FastBiCmrMLM: a fast and powerful compressed variance component mixed logistic model for big genomic case-control genome-wide association study.

Large sample datasets have been regarded as the primary basis for innovative discoveries and the solution to missing heritability in genome-wide association studies. However, their computational complexity cannot consider all comprehensive effects and all polygenic backgrounds, which reduces the effectiveness of large datasets. To address these challenges, we included all effects and polygenic backgrounds in a mixed logistic model for binary traits and compressed four variance components into two. The compressed model combined three computational algorithms to develop an innovative method, called FastBiCmrMLM, for large data analysis. These algorithms were tailored to sample size, computational speed, and reduced memory requirements. To mine additional genes, linkage disequilibrium markers were replaced by bin-based haplotypes, which are analyzed by FastBiCmrMLM, named FastBiCmrMLM-Hap. Simulation studies highlighted the superiority of FastBiCmrMLM over GMMAT, SAIGE and fastGWA-GLMM in identifying dominant, small α (allele substitution effect), and rare variants. In the UK Biobank-scale dataset, we demonstrated that FastBiCmrMLM could detect variants as small as 0.03% and with α ≈ 0. In re-analyses of seven diseases in the WTCCC datasets, 29 candidate genes, with both functional and TWAS evidence, around 36 variants identified only by the new methods, strongly validated the new methods. These methods offer a new way to decipher the genetic architecture of binary traits and address the challenges outlined above.

Drying without dying: A genome database for desiccation-tolerant plants and evolution of desiccation tolerance.

Desiccation is typically fatal, but a small number of land plants have evolved vegetative desiccation tolerance (VDT), allowing them to dry without dying through a process called anhydrobiosis. Advances in sequencing technologies have enabled the investigation of genomes for desiccation-tolerant plants over the past decade. However, a dedicated and integrated database for these valuable genomic resources has been lacking. Our prolonged interest in VDT plant genomes motivated us to create the "Drying without Dying" database, which contains a total of 16 VDT-related plant genomes (including 10 mosses) and incorporates 10 genomes that are closely related to VDT plants. The database features bioinformatic tools, such as blast and homologous cluster search, sequence retrieval, Gene Ontology term and metabolic pathway enrichment statistics, expression profiling, co-expression network extraction, and JBrowser exploration for each genome. To demonstrate its utility, we conducted tailored PFAM family statistical analyses, and we discovered that the drought-responsive ABA transporter AWPM-19 family is significantly tandemly duplicated in all bryophytes but rarely so in tracheophytes. Transcriptomic investigations also revealed that response patterns following desiccation diverged between bryophytes and angiosperms. Combined, the analyses provided genomic and transcriptomic evidence supporting a possible divergence and lineage-specific evolution of VDT in plants. The database can be accessed at http://desiccation.novogene.com. We expect this initial release of the "Drying without Dying" plant genome database will facilitate future discovery of VDT genetic resources.

Revealing *OOH key intermediates and regulating H2O2 photoactivation by surface relaxation of Fenton-like catalysts.

Hydrogen peroxide (H2O2) molecules play important roles in many green chemical reactions. However, the high activation energy limits their application efficiency, and there is still huge controversy about the activation path of H2O2 molecules over the presence of *OOH intermediates. Here, we confirmed the formation of the key species *OOH in the heterogeneous system, via in situ shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS), isotope labeling, and theoretical calculation. In addition, we found that compared with *H2O2, *OOH was more conducive to the charge transfer behavior with the catalyst and the activation of an O-O bond. Furthermore, we proposed to improve the local coordination structure and electronic density of the YFeO3 catalyst by regulating the surface relaxation with Ti modification so as to reduce the activation barrier of H2O2 and to improve the production efficiency of •OH. As a result, the kinetics rates of the Fenton-like (photo-Fenton) reaction had been significantly increased several times. The •OH free radical activity mechanism and molecular transformation pathways of 4-chloro phenol (4-CP) were also revealed. This may provide a clearer vision for the further study of H2O2 activation and suggest a means of designing catalysts for efficient H2O2 activation.

Identification of QTNs, QTN-by-environment interactions, and their candidate genes for salt tolerance related traits in soybean.

