Study of Root Mealiness and Other Texture-Associated Traits in Cassava

Frontiers in Plant Science ◽

10.3389/fpls.2021.770434 ◽

2021 ◽

Vol 12 ◽

Author(s):

Kelechi Uchendu ◽

Damian Ndubuisi Njoku ◽

Agre Paterne ◽

Ismail Yusuf Rabbi ◽

Daniel Dzidzienyo ◽

...

Keyword(s):

Candidate Genes ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Phenotypic Data ◽

Genome Wide ◽

A Genome ◽

Breeding Programmes ◽

Vegetables And Fruits ◽

Genomic Regions

Cassava breeders have made significant progress in developing new genotypes with improved agronomic characteristics such as improved root yield and resistance against biotic and abiotic stresses. However, these new and improved cassava (Manihot esculenta Crantz) varieties in cultivation in Nigeria have undergone little or no improvement in their culinary qualities; hence, there is a paucity of genetic information regarding the texture of boiled cassava, particularly with respect to its mealiness, the principal sensory quality attribute of boiled cassava roots. The current study aimed at identifying genomic regions and polymorphisms associated with natural variation for root mealiness and other texture-related attributes of boiled cassava roots, which includes fibre, adhesiveness (ADH), taste, aroma, colour, and firmness. We performed a genome-wide association (GWAS) analysis using phenotypic data from a panel of 142 accessions obtained from the National Root Crops Research Institute (NRCRI), Umudike, Nigeria, and a set of 59,792 high-quality single nucleotide polymorphisms (SNPs) distributed across the cassava genome. Through genome-wide association mapping, we identified 80 SNPs that were significantly associated with root mealiness, fibre, adhesiveness, taste, aroma, colour and firmness on chromosomes 1, 4, 5, 6, 10, 13, 17 and 18. We also identified relevant candidate genes that are co-located with peak SNPs linked to these traits in M. esculenta. A survey of the cassava reference genome v6.1 positioned the SNPs on chromosome 13 in the vicinity of Manes.13G026900, a gene recognized as being responsible for cell adhesion and for the mealiness or crispness of vegetables and fruits, and also known to play an important role in cooked potato texture. This study provides the first insights into understanding the underlying genetic basis of boiled cassava root texture. After validation, the markers and candidate genes identified in this novel work could provide important genomic resources for use in marker-assisted selection (MAS) and genomic selection (GS) to accelerate genetic improvement of root mealiness and other culinary qualities in cassava breeding programmes in West Africa, especially in Nigeria, where the consumption of boiled and pounded cassava is low.

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Genomic Regions Related to White/Black Tail Feather Color in Dwarf Chickens Identified Using a Genome-Wide Association Study

Frontiers in Genetics ◽

10.3389/fgene.2021.566047 ◽

2021 ◽

Vol 12 ◽

Author(s):

Changsheng Nie ◽

Liang Qu ◽

Xinghua Li ◽

Zhihua Jiang ◽

Kehua Wang ◽

...

Keyword(s):

Rhode Island ◽

Genome Wide Association Study ◽

The Body ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Tail Feather ◽

Body Feather ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

Although the genetic foundation of chicken body feather color has been extensively explored, that of tail feather color remains poorly understood. In the present study, we used a synthetic chicken dwarf line (DW), derived from hybrids bred between a black tail chicken breed, Rhode Island Red (RIR), and a white tail breed, dwarf layer (DL), to investigate the genetic rules associated white/black tail color. Even though the body feathers are predominantly red, the DW line still comprises individuals with black or white tails after more than 10 generations of self-crossing and selection for the body feather color. We first performed four crosses using the DW chickens, including black-tailed males to females, reciprocal crosses between the black and white, and white males to females to elucidate the inheritance pattern of the white/black tail. We also performed a genome-wide association (GWA) analysis to determine the candidate genomic regions underlying the tail feather color using black tail chickens from the RIR and DW lines and white individuals from the DW line. In the crossing experiment, we found that (i) the white/black tail feather color is independent of body feather color; (ii) the phenotype is a simple autosomal trait; and (iii) the white is dominant to the black in the DW line. The GWA results showed that seven single-nucleotide polymorphisms (SNPs) on chromosome 24 were significantly correlated with tail feather color. The significant region (3.97–4.26 Mb) comprises nine known genes (NECTIN1, THY1, gga-mir-1466, USP2, C1QTNF5, RNF26, MCAM, CBL, and CCDC153) and five anonymous genes. This study revealed that the white/black tail feather trait is autosome-linked in DW chickens. Fourteen genes were found in the significant ~0.29 Mb genomic region, and some, especially MCAM, are suggested to play critical roles in the determination of white/black tail feather color. Our research is the first study on the genetics underlying tail feather color and could help further the understanding of feather pigmentation in chickens.

