Recent progress in atomically precise metal nanoclusters for photocatalytic application.

Photocatalysis is a widely recognized green and sustainable technology that can harness inexhaustible solar energy to carry out chemical reactions, offering the opportunity to mitigate environmental issues and the energy crisis. Photocatalysts with wide spectral response and rapid charge transfer capability are crucial for highly efficient photocatalytic activity. Atomically precise metal nanoclusters (NCs), an emerging atomic-level material, have attracted great interests owing to their ultrasmall size, unique atomic stacking, abundant surface active sites, and quantum confinement effect. In particular, the molecule-like discrete electronic energy level endows them with small-band-gap semiconductor behavior, which allows for photoexcitation in order to generate electrons and holes to participate in the photoredox reaction. In addition, metal NCs exhibit strong light-harvesting ability in the wide spectral UV-near IR region, and the diversity of optical absorption properties can be precisely regulated by the composition and structure. These merits make metal NCs ideal candidates for photocatalysis. In this review, the recent advances in atomically-precise metal NCs for photocatalytic application are summarized, including photocatalytic water splitting, CO2 reduction, organic transformation, photoelectrocatalytic reactions, N2 fixation and H2O2 production. In addition, the strategy for promoting photostability, charge transfer and separation efficiency of metal NCs is highlighted. Finally, a perspective on the challenges and opportunities for NCs-based photocatalysts is provided.

Visualized electrochemiluminescence detection of trace copper in practical food samples.

Copper as a widely applied element in food supply chain can cause serious contamination issues that threats food safety. In this research, we present a quick and visible method for trace copper ion (Cu2+) quantification in practical food samples. Polymer dots (Pdots) were firstly conjugated with a copper-specific DNA aptamer and then tailored with rhodamine B (RhB) to extinguish the electrochemiluminescence (ECL) signal through a resonance energy transfer process. The selective release of RhB leads to signal restoration when exposed to trace Cu2+ levels, achieving remarkable linearity with the logarithm of Cu2+ concentration within the range of 1 ng/L to 10 µg/L with an impressively low limit of detection at 11.8 pg/L. Most notably, our device was also applicable on visualizing and quantifying trace Cu2+ (∼0.2 µg/g) in practical Glycyrrhiza uralensis Fisch. samples, underscoring its potential as a tool for the early prevention of potential copper contamination in food samples.

Genetic dissection of lint percentage in short-season cotton using combined QTL mapping and RNA-seq.

KEY MESSAGE: In total, 17 QTLs for lint percentage in short-season cotton, including three stable QTLs, were detected. Twenty-eight differentially expressed genes located within the stable QTLs were identified, and two genes were validated by qRT-PCR. The breeding and use of short-season cotton have significant values in addressing the question of occupying farmlands with either cotton or cereals. However, the fiber yields of short-season cotton varieties are significantly lower than those of middle- and late-maturing varieties. How to effectively improve the fiber yield of short-season cotton has become a focus of cotton research. Here, a high-density genetic map was constructed using genome resequencing and an RIL population generated from the hybridization of two short-season cotton accessions, Dong3 and Dong4. The map contained 4960 bin markers across the 26 cotton chromosomes and spanned 3971.08 cM, with an average distance of 0.80 cM between adjacent markers. Based on the genetic map, quantitative trait locus (QTL) mapping for lint percentage (LP, %), an important yield component trait, was performed. In total, 17 QTLs for LP, including three stable QTLs, qLP-A02, qLP-D04, and qLP-D12, were detected. Three out of 11 non-redundant QTLs overlapped with previously reported QTLs, whereas the other eight were novel QTLs. A total of 28 differentially expressed genes associated with the three stable QTLs were identified using RNA-seq of ovules and fibers at different seed developmental stages from the parental materials. The two genes, Ghir_A02G017640 and Ghir_A02G018500, may be related to LP as determined by further qRT-PCR validation. This study provides useful information for the genetic dissection of LP and promotes the molecular breeding of short-season cotton.

Physiological and Transcriptomic Comparison of Two Sunflower (Helianthus annuus L.) Cultivars With High/Low Cadmium Accumulation.

