scholarly journals The genetics of behavioral isolation in an island system

2018 ◽  
Author(s):  
Thomas Blankers ◽  
Kevin P. Oh ◽  
Kerry L. Shaw
Keyword(s):  
Mating Behavior ◽  
Species Pair ◽  
Song Variation ◽  
Behavioral Isolation ◽  
Island Species ◽  
Biogeographic History ◽  
Trait Locus ◽  
Island System ◽  
Cricket Song ◽  
Genomic Regions

AbstractMating behavior divergence can make significant contributions to reproductive isolation and speciation in various biogeographic contexts. However, whether the genetic architecture underlying mating behavior divergence is related to the biogeographic history and the tempo and mode of speciation remains poorly understood. Here, we use quantitative trait locus (QTL) mapping to infer the number, distribution, and effect size of mating song rhythm variation in the crickets Laupala eukolea and L. cerasina, which occur on different islands (Maui and Hawai’i). We then compare these results with a similar study of an independently evolving species pair that diverged within the same island. Finally, we annotate the L. cerasina transcriptome and test whether QTL fall in functionally enriched genomic regions. We document a polygenic architecture behind song rhythm divergence in the inter-island species pair that is remarkably similar to that previously found for an intra-island species pair in the same genus. Importantly, QTL regions were significantly enriched for potential homologs of genes involved in pathways that may be modulating cricket song rhythm. These clusters of loci could constrain the spatial genomic distribution of genetic variation underlying cricket song variation and harbor several candidate genes that merit further study.

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

Nutrients ◽  
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.

scholarly journals Integration of high-density genetic mapping with transcriptome analysis uncovers numerous agronomic QTL and reveals candidate genes for the control of tillering in sorghum

2021 ◽  
Author(s):  
Rajanikanth Govindarajulu ◽  
Ashley N Hostetler ◽  
Yuguo Xiao ◽  
Srinivasa R Chaluvadi ◽  
Margarita Mauro-Herrera ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Interspecific Cross ◽  
Crop Improvement ◽  
Differentially Expressed ◽  
Plant Domestication ◽  
Sorghum Propinquum ◽  
Ril Population ◽  
Trait Locus ◽  
Genomic Regions ◽  
Low Coverage

Abstract Phenotypes such as branching, photoperiod sensitivity, and height were modified during plant domestication and crop improvement. Here, we perform quantitative trait locus (QTL) mapping of these and other agronomic traits in a recombinant inbred line (RIL) population derived from an interspecific cross between Sorghum propinquum and Sorghum bicolor inbred Tx7000. Using low-coverage Illumina sequencing and a bin-mapping approach, we generated ∼1920 bin markers spanning ∼875 cM. Phenotyping data were collected and analyzed from two field locations and one greenhouse experiment for six agronomic traits, thereby identifying a total of 30 QTL. Many of these QTL were penetrant across environments and co-mapped with major QTL identified in other studies. Other QTL uncovered new genomic regions associated with these traits, and some of these were environment-specific in their action. To further dissect the genetic underpinnings of tillering, we complemented QTL analysis with transcriptomics, identifying 6189 genes that were differentially expressed during tiller bud elongation. We identified genes such as Dormancy Associated Protein 1 (DRM1) in addition to various transcription factors that are differentially expressed in comparisons of dormant to elongating tiller buds and lie within tillering QTL, suggesting that these genes are key regulators of tiller elongation in sorghum. Our study demonstrates the usefulness of this RIL population in detecting domestication and improvement-associated genes in sorghum, thus providing a valuable resource for genetic investigation and improvement to the sorghum community.

scholarly journals Genetic variation in recombination rate in the pig

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Martin Johnsson ◽  
Andrew Whalen ◽  
Roger Ros-Freixedes ◽  
Gregor Gorjanc ◽  
Ching-Yi Chen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Recombination Rate ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Genetic Material ◽  
A Genome ◽  
Pig Genome ◽  
Genetic Length ◽  
Trait Locus ◽  
Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