BACKGROUND: Salt stress significantly reduces soybean yield. To improve salt tolerance in soybean, it is important to mine the genes associated with salt tolerance traits. RESULTS: Salt tolerance traits of 286 soybean accessions were measured four times between 2009 and 2015. The results were associated with 740,754 single nucleotide polymorphisms (SNPs) to identify quantitative trait nucleotides (QTNs) and QTN-by-environment interactions (QEIs) using three-variance-component multi-locus random-SNP-effect mixed linear model (3VmrMLM). As a result, eight salt tolerance genes (GmCHX1, GsPRX9, Gm5PTase8, GmWRKY, GmCHX20a, GmNHX1, GmSK1, and GmLEA2-1) near 179 significant and 79 suggested QTNs and two salt tolerance genes (GmWRKY49 and GmSK1) near 45 significant and 14 suggested QEIs were associated with salt tolerance index traits in previous studies. Six candidate genes and three gene-by-environment interactions (GEIs) were predicted to be associated with these index traits. Analysis of four salt tolerance related traits under control and salt treatments revealed six genes associated with salt tolerance (GmHDA13, GmPHO1, GmERF5, GmNAC06, GmbZIP132, and GmHsp90s) around 166 QEIs were verified in previous studies. Five candidate GEIs were confirmed to be associated with salt stress by at least one haplotype analysis. The elite molecular modules of seven candidate genes with selection signs were extracted from wild soybean, and these genes could be applied to soybean molecular breeding. Two of these genes, Glyma06g04840 and Glyma07g18150, were confirmed by qRT-PCR and are expected to be key players in responding to salt stress. CONCLUSIONS: Around the QTNs and QEIs identified in this study, 16 known genes, 6 candidate genes, and 8 candidate GEIs were found to be associated with soybean salt tolerance, of which Glyma07g18150 was further confirmed by qRT-PCR.

A compressed variance component mixed model framework for detecting small and linked QTL-by-environment interactions.

Detecting small and linked quantitative trait loci (QTLs) and QTL-by-environment interactions (QEIs) for complex traits is a difficult issue in immortalized F2 and F2:3 design, especially in the era of global climate change and environmental plasticity research. Here we proposed a compressed variance component mixed model. In this model, a parametric vector of QTL genotype and environment combination effects replaced QTL effects, environmental effects and their interaction effects, whereas the combination effect polygenic background replaced the QTL and QEI polygenic backgrounds. Thus, the number of variance components in the mixed model was greatly reduced. The model was incorporated into our genome-wide composite interval mapping (GCIM) to propose GCIM-QEI-random and GCIM-QEI-fixed, respectively, under random and fixed models of genetic effects. First, potentially associated QTLs and QEIs were selected from genome-wide scanning. Then, significant QTLs and QEIs were identified using empirical Bayes and likelihood ratio test. Finally, known and candidate genes around these significant loci were mined. The new methods were validated by a series of simulation studies and real data analyses. Compared with ICIM, GCIM-QEI-random had 29.77 ± 18.20% and 24.33 ± 10.15% higher average power, respectively, in 0.5-3.0% QTL and QEI detection, 43.44 ± 9.53% and 51.47 ± 15.70% higher average power, respectively, in linked QTL and QEI detection, and identified 30 more known genes for four rice yield traits, because GCIM-QEI-random identified more small genes/loci, being 2.69 ± 2.37% for additional genes. GCIM-QEI-random was slightly better than GCIM-QEI-fixed. In addition, the new methods may be extended into backcross and genome-wide association studies. This study provides effective methods for detecting small-effect and linked QTLs and QEIs.

Lattice Oxygen in Photocatalytic Gas‒Solid Reactions: Participator vs. Dominator.

Lattice-oxygen activation has emerged as a popular strategy for optimizing the performance and selectivity of oxide-based thermocatalysis and electrolysis. However, the significance of lattice oxygen in oxide photocatalysts has been ignored, particularly in gas‒solid reactions. Here, using methane oxidation over a Ru1@ZnO single-atom photocatalyst as the prototypical reaction and via 18O isotope labelling techniques, we found that lattice oxygen can directly participate in gas‒solid reactions. Lattice oxygen played a dominant role in the photocatalytic reaction, as determined by estimating the kinetic constants in the initial stage. Furthermore, we discovered that dynamic diffusion between O2 and lattice oxygen proceeded even in the absence of targeted reactants. Finally, single-atom Ru can facilitate the activation of adsorbed O2 and the subsequent regeneration of consumed lattice oxygen, thus ensuring high catalyst activity and stability. The results provide guidance for next-generation oxide photocatalysts with improved activities and selectivities.