The toxic heavy metal cadmium (Cd) is easily absorbed and accumulated in crops and affects human health through the food chains. Sunflower (Helianthus annuus L.) is a globally important oil crop. In this study, two sunflower cultivars 62\3 (high Cd) and JB231AC (low Cd), were chosen to compare physiological and transcriptomic responses at different Cd concentrations (0, 25, 50, and 100 µM). The results showed that JB231AC had better Cd tolerance than 62\3. The contents of H2O2 and MDA (malondialdehyde) in 62\3 were lower than that in JB231AC under Cd stress, but the activities of SOD (superoxide dismutase) and POD (peroxidase) in JB231AC were higher than in 62\3, which indicated that JB231AC had a strong ability to remove reactive oxygen species (ROS)-induced toxic substances. Many deferentially expressed ABC (ATP-binding cassette) and ZIP (Zn-regulated transporter, Iron-regulated transporter-like protein) genes indicated that the two gene families might play important roles in different levels of Cd accumulation in the two cultivars. One up-regulated NRAMP (Natural resistance-associated macrophage protein) gene was identified and had a higher expression level in 62\3. These results provide valuable information to further understand the mechanism of Cd accumulation and provide insights into breeding new low Cd sunflower cultivars.

Identification of superior parents with high fiber quality using molecular markers and phenotypes based on a core collection of upland cotton (Gossypium hirsutum L.).

The combination of molecular markers and phenotypes to select superior parents has become the goal of modern breeders. In this study, 491 upland cotton (Gossypium hirsutum L.) accessions were genotyped using the CottonSNP80K array and then a core collection (CC) was constructed. Superior parents with high fiber quality were identified using molecular markers and phenotypes based on the CC. The Nei diversity index, Shannon's diversity index, and polymorphism information content among chromosomes for 491 accessions ranged from 0.307 to 0.402, 0.467 to 0.587, and 0.246 to 0.316, with mean values of 0.365, 0.542, and 0.291, respectively. A CC containing 122 accessions was established and was categorized into eight clusters based on the K2P genetic distances. From the CC, 36 superior parents (including duplicates) were selected, which contained the elite alleles of markers and ranked in the top 10% of phenotypic values for each fiber quality trait. Among the 36 materials, eight were for fiber length, four were for fiber strength, nine were for fiber micronaire, five were for fiber uniformity, and ten were for fiber elongation. In particular, the nine materials, 348 (Xinluzhong34), 319 (Xinluzhong3), 325 (Xinluzhong9), 397 (L1-14), 205 (XianIII9704), 258 (9D208), 464 (DP201), 467 (DP150), and 465 (DP208), possessed the elite alleles of markers for at least two traits and could be given priority in breeding applications for a more synchronous improvement of fiber quality. The work provides an efficient method for superior parent selection and will facilitate the application of molecular design breeding to cotton fiber quality. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01300-0.

Weakly Supervised 3D Semantic Segmentation Using Cross-Image Consensus and Inter-Voxel Affinity Relations.

We propose a novel weakly supervised approach for 3D semantic segmentation on volumetric images. Unlike most existing methods that require voxel-wise densely labeled training data, our weakly-supervised CIVA-Net is the first model that only needs image-level class labels as guidance to learn accurate volumetric segmentation. Our model learns from cross-image co-occurrence for integral region generation, and explores inter-voxel affinity relations to predict segmentation with accurate boundaries. We empirically validate our model on both simulated and real cryo-ET datasets. Our experiments show that CIVA-Net achieves comparable performance to the state-of-the-art models trained with stronger supervision.

Dissecting the genetic architecture of seed-cotton and lint yields in Upland cotton using genome-wide association mapping.

Seed-cotton yield (SY) and lint yield (LY) are the most important yield traits of cotton. Thus, it is critical to dissect their genetic architecture. Upland cotton (Gossypium hirsutum) is widely grown worldwide. In this study, a genome-wide association mapping was performed based on the CottonSNP80K array to dissect the genetic architecture of SY and LY in Upland cotton. Twenty-three significant associations were detected within four environments, including 11 associated with SY and 12 associated with LY. Seven single nucleotide polymorphisms (SNPs), TM234, TM237, TM247, TM255, TM256, TM263, and TM264, were co-associated with the two traits, which may indicate pleiotropy or intergenic tight linkages. Five SNPs, TM13332, TM39771, TM57119, TM81653, and TM81660, were coincided with those of previous reports and could be used in marker-assisted selection. Combining functional annotations with expression analyses of the genes identified within 400 kb of the significantly associated SNPs, we hypothesize that the three genes, Gh_D05G1077 and Gh_D13G1571 for SY, and Gh_A11G0775 for LY, may have the potential to increase cotton yield. The results would provide useful information for understanding the genetic basis of yield traits in Upland cotton and for facilitating its high-yield breeding through molecular design.

