scholarly journals Evolution and genetics of precocious burrowing behavior in Peromyscus mice

2017 ◽  
Author(s):  
Hillery C. Metz ◽  
Nicole L. Bedford ◽  
Linda Pan ◽  
Hopi E. Hoekstra
Keyword(s):  
Single Gene ◽  
Genomic Region ◽  
Life Stages ◽  
Tunnel Length ◽  
Closely Related Species ◽  
Peromyscus Polionotus ◽  
Early Life Environment ◽  
Burrowing Behavior ◽  
Juvenile Behavior ◽  
Innate Behaviors

A central challenge in biology is to understand how innate behaviors evolve between closely related species. One way to elucidate how differences arise is to compare the development of behavior in species with distinct adult traits. Here, we report that Peromyscus polionotus is strikingly precocious with regard to burrowing behavior, but not other behaviors, compared to its sister species P. maniculatus . In P. polionotus , burrows were excavated as early as 17 days of age, while P. maniculatus did not build burrows until 10 days later. Moreover, the well-known differences in burrow architecture between adults of these species -- P. polionotus adults excavate long burrows with an escape tunnel, while P. maniculatus dig short, single-tunnel burrows -- were intact in juvenile burrowers. To test whether this juvenile behavior is influenced by early-life environment, pups of both species were reciprocally cross-fostered. Fostering did not alter the characteristic burrowing behavior of either species, suggesting these differences are genetic. In backcross F2 hybrids, we show that precocious burrowing and adult tunnel length are genetically correlated, and that a single P. polionotus allele in a genomic region linked to adult tunnel length is predictive of precocious burrow construction. The co-inheritance of developmental and adult traits indicates the same genetic region -- either a single gene with pleiotropic effects, or closely linked genes -- acts on distinct aspects of the same behavior across life stages. Such genetic variants likely affect behavioral drive (i.e. motivation) to burrow, and thereby affect both the development and adult expression of burrowing behavior.

scholarly journals Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence

Genes ◽  
2020 ◽  
Vol 11 (9) ◽  
pp. 1026 ◽  
Author(s):  
K. N. S. Usha Kiranmayee ◽  
C. Tom Hash ◽  
S. Sivasubramani ◽  
P. Ramu ◽  
Bhanu Prakash Amindala ◽  
...  
Keyword(s):  
Drought Tolerance ◽  
Fine Mapping ◽  
Mapping Population ◽  
Single Gene ◽  
Genotyping By Sequencing ◽  
Introgression Line ◽  
Genomic Region ◽  
Stay Green ◽  
Delayed Senescence ◽  
Genomic Regions

This study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was developed from an introgression line cross—RSG04008-6 (stay-green) × J2614-11 (moderately senescent). The fine-mapping population with 1894 F2 was genotyped with eight SSRs and a set of 152 recombinants was identified, advanced to the F4 generation, field evaluated with three replications over 2 seasons, and genotyped with the GBS approach. A high-resolution linkage map was developed for SBI-10L using 260 genotyping by sequencing—Single Nucleotide Polymorphism (GBS–SNPs). Using the best linear unpredicted means (BLUPs) of the percent green leaf area (%GL) traits and the GBS-based SNPs, we identified seven quantitative trait loci (QTL) clusters and single gene, mostly involved in drought-tolerance, for each QTL cluster, viz., AP2/ERF transcription factor family (Sobic.010G202700), NBS-LRR protein (Sobic.010G205600), ankyrin-repeat protein (Sobic.010G205800), senescence-associated protein (Sobic.010G270300), WD40 (Sobic.010G205900), CPK1 adapter protein (Sobic.010G264400), LEA2 protein (Sobic.010G259200) and an expressed protein (Sobic.010G201100). The target genomic region was thus delimited from 15 Mb to 8 genes co-localized with QTL clusters, and validated using quantitative real-time (qRT)–PCR.