Genetic dissection of partial resistance to race 6 of Venturia inaequalis in apple

Genome ◽  
2003 ◽  
Vol 46 (2) ◽  
pp. 224-234 ◽  
Author(s):  
C E Durel ◽  
L Parisi ◽  
F Laurens ◽  
W E Van de Weg ◽  
R Liebhard ◽  
...  
Keyword(s):  
Resistance Gene ◽  
Malus Domestica ◽  
Quantitative Trait ◽  
Partial Resistance ◽  
Venturia Inaequalis ◽  
Genetic Dissection ◽  
Resistance Breakdown ◽  
Trait Locus ◽  
New Races ◽  
Genomic Regions

Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of apple (Malus × domestica). The major resistance gene, Vf, has been widely used in apple breeding programs, but two new races of the fungus (races 6 and 7) are able to overcome this gene. A mapped F1 progeny derived from a cross between the cultivars Prima and Fiesta has been inoculated with two monoconidial strains of race 6. These strains originated from sporulating leaves of 'Prima' and a descendant of 'Prima' that were grown in an orchard in northern Germany. 'Prima' carries the Vf resistance gene, whereas 'Fiesta' lacks Vf. A large variation in resistance and (or) susceptibility was observed among the individuals of the progeny. Several quantitative trait loci (QTLs) for resistance were identified that mapped on four genomic regions. One of them was located in the very close vicinity of the Vf resistance gene on linkage group LG-1 of the 'Prima' genetic map. This QTL is isolate specific because it was only detected with one of the two isolates. Two out of the three other genomic regions were identified with both isolates (LG-11 and LG-17). On LG-11, a QTL effect was detected in both parents. The genetic dissection of this QTL indicated a favourable intra-locus interaction between some parental alleles.Key words: Malus × domestica, partial resistance, Venturia inaequalis, resistance breakdown, quantitative trait locus.

scholarly journals Relationship between Yield Components and Partial Resistance to Lecanicillium fungicola in the Button Mushroom, Agaricus bisporus, Assessed by Quantitative Trait Locus Mapping

2012 ◽  
Vol 78 (7) ◽  
pp. 2435-2442 ◽  
Author(s):  
Marie Foulongne-Oriol ◽  
Anne Rodier ◽  
Jean-Michel Savoie
Keyword(s):  
Quantitative Trait ◽  
Wild Strain ◽  
Genomic Region ◽  
Yield Component ◽  
Phenotypic Variance ◽  
Button Mushroom ◽  
Content Type ◽  
Dry Bubble ◽  
Trait Locus ◽  
Genomic Regions

ABSTRACTDry bubble, caused byLecanicillium fungicola, is one of the most detrimental diseases affecting button mushroom cultivation. In a previous study, we demonstrated that breeding for resistance to this pathogen is quite challenging due to its quantitative inheritance. A second-generation hybrid progeny derived from an intervarietal cross between a wild strain and a commercial cultivar was characterized forL. fungicolaresistance under artificial inoculation in three independent experiments. Analysis of quantitative trait loci (QTL) was used to determine the locations, numbers, and effects of genomic regions associated with dry-bubble resistance. Four traits related to resistance were analyzed. Two to four QTL were detected per trait, depending on the experiment. Two genomic regions, on linkage group X (LGX) and LGVIII, were consistently detected in the three experiments. The genomic region on LGX was detected for three of the four variables studied. The total phenotypic variance accounted for by all QTL ranged from 19.3% to 42.1% over all traits in all experiments. For most of the QTL, the favorable allele for resistance came from the wild parent, but for some QTL, the allele that contributed to a higher level of resistance was carried by the cultivar. Comparative mapping with QTL for yield-related traits revealed five colocations between resistance and yield component loci, suggesting that the resistance results from both genetic factors and fitness expression. The consequences for mushroom breeding programs are discussed.

scholarly journals Linkage mapping of quantitative trait loci for fiber yield and its related traits in the population derived from cultivated ramie and wild B. nivea var. tenacissima

