Structural variants (SVs) significantly drive genome diversity and environmental adaptation for diverse species. Unlike the prevalent small SVs (< kilobase-scale) in higher eukaryotes, large-size SVs ...rarely exist in the genome, but they function as one of the key evolutionary forces for speciation and adaptation.
In this study, we discover and characterize several megabase-scale presence-absence variations (PAVs) in the maize genome. Surprisingly, we identify a 3.2 Mb PAV fragment that shows high integrity and is present as complete presence or absence in the natural diversity panel. This PAV is embedded within the nucleolus organizer region (NOR), where the suppressed recombination is found to maintain the PAV against the evolutionary variation. Interestingly, by analyzing the sequence of this PAV, we not only reveal the domestication trace from teosinte to modern maize, but also the footprints of its origin from Tripsacum, shedding light on a previously unknown contribution from Tripsacum to the speciation of Zea species. The functional consequence of the Tripsacum segment migration is also investigated, and environmental fitness conferred by the PAV may explain the whole segment as a selection target during maize domestication and improvement.
These findings provide a novel perspective that Tripsacum contributes to Zea speciation, and also instantiate a strategy for evolutionary and functional analysis of the "fossil" structure variations during genome evolution and speciation.
•A highly sensitive and simple colorimetric strategy for Hg2+ detection is developed using gold nanoparticles.•The assay was based on anti-aggregation of AuNPs which could lower false positive ...signals.•The assay was applied to detect Hg2+ in real water and milk powder samples.•The colorimetric assay showed excellent sensitivity compared to other assays.
A highly sensitive and simple colorimetric strategy for Hg2+ detection is introduced based on anti-aggregation of gold nanoparticles (AuNPs). 2-Mercaptobenzothiazole (MBT) can cause the aggregation of AuNPs due to strong covalent Au–S bond formation resulting in color change from red to blue. However, the presence of Hg2+ led the AuNPs to remain in the dispersed state because MBT prefers to interact with Hg2+ rather than AuNPs. Based on the anti-aggregation mechanism, Hg2+ can be detected by observing the color change of AuNPs solution containing MBT. The minimum detectable quantity is 0.1μM by the naked eyes, and the limit of the detection (LOD) is 6.0nM by UV–vis spectroscopy with the linear range from 0.05 to 1.0μM. Furthermore, the developed detection system is also environmental-friendly and inexpensive, which has been successfully used in lake water and milk powder samples detection.
Doubled haploid (DH) breeding based on in vivo haploid induction has led to a new approach for maize breeding
. All modern haploid inducers used in DH breeding are derived from the haploid inducer ...line Stock6. Two key quantitative trait loci, qhir1 and qhir8, lead to high-frequency haploid induction
. Mutation of the gene MTL/ZmPLA1/NLD in qhir1 could generate a ~2% haploid induction rate (HIR)
; nevertheless, this mutation is insufficient for modern haploid inducers whose average HIR is ~10%
. Therefore, cloning of the gene underlying qhir8 is important for illuminating the genetic basis of haploid induction. Here, we present the discovery that mutation of a non-Stock6-originating gene in qhir8, namely, ZmDMP, enhances and triggers haploid induction. ZmDMP was identified by map-based cloning and further verified by CRISPR-Cas9-mediated knockout experiments. A single-nucleotide change in ZmDMP leads to a 2-3-fold increase in the HIR. ZmDMP knockout triggered haploid induction with a HIR of 0.1-0.3% and exhibited a greater ability to increase the HIR by 5-6-fold in the presence of mtl/zmpla1/nld. ZmDMP was highly expressed during the late stage of pollen development and localized to the plasma membrane. These findings provide important approaches for studying the molecular mechanism of haploid induction and improving DH breeding efficiency in maize.
Auxin is a plant hormone that plays key roles in both shoot gravitropism and inflorescence development. However, these two processes appear to be parallel and to be regulated by distinct players. ...Here, we report that the maize (Zea mays) prostrate stem1 mutant, which is allelic to the classic mutant lazy plant1 (la1), displays prostrate growth with reduced shoot gravitropism and defective inflorescence development. Map-based cloning identified maize ZmLA1 as the functional ortholog of LAZY1 in rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana). It has a unique role in inflorescence development and displays enriched expression in reproductive organs such as tassels and ears. Transcription of ZmLA1 responds to auxin and is repressed by light. Furthermore, ZmLA1 physically interacts with a putative auxin transport regulator in the plasma membrane and a putative auxin signaling protein in the nucleus. RNA-SEQ data showed that dozens of auxin transport, auxin response, and light signaling genes were differentially expressed in la1 mutant stems. Therefore, ZmLA1 might mediate the cross talk between shoot gravitropism and inflorescence development by regulating auxin transport, auxin signaling, and probably light response in maize.
