High-density Map Research Articles

High-density genetic map construction and QTL mapping to identify genes for blight defense- and yield-related traits in sesame (Sesamum indicum L.).

Sesame (Sesamum indicum L.) is an important oilseed crop widely cultivated in subtropical and tropical areas. Low genetic yield potential and susceptibility to disease contribute to low productivity in sesame. However, the genetic basis of sesame yield- and disease-related traits remains unclear. Here, we represent the construction of a high-density bin map of sesame using whole genome sequencing of an F2 population derived from 'Yizhi' and 'Mingdeng Zhima'. A total of 2766 Bins were categorized into 13 linkage groups. Thirteen significant QTLs were identified, including ten QTLs related to yield, two QTLs related to Sesame Fusarium wilt (SFW) disease, and one QTL related to seed color. Among these QTLs, we found that SFW-QTL1.1 and SFW-QTL1.2 were major QTLs related to Fusarium wilt disease, explaining more than 20% of the phenotypic variation with LOD > 6. SCC-QTL1.1 was related to seed coat color, explaining 52% of the phenotypic variation with LOD equal to 25.3. This suggests that seed color traits were controlled by a major QTL. Candidate genes related to Fusarium wilt disease and seed color in the QTLs were annotated. We discovered a significant enrichment of genes associated with resistance to late blight. These genes could be spectral disease resistance genes and may have a role in the regulation of Fusarium wilt disease resistance. Our study will benefit the implementation of marker-assisted selection (MAS) for the genetic improvement of disease resistance and yield-related traits in sesame.

Heart Failure with Preserved Ejection Fraction Correlates with Fibrotic Atrial Myopathy in Patients Undergoing Atrial Fibrillation Ablation.

Background: The incidence of atrial fibrillation (AF) in patients with heart failure with preserved ejection fraction (HFpEF) is high. Impaired left atrial (LA) function is a major determinant in HFpEF. However, the extent of electrical LA tissue degeneration in HFpEF is unknown. Therefore, we sought to investigate the amount of arrhythmogenic and fibrotic LA tissue degeneration in HFpEF patients presenting for AF ablation. Methods: We prospectively screened consecutive patients presenting for first time AF ablation. The HFA-PEFF score was used to identify HFpEF patients. Bipolar high-density voltage mapping was created in sinus rhythm prior to ablation to evaluate the general LA bipolar voltage and quantify areas of low voltage. LVAs were defined as areas with bipolar voltage < 0.5 mV. Results: In total, 187 patients were prospectively enrolled (age 65 ± 11 years, 45% female, 46% persistent AF, 25% HFpEF) in this study. HFpEF patients were older and had a higher CHA2DS2-VASc score (70 ± 9 vs. 63 ± 11 years and 3.2 ± 1.5 vs. 2.3 ± 1.5, each p < 0.001, respectively). Overall, low-voltage areas (LVAs) were present in 97 patients (52%), whereas 76% of the HFpEF population had LVA, as compared to 44% of patients without HFpEF (p < 0.001). HFpEF was associated with generally decreased LA bipolar voltage (1.09 ± 0.64 vs. 1.83 ± 0.91 mV; p < 0.001) and predictive of the presence of low-voltage areas (76% vs. 44% p < 0.001). The HFA-PEFF score inversely correlated with LA bipolar voltage (=-0.454; p < 0.001). Conclusions: HFpEF closely relates to generally decreased LA bipolar voltage and to the existence of fibrotic and arrhythmogenic LA tissue degeneration.

Clinical efficacy of radiofrequency ablation guided by high-density mapping on persistent atrial fibrillation.

The study aimed to explore the clinical efficacy of radiofrequency ablation (RFA) guided by high-density mapping on persistent atrial fibrillation (PsAF). A total of 190 patients with PsAF undergoing RFA were divided into a routine group (n = 105) and a high-density mapping group (n = 85). The indicators of therapeutic efficacy were collected and compared. A statistically significant difference was found in the overall rate of post-operative recurrence between the two groups (11.58% vs. 23.81%, χ2 = 5.055, p = 0.025). The effects of different treatment methods on SF-36 score varied (FSF-36 treatment = 43.142, p < 0.05), and SF-36 scores at 3, 6, and 12 months of both groups were in the same order: the high-density mapping group > the routine group. While surgery guided by high-density substrate mapping (odds ratio = 0.453, 95% confidence interval: [0.232-0.784], p < 0.001) was a protective factor for recurrence. For patients with PsAF, more accurate mapping is conducted on the atrial substrate using a PentaRay electrode, which further verifies that the success rate of individualized ablation strategy is like mainstream procedures, and it significantly improves the subsequent health status of patients and reduces their incidence of adverse reactions.