Effects of N and P additions on twig traits of wild apple (Malus sieversii) saplings.

BACKGROUND: Wild apple (Malus sieversii) is under second-class national protection in China and one of the lineal ancestors of cultivated apples worldwide. In recent decades, the natural habitation area of wild apple trees has been seriously declining, resulting in a lack of saplings and difficulty in population regeneration. Artificial near-natural breeding is crucial for protecting and restoring wild apple populations, and adding nitrogen (N) and phosphorous (P) is one of the important measures to improve the growth performance of saplings. In this study, field experiments using N (CK, N1, N2, and N3: 0, 10, 20, and 40 g m- 2 yr- 1, respectively), P (CK, P1, P2, and P3: 0, 2, 4, and 8 g m- 2 yr- 1, respectively), N20Px (CK, N2P1, N2P2, and N2P3: N20P2, N20P4 and N20P8 g m- 2 yr- 1, respectively), and NxP4 (CK, N1P2, N2P2, and N3P2: N10P4, N20P4, and N40P4 g m- 2 yr- 1, respectively) treatments (totaling 12 levels, including one CK) were conducted in four consecutive years. The twig traits (including four current-year stem, 10 leaf, and three ratio traits) and comprehensive growth performance of wild apple saplings were analyzed under different nutrient treatments. RESULTS: N addition had a significantly positive effect on stem length, basal diameter, leaf area, and leaf dry mass, whereas P addition had a significantly positive effect on stem length and basal diameter only. The combination of N and P (NxP4 and N20Px) treatments evidently promoted stem growth at moderate concentrations; however, the N20Px treatment showed a markedly negative effect at low concentrations and a positive effect at moderate and high concentrations. The ratio traits (leaf intensity, leaf area ratio, and leaf to stem mass ratio) decreased with the increase in nutrient concentration under each treatment. In the plant trait network, basal diameter, stem mass, and twig mass were tightly connected to other traits after nutrient treatments, indicating that stem traits play an important role in twig growth. The membership function revealed that the greatest comprehensive growth performance of saplings was achieved after N addition alone, followed by that under the NxP4 treatment (except for N40P4). CONCLUSIONS: Consequently, artificial nutrient treatments for four years significantly but differentially altered the growth status of wild apple saplings, and the use of appropriate N fertilizer promoted sapling growth. These results can provide scientific basis for the conservation and management of wild apple populations.

2D Cobalt Chalcogenide Heteronanostructures Enable Efficient Alkaline Hydrogen Evolution Reaction.

The development of high-efficiency non-precious metal electrocatalysts for alkaline electrolyte hydrogen evolution reactions (HER) is of great significance in energy conversion to overcome the limited supply of fossil fuels and carbon emission. Here, a highly active electrocatalyst is presented for hydrogen production, consisting of 2D CoSe2 /Co3 S4 heterostructured nanosheets along Co3 O4 nanofibers. The different reaction rate between the ion exchange reaction and redox reaction leads to the heterogeneous volume swelling, promoting the growth of 2D structure. The 2D/1D heteronanostructures enable the improved the electrochemical active area, the number of active sites, and more favorable H binding energy compared to individual cobalt chalcogenides. The roles of the different composition of the heterojunction are investigated, and the electrocatalysts based on the CoSe2 /Co3 S4 @Co3 O4 exhibited an overpotential as low as 165 mV for 10 mA cm-2 and 393 mV for 200 mA cm-2 in 1 m KOH electrolyte. The as-prepared electrocatalysts remained active after 55 h operation without any significant decrease, indicating the excellent long-term operation stability of the electrode. The Faradaic efficiency of hydrogen production is close to 100% at different voltages. This work provides a new design strategy toward Co-based catalysts for efficient alkaline HER.

Room-Temperature Synthesis of Carbon Dot/TiO2 Composites with High Photocatalytic Activity.

Benefiting from the wide-range absorption and adjustable energy gap, carbon dots (C-dots) have attracted a great deal of attention and they have been used to sensitize semiconductor nanocomposites to boost the efficiency of energy conversion devices, while there is still a lack of fundamental understanding of the interaction between such materials and their influence on the catalytic activity on the reaction process. In this study, C-dots were used to modify TiO2 to form a direct Z-scheme (DZS) junction for enhancement of the photocatalytic activity. The C-dot/TiO2 composite was prepared by ultrasonication at room temperature through coupling between the Ti-O-C bond and electrostatic interaction. The C-dots can dramatically enhance the absorption of the composite by forming the DZS, and the composite is enabled to generate more free radicals, which facilitate ∼10 times higher photocatalytic activity compared to that of TiO2. As a proof of concept, the as-prepared C-dot/TiO2 was used for textile wastewater dye degradation. This study provides an efficient approach for room-temperature preparation of C-dot/TiO2 composites with high photocatalytic activity.

