Marker Interval Research Articles

The effect of tart cherry juice (TCJ) supplementation on exercise-induced muscle damage (EIMD) in an athletic population

Introduction: This systematic review and meta-analysis quantified the effect of tart cherry juice (TCJ) supplementation on exercise-induced muscle damage (EIMD). Evidence supported TCJ’s beneficial effects on muscular function and inflammatory biomarkers interleukin (IL)-6 and IL-8. Method: PubMed, Scopus, and Web of Science were searched up to January 2024. Risk of bias was assessed using RevMan® software. Mean differences and 95% confidence intervals (CIs) of maximal voluntary isometric contraction (MVIC), inflammatory markers, creatine kinase (CK), and visual analog scale (VAS) score were pooled using fixed- or random-effect models. Heterogeneity was assessed using Chi-square or I 2 statistics. Results: Ten trials were included in the analysis. TCJ supplementation significantly improved MVIC [weighted mean difference (WMD) = 9.13%, 95% CI (6.42–11.84), I 2 = 62.3%] and decreased IL-6 [WMD = −0.4 pg/ml, 95% CI (−0.68 to −0.11), I 2 = 62.2%] and IL-8 [WMD = −0.3 pg/ml, 95% CI (−0.6 to −0.0), I 2 = 46.3%]. No significant changes were found in CK, C-reactive protein, IL-1β, tumor necrosis factor-alpha, or VAS score. Dose–response analysis revealed a significant non-linear association between daily TCJ dose and MVIC effect size. Conclusion: TCJ supplementation may improve muscle function and some inflammatory biomarkers in EIMD. Further high-quality studies with larger sample sizes are needed to determine TCJ’s long-term effects.

Genetic mapping and validation of QTL controlling fruit diameter in cucumber

Fruit diameter is one of important agronomy traits that has greatly impacts fruit yield and commercial value in cucumber (Cucumis sativus L.). Hence, we preliminary mapping of fruit diameter was conducted to refine its genetic locus. In this study, to genetic mapping of QTLs that control cucumber fruit diameter, a F2 population with 120 individuals was developed by the East Asian line ‘9930’ (known as narrow fruit diameter) and the European-type cucumber ‘EU224’ (known as wide fruit diameter). Then a Genotyping-by-Sequencing (GBS)-based genetic map with 5662 markers was constructed and the total length is 656.177 cM, with average marker interval of 0.116 cM. Based on this high-density genetic map, a major QTL qfd1.1 related to fruit diameter was detected with a markedly high LOD score 4.07 located approximately 300 kb interval on Chromosome 1 (located between Chr1:1654704–1958556). To confirm qfd1.1 that detected by F2 population, we performed genetic mapping of fruit diameter with an introgression line (IL) about fruit diameter. We developed two KASP markers (FD-1 and FD-2) related to the fruit diameter. Based on this, we inserted the European cucumber EU224 into the qfd1.1 range and targeted widening the fruit diameter of the 9930 cucumber variety, further indicating that qfd1.1 is a new locus regulating the fruit diameter of cucumber. Our findings will support breeders in their research on cucumber fruit diameter.

Reference Intervals (RIs) of the Bone Turnover Markers (BTMs) in Children and Adolescents: A Proposal for Effective Use.

Bone turnover markers (BTMs) can provide information on the bone growth of apparently healthy children and adolescents or useful results in the diagnosis and monitoring of the disease condition, comparing them with appropriate reference intervals (RIs). The aim of this study was to establish the RI for the BTM [specific bone alkaline phosphatase (BALP), carboxy-terminal cross-linked collagen type I telopeptide (CTX), N-terminal propeptide pro-collagen type I (PINP), osteocalcin (OC), resistant to acid tartrate phosphatase isoform 5b (TRAcP-5b)] on serum samples from children and adolescents. 202 samples from children and adolescents (ages 1-18 years) (51.48% male), considered apparently healthy. The biomarker was analyzed on automatic immunometric equipment (TGSTA Technogenetics) and the IDS-iSYS automated system kits The RI of the studied parameters was calculated according to CLSI Guideline C28-A3 with stratification by age and sex. Evaluation of the distribution of values and the meaning of the biomarker concentrations were used to calculate general and specific RI for an age group. BTM concentrations vary with pubertal growth. The pattern of change differs for each bone marker. General and age-specific RI were calculated: 1-14 years, 15-18 years for BALP and CTX; 1-13 years, 14-18 years for Oc and PINP and 1-12 years, 13-18 years for TRAcP. Concentrations for biomarker studied vary with age and gender. The proof of concentrations with insignificant changes until puberty led to identification of two groups of RI relating to the covariables (age and sex) for each biomarker.