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Zheng Zeng ◽  
Yanzhou Wang ◽  
Chan Liu ◽  
Xiufeng Yang ◽  
Hengyun Wang ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Linkage Mapping ◽  
Genetic Basis ◽  
Natural Fiber ◽  
Stem Bark ◽  
High Yield ◽  
Fiber Yield ◽  
Wild Allele ◽  
Trait Locus ◽  
Genomic Regions

AbstractRamie is an important natural fiber crop, and the fiber yield and its related traits are the most valuable traits in ramie production. However, the genetic basis for these traits is still poorly understood, which has dramatically hindered the breeding of high yield in this fiber crop. Herein, a high-density genetic map with 6,433 markers spanning 2476.5 cM was constructed using a population derived from two parents, cultivated ramie Zhongsizhu 1 (ZSZ1) and its wild progenitor B. nivea var. tenacissima (BNT). The fiber yield (FY) and its four related traits—stem diameter (SD) and length (SL), stem bark weight (BW) and thickness (BT)—were performed for quantitative trait locus (QTL) analysis, resulting in a total of 47 QTLs identified. Forty QTLs were mapped into 12 genomic regions, thus forming 12 QTL clusters. Among 47 QTLs, there were 14 QTLs whose wild allele from BNT was beneficial. Interestingly, all QTLs in Cluster 10 displayed overdominance, indicating that the region of this cluster was likely heterotic loci. In addition, four fiber yield-related genes underwent positive selection were found either to fall into the FY-related QTL regions or to be near to the identified QTLs. The dissection of FY and FY-related traits not only improved our understanding to the genetic basis of these traits, but also provided new insights into the domestication of FY in ramie. The identification of many QTLs and the discovery of beneficial alleles from wild species provided a basis for the improvement of yield traits in ramie breeding.

scholarly journals Identification of Neuronal Enhancers of the Proopiomelanocortin Gene by Transgenic Mouse Analysis and Phylogenetic Footprinting

2005 ◽  
Vol 25 (8) ◽  
pp. 3076-3086 ◽  
Author(s):  
Flávio S. J. de Souza ◽  
Andrea M. Santangelo ◽  
Viviana Bumaschny ◽  
María Elena Avale ◽  
James L. Smart ◽  
...  
Keyword(s):  
Energy Homeostasis ◽  
Significant Quantitative Trait Locus ◽  
Phylogenetic Footprinting ◽  
Transcriptional Unit ◽  
Human Populations ◽  
Chromosome 2 ◽  
Loss Of Function ◽  
Trait Locus ◽  
Genomic Regions ◽  
Arcuate Neurons

ABSTRACT The proopiomelanocortin (POMC) gene is expressed in the pituitary and arcuate neurons of the hypothalamus. POMC arcuate neurons play a central role in the control of energy homeostasis, and rare loss-of-function mutations in POMC cause obesity. Moreover, POMC is the prime candidate gene within a highly significant quantitative trait locus on chromosome 2 associated with obesity traits in several human populations. Here, we identify two phylogenetically conserved neuronal POMC enhancers designated nPE1 (600 bp) and nPE2 (150 bp) located approximately 10 to 12 kb upstream of mammalian POMC transcriptional units. We show that mouse or human genomic regions containing these enhancers are able to direct reporter gene expression to POMC hypothalamic neurons, but not the pituitary of transgenic mice. Conversely, deletion of nPE1 and nPE2 in the context of the entire transcriptional unit of POMC abolishes transgene expression in the hypothalamus without affecting pituitary expression. Our results indicate that the nPEs are necessary and sufficient for hypothalamic POMC expression and that POMC expression in the brain and pituitary is controlled by independent sets of enhancers. Our study advances the understanding of the molecular nature of hypothalamic POMC neurons and will be useful to determine whether polymorphisms in POMC regulatory regions play a role in the predisposition to obesity.

scholarly journals Genetic analysis of albuminuria in a cross between C57BL/6J and DBA/2J mice