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A GWAS in Latin Americans identifies novel face shape loci, implicating VPS13B and a Denisovan introgressed region in facial variation

Science Advances ◽

10.1126/sciadv.abc6160 ◽

2021 ◽

Vol 7 (6) ◽

pp. eabc6160

Author(s):

Betty Bonfante ◽

Pierre Faux ◽

Nicolas Navarro ◽

Javier Mendoza-Revilla ◽

Morgane Dubied ◽

...

Keyword(s):

Native Americans ◽

Genome Wide Association Study ◽

Regulatory Sequences ◽

Nucleotide Polymorphisms ◽

Latin Americans ◽

Face Shape ◽

Genome Wide ◽

A Genome ◽

Genomic Regions ◽

Face Morphology

To characterize the genetic basis of facial features in Latin Americans, we performed a genome-wide association study (GWAS) of more than 6000 individuals using 59 landmark-based measurements from two-dimensional profile photographs and ~9,000,000 genotyped or imputed single-nucleotide polymorphisms. We detected significant association of 32 traits with at least 1 (and up to 6) of 32 different genomic regions, more than doubling the number of robustly associated face morphology loci reported until now (from 11 to 23). These GWAS hits are strongly enriched in regulatory sequences active specifically during craniofacial development. The associated region in 1p12 includes a tract of archaic adaptive introgression, with a Denisovan haplotype common in Native Americans affecting particularly lip thickness. Among the nine previously unidentified face morphology loci we identified is the VPS13B gene region, and we show that variants in this region also affect midfacial morphology in mice.

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Genome-wide association study in almost 195,000 individuals identifies 50 previously unidentified genetic loci for eye color

Science Advances ◽

10.1126/sciadv.abd1239 ◽

2021 ◽

Vol 7 (11) ◽

pp. eabd1239

Author(s):

Mark Simcoe ◽

Ana Valdes ◽

Fan Liu ◽

Nicholas A. Furlotte ◽

David M. Evans ◽

...

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Color Variation ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Melanin Pigmentation ◽

Eye Color ◽

Human Eye ◽

Genome Wide ◽

Genomic Regions

Human eye color is highly heritable, but its genetic architecture is not yet fully understood. We report the results of the largest genome-wide association study for eye color to date, involving up to 192,986 European participants from 10 populations. We identify 124 independent associations arising from 61 discrete genomic regions, including 50 previously unidentified. We find evidence for genes involved in melanin pigmentation, but we also find associations with genes involved in iris morphology and structure. Further analyses in 1636 Asian participants from two populations suggest that iris pigmentation variation in Asians is genetically similar to Europeans, albeit with smaller effect sizes. Our findings collectively explain 53.2% (95% confidence interval, 45.4 to 61.0%) of eye color variation using common single-nucleotide polymorphisms. Overall, our study outcomes demonstrate that the genetic complexity of human eye color considerably exceeds previous knowledge and expectations, highlighting eye color as a genetically highly complex human trait.

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Genome-Wide Association Study (GWAS) for Examining the Genomics Controlling Prickle Production in Red Raspberry (Rubus idaeus L.)

Agronomy ◽

10.3390/agronomy11010027 ◽

2020 ◽

Vol 11 (1) ◽

pp. 27

Author(s):

Archana Khadgi ◽

Courtney A. Weber

Keyword(s):

Association Study ◽

Genome Wide Association Study ◽

Genomic Region ◽

Rubus Idaeus ◽

Genome Wide Association ◽

Nucleotide Polymorphisms ◽

Red Raspberry ◽

Genome Wide ◽

A Genome ◽

Genotype By Sequencing

Red raspberry (Rubus idaeus L.) is an expanding high-value berry crop worldwide. The presence of prickles, outgrowths of epidermal tissues lacking vasculature, on the canes, petioles, and undersides of leaves complicates both field management and harvest. The utilization of cultivars with fewer prickles or prickle-free canes simplifies production. A previously generated population segregating for prickles utilizing the s locus between the prickle-free cultivar Joan J (ss) and the prickled cultivar Caroline (Ss) was analyzed to identify the genomic region associated with prickle development in red raspberry. Genotype by sequencing (GBS) was combined with a genome-wide association study (GWAS) using fixed and random model circulating probability unification (FarmCPU) to analyze 8474 single nucleotide polymorphisms (SNPs) and identify significant markers associated with the prickle-free trait. A total of four SNPs were identified on chromosome 4 that were associated with the phenotype and were located near or in annotated genes. This study demonstrates how association genetics can be used to decipher the genetic control of important horticultural traits in Rubus, and provides valuable information about the genomic region and potential genes underlying the prickle-free trait.