Simple sequence repeat markers associated/linked with agronomic traits, as core primers, are eminently suitable for DNA fingerprinting in Upland cotton.

Analyzing the genetic differences among crop germplasm resources scientifically and accurately is very important for the selection of core accessions, the identification of new cultivars, and the determination of seed purity. However, phenotypic selection per se is not sufficient to identify genetically distinct accessions. In this study, 26 out of 83 simple sequence repeat markers associated/linked with cotton important agronomic traits derived from our previous and other published research, corresponding to the 26 chromosomes of Upland cotton (Gossypium hirsutum L.), were selected as core primers for DNA fingerprinting construction. The 26 markers showed clear band patterns, good repeatability and high polymorphism. The average alleles, gene diversity index and polymorphism information content were 3.12, 0.4312 and 0.3830, respectively. Using TM-1, a genetic standard line for Upland cotton, as the control, DNA fingerprinting pattern and DNA barcodes were obtained based on the core primers. There was a significant positive correlation between genetic distance matrix determined using 26 core primers and that determined using more primers (335) derived from previous research, further suggesting that the core primers were eminently suitable for DNA fingerprinting in Upland cotton. This study provides a molecular basis for assessing identification, authenticity and seed purity of cotton cultivars.

Single-Locus and Multi-Locus Genome-Wide Association Studies in the Genetic Dissection of Fiber Quality Traits in Upland Cotton (Gossypium hirsutum L.).

A major breeding target in Upland cotton (Gossypium hirsutum L.) is to improve the fiber quality. To address this issue, 169 diverse accessions, genotyped by 53,848 high-quality single-nucleotide polymorphisms (SNPs) and phenotyped in four environments, were used to conduct genome-wide association studies (GWASs) for fiber quality traits using three single-locus and three multi-locus models. As a result, 342 quantitative trait nucleotides (QTNs) controlling fiber quality traits were detected. Of the 342 QTNs, 84 were simultaneously detected in at least two environments or by at least two models, which include 29 for fiber length, 22 for fiber strength, 11 for fiber micronaire, 12 for fiber uniformity, and 10 for fiber elongation. Meanwhile, nine QTNs with 10% greater sizes (R2) were simultaneously detected in at least two environments and between single- and multi-locus models, which include TM80185 (D13) for fiber length, TM1386 (A1) and TM14462 (A6) for fiber strength, TM18616 (A7), TM54735 (D3), and TM79518 (D12) for fiber micronaire, TM77489 (D12) and TM81448 (D13) for fiber uniformity, and TM47772 (D1) for fiber elongation. This indicates the possibility of marker-assisted selection in future breeding programs. Among 455 genes within the linkage disequilibrium regions of the nine QTNs, 113 are potential candidate genes and four are promising candidate genes. These findings reveal the genetic control underlying fiber quality traits and provide insights into possible genetic improvements in Upland cotton fiber quality.

A genome-wide association study of early-maturation traits in upland cotton based on the CottonSNP80K array.

Genome-wide association studies (GWASs) efficiently identify genetic loci controlling traits at a relatively high resolution. In this study, variations in major early-maturation traits, including seedling period (SP), bud period (BP), flower and boll period (FBP), and growth period (GP), of 169 upland cotton accessions were investigated, and a GWAS of early maturation was performed based on a CottonSNP80K array. A total of 49,650 high-quality single-nucleotide polymorphisms (SNPs) were screened, and 29 significant SNPs located on chromosomes A6, A7, A8, D1, D2, and D9, were repeatedly identified as associated with early-maturation traits, in at least two environments or two algorithms. Of these 29 significant SNPs, 1, 12, 11, and 5 were related to SP, BP, FBP, and GP, respectively. Six peak SNPs, TM47967, TM13732, TM20937, TM28428, TM50283, and TM72552, exhibited phenotypic contributions of approximately 10%, which could allow them to be used for marker-assisted selection. One of these, TM72552, as well as four other SNPs, TM72554, TM72555, TM72558, and TM72559, corresponded to the quantitative trait loci previously reported. In total, 274 candidate genes were identified from the genome sequences of upland cotton and were categorized based on their functional annotations. Finally, our studies identified Gh_D01G0340 and Gh_D01G0341 as potential candidate genes for improving cotton early maturity.

