Resolution enhancement for interrogating fiber Bragg grating sensor network using dilated U-Net.

In the fiber Bragg grating (FBG) sensor network, the signal resolution of the reflected spectrum is correlated with the network's sensing accuracy. The interrogator determines the signal resolution limits, and a coarser resolution results in an enormous uncertainty in sensing measurement. In addition, the multi-peak signals from the FBG sensor network are often overlapped; this increases the complexity of the resolution enhancement task, especially when the signals have a low signal-to-noise ratio (SNR). Here, we show that deep learning with U-Net architecture can enhance the signal resolution for interrogating the FBG sensor network without hardware modifications. The signal resolution is effectively enhanced by 100 times with an average root mean square error (RMSE) < 2.25 pm. The proposed model, therefore, allows the existing low-resolution interrogator in the FBG setup to function as though it contains a much higher-resolution interrogator.

Dilated convolutional neural networks for fiber Bragg grating signal demodulation.

In quasi-distributed fiber Bragg grating (FBG) sensor networks, challenges are known to arise when signals are highly overlapped and thus hard to separate, giving rise to substantial error in signal demodulation. We propose a multi-peak detection deep learning model based on a dilated convolutional neural network (CNN) that overcomes this problem, achieving extremely low error in signal demodulation even for highly overlapped signals. We show that our FBG demodulation scheme enhances the network multiplexing capability, detection accuracy and detection time of the FBG sensor network, achieving a root-mean-square (RMS) error in peak wavelength determination of < 0.05 pm, with a demodulation time of 15 ms for two signals. Our demodulation scheme is also robust against noise, achieving an RMS error of < 0.47 pm even with a signal-to-noise ratio as low as 15 dB. A comparison on our high-performance computer with existing signal demodulation methods shows the superiority in RMS error of our dilated CNN implementation. Our findings pave the way to faster and more accurate signal demodulation methods, and testify to the substantial promise of neural network algorithms in signal demodulation problems.

Strain sensitivity enhancement based on periodic deformation in hollow core fiber.

Recent progress in optical fiber Mach-Zehnder interferometers (MZIs) has gained many achievements in sensing application. However, the strain sensitivity of optical fiber MZIs is low due to the low elasto-optical coefficient of silica. In this Letter, we propose and demonstrate a method to modulate the guided modes in an MZI based on a special hollow core microstructured optical fiber (HCMOF) by fabricating periodical deformations. Specifically, periodical deformations reduce the extinction ratio of the transmission spectrum. Furthermore, the axial tension modulates these periodical deformations, leading to the enhanced strain sensitivity in comparison to the configuration without deformations. In our experiment, the strain response from 0 to 1000µÎµ is obtained with a sensitivity of 0.00359dB/µÎµ corresponding to an improvement of 13 times compared with a sensor based on same HCMOF without deformations.

Dietary supplementation with an amino acid blend enhances intestinal function in piglets.

The traditionally classified nutritionally non-essential amino acids are now known to be insufficiently synthesized for maximal growth and optimal health in piglets. This study determined the effects of dietary supplementation with an amino acid blend (AAB; glutamate:glutamine:glycine:arginine:N-acetylcysteine = 5:2:2:1:0.5) on piglet growth performance and intestinal functions. Sixteen piglets (24-day-old) were randomly assigned to a corn and soybean meal-based diet supplemented with 0.99% alanine (isonitrogenous control) or 1% AAB. On day 20 of the trial, blood and intestinal tissue samples were obtained from piglets. Compared with the control, AAB supplementation reduced (P < 0.05) diarrhoea incidence; plasma alanine aminotransferase and diamine oxidase activities; intestinal concentrations of hydrogen peroxide, malondialdehyde, and heat shock protein-70, and intestinal mRNA levels for interleukin-1ß, interferon-γ, and chemokine (C-X-C motif) ligand-9; and the numbers of Enterobacterium family, Enterococcus genus and Clostridium coccoides in the colon digesta. Furthermore, AAB supplementation enhanced (P < 0.05): the plasma concentrations of serine, aspartate, glutamate, cysteine, tyrosine, phenylalanine, tryptophan, lysine, arginine, citrulline, ornithine, taurine, and γ-aminobutyric acid; intestinal villus height and surface area, villus height/crypt depth ratio, antioxidative enzyme activities, and mRNA levels for porcine ß-defensin-1, sodium-independent amino acid transporters (b0,+AT and y+LAT1), aquaporin (AQP) 3, AQP8, AQP10, nuclear factor erythroid 2-related factor 2 and glutathione S-transferase omega-2, and protein abundances of AQP3, AQP4, claudin-1, occludin and myxovirus resistance 1; and the numbers of Bifidobacterium genus and Lactobacillus genus in the colon digesta. Collectively, these comprehensive results indicate that dietary AAB supplementation plays an important role in improving piglet growth and intestinal function.