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Genome-Wide Association Analysis of Growth Curve Parameters in Chinese Simmental Beef Cattle

Animals ◽

10.3390/ani11010192 ◽

2021 ◽

Vol 11 (1) ◽

pp. 192

Author(s):

Xinghai Duan ◽

Bingxing An ◽

Lili Du ◽

Tianpeng Chang ◽

Mang Liang ◽

...

Keyword(s):

Beef Cattle ◽

Candidate Genes ◽

Growth Curve ◽

Growth And Development ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Coefficient Of Determination ◽

Nucleotide Polymorphisms ◽

Genome Wide ◽

A Genome

The objective of the present study was to perform a genome-wide association study (GWAS) for growth curve parameters using nonlinear models that fit original weight–age records. In this study, data from 808 Chinese Simmental beef cattle that were weighed at 0, 6, 12, and 18 months of age were used to fit the growth curve. The Gompertz model showed the highest coefficient of determination (R2 = 0.954). The parameters’ mature body weight (A), time-scale parameter (b), and maturity rate (K) were treated as phenotypes for single-trait GWAS and multi-trait GWAS. In total, 9, 49, and 7 significant SNPs associated with A, b, and K were identified by single-trait GWAS; 22 significant single nucleotide polymorphisms (SNPs) were identified by multi-trait GWAS. Among them, we observed several candidate genes, including PLIN3, KCNS3, TMCO1, PRKAG3, ANGPTL2, IGF-1, SHISA9, and STK3, which were previously reported to associate with growth and development. Further research for these candidate genes may be useful for exploring the full genetic architecture underlying growth and development traits in livestock.

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Epigenome-Wide Study Identified Methylation Sites Associated with the Risk of Obesity

Nutrients ◽

10.3390/nu13061984 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1984

Author(s):

Majid Nikpay ◽

Sepehr Ravati ◽

Robert Dent ◽

Ruth McPherson

Keyword(s):

Quantitative Trait Locus ◽

Quantitative Trait ◽

Rare Variants ◽

Genome Wide ◽

A Genome ◽

Genome Wide Search ◽

Risk Snps ◽

Trait Locus ◽

Genomic Regions ◽

Eqtl Data

Here, we performed a genome-wide search for methylation sites that contribute to the risk of obesity. We integrated methylation quantitative trait locus (mQTL) data with BMI GWAS information through a SNP-based multiomics approach to identify genomic regions where mQTLs for a methylation site co-localize with obesity risk SNPs. We then tested whether the identified site contributed to BMI through Mendelian randomization. We identified multiple methylation sites causally contributing to the risk of obesity. We validated these findings through a replication stage. By integrating expression quantitative trait locus (eQTL) data, we noted that lower methylation at cg21178254 site upstream of CCNL1 contributes to obesity by increasing the expression of this gene. Higher methylation at cg02814054 increases the risk of obesity by lowering the expression of MAST3, whereas lower methylation at cg06028605 contributes to obesity by decreasing the expression of SLC5A11. Finally, we noted that rare variants within 2p23.3 impact obesity by making the cg01884057 site more susceptible to methylation, which consequently lowers the expression of POMC, ADCY3 and DNAJC27. In this study, we identify methylation sites associated with the risk of obesity and reveal the mechanism whereby a number of these sites exert their effects. This study provides a framework to perform an omics-wide association study for a phenotype and to understand the mechanism whereby a rare variant causes a disease.