Differential expression of microRNAs during fiber development between fuzzless-lintless mutant and its wild-type allotetraploid cotton.

Cotton is one of the most important textile crops but little is known how microRNAs regulate cotton fiber development. Using a well-studied cotton fiberless mutant Xu-142-fl, we compared 54 miRNAs for their expression between fiberless mutant and its wildtype. In wildtype Xu-142, 26 miRNAs are involved in cotton fiber initiation and 48 miRNAs are related to primary wall synthesis and secondary wall thickening. Thirty three miRNAs showed different expression in fiber initiation between Xu-142 and Xu-142-fl. These miRNAs potentially target 723 protein-coding genes, including transcription factors, such as MYB, ARF, and LRR. ARF18 was newly predicted targets of miR160a, and miR160a was expressed at higher level in -2DPA of Xu-142-fl compared with Xu-142. Furthermore, the result of Gene Ontology-based term classification (GO), EuKaryotic Orthologous Groups (KOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis shows that miRNA targets were classified to 222 biological processes, 64 cellular component and 42 molecular functions, enriched in 22 KOG groups, and classified into 28 pathways. Together, our study provides evidence for better understanding of miRNA regulatory roles in the process of fiber development, which is helpful to increase fiber yield and improve fiber quality.

Chemical shift MR imaging in the lumbar vertebra: the effect of field strength, scanner vendors and flip angles in repeatability of signal intensity index measurement.

BACKGROUND: To evaluate the reproducibility of signal intensity index (SII) measurements with MRI systems from different vendors and with different field strengths, and to test the effectiveness of flip angle. METHODS: Thirty-two healthy volunteers (mean age 35.3 ± 9.3 years) were enrolled in this ethics committee-approved study. Chemical shift MR imaging was performed on 1.5- and 3.0-T MR systems from three vendors. Two independent observers measured SII values in five lumbar segments. Inter- and intraobserver agreement was assessed using the interclass correlation coefficients (ICCs). Differences of mean SII values between different field strengths and MR vendors as well as flip angles were compared by using repeated-measures analysis of variance. Differences of mean SII values between different flip angles were also compared by using paired-sample t test. RESULTS: Inter- and intra-observer correlation coefficients showed good agreement (all ICC > 0.75) when measuring SII values at different MR systems (ICCs ranging from 0.896 to 0.983) and flip angles (ICCs ranging from 0.824 to 0.983). There were no significant differences in mean SII values measured by different MR vendors with different field strengths (all p > 0.05 ranging from 0.337 to 0.824). The differences in the mean SII between the four different flip angles were statistically significant (all p < 0.05 ranging from < 0.001 to 0.004) except the group of flip angle 50° versus 70° (p = 0.116). CONCLUSION: The SII measurement using chemical shift MR imaging may be comparable between different MR systems. Also high flip angles showed better stability to quantitate lumbar fat content.

Quantitative trait loci mapping and genetic dissection for lint percentage in upland cotton (Gossypium hirsutum).