Dietary Supplementation with α-Ketoglutarate Activates mTOR Signaling and Enhances Energy Status in Skeletal Muscle of Lipopolysaccharide-Challenged Piglets.

BACKGROUND: Skeletal muscle undergoes rapid loss in response to inflammation. α-Ketoglutarate (AKG) has been reported to enhance muscle growth in piglets, but the underlying mechanisms are largely unknown. OBJECTIVES: This study tested the hypothesis that dietary AKG supplementation activates mechanistic target of rapamycin (mTOR) signaling and improves skeletal muscle energy metabolism in lipopolysaccharide (LPS)-challenged piglets. METHODS: Forty-eight male piglets (Duroc × Landrace × Yorkshire) were weaned at 21 d of age to a corn- and soybean meal-based diet. After a 3-d period of adaptation, piglets with a mean weight of 7.21 kg were randomly assigned to control, LPS (intraperitoneal administration of 80 µg LPS/kg body weight on days 10, 12, 14, and 16), or LPS plus 1% dietary AKG (LPS+AKG) groups. On day 16, blood samples were collected from 8 piglets/group 3 h after LPS administration. On day 17, piglets were killed to obtain gastrocnemius muscle from 8 piglets/group for biochemical analysis. RESULTS: Compared with the control group, LPS administration increased (P < 0.05) plasma concentrations of globulin (by 14%) and tumor necrosis factor α (by 59%) and the intramuscular ratio of AMP to ATP (by 93%) and abundance of phosphorylated acetyl-coenzyme A carboxylase (ACC) ß protein (by 64%). Compared with the control group, LPS administration reduced (P < 0.05) weight gain (by 15%); plasma concentrations of glutamine (by 20%), glucose (by 23%), insulin, insulin-like growth factor I, and epidermal growth factor; intramuscular concentrations of glutamine (by 27%), ATP (by 12%), ADP (by 22%), and total adenine nucleotides; and intramuscular ratios of phosphorylated mTOR to total mTOR (by 38%) and of phosphorylated 70-kDa ribosomal protein S6 kinase (p70S6K) to total p70S6K (by 39%). These adverse effects of LPS were ameliorated (P < 0.05) by AKG supplementation. CONCLUSIONS: Dietary AKG supplementation activated mTOR signaling, inhibited ACC-ß, and improved energy status in skeletal muscle of LPS-challenged piglets. These results provide a biochemical basis for the use of AKG to enhance piglet growth under inflammatory or practical postweaning conditions.

Hybrid Photoacoustic Ultrasound Imaging System for Cold-Induced Vasoconstriction and Vasodilation Monitoring.

Lewis hunting reaction refers to the alternating cold-induced vasoconstriction and dilation in extremities, whose underlying mechanism is complex. While numerous studies reported this intriguing phenomenon by measuring cutaneous temperature fluctuation under cold exposure, few of them tracked peripheral vascular responses in real-time, lacking a non-invasive and quantitative imaging tool. To better monitor hunting reaction and diagnose relevant diseases, we developed a hybrid photoacoustic ultrasound (PAUS) tomography system to monitor finger vessels' dynamic response to cold, together with simultaneous temperature measurement. We also came out a standard workflow for image analysis with self-defined indices. In the small cohort observational study, vascular changes in the first cycle of hunting reaction were successfully captured by the image series and quantified. Time difference between vasodilation and temperature recovery was noticed and reported for the first time, thanks to the unique capability of the PAUS imaging system in real-time and continuous vascular monitoring. The developed imaging system and indices enabled more objective and quantitative monitoring of peripheral vascular activities, indicating its great potential in numerous clinical applications.