Effects of potassium channel knockdown on peripheral blood T lymphocytes and NFAT signaling pathway in Xinjiang Kazak patients with hypertension.

BACKGROUD AND AIM: T lymphocytes are involved in the occurrence and development of essential hypertension, and potassium channels are thought to be critical for lymphocyte activation. This study is to examine the roles of the voltage-gated potassium channels (Kv1.3) and calcium-activated potassium channels (KCa3.1) in peripheral blood T lymphocytes in Kazakh hypertensive patients of Xinjiang, China, mainly focusing on the effects of these channels on nuclear factor of activated T cells (NFAT) and inflammatory cytokines of T lymphocytes. METHOD: Kv1.3 and KCa3.1 gene silencing were performed in cultured T lymphocytes from Kazakh patients with severe hypertension. T cell proliferation after gene silencing was measured using CCK-8. The mRNA and protein expression levels were measured using RT-qPCR and Western blot analysis, respectively. Nuclear translocation of NFAT was observed using laser confocal fluorescence microscopy. Inflammatory cytokine levels were detected with ELISA. RESULTS: Compared with control group, gene silencing of Kv1.3 and KCa3.1 respectively inhibited the proliferation of T cells. Moreover, compared with the control group, the mRNA expression levels of NFAT, IL-6 and IFN-γ were significantly decreased after gene silencing. Furthermore, the NFAT protein expression level was significantly down-regulated. In addition, the levels of IFN-γ and IL-6 in the cell culture supernatant were significantly decreased. CONCLUSION: Both Kv1.3 and KCa3.1 potassium channels activated T lymphocytes and enhanced the cytokine secretion possibly through CaN/NFAT signaling pathway, which may in turn induce micro-inflammatory responses and trigger the occurrence and progression of hypertension.

Genome-Wide Analysis and Functional Characterization of LACS Gene Family Associated with Lipid Synthesis in Cotton (Gossypium spp.).

Cotton (Gossypium spp.) is the fifth largest oil crop in the world, and cottonseed provides abundant vegetable oil resources and industrial bioenergy fuels for people; therefore, it is of practical significance to increase the oil content of cotton seeds for improving the oil yield and economic benefits of planting cotton. Long-chain acyl-coenzyme A (CoA) synthetase (LACS) capable of catalyzing the formation of acyl-CoAs from free fatty acids has been proven to significantly participate in lipid metabolism, of which whole-genome identification and functional characterization of the gene family have not yet been comprehensively analyzed in cotton. In this study, a total of sixty-five LACS genes were confirmed in two diploid and two tetraploid Gossypium species, which were divided into six subgroups based on phylogenetic relationships with twenty-one other plants. An analysis of protein motif and genomic organizations displayed structural and functional conservation within the same group but diverged among the different group. Gene duplication relationship analysis illustrates the LACS gene family in large scale expansion through WGDs/segmental duplications. The overall Ka/Ks ratio indicated the intense purifying selection of LACS genes in four cotton species during evolution. The LACS genes promoter elements contain numerous light response cis-elements associated with fatty acids synthesis and catabolism. In addition, the expression of almost all GhLACS genes in high seed oil were higher compared to those in low seed oil. We proposed LACS gene models and shed light on their functional roles in lipid metabolism, demonstrating their engineering potential for modulating TAG synthesis in cotton, and the genetic engineering of cottonseed oil provides a theoretical basis.

Analysis of complete chloroplast genome sequences and insight into the phylogenetic relationships of Ferula L.