Uncovering QTLs for uppermost internode length and panicle exsertion in rice (Oryza sativa L.)

Uppermost internode length (UIL) and panicle exsertion are two important traits that contribute significantly to increased yield in rice. The present study was conducted using recombinant inbred lines (RILs) comprising 201 lines derived from RTN10B and IRG213. These RILs were evaluated at three different locations— Delhi, Karnal, and Aduthurai. We report the mapping of quantitative trait loci (QTLs) for uppermost internode length and the panicle exsertion ratio (PER), as well as QTLs for plant height (PH), tiller number, length of the second internode, length of the third internode, length from the flag leaf to the panicle tip (PFL), and panicle length (PL). Mapping was performed using a custom microsatellite linkage map constructed for the population, having a total span of 2077.1 cM with 104 markers. A total of 22 QTLs were identified for various traits, among which 19 were found distributed in four hotspots. A total of 11 major effect QTLs and 11 minor effect QTLs were identified for various internode length-related traits. Among the four QTLs identified for PFL, three QTLs—qPFL1.1, qPFL1.2, and qPFL2.1—co-localized with previously reported QTLs, while qPFL8.1 was a novel QTL. A major QTL hotspot was identified on chromosome 1, located at the marker interval of RM12055-RM320. The size of the major QTL hotspot on chromosome 1 was 1.4 Mb and contained a total of seven HEs for PER, PFL, PH, PL, UIL, SIL, and TIL. Based on the in-silico analysis of the major QTL hotspot on chromosome 1, we identified 15 putative candidate genes associated with internode length- and panicle-related traits. Furthermore, narrowing the genomic region through the fine mapping of the marker intervals facilitated the identification of candidate genes to enable more precise marker-assisted selection for uppermost internode length and panicle exsertion.

QTL mapping and candidate gene mining of seed size and seed weight in castor plant (Ricinus communis L.).

Castor (Ricinus communis L., 2n = 2x = 20) is an important industrial crop, due to its oil is very important to the global special chemical industry. Seed size and seed weight are fundamentally important in determining castor yield, while little is known about it. In this study, QTL analysis and candidate gene mining of castor seed size and seed weight were conducted with composite interval mapping (CIM), inclusive composite interval mapping (ICIM) and marker enrichment strategy in 4 populations, i.e., populations F2, BC1, S1-1 and S1-2, derived from 2 accessions with significant phenotypic differences. In the QTL primary mapping, 2 novel QTL clusters were detected in marker intervals RCM520-RCM76 and RCM915-RCM950. In order to verify their accuracy and to narrow their intervals, QTL remapping was carried out in populations F2 and BC1. Among them, 44 and 30 QTLs underlying seed size and seed weight were detected in F2 population using methods CIM and ICIM-ADD respectively, including 4-9 and 3-5 ones conferring each trait were identified with a phenotypic variation explained ranged from 37.92 to 115.81% and 32.86-45.98% respectively. The remapping results in BC1 population were consistent with those in F2 population. Importantly, 3 QTL clusters (i.e. QTL-cluster1, QTL-cluster2 and QTL-cluster3) were found in marker intervals RCM74-RCM76 (37.1kb), RCM930-RCM950 (259.8kb) and RCM918-RCM920 (172.9kb) respectively; in addition, all of them were detected again, the former one was found in the S1-2 population, and the latter two were found simultaneously in the populations S1-1 and S1-2. Finally, 6 candidate genes (i.e. LOC8266555, LOC8281168, LOC8281151, LOC8259066, LOC8258591 and LOC8270077) were screened in the above QTL clusters, they were differentially expressed in multiple seed tissues of both parents, signifying the potential role in regulating seed size and seed weight. The above results not only provide new insights into the genetic structure of seed size and seed weight in castor, but also lay the foundation for the functional identification of these candidate genes.

Establishment of Reference Intervals for Bone Turnover Biomarkers in Healthy Populations in Northern China.

