Conservation Genetics, Journal Year: 2023, Volume and Issue: 24(4), P. 523 - 535
Published: April 17, 2023
Language: Английский
Molecular Ecology Resources, Journal Year: 2020, Volume and Issue: 20(6), P. 1505 - 1516
Published: June 10, 2020
Abstract Noninvasive genotyping methods have become key elements of wildlife research over the last two decades, but their widespread adoption is limited by high costs, low success rates and error rates. The information lost when may lead to decreased precision in animal population densities, which could misguide conservation management actions. Single nucleotide polymorphisms (SNPs) provide a promising alternative traditionally used microsatellites as SNPs allow amplification shorter DNA fragments, are less prone errors produce results that easily shared among laboratories. Here, we outline detailed protocol for cost‐effective accurate noninvasive SNP using multiplexed amplicon sequencing optimized degraded DNA. We validated this method individual identification 216 scats, 18 hairs 15 tissues from coyotes ( Canis latrans ) 26 SNPs. Our rate scat samples was 93%, 100% hair tissue, representing substantial increase compared previous microsatellite‐based studies while remaining at cost under $5 per PCR replicate (excluding labour). accuracy genotypes further corroborated scats matching known, GPS‐collared were always located within territory known individual. also show different levels multiplexing produced similar results, product cleanup strategies can effects on success. By making more affordable, efficient, use monitor conserve free‐ranging populations.
Language: Английский
Citations
74
Proceedings of the National Academy of Sciences, Journal Year: 2022, Volume and Issue: 119(23)
Published: June 3, 2022
Significance Although turnover of sex chromosomes is very common in many vertebrate lineages, the transition process still elusive. We studied sex-determining region (SDR) 12 congeneric fish species Takifugu that compose an important model for study genomics and determination. found while nine retained their ancestral SDR, three had acquired derived SDRs. SDRs resided different chromosomes, they harbored a shared supergene flanked by two putative transposable elements. The results highlight underestimated role mobile vertebrates.
Language: Английский
Citations
32
Molecular Biology and Evolution, Journal Year: 2021, Volume and Issue: 38(11), P. 4683 - 4699
Published: July 11, 2021
How early stages of speciation in free-spawning marine invertebrates proceed is poorly understood. The Western Pacific abalones, Haliotis discus, H. madaka, and gigantea, occur sympatry with shared breeding season are capable producing viable F1 hybrids spite being ecologically differentiated. Population genomic analyses revealed that although the three species genetically distinct, there evidence for historical ongoing gene flow among these species. Evidence from demographic modeling suggests reproductive isolation started to build allopatry has proceeded flow, possibly driven by ecological selection. We identified 27 differentiation islands between closely related discus madaka characterized high FST dA, but not dXY values, as well genetic diversity one population. These signatures suggest recent divergent selection presence outside differentiation. showed low polymorphism both FST, dXY, dA values gigantea. Collectively, abalones appear occupy continuum, associated divergence do have acted barrier loci younger divergences so older divergences.
Language: Английский
Citations
32
Horticulture Research, Journal Year: 2024, Volume and Issue: 11(7)
Published: July 1, 2024
Abstract With advances in next-generation sequencing technologies, various marker genotyping systems have been developed for genomics-based approaches such as genomic selection (GS) and genome-wide association study (GWAS). As new platforms are developed, data from different must be combined. However, the potential use of combined GS GWAS has not yet clarified. In this study, accuracy prediction (GP) detection power increased most fruit quality traits apples when using systems, Illumina Infinium single-nucleotide polymorphism array by random amplicon sequencing-direct (GRAS-Di) systems. addition, GP model, which considered inbreeding effect, further improved seven traits. Runs homozygosity (ROH) islands overlapped with significantly associated regions detected several Breeders may exploited these to select promising breeders, increasing homozygosity. These results suggest that combining genotypic benefits apples. Information on could beneficial improving apples; however, analysis is required elucidate relationship between depression (e.g. decreased vigor).