scholarly journals An Interstitial 20q11.21 Microdeletion Causing Mild Intellectual Disability and Facial Dysmorphisms

2013 ◽  
Vol 2013 ◽  
pp. 1-5 ◽  
Author(s):  
Ivan Y. Iourov ◽  
Svetlana G. Vorsanova ◽  
Oxana S. Kurinnaia ◽  
Yuri B. Yurov
Keyword(s):  
Intellectual Disability ◽  
Single Gene ◽  
Index Patient ◽  
Genomic Region ◽  
Comparative Genomic ◽  
Mild Intellectual Disability ◽  
Present Case Report ◽  
Facial Dysmorphisms ◽  
Genomic Variations ◽  
Opitz Syndrome

We report a case of an interstitial chromosome 20q11.21 microdeletion in a 7-year-old male child presenting with mild intellectual disability and facial dysmorphisms. Array comparative genomic hybridization (CGH) has shown that the deletion resulted in the loss of 68 genes, among which 5 genes (COX4I2,MYLK2,ASXL1,DNMT3B, andSNTA1) are disease causing. The size of the deletion was estimated to span 2.6 Mb. Only three cases of deletions encompassing this chromosomal region have been reported. The phenotype of the index patient was found to resemble the mildest cases of Bohring-Opitz syndrome that is caused byASXL1mutations. Anin silicoevaluation of the deleted genomic region has shown that benign genomic variations have never been observed to affect theASXL1gene, in contrast to the other disease-causing genes. As a result, it was suggested thatASXL1loss is likely to be the main cause of the phenotypic manifestations. The present case report indicates that a loss of the disease-causing gene can produce a milder phenotype of a single gene condition.

scholarly journals Recurrent erosion of COA1/MITRAC15 demonstrates gene dispensability in oxidative phosphorylation

2021 ◽  
Author(s):  
Sagar Sharad Shinde ◽  
Sandhya Sharma ◽  
Lokdeep Teekas ◽  
Ashutosh Sharma ◽  
Nagarjun Vijay
Keyword(s):  
Skeletal Muscle ◽  
Oxidative Phosphorylation ◽  
Gene Loss ◽  
Chromosomal Rearrangements ◽  
Genomic Region ◽  
Glycolytic Pathway ◽  
Mitochondrial Translation ◽  
Closely Related Species ◽  
Genome Assemblies

Skeletal muscle fibers rely upon either oxidative phosphorylation or glycolytic pathway to achieve muscular contractions that power mechanical movements. Species with energy-intensive adaptive traits that require sudden bursts of energy have a greater dependency on fibers that use the glycolytic pathway. Glycolytic fibers have decreased reliance on OXPHOS and lower mitochondrial content compared to oxidative fibers. Hence, we hypothesized that adaptive gene loss might have occurred within the OXPHOS pathway in lineages that largely depend on glycolytic fibers. The protein encoded by the COA1/MITRAC15 gene with conserved orthologs found in budding yeast to humans promotes mitochondrial translation. We show that gene disrupting mutations have accumulated within the COA1/MITRAC15 gene in the cheetah, several species of galliforms, and rodents. The genomic region containing COA1/MITRAC15 is a well-established evolutionary breakpoint region in mammals. Careful inspection of genome assemblies of closely related species of rodents and marsupials suggests two independent COA1/MITRAC15 gene loss events co-occurring with chromosomal rearrangements. Besides recurrent gene loss events, we document changes in COA1/MITRAC15 exon structure in primates and felids. The detailed evolutionary history presented in this study reveals the intricate link between skeletal muscle fiber composition and dispensability of the chaperone-like role of the COA1/MITRAC15 gene.

scholarly journals Molecular parallelisms between pigmentation in the avian iris and the integument of ectothermic vertebrates