This study was intended to establish the reference intervals of bone turnover markers (BTMs) for healthy populations. According to the Clinical Laboratory Standards Institute (CLSI) EP28-A3c, we recruited 774 healthy Chinese and investigated their clinical characteristics and relationships among gender, age, season and BTMs. The reference intervals of BTMs for healthy populations in Hebei of China were established through defining the central 95% range of all observations. We found that gender were associated with 25(OH)D, OC, β-CTX, and P1NP (P < 0.05), but not PTH1-84 (P=0.138). All serum BTMs showed differences among different age groups (P < 0.01). The level of 25 (OH) D in winter showed statistical differences with spring, summer, and autumn (P<0.05). The OC level showed statistical difference between summer and winter (P=0.000). The P1NP levels showed statistical difference between spring and winter (P=0.019), summer and winter (P=0.000), and summer and autumn (P=0.012), respectively. The PTH1-84 levels in winter showed statistical differences with spring, and summer (all P=0.000), while there was no statistically significant difference in β- CTX levels between seasons. We have established the reference intervals of several BTMs for healthy individuals in Hebei of China, which have statistical significance across different age groups and genders, and there are also significant differences between different seasons. Therefore, the Chinese medical laboratories in different locations should group individuals according to gender and age groups in different seasons, and establish corresponding biological reference intervals.

The correlation between indicators of time intervals of left ventricular activity and markers of myocardial damage in patients with non-ST-segment elevation acute coronary syndrome

The correlation between indicators of time intervals of left ventricular activity and markers of myocardial damage in patients with non-ST-segment elevation acute coronary syndrome

High-Density Genetic Map Construction and Quantitative Trait Locus Analysis of Fruit- and Oil-Related Traits in Camellia oleifera Based on Double Digest Restriction Site-Associated DNA Sequencing.

Camellia oleifera, an important tree species and source of edible oil in China, has received significant attention owing to the oil's high unsaturated fatty acid content, which has benefits for human health. However, the mechanisms underlying C. oleifera yield and oil quality are largely unknown. In this study, 180 F1 progenies were obtained from two parents with obvious differences in fruit- and oil-related traits. We constructed a high-density genetic map using a double digest restriction site-associated DNA sequencing (ddRAD-Seq) strategy in C. oleifera. This map spanned 3327 cM and anchored 2780 markers in 15 linkage groups (LGs), with an average marker interval of 1.20 cM. A total of 221 quantitative trait loci (QTLs) associated with fruit- and oil-related traits were identified across three years' worth of phenotypic data. Nine QTLs were detected simultaneously in at least two different years, located on LG02, LG04, LG05, LG06, and LG11, and explained 8.5-16.6% of the phenotypic variation in the corresponding traits, respectively. Seventeen major QTLs were obtained that explained 13.0-16.6% of the phenotypic variance. Eleven and five flanking SNPs of major QTLs for fruit- and oil-related traits were detected which could be used for marker-assisted selection in C. oleifera breeding programs. Furthermore, 202 potential candidate genes in QTL regions were identified based on the collinearity of the genetic map and the C. oleifera "CON" genome. A potential regulatory network controlling fruit development and oil biosynthesis was constructed to dissect the complex mechanism of oil accumulation. The dissection of these QTLs will facilitate the gene cloning underlying lipid synthesis and increase our understanding in order to enhance C. oleifera oil yield and quality.

Construction of a high-density linkage map and QTL detection for growth traits in South African abalone (Haliotis midae).

Haliotis midae is one of the most important molluscs in South African commercial aquaculture. In this study, a high-resolution integrated linkage map was constructed, and QTL identified using 2b-RADseq for genotyping SNPs in three families. The final integrated linkage map was composed by merging the individual family maps, resulting in 3290 informative SNPs mapping to 18 linkage groups, conforming to the known haploid chromosome number for H. midae. The total map spanned 1798.25 cM with an average marker interval of 0.55 cM, representing a genome coverage of 98.76%. QTL analysis, across all three families, resulted in a total of five QTL identified for growth-related traits, shell width, shell length, and total body weight. For shell width and total body weight, one QTL was identified for each trait respectively, whilst three QTL were identified for shell length. The identified QTL respectively explained between 7.20% and 11.40% of the observed phenotypic variance. All three traits were significantly correlated (r = 0.862-0.970; p < 0.01) and shared overlapping QTL. The QTL for growth traits were mapped back to the H. midae draft genome and BLAST searches revealed the identity of candidate genes, such as egf-1, megf10, megf6, tnx, sevp1, kcp, notch1, and scube2 with possible functional roles in H. midae growth. The constructed high-density linkage map and mapped QTL have given valuable insights regarding the genetic architecture of growth-related traits and will be important genetic resources for marker-assisted selection. It remains, however, important to validate causal variants through linkage disequilibrium fine mapping in future.