2007 ◽  
Vol 293 (5) ◽  
pp. F1649-F1656 ◽  
Author(s):  
Susan Sheehan ◽  
Shirng-Wern Tsaih ◽  
Benjamin L. King ◽  
Caitlin Stanton ◽  
Gary A. Churchill ◽  
...  
Keyword(s):  
Kidney Disease ◽  
Genetic Basis ◽  
Significant Risk ◽  
Significant Risk Factor ◽  
Medical Problem ◽  
Progression Of Kidney Disease ◽  
Trait Locus ◽  
Stage Renal Disease ◽  
End Stage ◽  
Genomic Regions

Chronic kidney disease (CKD) is a growing medical problem and a significant risk factor for the development of end-stage renal disease, cardiovascular disease, and cardiovascular mortality. The genetic basis of CKD is recognized, but knowledge of the specific genes that contribute to the onset and progression of kidney disease is limited, mainly because of the difficulty and expense of identifying genes underlying CKD in humans. Results from genetic studies of CKD in rodents often correspond to findings in humans; therefore, we used quantitative trait locus (QTL) analysis to detect genomic regions affecting albuminuria in a cross between C57BL/6J and DBA/2J mice, strains resistant and susceptible to CKD, respectively. We identified several independent and interacting loci affecting albuminuria, including one QTL on mouse chromosome (Chr) 2 that is concordant with QTL influencing urinary albumin excretion on rat Chr 3 and diabetic nephropathy on human Chr 20p. Because this QTL was identified in multiple mouse crosses, as well as in rats and in humans, we used comparative genomics, haplotype analysis, and expression profiling to narrow the initial QTL interval from 386 genes to 10 genes with known coding sequence polymorphisms or expression differences between the strains. These results support the continued use of multiple cross-mapping and cross-species comparisons to further our understanding of the genetic basis of kidney disease.

scholarly journals Explaining the heritability of an ecologically significant trait in terms of individual quantitative trait loci

2011 ◽  
Vol 7 (6) ◽  
pp. 896-898 ◽  
Author(s):  
Alison G. Scoville ◽  
Young Wha Lee ◽  
John H. Willis ◽  
John K. Kelly
Keyword(s):  
Qtl Mapping ◽  
Quantitative Trait ◽  
Complex Traits ◽  
Genetic Variance ◽  
Balancing Selection ◽  
Natural Populations ◽  
Population Based ◽  
Population Variation ◽  
Trait Locus ◽  
Genomic Regions

Most natural populations display substantial genetic variation in behaviour, morphology, physiology, life history and the susceptibility to disease. A major challenge is to determine the contributions of individual loci to variation in complex traits. Quantitative trait locus (QTL) mapping has identified genomic regions affecting ecologically significant traits of many species. In nearly all cases, however, the importance of these QTLs to population variation remains unclear. In this paper, we apply a novel experimental method to parse the genetic variance of floral traits of the annual plant Mimulus guttatus into contributions of individual QTLs. We first use QTL-mapping to identify nine loci and then conduct a population-based breeding experiment to estimate V Q , the genetic variance attributable to each QTL. We find that three QTLs with moderate effects explain up to one-third of the genetic variance in the natural population. Variation at these loci is probably maintained by some form of balancing selection. Notably, the largest effect QTLs were relatively minor in their contribution to heritability.

scholarly journals Quantitative Trait Locus Analysis Identifies Rat Genomic Regions Related to Amphetamine-Induced Locomotion and Gαi3 Levels in Nucleus Accumbens

2008 ◽  
Vol 33 (11) ◽  
pp. 2735-2746 ◽  
Author(s):  
Marc N Potenza ◽  
Edward S Brodkin ◽  
Bao-Zhu Yang ◽  
Shari G Birnbaum ◽  
Eric J Nestler ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Nucleus Accumbens ◽  
Quantitative Trait Locus Analysis ◽  
Quantitative Trait ◽  
Trait Locus ◽  
Genomic Regions
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