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Drosophila Gain-of-Function Mutant RTK Torso Triggers Ectopic Dpp and STAT Signaling

Genetics ◽

10.1093/genetics/164.1.247 ◽

2003 ◽

Vol 164 (1) ◽

pp. 247-258 ◽

Cited By ~ 1

Author(s):

Jinghong Li ◽

Willis X Li

Keyword(s):

Tyrosine Kinases ◽

Target Genes ◽

Tor Signaling ◽

Gain Of Function ◽

Essential Requirement ◽

Downstream Target ◽

Rtk Signaling ◽

Genome Wide ◽

A Genome ◽

Genomic Regions

Abstract Overactivation of receptor tyrosine kinases (RTKs) has been linked to tumorigenesis. To understand how a hyperactivated RTK functions differently from wild-type RTK, we conducted a genome-wide systematic survey for genes that are required for signaling by a gain-of-function mutant Drosophila RTK Torso (Tor). We screened chromosomal deficiencies for suppression of a gain-of-function mutation tor (torGOF), which led to the identification of 26 genomic regions that, when in half dosage, suppressed the defects caused by torGOF. Testing of candidate genes in these regions revealed many genes known to be involved in Tor signaling (such as those encoding the Ras-MAPK cassette, adaptor and structural molecules of RTK signaling, and downstream target genes of Tor), confirming the specificity of this genetic screen. Importantly, this screen also identified components of the TGFβ (Dpp) and JAK/STAT pathways as being required for TorGOF signaling. Specifically, we found that reducing the dosage of thickveins (tkv), Mothers against dpp (Mad), or STAT92E (aka marelle), respectively, suppressed torGOF phenotypes. Furthermore, we demonstrate that in torGOF embryos, dpp is ectopically expressed and thus may contribute to the patterning defects. These results demonstrate an essential requirement of noncanonical signaling pathways for a persistently activated RTK to cause pathological defects in an organism.

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Learning a genome-wide score of human–mouse conservation at the functional genomics level

Nature Communications ◽

10.1038/s41467-021-22653-8 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Soo Bin Kwon ◽

Jason Ernst

Keyword(s):

Mouse Model ◽

Functional Genomics ◽

Functional Genomic ◽

Transcriptomic Data ◽

Model Studies ◽

Genome Wide ◽

A Genome ◽

Important Challenge ◽

Genomic Regions ◽

Human And Mouse

AbstractIdentifying genomic regions with functional genomic properties that are conserved between human and mouse is an important challenge in the context of mouse model studies. To address this, we develop a method to learn a score of evidence of conservation at the functional genomics level by integrating information from a compendium of epigenomic, transcription factor binding, and transcriptomic data from human and mouse. The method, Learning Evidence of Conservation from Integrated Functional genomic annotations (LECIF), trains neural networks to generate this score for the human and mouse genomes. The resulting LECIF score highlights human and mouse regions with shared functional genomic properties and captures correspondence of biologically similar human and mouse annotations. Analysis with independent datasets shows the score also highlights loci associated with similar phenotypes in both species. LECIF will be a resource for mouse model studies by identifying loci whose functional genomic properties are likely conserved.

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Genome-Wide Analyses Identifies Known and New Markers Responsible of Chicken Plumage Color

Animals ◽

10.3390/ani10030493 ◽

2020 ◽

Vol 10 (3) ◽

pp. 493

Author(s):

Salvatore Mastrangelo ◽

Filippo Cendron ◽

Gianluca Sottile ◽

Giovanni Niero ◽

Baldassare Portolano ◽

...

Keyword(s):

Genome Wide Association Study ◽

Snp Array ◽

Fixation Index ◽

Phenotypic Traits ◽

Plumage Color ◽

Phenotypic Marker ◽

Genome Wide ◽

A Genome ◽

The Difference ◽

Genomic Regions

Through the development of the high-throughput genotyping arrays, molecular markers and genes related to phenotypic traits have been identified in livestock species. In poultry, plumage color is an important qualitative trait that can be used as phenotypic marker for breed identification. In order to assess sources of genetic variation related to the Polverara chicken breed plumage colour (black vs. white), we carried out a genome-wide association study (GWAS) and a genome-wide fixation index (FST) scan to uncover the genomic regions involved. A total of 37 animals (17 white and 20 black) were genotyped with the Affymetrix 600 K Chicken single nucleotide polymorphism (SNP) Array. The combination of results from GWAS and FST revealed a total of 40 significant markers distributed on GGA 01, 03, 08, 12 and 21, and located within or near known genes. In addition to the well-known TYR, other candidate genes have been identified in this study, such as GRM5, RAB38 and NOTCH2. All these genes could explain the difference between the two Polverara breeds. Therefore, this study provides the basis for further investigation of the genetic mechanisms involved in plumage color in chicken.

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