Identification of quantitative trait loci for sweetening genes of Stevia rebaudiana Bertoni with multiple marker system

Stevia rebaudiana Bertoni, belonging to the family Asteraceae, is one of the most important perennial medicinal plants. It is used as a no-calorie sweetener therefore; mining of sweetening genes using molecular markers is a thrust area. In the present study combinations of markers were screened. Out of 170 RAPD, 26 ISSR, and 89 EST-SSR primers, it was observed that 36 RAPD, 10 ISSR, and 33 EST-SSR were found to be polymorphic. Using MAPMAKER/EXP version 3.0 b, four linkage groups were constructed spanning a distance of 927.3 cM with an average distance between loci of 16.29 cM. On QTL identification, a total of 53 locations were found for both trait 1 (rebaudioside-A) and trait 2 (stevioside). Among 53 QTL locations of trait 1, two major QTL were found for rebaudioside-A namely, in the marker interval of L67–L71 (ISSR HB-11)–(IISRS-3-L) in LG1 and the marker interval of L38–L40 (Sigma-5383–027)- (Sigma-5383-029) in LG3 at LOD of 2.5 and 2.7, respectively. The map constructed and QTL identified will greatly facilitate further genetic studies. It is hoped that this work will have a practical impact on the advancement of stevia breeding and genome analysis.

Genetic Analysis of an F2 Population Derived from the Cotton Landrace Hopi Identified Novel Loci for Boll Glanding.

Landraces are an important reservoir of genetic variation that can expand the narrow genetic base of cultivated cotton. In this study, quantitative trait loci (QTL) analysis was conducted using an F2 population developed from crosses between the landrace Hopi and inbred TM-1. A high-density genetic map spanning 2253.11 and 1932.21 cM for the A and D sub-genomes, respectively, with an average marker interval of 1.14 cM, was generated using the CottonSNP63K array. The linkage map showed a strong co-linearity with the physical map of cotton. A total of 21 QTLs were identified, controlling plant height (1), bract type (1), boll number (1), stem color (2), boll pitting (2), fuzz fiber development (2), boll shape (3), boll point (4), and boll glanding (5). In silico analysis of the novel QTLs for boll glanding identified a total of 13 candidate genes. Analysis of tissue-specific expression of the candidate genes suggests roles for the transcription factors bHLH1, MYB2, and ZF1 in gland formation. Comparative sequencing of open reading frames identified early stop codons in all three transcription factors in Hopi. Functional validation of these genes offers avenues to reduce glanding and, consequently, lower gossypol levels in cottonseeds without compromising the defense mechanisms of the plant against biotic stresses.

Construction of a high-density genetic map and QTL localization of body weight and wool production related traits in Alpine Merino sheep based on WGR

BackgroundThe Alpine Merino is a new breed of fine-wool sheep adapted to the cold and arid climate of the plateau in the world. It has been popularized in Northwest China due to its superior adaptability as well as excellent production performance. Those traits related to body weight, wool yield, and wool fiber characteristics, which are economically essential traits in Alpine Merino sheep, are controlled by QTL (Quantitative Trait Loci). Therefore, the identification of QTL and genetic markers for these key economic traits is a critical step in establishing a MAS (Marker-Assisted Selection) breeding program.ResultsIn this study, we constructed the high-density genetic linkage map of Alpine Merino sheep by sequencing 110 F1 generation individuals using WGR (Whole Genome Resequencing) technology. 14,942 SNPs (Single Nucleotide Polymorphism) were identified and genotyped. The map spanned 2,697.86 cM, with an average genetic marker interval of 1.44 cM. A total of 1,871 high-quality SNP markers were distributed across 27 linkage groups, with an average of 69 markers per LG (Linkage Group). Among them, the smallest genetic distance is 19.62 cM for LG2, while the largest is 237.19 cM for LG19. The average genetic distance between markers in LGs ranged from 0.24 cM (LG2) to 3.57 cM (LG17). The marker density in the LGs ranged from LG14 (39 markers) to LG1 (150 markers).ConclusionsThe first genetic map of Alpine Merino sheep we constructed included 14,942 SNPs, while 46 QTLs associated with body weight, wool yield and wool fiber traits were identified, laying the foundation for genetic studies and molecular marker-assisted breeding. Notably, there were QTL intervals for overlapping traits on LG4 and LG8, providing potential opportunities for multi-trait co-breeding and further theoretical support for selection and breeding of ultra-fine and meaty Alpine Merino sheep.