Effects of Dietary l-Glutamine Supplementation on the Intestinal Function and Muscle Growth of Piglets.

The aim of this study was to investigate the effects of dietary l-glutamine (Gln) supplementation on the morphology and function of the intestine and the growth of muscle in piglets. In this study, sixteen 21-day-old piglets were randomly divided into two groups: the Control group (fed a basal diet) and the Gln group (fed a basal diet supplemented with 0.81% Gln). Blood, gut, and muscle samples were collected from all piglets on Day 20 of the trial. Compared with the Control group, the supplementation of Gln increased (p < 0.05) the villus height, villus width, villus surface area, and villus height/crypt depth ratio of the small intestine. Furthermore, the supplementation of Gln increased (p < 0.05) total protein, total protein/DNA, and RNA/DNA in both the jejunum and ileum. It also increased (p < 0.05) the concentrations of carnosine and citrulline in the jejunal mucosa, as well as citrulline and cysteine concentrations in the ileum. Conversely, Gln supplementation decreased (p < 0.05) Gln concentrations in both the jejunum and ileum, along with ß-aminoisobutyric acid and 1-Methylhistidine concentrations, specifically in the ileum. Subsequent research revealed that Gln supplementation increased (p < 0.05) the mRNA levels for glutathione-S-transferase omega 2 and interferon-ß in the duodenum. In addition, Gln supplementation led to an increase (p < 0.05) in the number of Lactobacillus genus in the colon, but a decrease (p < 0.05) in the level of HSP70 in the jejunum and the activity of diamine oxidase in plasma. Also, Gln supplementation reduced (p < 0.05) the mRNA levels of glutathione-S-transferase omega 2 and interferon stimulated genes, such as MX1, OAS1, IFIT1, IFIT2, IFIT3, and IFIT5 in both the jejunum and ileum, and the numbers of Clostridium coccoides, Enterococcus genus, and Enterobacterium family in the colon. Moreover, Gln supplementation enhanced (p < 0.05) the concentrations of total protein, RNA/DNA, and total protein/DNA ratio in the longissimus dorsi muscle, the concentrations of citrulline, ornithine, arginine, and hydroxyproline, and the mRNA level of peptide transporter 1, while reducing the contents of hydrogen peroxide and malondialdehyde and the mRNA level of glutathione-S-transferase omega 2 in the longissimus dorsi muscle. In conclusion, dietary Gln supplementation can improve the intestinal function of piglets and promote the growth of the longissimus dorsi muscle.

The Mediating Role of Sarcopenia in the Association between Physical Activity and Falls among Chinese Older Adults: A Cross-Sectional Study.

Physical inactivity and sarcopenia are potentially modifiable risk factors for falls in older adults, but the strength of the association between physical activity (PA), sarcopenia, and falls in Chinese older adults is unclear. This study sought to investigate the potential mediation mechanism relationship in the connection between PA, sarcopenia, including its elements (muscle strength, physical performance, and skeletal muscle mass), and falls among Chinese older people. The subjects were 3592 community-dwelling Chinese aged 60 or over, selected from the China Health and Retirement Longitudinal Study (CHARLS). PA was evaluated through the International Physical Activity Questionnaire (IPAQ), and sarcopenia was determined through the Asian Working Group on Sarcopenia (AWGS) 2019 guidelines. We employed logistic regression to explore the link between physical activity, sarcopenia, and falls. Additionally, we applied Karlson, Holm and Breen's (KHB) method to estimate two different mediation models. The results demonstrated that PA lowers the risk of falls [odds ratio (OR) 0.54, 95% confidence interval (CI) 0.48-0.61], whereas sarcopenia increases the risk of falls (OR 1.34, 95% CI 1.16-1.55). Sarcopenia mediated the association between PA and falls, explaining a total of 2.69% of the association (indirect effect = -0.02). PA also had a significant mediating effect on the association between sarcopenia and falls, explaining a total of 20.12% of the association (indirect effect = 0.06). The proportion mediated by sarcopenia was 2.69% for PA and falls (indirect effect = -0.02). Our findings suggest that PA and sarcopenia have a direct effect on falls as well as an indirect effect through each other. Enhancing PA levels and preventing sarcopenia may help prevent falls in older adults.