BACKGROUND: Ferula L. is one of the largest and most taxonomically complicated genera as well as being an important medicinal plant resource in the family Apiaceae. To investigate the plastome features and phylogenetic relationships of Ferula and its neighboring genera Soranthus Ledeb., Schumannia Kuntze., and Talassia Korovin, we sequenced 14 complete plastomes of 12 species.  RESULTS: The size of the 14 complete chloroplast genomes ranged from 165,607 to 167,013 base pairs (bp) encoding 132 distinct genes (87 protein-coding, 37 tRNA, and 8 rRNA genes), and showed a typical quadripartite structure with a pair of inverted repeats (IR) regions. Based on comparative analysis, we found that the 14 plastomes were similar in codon usage, repeat sequence, simple sequence repeats (SSRs), and IR borders, and had significant collinearity. Based on our phylogenetic analyses, Soranthus, Schumannia, and Talassia should be considered synonymous with Ferula. Six highly divergent regions (rps16/trnQ-UUG, trnS-UGA/psbZ, psbH/petB, ycf1/ndhF, rpl32, and ycf1) were also detected, which may represent potential molecular markers, and combined with selective pressure analysis, the weak positive selection gene ccsA may be a discriminating DNA barcode for Ferula species. CONCLUSION: Plastids contain abundant informative sites for resolving phylogenetic relationships. Combined with previous studies, we suggest that there is still much room for improvement in the classification of Ferula. Overall, our study provides new insights into the plastome evolution, phylogeny, and taxonomy of this genus.

Biocrust diazotrophs and bacteria rather than fungi are sensitive to chronic low N deposition.

Anthropogenic long-term nitrogen (N) deposition may dramatically impact biocrusts due to the overarching N limitation of soil biota in deserts. Even low levels of N may reach a critical loading threshold altering biocrust constituents and function. To identify the impact of chronic and continuous low levels of N deposition on biocrusts, we created a realistic gradient mirroring anthropogenic N addition rate (2:1 NH4 + : NO3 - rates: 0.3, 0.5, 1.0, 1.5, 3 g N m-2  yr-1 ) and measured the response of bacteria and fungi within cyanobacterial-dominated biocrusts over 8 years in a temperate desert, the Gurbantunggut Desert, China. We found that once N deposition reached 1.5 g N m-2  yr-1 biocrust bacterial communities, including diazotrophs, were altered while no such tipping point existed for fungi. Above the threshold, bacterial richness was enhanced, the relative abundance of Chloroflexi, FBP and Gemmatimonadetes was elevated, and diazotrophs shifted from being dominated by Nostocaceae and Scytonemataceae (Cyanobacteria) to free-living Bradyrhizobiaceae (Alphaproteobacteria). Alternatively, the relative recovery of a few fungal species within the Lecanorales, Pleosporales and Verrucariales became either enriched or diminished due to N deposition. The chronic addition of N resulted in a dense and interconnected bacterial co-occurrence network that accentuated a functional shift from networks dominated by phototrophic species within the Nostocaceae, Xenococcaceae, Phormidiaceae and Scytonemataceae (Cyanobacteria) to ammonia-oxidizing species within the Nitrosomonadaceae (Betaproteobacteria) and nitrifying bacteria [i.e. Nitrospiraceae (Nitrospirae)]. Based on structural equation models, the effects of N additions on biocrust constituents were imposed through indirect effects on pH, soil electrical conductivity and ammonium concentrations. In summary, biocrust constituents are generally insensitive to chronic low levels of N depositions until rates reach above 1.5 g N m-2  yr-1 with diazotrophs being the most sensitive biocrust constituents followed by bacteria and finally fungi. Ultimately once the threshold is reached N deposition favours biocrust constituents utilizing inorganic N and other C sources over relying on phototrophic and/or N-fixing cyanobacteria for C and N.

Efficient Oxygen Evolution Reaction on Polyethylene Glycol-Modified BiVO4 Photoanode by Speeding up Proton Transfer.

The rate-determining step of the oxygen evolution reaction based on a semiconductor photoanode is the formation of the OO bond. Herein, polyethylene glycol (PEG)-modified BiVO4 photoanodes are reported, in which protons can be transferred quickly due to the high proton conductivity of PEG, resulting in the acceleration of the OO bond formation rate. These are fully demonstrated by different kinetic isotope effect values. Moreover, the open-circuit voltage (Uoc ) further illustrates that PEG passivates the surface states and surface charge recombination is reduced. The composite photoanode can achieve a maximum photocurrent density of 3.64 mA cm-2 at 1.23 V compared to 1.04 mA cm-2 for pure BiVO4 , and an onset potential of 170 mV, which is a 230 mV negative shift compared to pure BiVO4 . This work provides a new strategy to accelerate water oxidation kinetics for photoanodes by speeding up the transfer of the proton and the OO bond formation rate.

AAQSP increases mapping resolution of stable QTLs through applying NGS-BSA in multiple genetic backgrounds.