High-density genetic map construction and QTL mapping of a zigzag-shaped stem trait in tea plant (Camellia sinensis)

The highly unique zigzag-shaped stem phenotype in tea plants boasts significant ornamental value and is exceptionally rare. To investigate the genetic mechanism behind this trait, we developed BC1 artificial hybrid populations. Our genetic analysis revealed the zigzag-shaped trait as a qualitative trait. Utilizing whole-genome resequencing, we constructed a high-density genetic map from the BC1 population, incorporating 5,250 SNP markers across 15 linkage groups, covering 3,328.51 cM with an average marker interval distance of 0.68 cM. A quantitative trait locus (QTL) for the zigzag-shaped trait was identified on chromosome 4, within a 61.2 to 97.2 Mb range, accounting for a phenotypic variation explained (PVE) value of 13.62%. Within this QTL, six candidate genes were pinpointed. To better understand their roles, we analyzed gene expression in various tissues and individuals with erect and zigzag-shaped stems. The results implicated CsXTH (CSS0035625) and CsCIPK14 (CSS0044366) as potential key contributors to the zigzag-shaped stem formation. These discoveries lay a robust foundation for future functional genetic mapping and tea plant genetic enhancement.

Genome-wide QTL and eQTL mapping reveal genes associated with growth rate trait of the Pacific white shrimp (Litopenaeus vannamei)

BackgroundGrowth rate is a crucial economic trait for farmed animals, but the genetic regulation of this trait is largely unknown in non-model organisms such as shrimp.ResultsIn this study, we performed genome-wide phenotypic quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) mapping analyses to identify genes affecting the growth rate of Pacific white shrimp (Litopenaeus vannamei), which is the most commercially-farmed crustacean worldwide. We used RNA-sequencing of 268 individuals in a mapping population, and subsequently validated our findings through gene silencing and shrimp growth experiments. We constructed a high-density genetic linkage map comprising 5533 markers spanning 44 linkage groups, with a total distance of 6205.75 cM and an average marker interval of 1.12 cM. Our analyses identified 11 QTLs significantly correlated with growth rate, and 117,525 eQTLs. By integrating QTL and eQTL data, we identified a gene (metalloreductase STEAP4) highly associated with shrimp growth rate. RNA interference (RNAi) analysis and growth experiments confirmed that STEAP4 was significantly correlated with growth rate in L. vannamei.ConclusionsOur results indicate that the comprehensive analysis of QTL and eQTL can effectively identify genes involved in complex animal traits. This is important for marker-assisted selection (MAS) of animals. Our work contributes to the development of shrimp breeding and available genetic resources.

First ever probable oats (Avena sativa) QTLs mapped on chromosome 1 and 7 for pyrenophora leaf spot resistance in India

An experiment was conducted during 2021–22 at Punjab Agricultural University, Ludhiana, Punjab for the development of linkage map and identification of QTLs for pyrenophora or Helminthosporium leaf spot resistance in oats (Avena sativa L.). A total of 96 F2 plants were used which was derived from the cross EC/0007662 (resistant source) and EC/0131291 (susceptible source). Linkage map was constructed for genotypic data of 96 population lines with 24 polymorphic SSR markers using QTL cartographer. A total of 7 linkage groups (LGs) had been generated from this data. But out of 7 LGs, 5 LGs remained individually at 0 position (unlinked) i.e. belonged to different group each and LG1 and LG7 were grouped. First LG included ABAM232, ABAM493 and ABAM077 from 0 to 66.5 cM. Similarly, 7th LG had two marker position i.e. ABAM342 and ABAM425. Maximum distance between the two markers was found to be 33.4 cM (between the marker interval of ABAM232 and ABAM497. Further QTL analysis was done using cartographer with composite interval mapping to identify the QTLs associated with disease resistance by comparing the phenotypic data of F2 population for disease and genotypic data of the population. The work reported here constitutes a major step toward identification of genetic regions responsible for disease resistance. However, the utility of QTL for marker assisted selection requires that QTLs are localized in a narrow region tightly linked with associated markers. The result of the experiment can be used for marker assisted breeding to transfer such genes identified as part of our research in order to reduce disease severity and yield losses in oats.