Circular RNA circ_0002360 regulates the Taxol resistance and malignant behaviors of Taxol-resistant non-small cell lung cancer cells by microRNA-585-3p-dependent modulation of G protein regulated inducer of neurite outgrowth 1.

Drug resistance has become the major obstacle for the treatment of non-small cell lung cancer (NSCLC). Circular RNAs (circRNAs) are tightly linked to the development of drug resistance of NSCLC. Herein, we tested the function of circ_0002360 in the Taxol resistance of NSCLC. Circ_0002360, microRNA (miR)-585-3p and G protein regulated inducer of neurite outgrowth 1 (GPRIN1) were quantified by quantitative real-time PCR (qRT-PCR). To identify the circular structure of circ_0002360, RNase R digestion was applied. To detect cell proliferation, colony formation and 5-ethynyl-2'-deoxyuridine (EdU) assays were used. For assessment of cell apoptosis, flow cytometry was adopted. For motility and invasion analyses, transwell assay was employed. Our data showed that circ_0002360 was mainly located in the cytoplasm and was highly expressed in the Taxol-resistant NSCLC. Silencing of circ_0002360 inhibited cell Taxol resistance, proliferation, motility, and invasiveness and induced apoptosis in vitro. MiR-585-3p was underexpressed in Taxol-resistant NSCLC and was targeted by circ_0002360. MiR-585-3p knockdown alleviated the influence of circ_0002360 silence on Taxol-resistant cells. GPRIN1 was directly targeted by miR-585-3p. The influence of miR-585-3p on cell Taxol resistance and functional behaviors was reversed by GPRIN1 overexpression. Moreover, circ_0002360 modulated GPRIN1 through miR-585-3p. Additionally, silencing of circ_0002360 weakened the growth of xenografts in vivo. Our study demonstrated that silencing of circ_0002360 enhanced the Taxol sensitivity and suppressed the malignant behaviors of Taxol-resistant NSCLC cells by miR-585-3p/GPRIN1 axis, providing novel targets for improving the anti-tumor efficacy of Taxol in NSCLC.

Applications of Optical Fiber in Label-Free Biosensors and Bioimaging: A Review.

Biosensing and bioimaging are essential in understanding biological and pathological processes in a living system, for example, in detecting and understanding certain diseases. Optical fiber has made remarkable contributions to the biosensing and bioimaging areas due to its unique advantages of compact size, immunity to electromagnetic interference, biocompatibility, fast response, etc. This review paper will present an overview of seven common types of optical fiber biosensors and optical fiber-based ultrasound detection in photoacoustic imaging (PAI) and the applications of these technologies in biosensing and bioimaging areas. Of course, there are many types of optical fiber biosensors. Still, this paper will review the most common ones: optical fiber grating, surface plasmon resonance, Sagnac interferometer, Mach-Zehnder interferometer, Michelson interferometer, Fabry-Perot Interferometer, lossy mode resonance, and surface-enhanced Raman scattering. Furthermore, different optical fiber techniques for detecting ultrasound in PAI are summarized. Finally, the main challenges and future development direction are briefly discussed.

Dietary tributyrin intervention improves the carcass traits, organ indices, and blood biomarker profiles in broilers under the isocaloric diets administration.

The objective of the current study was to investigate the effect of dietary tributyrin (TB) intervention on carcass traits, visceral and immune organ indices, and blood biomarker profiles in Arbor Acres (AA) broilers under the isocaloric diets administration. A total of 432-day-old healthy AA broiler chickens were assigned to 4 treatments, with 12 replicates per treatment and 9 birds per cage, for 42 d. The dietary treatments were a basal diet (control) and the basal diet supplemented with a TB product (Eucalorie) at doses of 0.50 g/kg (TB1), 1.0 g/kg (TB2), and 2.0 g/kg (TB3). The results showed that dietary TB treatment quadratically improved the average daily gain and average daily feed intake in the second (22-42 d) and overall (0-42 d) feeding periods (P < 0.05) while decreasing the feed conversion ratio in the second feeding period (P < 0.05). Dietary TB treatment improved the carcass traits, as evidenced by a higher eviscerated carcass rate and lower abdominal fat yield than those in the control group (P < 0.05). The breast meat yield rate was quadratically improved in response to dietary TB administration (P < 0.05). Dietary TB treatment improved the kidney, spleen, thymus, and bursa indices (P < 0.05) and reduced the lung indices compared with those in the control group (P < 0.05). In particular, the spleen and thymus indices were improved quadratically in response to dietary TB administration (P < 0.05). Dietary TB treatment improved the white and red blood cell counts, platelet count, hemoglobin and hematocrit at d 21, and platelet count at d 42 (P < 0.05), with those in the TB3 group being most affected. Dietary TB administration quadratically decreased the plasma content of uric acid at both d 21 and d 42 as well as that of creatine kinase at d 42 (P < 0.05), while it quadratically increased the plasma albumin/globulin ratio at both d 21 and d 42 (P < 0.05). Collectively, these results demonstrated that dietary TB intervention improved the growth performance, carcass traits, selected visceral and immune organ indices, and some blood biochemical markers under the isocaloric diets administration, which may facilitate better economic profit returns in poultry industry application.