PLoS Genetics ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. e1009404
Author(s):  
Pedro Andrade ◽  
Małgorzata A. Gazda ◽  
Pedro M. Araújo ◽  
Sandra Afonso ◽  
Jacob. A. Rasmussen ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Stop Codon ◽  
Expression Profiles ◽  
Single Gene ◽  
Skin Pigmentation ◽  
Premature Stop Codon ◽  
Gene Expression Profiles ◽  
Genomic Region ◽  
Pigment Cells ◽  
Eye Color

Birds exhibit striking variation in eye color that arises from interactions between specialized pigment cells named chromatophores. The types of chromatophores present in the avian iris are lacking from the integument of birds or mammals, but are remarkably similar to those found in the skin of ectothermic vertebrates. To investigate molecular mechanisms associated with eye coloration in birds, we took advantage of a Mendelian mutation found in domestic pigeons that alters the deposition of yellow pterin pigments in the iris. Using a combination of genome-wide association analysis and linkage information in pedigrees, we mapped variation in eye coloration in pigeons to a small genomic region of ~8.5kb. This interval contained a single gene, SLC2A11B, which has been previously implicated in skin pigmentation and chromatophore differentiation in fish. Loss of yellow pigmentation is likely caused by a point mutation that introduces a premature STOP codon and leads to lower expression of SLC2A11B through nonsense-mediated mRNA decay. There were no substantial changes in overall gene expression profiles between both iris types as well as in genes directly associated with pterin metabolism and/or chromatophore differentiation. Our findings demonstrate that SLC2A11B is required for the expression of pterin-based pigmentation in the avian iris. They further highlight common molecular mechanisms underlying the production of coloration in the iris of birds and skin of ectothermic vertebrates.

scholarly journals Recurrent erosion of COA1/MITRAC15 exemplifies conditional gene dispensability in oxidative phosphorylation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sagar Sharad Shinde ◽  
Sandhya Sharma ◽  
Lokdeep Teekas ◽  
Ashutosh Sharma ◽  
Nagarjun Vijay
Keyword(s):  
Skeletal Muscle ◽  
Oxidative Phosphorylation ◽  
Gene Loss ◽  
Chromosomal Rearrangements ◽  
Genomic Region ◽  
Mitochondrial Translation ◽  
Closely Related Species ◽  
Genome Assemblies ◽  
Exon Structure

AbstractSkeletal muscle fibers rely upon either oxidative phosphorylation or the glycolytic pathway with much less reliance on oxidative phosphorylation to achieve muscular contractions that power mechanical movements. Species with energy-intensive adaptive traits that require sudden bursts of energy have a greater dependency on glycolytic fibers. Glycolytic fibers have decreased reliance on OXPHOS and lower mitochondrial content compared to oxidative fibers. Hence, we hypothesized that gene loss might have occurred within the OXPHOS pathway in lineages that largely depend on glycolytic fibers. The protein encoded by the COA1/MITRAC15 gene with conserved orthologs found in budding yeast to humans promotes mitochondrial translation. We show that gene disrupting mutations have accumulated within the COA1 gene in the cheetah, several species of galliform birds, and rodents. The genomic region containing COA1 is a well-established evolutionary breakpoint region in mammals. Careful inspection of genome assemblies of closely related species of rodents and marsupials suggests two independent COA1 gene loss events co-occurring with chromosomal rearrangements. Besides recurrent gene loss events, we document changes in COA1 exon structure in primates and felids. The detailed evolutionary history presented in this study reveals the intricate link between skeletal muscle fiber composition and the occasional dispensability of the chaperone-like role of the COA1 gene.

scholarly journals The Loci of Behavioral Evolution: Evidence That Fas2 and tilB Underlie Differences in Pupation Site Choice Behavior between Drosophila melanogaster and D. simulans