KEY MESSAGE: In this study, we present AAQSP as an extension of existing NGS-BSA applications for identifying stable QTLs at high resolution. GhPAP16 and GhIQD14 fine mapped on chromosome D09 of upland cotton are identified as important candidate genes for lint percentage (LP). Bulked segregant analysis combined with next generation sequencing (NGS-BSA) allows rapid identification of genome sequence differences responsible for phenotypic variation. The NGS-BSA approach applied to crops mainly depends on comparing two bulked DNA samples of individuals from an F2 population. Since some F2 individuals still maintain high heterozygosity, heterosis will exert complications in pursuing NGS-BSA in such populations. In addition, the genetic background influences the stability of gene expression in crops, so some QTLs mapped in one segregating population may not be widely applied in crop improvement. The AAQSP (Association Analysis of QTL-seq on Semi-homologous Populations) reported in our study combines the optimized scheme of constructing BSA bulks with NGS-BSA analysis in two (or more) different parental genetic backgrounds for isolating the stable QTLs. With application of AAQSP strategy and construction of a high-density linkage map, we have successfully identified a QTL significantly related to lint percentage (LP) in cultivated upland cotton, followed by map-based cloning to dissect two candidate genes, GhPAP16 and GhIQD14. This study demonstrated that AAQSP can efficiently identify stable QTLs for complex traits of interest, and thus accelerate the genetic improvement of upland cotton and other crop plants.

Leaf-root-soil N:P stoichiometry of ephemeral plants in a temperate desert in Central Asia.

Ephemeral plants are a crucial vegetation component in temperate deserts of Central Asia, and play an important role in biogeochemical cycle and biodiversity maintenance in desert ecosystems. However, the nitrogen (N) and phosphorus (P) status and interrelations of leaf-root-soil of ephemeral plants remain unclear. A total of 194 leaf-root-soil samples of eight ephemeral species at 37 sites in the Gurbantunggut Desert, China were collected, and then the corresponding N and P concentrations, and the N:P ratio were measured. Results showed that soil parameters presented no significant difference among the eight species. The total soil N:P was only 0.116 (geomean), indicating limited soil N, while the available soil N:P (4.896, geomean) was significantly larger than the total N:P. The leaf N (averagely 30.995 mg g-1) and P (averagely 1.523 mg g-1) concentrations were 2.64-8.46 and 0.93-3.99 times higher than the root N (averagely 8.014 mg g-1) and P (averagely 0.802 mg g-1) concentrations, respectively. Thus, leaf N:P (averagely 21.499) was 1.410-2.957 times higher than root N:P (averagely 11.803). Meanwhile, significant interspecific differences existed in plant stoichiometric traits. At the across-species level, N content scaled as the 3/4-power of P content in both leaves and roots. Leaf and root N:P ratios were mainly influenced by P; however, the leaf-to-root N or P ratio was dominated by roots. Leaf and root N, P contents and N:P were generally unrelated to soil nutrients, and the former presented lower variation than the latter, indicating a strong stoichiometric homeostasis for ephemerals. These results demonstrate that regardless of soil nutrient supply capacity in this region, the fast-growing ephemeral plants have formed a specific leaf-root-soil stoichiometric relation and nutrient use strategy adapting to the extreme desert environment.

Three-dimensional genetic networks among seed oil-related traits, metabolites and genes reveal the genetic foundations of oil synthesis in soybean.

Although the biochemical and genetic basis of lipid metabolism is clear in Arabidopsis, there is limited information concerning the relevant genes in Glycine max (soybean). To address this issue, we constructed three-dimensional genetic networks using six seed oil-related traits, 52 lipid metabolism-related metabolites and 54 294 SNPs in 286 soybean accessions in total. As a result, 284 and 279 candidate genes were found to be significantly associated with seed oil-related traits and metabolites by phenotypic and metabolic genome-wide association studies and multi-omics analyses, respectively. Using minimax concave penalty (MCP) and smoothly clipped absolute deviation (SCAD) analyses, six seed oil-related traits were found to be significantly related to 31 metabolites. Among the above candidate genes, 36 genes were found to be associated with oil synthesis (27 genes), amino acid synthesis (four genes) and the tricarboxylic acid (TCA) cycle (five genes), and four genes (GmFATB1a, GmPDAT, GmPLDα1 and GmDAGAT1) are already known to be related to oil synthesis. Using this information, 133 three-dimensional genetic networks were constructed, 24 of which are known, e.g. pyruvate-GmPDAT-GmFATA2-oil content. Using these networks, GmPDAT, GmAGT and GmACP4 reveal the genetic relationships between pyruvate and the three major nutrients, and GmPDAT, GmZF351 and GmPgs1 reveal the genetic relationships between amino acids and seed oil content. In addition, GmCds1, along with average temperature in July and the rainfall from June to September, influence seed oil content across years. This study provides a new approach for the construction of three-dimensional genetic networks and reveals new information for soybean seed oil improvement and the identification of gene function.