Language: Английский
Citations
4
Scientific Reports, Journal Year: 2020, Volume and Issue: 10(1)
Published: Dec. 8, 2020
Due to large and complex genomes of Triticeae species, skim sequencing approaches have cost analytical advantages for detecting genetic markers building linkage maps. Here, we develop a high-density map identify quantitative trait loci (QTLs) recombinant inbred lines Aegilops tauschii, D-genome donor bread wheat, using the recently developed genotyping by Random Amplicon Sequencing-Direct (GRAS-Di) system, which facilitates skimming complicated genome generates number markers. The deduced groups based on GRAS-Di corresponded chromosome Ae. tauschii. We successfully identified stable QTLs flowering time spikelet shape-related traits. Genotype differences RILs at QTL-linked were significantly associated with variations. In particular, one was mapped close VRN3 (also known as FLOWERING LOCUS T), controls flowering. system is, therefore, an efficient useful application mapping in species genomes, such species.
Language: Английский
Citations
29
Life, Journal Year: 2022, Volume and Issue: 12(11), P. 1752 - 1752
Published: Nov. 1, 2022
Molecular markers play a crucial role in the improvement of rice. To benefit from these markers, genotyping is carried out to identify differences at specific position genome individuals. The advances sequencing technologies have led development different techniques such as genotyping-by-sequencing. Unlike PCR-fragment-based genotyping, genotyping-by-sequencing has enabled parallel and hundreds samples single run, making it more cost-effective. Currently, GBS being used several pre-breeding programs rice beneficial genes QTL genetic resources. In this review, we present current utilization for materials existing cultivars. challenges perspectives using approach are also highlighted.
Language: Английский
Citations
17
Aquaculture, Journal Year: 2025, Volume and Issue: 600, P. 742266 - 742266
Published: Feb. 6, 2025
Language: Английский
Citations
0
Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(2)
Published: Feb. 1, 2025
ABSTRACT Mutualistic relationships such as the one between Trapezia crabs and coral colonies are common in reef organisms play a crucial role resilience resistance to climate‐induced stressor, yet very little is known about taxonomic diversity evolutionary history of species involved. Despite being essential actors reefs threatened by ongoing degradation their habitat, genetic information available for crabs, including exact number relationships. To overcome this limitation, we sampled Natural History Collections, an important underutilized source genomic data. We used novel approach optimized degraded DNA generate high‐quality data from combination 166 museum tissues freshly collected samples recovered strongly supported phylogeny genus, clarifying majority taxa suggesting potential division into two genera. then focused on most widespread T. bidentata identified four distinct clusters, high divergence cryptic speciation Indian Ocean Marquesas Islands. Populations Central West Pacific showed signs admixture across heterogeneous seascape, attributing potentially long pelagic dispersal phase expansive gene pool. Our results highlight need further explore within other coral‐associated organisms, they likely exhibit more complex patterns than previously understood.
Language: Английский
Citations
0
Aquaculture International, Journal Year: 2025, Volume and Issue: 33(3)
Published: March 12, 2025
Language: Английский
Citations
0
Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(4)
Published: April 1, 2025
ABSTRACT Assessing population vulnerability to climate change is essential for informing management and conservation strategies, particularly amphibians. We integrated genetics ecological niche modeling (ENM) assess the effect of on distribution genetic structure two species Asian warty newts ( Paramesotriton deloustali P. guangxiensis ) in northern Vietnam. analyzed using a genome‐wide SNP dataset generated with MIG‐seq method. Additionally, we applied ensemble predict potential under scenarios (SSP2‐4.5 SSP5‐8.5) periods 2050 2090. Population revealed three primary groups: West, East + Cao Bang (CB), Quang Ninh (QN). CB exhibited discordance between mitochondrial DNA single‐nucleotide nuclear polymorphism data. Furthermore, gene flow within populations was restricted, West QN. Spatial analyses clusters conditioned by environmental variables predicted that cluster would expand, whereas those QN decrease. The introgression structures probably reduces change. ENM analysis these are susceptible change, resulting reduction their suitable habitat areas across all scenarios. also observed shift toward higher elevations. Our results suggest mountainous Vietnam could serve as refugia effects intensify.
Language: Английский
Citations
0