Association of white blood cell parameters with metabolic syndrome: A systematic review and meta-analysis of 168,000 patients.

Leukocyte parameters are predicted to be affected in patients with metabolic syndrome (MetS). We conducted a systematic review and meta-analysis to study the association between white blood cell parameters (WBC) in people with and without MetS. PubMed, EMBASE, Scopus and Cochrane Library databases were searched according to the study protocol. The standardized mean difference (SMD) and 95% confidence intervals (CI) of leukocyte markers between individuals with and without MetS were pooled using an inverse variance model. Additionally, a subgroup analysis by sex was performed where possible. Methodological quality assessment was conducted using the Newcastle-Ottawa scale (NOS) for observational studies and the Cochrane Risk of Bias tool 2.0 for Randomized Controlled Trials (RCTs). Of 6068 articles identified, 63 were eligible for the study. Compared to controls, individuals with MetS showed significantly higher concentrations of total leukocyte count (SMD [95% CI]: 0.60 [0.55-0.65]; P < .00001; I2 = 100%), neutrophil counts (0.32 [0.28-0.37]; P < .00001; I2 = 99%), lymphocyte counts (0.15 [0.07-0.23]; P = .0004; I2 = 100%), basophil counts (0.01 [0.00-0.02]; P = .02; I2 = 98%), monocyte counts (0.05 [0.02-0.09]; P = .003; I2 = 99%), and neutrophil-to-lymphocyte ratio (0.24 [0.15-0.33]; P < .00001; I2 = 98%). There were no significant differences in the eosinophil count (0.02 [-0.01 to 0.05]; P = .19; I2 = 96%) and monocyte-to-lymphocyte ratio (0.06 [-0.05 to 0.17]; P = .27; I2 = 100%) between patients with and without MetS, however, the lymphocyte-to-monocyte ratio (0.52 [-0.81 to -0.23]; P = .0005; I2 = 52%) tended to be significantly lower in patients with MetS. Biomarkers such as total leukocyte count, neutrophil count, lymphocyte count, basophil count, monocyte count and neutrophil-to-lymphocyte ratio are associated with higher levels in patients in MetS and thus can potentially be used for early detection of MetS.

QTL Mapping of Trichome Traits and Analysis of Candidate Genes in Leaves of Wheat (Triticum aestivum L.).

Trichome plays an important role in heat dissipation, cold resistance, water absorption, protection of leaves from mechanical damage, and direct exposure to ultraviolet rays. It also plays an important role in the photosynthesis, transpiration, and respiration of plants. However, the genetic basis of trichome traits is not fully understood in wheat. In this study, wheat DH population (Hanxuan 10 × Lumai 14) was used to map quantitative trait loci (QTL) for trichome traits in different parts of flag leaf at 10 days after anther with growing in Zhao County, Hebei Province, and Taigu County, Shanxi Province, respectively. The results showed that trichome density (TD) was leaf center > leaf tip > leaf base and near vein > middle > edge, respectively, in both environments. The trichome length (TL) was leaf tip > leaf center > leaf base and edge > middle > near vein. Significant phenotypic positive correlations were observed between the trichome-related traits of different parts. A total of 83 QTLs for trichome-related traits were mapped onto 18 chromosomes, and each one accounted for 2.41 to 27.99% of the phenotypic variations. Two QTL hotspots were detected in two marker intervals: AX-95232910~AX-95658735 on 3A and AX-94850949~AX-109507404 on 7D. Six possible candidate genes (TraesCS3A02G406000, TraesCS3A02G414900, TraesCS3A02G440900, TraesCS7D02G145200, TraesCS7D02G149200, and TraesCS7D02G152400) for trichome-related traits of wheat leaves were screened out according to their predicted expression levels in wheat leaves. The expression of these genes may be induced by a variety of abiotic stresses. The results provide the basis for further validation and functional characterization of the candidate genes.