2019 ◽  
Vol 37 (3) ◽  
pp. 864-880
Author(s):  
Alison Pischedda ◽  
Michael P Shahandeh ◽  
Thomas L Turner
Keyword(s):  
Drosophila Melanogaster ◽  
X Chromosome ◽  
Related Species ◽  
Choice Behavior ◽  
Genetic Basis ◽  
Association Studies ◽  
Single Gene ◽  
Closely Related Species ◽  
Environmentally Sensitive ◽  
Pupation Site

Abstract The behaviors of closely related species can be remarkably different, and these differences have important ecological and evolutionary consequences. Although the recent boom in genotype–phenotype studies has led to a greater understanding of the genetic architecture and evolution of a variety of traits, studies identifying the genetic basis of behaviors are, comparatively, still lacking. This is likely because they are complex and environmentally sensitive phenotypes, making them difficult to measure reliably for association studies. The Drosophila species complex holds promise for addressing these challenges, as the behaviors of closely related species can be readily assayed in a common environment. Here, we investigate the genetic basis of an evolved behavioral difference, pupation site choice, between Drosophila melanogaster and D. simulans. In this study, we demonstrate a significant contribution of the X chromosome to the difference in pupation site choice behavior between these species. Using a panel of X-chromosome deficiencies, we screened the majority of the X chromosome for causal loci and identified two regions associated with this X-effect. We then collect gene disruption and RNAi data supporting a single gene that affects pupation behavior within each region: Fas2 and tilB. Finally, we show that differences in tilB expression correlate with the differences in pupation site choice behavior between species. This evidence associating two genes with differences in a complex, environmentally sensitive behavior represents the first step toward a functional and evolutionary understanding of this behavioral divergence.

scholarly journals The 22q11.2 Deletion Syndrome: A Gene Dosage Perspective

2006 ◽  
Vol 6 ◽  
pp. 1881-1887 ◽  
Author(s):  
Antonio Baldini
Keyword(s):  
Developmental Stages ◽  
Gene Dosage ◽  
Single Gene ◽  
22Q11.2 Deletion Syndrome ◽  
Genomic Region ◽  
Deletion Syndrome ◽  
Genomic Disorder ◽  
22Q11.2 Deletion ◽  
Developmental Context

The 22q11.2 deletion/DiGeorge syndrome is a relatively common “genomic” disorder that results from heterozygous deletion of a 3-Mbp segment of chromosome 22. Of the more than 30 genes deleted in this syndrome,TBX1is the only one that has been found to be mutated in some patients with a phenotype that is very similar to that of patients with the full deletion, suggesting thatTBX1haploinsufficiency is a major contributor to the syndrome’s phenotype. Multi- and single-gene mouse models have provided a considerable amount of information about the consequences of decreased and increased dosage of the genomic region (and in particular of theTbx1gene) on mouse embryonic development. Modified alleles ofTbx1, as well as conditional ablation strategies have been utilized to mapin vivothe tissues and developmental stages most sensitive to gene dosage. These experiments have revealed substantially different sensitivity to gene dosage in different tissues and at different times, underlying the importance of the developmental context within which gene dosage reduction occurs.

Genetics and molecular mapping of resistance to Plasmodiophora brassicae pathotypes 2, 3, 5, 6, and 8 in rutabaga (Brassica napus var. napobrassica)

Genome ◽  
2016 ◽  
Vol 59 (10) ◽  
pp. 805-815 ◽  
Author(s):  
Muhammad Jakir Hasan ◽  
Habibur Rahman
Keyword(s):  
Brassica Napus ◽  
Doubled Haploid ◽  
Genetic Basis ◽  
Molecular Mapping ◽  
Plasmodiophora Brassicae ◽  
Single Gene ◽  
Genomic Region ◽  
Clubroot Disease ◽  
Dh Population ◽  
Brassica Crops