Dietary Tributyrin Administration Improves Intestinal Morphology and Selected Bacterial and Short-Chain Fatty Acid Profiles in Broilers Under an Isocaloric Feeding Regime.

The current study was conducted to investigate the effect of dietary tributyrin (TB) administration on the intestinal and growth performances in Arbor Acres (AA) broilers under an isocaloric feeding regime. A total of 540 day-old healthy AA broilers were randomly assigned to five treatments with 12 replicates (pens) per treatment and nine birds per pen for 42 days. The dietary treatments were basal diet (control) and basal diet with TB at doses of 0.23 g/kg (TB1), 0.46 g/kg (TB2), 0.92 g/kg (TB3), and 1.84 g/kg (TB4). Particularly, to achieve the isocaloric and cost-saving experimental diets, soybean oil was replaced by the TB product (Eucalorie®) with equivalent metabolic energy contents, and the formulas were rebalanced with zeolite to get the sum of all the feed ingredients to 100%. On days 21 and 42, after weighing, the birds (one bird per replicate) whose body weight was close to the replicate average were euthanized to investigate the effect of dietary TB on intestinal morphology, intestinal bacterial population, and short-chain fatty acid contents. The results revealed that dietary TB administration increased the average daily gain, gain/feed ratio, and European broiler index (P < 0.05) and improved the intestinal morphology (P < 0.05) as indicated by higher villus height and the ratios of villus height/crypt depth in broilers. The incremental levels of TB increased the ileal Lactobacillus content (P = 0.05) and cecal Bacillus content (P = 0.02), respectively. Moreover, dietary TB administration also increased the contents of most of the selected short-chain fatty acids in ileal and cecal digesta (P < 0.05). Collectively, dietary TB administration quadratically improved the growth performance, intestinal morphology, beneficial bacterial population, and short-chain fatty acid levels under the isocaloric feeding regime, indicating better profit return potential in practical poultry operation.

The Formation of 14H-LPSO in Mg-9Gd-2Y-2Zn-0.5Zr Alloy during Heat Treatment.

There is a new long-period stacking ordered structure in Mg-RE-Zn magnesium alloys, namely the LPSO phase, which can effectively improve the yield strength, elongation, and corrosion resistance of Mg alloys. According to different types of Mg-RE-Zn alloy systems, two transformation modes are involved in the heat treatment transformation process. The first is the alloy without LPSO phase in the as-cast alloy, and the MgxRE phase changes to 14H-LPSO phase. The second is the alloy containing LPSO phase in the as-cast state, and the 14H-LPSO phase is obtained by the transformations of 6H, 18R, and 24R. The effects of different solution parameters on the second phase of Mg-9Gd-2Y-2Zn-0.5Zr alloy were studied by scanning electron microscopy (SEM), transmission electron microscopy (TEM), and X-ray diffraction (XRD). The precipitation mechanism of 14H-LPSO phase during solution treatment was further clarified. At a solution time of 13 h, the grain size increased rapidly initially and then decreased slightly with increasing solution temperature. The analysis of the volume fraction of the second phase and lattice constant showed that Gd and Y elements in the alloy precipitated from the matrix and formed 14H-LPSO phase after solution treatment at 490 °C for 13 h. At this time, the hardness of the alloy reached the maximum of 74.6 HV. After solution treatment at 500 °C for 13 h, the solid solution degree of the alloy increases, and the grain size and hardness of the alloy remain basically unchanged.