Markers of insulin resistance associated with non-alcoholic fatty liver disease in non-diabetic population

Insulin resistance (IR) plays an important role in the development of non-alcoholic fatty liver disease (NAFLD). IR markers are divided into two types: (1) insulin-based IR marker, homeostatic model assessment of IR (HOMA-IR); and (2) non-insulin-based IR markers, such as triglyceride-glucose (TyG) index, TyG index with body mass index (TyG-BMI), triglyceride/high-density lipoprotein cholesterol ratio (TG/HDL-c), and metabolic score for IR (METS-IR). The non-insulin-based IR markers are often associated with lipids. The aim of this study was to analyse the association between IR markers and NAFLD in non-diabetic population. Baseline data of NAFLD and non-NAFLD groups were compared. Logistic regression was used to evaluate the relationship between five IR markers and NAFLD risk. The odds ratios (ORs) and 95% confidence intervals (CIs) of IR markers were calculated. Receiver operating characteristic (ROC) curves and area under the curve (AUC) were used to evaluate the ability of different IR markers to detect NAFLD. Subgroup analyses were performed in obese and non-obese subgroups. This study found a positive correlation between NAFLD risk and elevation in five IR markers (HOMA-IR, TyG, TyG-BMI, TG/HDL-c, and METS-IR). In non-obese subjects, the AUC of TyG-BMI was larger than that of the other four IR markers to detect NAFLD. The AUC of HOMA-IR was larger than that of the other four IR markers to detect NAFLD in obese subjects. In non-diabetic population, the five IR markers are associated with the risk of NAFLD, including non-obese and obese NAFLD. TyG-BMI and HOMA-IR can be used to detect non-obese and obese NAFLD, respectively, with better detection ability compared with the other IR markers.

Hub Genes in Stable QTLs Orchestrate the Accumulation of Cottonseed Oil in Upland Cotton via Catalyzing Key Steps of Lipid-Related Pathways

Upland cotton is the fifth-largest oil crop in the world, with an average supply of nearly 20% of vegetable oil production. Cottonseed oil is also an ideal alternative raw material to be efficiently converted into biodiesel. However, the improvement in kernel oil content (KOC) of cottonseed has not received sufficient attention from researchers for a long time, due to the fact that the main product of cotton planting is fiber. Previous studies have tagged QTLs and identified individual candidate genes that regulate KOC of cottonseed. The regulatory mechanism of oil metabolism and accumulation of cottonseed are still elusive. In the current study, two high-density genetic maps (HDGMs), which were constructed based on a recombinant inbred line (RIL) population consisting of 231 individuals, were used to identify KOC QTLs. A total of forty-three stable QTLs were detected via these two HDGM strategies. Bioinformatic analysis of all the genes harbored in the marker intervals of the stable QTLs revealed that a total of fifty-one genes were involved in the pathways related to lipid biosynthesis. Functional analysis via coexpression network and RNA-seq revealed that the hub genes in the co-expression network that also catalyze the key steps of fatty acid synthesis, lipid metabolism and oil body formation pathways (ACX4, LACS4, KCR1, and SQD1) could jointly orchestrate oil accumulation in cottonseed. This study will strengthen our understanding of oil metabolism and accumulation in cottonseed and contribute to KOC improvement in cottonseed in the future, enhancing the security and stability of worldwide food supply.

Application of a High-Density Single Nucleotide Polymorphism Genetic Map in Mapping Quantitative Trait Loci of Early-Maturing Traits in Upland Cotton

(1) Background: Mapping QTLs for early-maturing traits is necessary for the development of early-maturing variety breeding. (2) Methods: In this research, a high-density genetic map (HDGM) was constructed using an F2 population with 100 individuals and single nucleotide polymorphism markers (SNPs) developed using the genotyping-by-sequencing (GBS) method. (3) Results: The HDGM, which covered a total distance of 3167.14 cM, harbored 5454 SNPs with an average marker interval of 0.58 cM. In total, 18 QTLs for four early-maturing characters were detected and explained 11.6–46.4% of phenotypic variation (PV). Two QTLs of the whole growing period (WGP) and height of the node of the first fruiting branch (HNFFB) were identified as stable QTLs. In total, 125 candidate genes were identified in the confidence intervals of these stable QTLs. Presumably, Gh_D03G0857 may play an important role in regulating earliness. (4) Conclusions: This research will provide new information about fine mapping of QTLs for earliness traits, molecular marker assisted selection (MAS) of earliness traits, and pyramiding breeding as well.