Inference of Chromosome-Length Haplotypes Using Genomic Data of Three or a Few More Single Gametes.

Compared with genomic data of individual markers, haplotype data provide higher resolution for DNA variants, advancing our knowledge in genetics and evolution. Although many computational and experimental phasing methods have been developed for analyzing diploid genomes, it remains challenging to reconstruct chromosome-scale haplotypes at low cost, which constrains the utility of this valuable genetic resource. Gamete cells, the natural packaging of haploid complements, are ideal materials for phasing entire chromosomes because the majority of the haplotypic allele combinations has been preserved. Therefore, compared with the current diploid-based phasing methods, using haploid genomic data of single gametes may substantially reduce the complexity in inferring the donor's chromosomal haplotypes. In this study, we developed the first easy-to-use R package, Hapi, for inferring chromosome-length haplotypes of individual diploid genomes with only a few gametes. Hapi outperformed other phasing methods when analyzing both simulated and real single gamete cell sequencing data sets. The results also suggested that chromosome-scale haplotypes may be inferred by using as few as three gametes, which has pushed the boundary to its possible limit. The single gamete cell sequencing technology allied with the cost-effective Hapi method will make large-scale haplotype-based genetic studies feasible and affordable, promoting the use of haplotype data in a wide range of research.

Large-fragment insertion activates gene GaFZ (Ga08G0121) and is associated with the fuzz and trichome reduction in cotton (Gossypium arboreum).

Cotton seeds are typically covered by lint and fuzz fibres. Natural 'fuzzless' mutants are an ideal model system for identifying genes that regulate cell initiation and elongation. Here, using a genome-wide association study (GWAS), we identified a ~ 6.2 kb insertion, larINDELFZ , located at the end of chromosome 8, composed of a ~ 5.0 kb repetitive sequence and a ~ 1.2 kb fragment translocated from chromosome 12 in fuzzless Gossypium arboreum. The presence of larINDELFZ was associated with a fuzzless seed and reduced trichome phenotypes in G. arboreum. This distant insertion was predicted to be an enhancer, located ~ 18 kb upstream of the dominant-repressor GaFZ (Ga08G0121). Ectopic overexpression of GaFZ in Arabidopsis thaliana and G. hirsutum suggested that GaFZ negatively modulates fuzz and trichome development. Co-expression and interaction analyses demonstrated that GaFZ might impact fuzz fibre/trichome development by repressing the expression of genes in the very-long-chain fatty acid elongation pathway. Thus, we identified a novel regulator of fibre/trichome development while providing insights into the importance of noncoding sequences in cotton.

An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2.

In the genetic system that regulates complex traits, metabolites, gene expression levels, RNA editing levels and DNA methylation, a series of small and linked genes exist. To date, however, little is known about how to design an efficient framework for the detection of these kinds of genes. In this article, we propose a genome-wide composite interval mapping (GCIM) in F2. First, controlling polygenic background via selecting markers in the genome scanning of linkage analysis was replaced by estimating polygenic variance in a genome-wide association study. This can control large, middle and minor polygenic backgrounds in genome scanning. Then, additive and dominant effects for each putative quantitative trait locus (QTL) were separately scanned so that a negative logarithm P-value curve against genome position could be separately obtained for each kind of effect. In each curve, all the peaks were identified as potential QTLs. Thus, almost all the small-effect and linked QTLs are included in a multi-locus model. Finally, adaptive least absolute shrinkage and selection operator (adaptive lasso) was used to estimate all the effects in the multi-locus model, and all the nonzero effects were further identified by likelihood ratio test for true QTL identification. This method was used to reanalyze four rice traits. Among 25 known genes detected in this study, 16 small-effect genes were identified only by GCIM. To further demonstrate GCIM, a series of Monte Carlo simulation experiments was performed. As a result, GCIM is demonstrated to be more powerful than the widely used methods for the detection of closely linked and small-effect QTLs.