Stem signatures associated antibodies yield early diagnosis and precise prognosis predication of patients with non-small cell lung cancer.

BACKGROUND: This study was designed to detect patients with early NSCLC with tentatively using the stem signatures associated autoantibodies (AAbs), and to evaluate its latent values in the early diagnosis and precise prognosis prediction. METHODS: The serum concentrations of selective antibodies were quantitated by enzyme-linked immunosorbent assay (ELISA), and a total of 458 cases were enrolled (training set = 401; validation set = 57). TCGA databases were used to analyze the distinct expressions and prognostic values of related genes. The optimal cut-off values were 11.60 U/ml for P53, 4.90 U/ml for MAGEA1, 3.85 U/ml for SOX2, and 7.05U/ml for PGP9.5. RESULTS: We found that the stem signatures associated antibodies of MAGEA1, PGP9.5, SOX2, and TP53 exhibited high expressions in NSCLC, negatively correlating with the overall survival (OS) (P < 0.05). In the test groups, the diagnosis sensitivity of P53, PGP9.5, SOX2, and MAGEA1 reached to 21.5%, 39.0%, 50.3%, and 35.0%, respectively, and the specificity reached to 98.7%, 99.4%, 92.2%, and 97.4%. The four candidates' panel gave a sensitivity of 71.8% with a specificity of 89%. In the validation group, the detection of the four antibodies in early diagnosis of NSCLC also exhibited high specificity and sensitivity, further consolidating their potential application. CONCLUSIONS: The detection regarding stem signatures associated antibodies could be used as effective tools in early NSCLC diagnosis, but not for localized screening of cancers, and their abnormal expression was in accordance with poorer survival.

Analysis of the In Situ Crack Evolution Behavior in a Solid Solution Mg-13Gd-5Y-3Zn-0.3Zr Alloy.

The low plasticity of high strength Mg-Gd-Y alloy has become the main obstacle to its application in engineering. In this paper, the origin, propagation and fracture processes of cracks of a solution of treated Mg-13Gd-5Y-3Zn-0.3Zr alloy were observed and studied with scanning electron microscopy (SEM) in an in situ tensile test to provide theoretical references for the development of a new high-performance Mg-Gd-Y alloy. The results showed that there was still some bulk long period stacking order (LPSO) phase remaining in solid solution Mg-13Gd-5Y-3Zn-0.3Zr alloy. Most importantly, it was found that the locations of micro-cracks vary with the different solution treatment processes, mainly including the following three types. (1) At 480 × 10 h and 510 °C × 10 h, much bulk LPSO phase with higher elastic modulus remains in the alloy, which can lead to micro-cracks in the LPSO phase due to stress concentration. (2) At 510 °C × 13 h and 510 °C × 16 h, the phase structure of bulk LPSO changes, and the stress concentration easily appears at the LPSO/α-Mg interface, which leads to micro-cracks at the interface. (3) At 510 °C × 19 h and 510 °C × 22 h, the grain size increases, and the stress concentration is obvious at the grain boundary of coarse grains, which leads to the formation of micro-cracks.

Using three overlapped RILs to dissect genetically clustered QTL for fiber strength on Chro.D8 in Upland cotton.

Fiber strength is an important trait among cotton fiber qualities due to ongoing changes in spinning technology. Major quantitative trait loci (QTL) for fiber quality enable molecular marker-assisted selection (MAS) to effectively improve fiber quality of cotton cultivars. We previously identified a major QTL for fiber strength derived from 7235 in Upland cotton. In the present study, in order to fine-map fiber strength QTL, we chose three recombinant inbred lines (RIL), 7TR-133, 7TR-132, and 7TR-214, developed from a cross between 7235 and TM-1 for backcrossing to TM-1 to develop three large mapping populations. Phenotypic data for fiber strength traits were collected in Nanjing (JES/NAU) and Xinjiang (BES/XJ) in 2006 and 2007. Three simple sequence repeat (SSR) genetic linkage maps on Chro.24(D8) were constructed using these three backcrossed populations. The SSR genetic maps were constructed using 907 individuals in (7TR-133 x TM-1)F(2) (Pop A), 670 in (7TR-132 x TM-1)F(2) (Pop B), and 940 in (7TR-214 x TM-1)F(2) (Pop C). The average distance between SSR loci was 0.62, 1.7, and 0.56 cM for the three maps. MapQTL 5 software detected five-clustered QTL (2.5 < LOD < 29.8) on Chro.D8 for fiber strength following analysis of three RIL backcrossed F(2)/F(2:3) progenies at JES/NAU and BES/XJ over 2 years. Five QTL for fiber strength exhibited a total phenotypic variance (PV) of 28.8-59.6%.