Clubroot disease, caused by Plasmodiophora brassicae, is a threat to the production of Brassica crops including oilseed B. napus. In Canada, several pathotypes of this pathogen, such as pathotypes 2, 3, 5, 6, and 8, were identified, and resistance to these pathotypes was found in a rutabaga (B. napus var. napobrassica) genotype. In this paper, we report the genetic basis and molecular mapping of this resistance by use of F2, backcross (BC1), and doubled haploid (DH) populations generated from crossing of this rutabaga line to a susceptible spring B. napus canola line. The F1, F2, and BC1 populations were evaluated for resistance to pathotype 3, and the DH population was evaluated for resistance to pathotypes 2, 3, 5, 6, and 8. A 3:1 segregation in F2 and a 1:1 segregation in BC1 were found for resistance to pathotype 3, and a 1:1 segregation was found in the DH population for resistance to all pathotypes. Molecular mapping by using the DH population identified a genomic region on chromosome A8 carrying resistance to all five pathotypes. This suggests that a single gene or a cluster of genes, located in this genomic region, is involved in the control of resistance to these pathotypes.

A complex phenotype in salmon controlled by a simple change in migratory timing

Science ◽  
2020 ◽  
Vol 370 (6516) ◽  
pp. 609-613 ◽  
Author(s):  
Neil F. Thompson ◽  
Eric C. Anderson ◽  
Anthony J. Clemento ◽  
Matthew A. Campbell ◽  
Devon E. Pearse ◽  
...  
Keyword(s):  
Chinook Salmon ◽  
Sexual Maturity ◽  
Single Gene ◽  
Genomic Region ◽  
Seasonal Patterns ◽  
Diverse Population ◽  
Complex Phenotype ◽  
Migration Timing ◽  
Simple Change ◽  
Migratory Phenotype

Differentiation between ecotypes is usually presumed to be complex and polygenic. Seasonal patterns of life history in salmon are used to categorize them into ecotypes, which are often considered “distinct” animals. Using whole-genome sequencing and tribal fishery sampling of Chinook salmon, we show that a single, small genomic region is nearly perfectly associated with spawning migration timing but not with adiposity or sexual maturity, traits long perceived as central to salmon ecotypes. Distinct migration timing does not prevent interbreeding between ecotypes, which are the result of a simple, ancient polymorphism segregating within a diverse population. Our finding that a complex migratory phenotype results from a single gene region will facilitate conservation and restoration of this iconic fish.

scholarly journals Sequences, sequence clusters and bacterial species

2006 ◽  
Vol 361 (1475) ◽  
pp. 1917-1927 ◽  
Author(s):  
William P Hanage ◽  
Christophe Fraser ◽  
Brian G Spratt
Keyword(s):  
Single Gene ◽  
Bacterial Species ◽  
Rrna Gene ◽  
Similar Species ◽  
Gene Sequences ◽  
Closely Related Species ◽  
Microbiological Methods ◽  
Large Populations ◽  
Interspecies Recombination ◽  
Clustering Patterns

Whatever else they should share, strains of bacteria assigned to the same species should have house-keeping genes that are similar in sequence. Single gene sequences (or rRNA gene sequences) have very few informative sites to resolve the strains of closely related species, and relationships among similar species may be confounded by interspecies recombination. A more promising approach (multilocus sequence analysis, MLSA) is to concatenate the sequences of multiple house-keeping loci and to observe the patterns of clustering among large populations of strains of closely related named bacterial species. Recent studies have shown that large populations can be resolved into non-overlapping sequence clusters that agree well with species assigned by the standard microbiological methods. The use of clustering patterns to inform the division of closely related populations into species has many advantages for poorly studied bacteria (or to re-evaluate well-studied species), as it provides a way of recognizing natural discontinuities in the distribution of similar genotypes. Clustering patterns can be used by expert groups as the basis of a pragmatic approach to assigning species, taking into account whatever additional data are available (e.g. similarities in ecology, phenotype and gene content). The development of large MLSA Internet databases provides the ability to assign new strains to previously defined species clusters and an electronic taxonomy. The advantages and problems in using sequence clusters as the basis of species assignments are discussed.

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