Since the Arabidopsis genome was completed, draft sequences or pseudomolecules have been published for more than 100 plant genomes including green algae, in large part due to advances in sequencing technologies. Advanced DNA sequencing technologies have also conferred new opportunities for high-throughput low-cost crop genotyping, based on single-nucleotide polymorphisms (SNPs). However, a recurring complication in crop genotyping that differs from other taxa is a higher level of DNA sequence duplication, noting that all angiosperms are thought to have polyploidy in their evolutionary history. In the current article, we briefly review current genotyping methods using next-generation sequencing (NGS) technologies. We also explore case studies of genotyping-by-sequencing (GBS) applications to several crops differing in genome size, organization and breeding system (paleopolyploids, neo-allopolyploids, neo-autopolyploids). GBS typically shows good results when it is applied to an inbred diploid species with a well-established reference genome. However, we have also made some progress toward GBS of outcrossing species lacking reference genomes and of polyploid populations, which still need much improvement. Regardless of some limitations, low-cost and multiplexed genotyping offered by GBS will be beneficial to breed superior cultivars in many crop species.
BackgroundDomestication has played an important role in shaping characteristics of the inflorescence and plant height in cultivated cereals. Taking advantage of meta-analysis of QTLs, phylogenetic analyses in 502 diverse sorghum accessions, GWAS in a sorghum association panel (n = 354) and comparative data, we provide insight into the genetic basis of the domestication traits in sorghum and rice.ResultsWe performed genome-wide association studies (GWAS) on 6 traits related to inflorescence morphology and 6 traits related to plant height in sorghum, comparing the genomic regions implicated in these traits by GWAS and QTL mapping, respectively. In a search for signatures of selection, we identify genomic regions that may contribute to sorghum domestication regarding plant height, flowering time and pericarp color. Comparative studies across taxa show functionally conserved ‘hotspots’ in sorghum and rice for awn presence and pericarp color that do not appear to reflect corresponding single genes but may indicate co-regulated clusters of genes. We also reveal homoeologous regions retaining similar functions for plant height and flowering time since genome duplication an estimated 70 million years ago or more in a common ancestor of cereals. In most such homoeologous QTL pairs, only one QTL interval exhibits strong selection signals in modern sorghum.ConclusionsIntersections among QTL, GWAS and comparative data advance knowledge of genetic determinants of inflorescence and plant height components in sorghum, and add new dimensions to comparisons between sorghum and rice.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0477-6) contains supplementary material, which is available to authorized users.
Bromophenols occur naturally and are used globally as man-made additives in various industrial products. They are decomposition products of many emerging organic pollutants, such as tetrabromobisphenol A, polybrominated dibenzo-p-dioxin (PBDD), polybrominated diphenyl ethers (PBDE), and others. To characterize their biotransformation pathways, bromophenol congener 2,4,6-tribromophenol, being used most frequently in the synthesis of brominated flame retardants and having the greatest environmental abundance, was selected to hydroponically expose rice plants. After exposure for 5 days, 99.2% of 2,4,6-tribromophenol was metabolized by rice. Because of the lack of relative reference standards, an effective screening strategy was used to screen for potential metabolites that were further qualitatively identified by gas and liquid chromatography combined with high-resolution mass spectrometry. Forty transformation products were confirmed or tentatively identified at different confidence levels, including 9 phase I and 31 phase II metabolites. A large number of metabolites (39) were found in rice root, and 10 of them could be translocated and detected in rice stems or leaves. Many transformation pathways were proposed, including debromination, hydroxylation, methylation, coupling reactions, sulfation, and glycosylation. It was remarkable that a total of seven hydrophobic, persistent, and toxic OH-PBDEs and PBDD/Fs were found, indicating the biotic dimeric reactions of 2,4,6-tribromophenol that occurred in the rice plants. These results improve our understanding of the transformation and environmental fates of bromophenols, and they indicate new potential sources for OH-PBDEs and PBDD/Fs in the environment, especially in food chains.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.