Detection of favorable alleles for yield and yield components by association mapping in upland cotton.

Association mapping based on linkage disequilibrium provides a promising tool for dissecting the genetic basis underlying complex traits. To reveal the genetic variations of yield and yield components traits in upland cotton, 403 upland cotton accessions were collected and analyzed by 560 genome-wide simple sequence repeats (SSRs). A diverse panel consisting of 403 upland cotton accessions was grown in six different environments, and the yield and yield component traits were measured, and 560 SSR markers covering the whole genome were mapped. Association studies were performed to uncover the genotypic and phenotypic variations using a mixed linear model. Favorable alleles and typical accessions for yield traits were identified. A total of 201 markers were polymorphic, revealing 394 alleles. The average gene diversity and polymorphism information content were 0.556 and 0.483, respectively. Based on a population structure analysis, 403 accessions were divided into two subgroups. A mixed linear model analysis of the association mapping detected 43 marker loci according to the best linear unbiased prediction and in at least three of the six environments(- lgP > 1.30, P < 0.05). Among the 43 associated markers, five were associated with more than two traits simultaneously and nine were coincident with those identified previously. Based on phenotypic effects, favorable alleles and typical accessions that contained the elite allele loci related to yield traits were identified and are widely used in practical breeding. This study detected favorable quantitative trait loci's alleles and typical accessions for yield traits, these are excellent genetic resources for future high-yield breeding by marker-assisted selection in upland cotton in China.

Association mapping and favourable QTL alleles for fibre quality traits in Upland cotton (Gossypium hirsutum L.).

Improving cotton fibre quality is a major breeding goal for Upland cotton in China.To investigate the genetic mechanisms of fibre quality, a diverse panel of 403 Upland cotton accessions was grown, and the fibre quality traits were measured in six different environments. Genotyping was performed with genomewide simple sequence repeats. A total of 201 markers were polymorphic and generated 394 allele loci, and 403 accessions were arranged into two subgroups using Structure software. Of the marker loci, 18.94% showed significant linkage disequilibrium (P < 0.05). A mixed linear model in association mapping showed that 51 associations were significant between 39 polymorphic loci and five fibre quality traits, according to best linear unbiased prediction, and in at least three of six environments. Of the 39 associated marker loci, 12 were coincident with previous studies. There were 41 typical accessions identified as containing favourable allele loci related to fibre quality traits. The identified favourable QTL alleles and typical accessions for fibre quality are excellent genetic resources for future cotton breeding in China.

Identifying Functional Genes Influencing Gossypium hirsutum Fiber Quality.

Fiber quality is an important economic index and a major breeding goal in cotton, but direct phenotypic selection is often hindered due to environmental influences and linkage with yield traits. A genome-wide association study (GWAS) is a powerful tool to identify genes associated with phenotypic traits. In this study, we identified fiber quality genes in upland cotton (Gossypium hirsutum L.) using GWAS based on a high-density CottonSNP80K array and multiple environment tests. A total of 30 and 23 significant single nucleotide polymorphisms (SNPs) associated with five fiber quality traits were identified across the 408 cotton accessions in six environments and the best linear unbiased predictions, respectively. Among these SNPs, seven loci were the same, and 128 candidate genes were predicted in a 1-Mb region (±500 kb of the peak SNP). Furthermore, two major genome regions (GR1 and GR2) associated with multiple fiber qualities in multiple environments on chromosomes A07 and A13 were identified, and within them, 22 candidate genes were annotated. Of these, 11 genes were expressed [log2(1 + FPKM)>1] in the fiber development stages (5, 10, 20, and 25 dpa) using RNA-Seq. This study provides fundamental insight relevant to identification of genes associated with fiber quality and will accelerate future efforts toward improving fiber quality of upland cotton.