We have resequenced a group of six elite maize inbred lines, including the parents of the most productive commercial hybrid in China. This effort uncovered more than 1,000,000 SNPs, 30,000 indel ...polymorphisms and 101 low-sequence-diversity chromosomal intervals in the maize genome. We also identified several hundred complete genes that show presence/absence variation among these resequenced lines. We discuss the potential roles of complementation of presence/absence variations and other deleterious mutations in contributing to heterosis. High-density SNP and indel polymorphism markers reported here are expected to be a valuable resource for future genetic studies and the molecular breeding of this important crop.
Clementine mandarin (Citrus clementina Hort. ex Tan.) is one of the most famous and widely grown citrus cultivars worldwide. Variations in relation to the composition and distribution of repetitive ...DNA sequences that dominate greatly in eukaryote genomes are considered to be species-, genome-, or even chromosome-specific. Repetitive DNA-based fluorescence in situ hybridization (FISH) is a powerful tool for molecular cytogenetic study. However, to date few studies have involved in the repetitive elements and cytogenetic karyotype of Clementine.
A graph-based similarity sequence read clustering methodology was performed to analyze the repetitive DNA families in the Clementine genome. The bioinformatics analysis showed that repetitive DNAs constitute 41.95% of the Clementine genome, and the majority of repetitive elements are retrotransposons and satellite DNAs. Sequential multicolor FISH using a probe mix that contained CL17, four satellite DNAs, two rDNAs and an oligonucleotide of (TTTAGGG)
was performed with Clementine somatic metaphase chromosomes. An integrated karyotype of Clementine was established based on unequivocal and reproducible chromosome discriminations. The distribution patterns of these probes in several Citrus, Poncirus and Fortunella species were summarized through extensive FISH analyses. Polymorphism and heterozygosity were commonly observed in the three genera. Some asymmetrical FISH loci in Clementine were in agreement with its hybrid origin.
The composition and abundance of repetitive elements in the Clementine genome were reanalyzed. Multicolor FISH-based karyotyping provided direct visual proof of the heterozygous nature of Clementine chromosomes with conspicuous asymmetrical FISH hybridization signals. We detected some similar and variable distribution patterns of repetitive DNAs in Citrus, Poncirus, and Fortunella, which revealed notable conservation among these genera, as well as obvious polymorphism and heterozygosity, indicating the potential utility of these repetitive element markers for the study of taxonomic, phylogenetic and evolutionary relationships in the future.
Organic selenides were efficient regioselective synthesized by palladium-catalyzed switchable mono- and diselenylation of arenes sp2 C–H bonds through simply tuning the DMSO to water ratio. The ...present protocol was also successfully extended to the monoselenylation of 2-phenoxypyridines, which bore a removable directing group, in modest yields.
A Ru(II) catalyst bearing pyridyl-functionalized and butenyl-tethered N-heterocyclic carbene (NHC) ligand selectively hydrogenates nitriles to secondary amines, and affords unsymmetrical secondary amines with external amines Display omitted
•An efficient regioselective synthetic route to organic selenides via Palladium-catalyzed C–H bonds activation.•The selectivity for mono- and diselenylation of 2-arylpyridines was tuned by solvent effect.•This methodology shows good functional group tolerance and broad substrate scope.•A possible Pd(II)/Pd(IV) mechanism is proposed.
Abstract
In this paper, multiple evaluation means including the fuzzy evaluation method, the analytic hierarchy process and the expert evaluation method are used to evaluate the suitability of sunken ...and submerged oil containment technology in a specific scenario. The results show that the containment technology has a good effect of disposal of submerged oil and floating oil, especially when they may affect sensitive areas.
Production of maternal haploids via a male inducer can greatly accelerate maize breeding and is an interesting biological phenomenon in double fertilization. However, the mechanism behind haploid ...induction remains elusive. Segregation distortion, which is increasingly recognized as a potentially powerful evolutionary force, has recently been observed during maternal haploid induction in maize. The results present here showed that both male gametophytic and zygotic selection contributed to severe segregation distortion of a locus, named segregation distortion 1 (sed1), during maternal haploid induction in maize. Interestingly, analysis of reciprocal crosses showed that sed1 is expressed in the male gametophyte. A novel mapping strategy based on segregation distortion has been used to fine-map this locus. Strong selection for the presence of the sed1 haplotype from inducers in kernels with haploid formation and defects could be detected in the segregating population. Dual-pollination experiments showed that viable pollen grains from inducers had poor pollen competitive ability against pollen from normal genotypes. Although defective kernels and haploids have different phenotypes, they are most probably caused by the sed1 locus, and possible mechanisms for production of maternal haploids and the associated segregation distortion are discussed. This research also provides new insights into the process of double fertilization.
PDF