Lint percentage is an important character of cotton yield components and it is also correlated with cotton fibre development. In this study, we used a high lint percentage variety, Baimian1, and a low lint percentage, TM-1 genetic standard for Gossypium hirsutum, as parents to construct a mapping populations in upland cotton (G. hirsutum). A quantitative trait locus/loci (QTL) analysis of lint percentage was performed by using two mapping procedures; composite interval mapping (CIM), inclusive composite interval mapping (ICIM) and the F2:3 populations in 2 years. Six main-effect QTL (M-QTL) for lint percentage (four significant and two suggestive) were detected in both years by CIM, and were located on chr. 3, chr. 19, chr. 26 and chr. 5/chr. 19. Of the six QTL, marker intervals and favourable gene sources of the significant M-QTL, qLP-3(2010) and qLP-3(2011) were consistent. These QTL were also detected by ICIM, and therefore, should preferentially be used for markerassisted selection (MAS) of lint percentage. Another M-QTL, qLP-19(2010), was detected by two mapping procedures, and it could also be a candidate for MAS. We detected the interaction between two M-QTL and environment, and 11 epistatic QTL (E-QTL) and their interaction with environment by using ICIM. The study also found two EST-SSRs, NAU1187 and NAU1255, linked to M-QTL for lint percentage that could be candidate markers affecting cotton fibre development.

QTL analysis for early-maturing traits in cotton using two upland cotton (Gossypium hirsutum L.) crosses.

Making use of the markers linked closely to QTL for early-maturing traits for MAS (Marker-assisted selection) is an effective method for the simultaneous improvement of early maturity and other properties in cotton. In this study, two F2 populations and their F2:3 families were generated from the two upland cotton (Gossypium hirsutum L.) crosses, Baimian2 × TM-1 and Baimian2 × CIR12. QTL for early-maturing traits were analyzed using F2:3 families. A total of 54 QTL (31 suggestive and 23 significant) were detected. Fourteen significant QTL had the LOD scores not only > 3 but also exceeding permutation threshold. At least four common QTL, qBP-17 for bud period (BP), qGP-17a/qGP-17b (qGP-17) for growth period (GP), qYPBF-17a/qYPBF-17b (qYPBF-17) for yield percentage before frost (YPBF) and qHFFBN-17 for height of first fruiting branch node (HFFBN), were found in both populations. These common QTL should be reliable and could be used for MAS to facilitate early maturity. The common QTL, qBP-17, had a LOD score not only > 3 but also exceeding permutation threshold, explaining 12.6% of the phenotypic variation. This QTL should be considered preferentially in MAS. Early-maturing traits of cotton are primarily controlled by dominant and over-dominant effects.

Overexpression of miR 156 in cotton via Agrobacterium-mediated transformation.

microRNAs (miRNAs) are an extensive class of newly identified endogenous small regulatory molecules. Many studies show that miRNAs play a critical role in almost all biological and metabolic progresses through targeting protein-coding genes for mRNA cleavage or translation inhibition. Many miRNAs are also identified from cotton using computational and/or experimental approaches, including the next generation deep sequencing technology. However, the function of the majority of miRNAs are unclear. In this chapter, we describe a detailed method for overexpressing miR 156 in cotton using Agrobacterium-mediated genetic transformation. This provides an approach to investigate the function and regulatory mechanism of miRNAs in cotton.

[QTL mapping for "pre-summer boll, summer boll and autumn boll" traits in cotton].

"Pre-summer boll, summer boll and autumn boll" have long been regarded as an important index for prematurity and high-yield in cotton. In this study, the prematurity and high-yield cotton cultivar, Baimian 2, was used as the central parent to cross separately with the middle-late-matury lines TM-1 and CIR12, and then two populations of F2 and F2:3 family lines were obtained, which was used to construct two genetic linkage maps. These maps were comprised of 269 and 127 marker loci with the total length 1837.8 cM and 1244.3 cM, respectively. Results of QTL location showed that a total of 29 QTLs were detected in the two combinations, including 16 suggestive QTLs and 13 significant QTLs, of which 5 significant QTLs had higher LOD values that was not only greater than 3 but also greater than the threshold calculated by permutation test. The contribution rate of 16 QTLs explained 10.9%-44.5% of the phenotypic variations. Four common QTLs, qPSB-17 for pre-summer boll, qSB-17 (qSB-17a/17b) for summer boll, and qAB-17 and qAB-12/26 for autumn boll, were detected close to common markers of the same chromosome in the two combinations, which could be applied in marker-assisted selection. Moreover, the contribution rate of qSB-17 (qSB-17a/17b) for summer boll in the two combinations was greater than 10%, and that of qAB-17, qAB-12/26 for autumn boll in one combination were greater than 10%. These common QTLs with greater contribution rates should take into consideration firstly in marker-assisted selection.