Theoretical and Applied Genetics, Journal Year: 2023, Volume and Issue: 136(11)
Published: Oct. 25, 2023
Language: Английский
Frontiers in Plant Science, Journal Year: 2024, Volume and Issue: 14
Published: Jan. 4, 2024
The World Collection of Sugarcane and Related Grasses, maintained at the USDA-ARS in Miami, FL, is one largest sugarcane germplasm repositories world. However, genetic integrity Saccharum spp. this collection has not been fully analyzed. In study, we employed a single-dose SNP panel to genotype 901 accessions, representing six species various hybrids. Our analysis uncovered high rate clone mislabeling collection. Specifically, identified 86 groups duplicates, characterized by identical genotypes, which encompassed 211 accessions (23% total clones), while 135 groups, constituting 471 clones (52% total), exhibited near-identical genotypes. addition, twenty-seven homonymous were detected, shared same name but differed Hierarchical population structure partitioned into five clusters, corresponding S. barberi, sinense, officinarum, spontaneum robustum/S. edule . An assignment test, based on species, enabled correcting 141 instances mislabeled memberships inaccuracies. Moreover, clarified membership parentage 298 that had ambiguous passport records (e.g., ‘ spp ’, ‘unknown’, ‘hybrid’). Population diversity these further supported Principal Coordinate Analysis neighbor-joining clustering analysis. Molecular Variance revealed within-species variations accounted for 85% molecular variance, with remaining 15% attributed among-species variations. markers developed study offer robust tool characterizing worldwide. These findings have important implications genebank management, exchange, crop improvement.
Language: Английский
Citations
4
Foods, Journal Year: 2023, Volume and Issue: 12(3), P. 455 - 455
Published: Jan. 18, 2023
Similar to genetically modified organisms (GMOs) produced by classical genetic engineering, gene-edited (GE) and their derived food/feed products commercialized on the European Union market fall within scope of Directive 2001/18/EC. Consequently, control in chain GMO enforcement laboratories is required competent authorities guarantee safety traceability (2003/1829/EC; 2003/1830/EC). However, detection potentially challenging at both analytical interpretation levels since this requires methodological approaches that can target detect a specific single nucleotide variation (SNV) introduced into GE organism. In study, we propose targeted high-throughput sequencing approach, including (i) prior PCR-based enrichment step amplify regions interest, (ii) step, (iii) data analysis methodology identify SNVs interest. To investigate if performance approach compatible with criteria used field, several samples containing different percentages rice line carrying adenosine insertion OsMADS26 were prepared analyzed. The SNV interest could successfully be detected, high low percentages. No impact related food processing or presence other crop species was observed. present proof-of-concept study has allowed us deliver first experimental-based evidence indicating proposed may constitute, future, sensitive tool support regarding plants SNVs.
Language: Английский
Citations
10
Ecology and Evolution, Journal Year: 2022, Volume and Issue: 12(6)
Published: June 1, 2022
Abstract Studies in ecology, evolution, and conservation often rely on noninvasive samples, making it challenging to generate large amounts of high‐quality genetic data for many elusive at‐risk species. We developed optimized a Genotyping‐in‐Thousands by sequencing (GT‐seq) panel using samples inform the management invasive Sitka black‐tailed deer ( Odocoileus hemionus sitkensis ) Haida Gwaii (Canada). validated our paired tissue fecal hair simultaneously distinguish individuals, identify sex, reconstruct kinship among sampled across archipelago, then provided proof‐of‐concept application field‐collected feces SGang Gwaay, an island high ecological cultural value. Genotyping success 244 loci was (90.3%) comparable that genotyped restriction‐site associated DNA (92.4%), while genotyping discordance between low (0.50%). The will be used future species operations providing individual population information management. More broadly, GT‐seq workflow includes quality control analyses targeted SNP selection modified protocol may wider utility other studies systems where sampling is employed.
Language: Английский
Citations
14
Sustainability Sciences in Asia and Africa, Journal Year: 2024, Volume and Issue: unknown, P. 65 - 78
Published: Jan. 1, 2024
Language: Английский
Citations
1
G3 Genes Genomes Genetics, Journal Year: 2024, Volume and Issue: unknown
Published: Dec. 19, 2024
Abstract Amplicon panels using genotyping by sequencing methods are now common, but have focused on characterizing SNP markers. We investigate how microhaplotype (MH) discovery within a recently developed Pacific oyster (Magallana gigas) amplicon panel could increase the statistical power for relationship assignment. Trios (offspring and two parents) from three populations in newly established breeding program were genotyped 592 locus panel. After processing, 92% of retained amplicons contained polymorphic MH variants 85% monomorphic markers variation. The increased allelic richness resulted substantially improved assignment with much lower estimated false positive rates. No substantive differences accuracy occurred between datasets, MHs separation log-likelihood values true parents highly related potential (aunts uncles). A high number Mendelian incompatibilities among trios observed, likely due to null alleles. Further development panel, including removing loci rates alleles, would enable high-throughput reducing size therefore cost research programs.
Language: Английский
Citations
1
Theoretical and Applied Genetics, Journal Year: 2023, Volume and Issue: 136(11)
Published: Oct. 25, 2023
Language: Английский
Citations
2