The Functional substrate in patients with atrial fibrillation is predictive of recurrences after catheter ablation

BackgroundEnhanced characterization of the atrial electrical substrate may lead to better comprehension of atrial fibrillation (AF) pathophysiology. ObjectiveWith the use of high-density substrate mapping, we sought to investigate the occurrence of functional electrophysiological phenomena in the left atrium and to assess potential association with arrhythmia recurrences after catheter ablation. MethodsSixty-three consecutive patients with AF referred for ablation were enrolled. Analysis of conduction abnormalities relied on two acquired left atrial electroanatomic maps (sinus and atrial paced rhythm). We classified conduction abnormalities as fixed (if these were present in both rhythms) or functional rhythm dependent (if unmasked in one of the two rhythms). Esophagus and aorta locations were recorded to check the correspondence with abnormal conduction sites. ResultsThere were 234 conduction abnormalities detected, of which 125 (53.4%) were functional rhythm dependent. The most frequent anatomic site of functional phenomena was the anterior wall, followed by the posterior wall, in sinus rhythm and the pulmonary venous antra in paced rhythm. Sites of functional phenomena in 82.6% of cases corresponded with extracardiac structures, such as sinus of Valsalva of ascending aorta anteriorly and the esophagus posteriorly. Most (88%) areas with functional phenomena had normal bipolar voltage. After pulmonary vein ablation, the number of residual functional phenomena is an independent predictor of AF recurrence (hazard ratio, 2.539 [1.458–4.420]; P = .001) with a risk of recurrences at multivariable Cox analysis. ConclusionDual high-density mapping (during sinus and paced rhythms) is able to unmask functional, rhythm-dependent phenomena that are predictive of AF recurrences during follow-up.

Localized three-dimensional reentrant ventricular tachycardia visualized by high-density mapping in arrhythmogenic right ventricular cardiomyopathy.

Localized three-dimensional reentrant ventricular tachycardia visualized by high-density mapping in arrhythmogenic right ventricular cardiomyopathy.

Relationships between biatrial substrate and recurrence after radiofrequency ablation in patients with persistent atrial fibrillation.

Global longitudinal strain (GLS) and atrial voltage are acknowledged markers for worse rhythm outcome after ablation of persistent atrial fibrillation (PeAF). The majority of research efforts have been directed towards the left atrium (LA), with relatively fewer studies focusing on the right atrium (RA). The aim of this study was to investigate the effect of the biatrial substrate on the outcome following radiofrequency catheter ablation (RFCA). All patients underwent two-dimensional speckle tracking echocardiography (2D-STE) and high-density mapping (HDM) on LA and RA in preoperative and postoperative stages of RFCA. Atrial substrate was assessed by GLS, average voltage, and low voltage zone (LVZ). This retrospective study enrolled 48 patients. With a follow-up of 385.98±161.78days, 22.92% (11/48) of all patients had AF recurrence and 63.64% in low strain group. Left atrial-low voltage zone (LA-LVZ) prior to RFCA was 67.52±15.27% and 54.21±20.07%, respectively, in the recurrence group and non-recurrence group. Multivariate regression analysis showed that preoperative LA-GLS (OR 0.047, 95%CI 0.002-0.941, p=.046) was independent predictors of AF recurrence. Biatrial average voltage in preoperative and postoperative stages were positively correlated (preoperative: r=0.563 p<.001; postoperative: r=0.464 p=.002). There was no significant difference in the proportion of RA in the recurrence group except the septum in preoperative and postoperative stages. Low LA-GLS and high LA-LVZ may be predictors of RFCA recurrence in PeAF patients. Biatrial average voltage were positively correlated in preoperative and postoperative stages.

A high-density linkage map reveals broad- and fine-scale sex differences in recombination in the hihi (stitchbird; Notiomystis cincta)

Recombination, the process of DNA exchange between homologous chromosomes during meiosis, plays a major role in genomic diversity and evolutionary change. Variation in recombination rate is widespread despite recombination often being essential for progression of meiosis. One such variation is heterochiasmy, where recombination rates differ between sexes. Heterochiasmy has been observed across broad taxonomic groups, yet it remains an evolutionary enigma. We used Lep-MAP3, a pedigree-based software that is efficient in handling large datasets, to generate linkage maps for the hihi or stitchbird (Notiomystis cincta), utilising information from >36 K SNPs and 36 families. We constructed 29 linkage maps, including for the previously unscaffolded Z chromosome. The hihi is an endangered passerine endemic to Aotearoa New Zealand that is sexually dimorphic and exhibits high levels of sexual conflict, including sperm competition. Patterns in recombination in the hihi are consistent with those in other birds, including higher recombination rates in micro-chromosomes. Heterochiasmy in the hihi is male-biased, in line with predictions of the Haldane-Huxley rule, with the male linkage map being 15% longer. Micro-chromosomes exhibit heterochiasmy to a greater extent, contrary to that reported in other birds. At the intra-chromosomal level, heterochiasmy is higher nearer to chromosome ends and in gene-rich regions. Regions of extreme heterochiasmy are enriched for genes implicated in cell structure. This study adds an important contribution in assessing evolutionary theories of heterochiasmy and provides a framework for future studies investigating fine-scale heterochiasmy.

Optimized isochronal late activation methods in the visualization and isthmus identification of ventricular tachycardia

BackgroundCatheter ablation of ventricular tachycardia (VT) during sinus rhythm often relies on isochronal late activation mapping (ILAM), a validated means of isthmus identification, whereby points are binned by local activation time (LAT) into 8 isochrones, and isthmus regions are identified as regions with isochronal crowding. The resulting output, however, is inherently discretized, and loss of LAT data occurs. To improve the precision of isthmus identification, we quantify isochronal density and assess the effect of increasing the number of isochrones used and the effectiveness of continuous metrics analogous to ILAM. ObjectiveThe objective of this study was to determine whether current practices in ILAM calculation are optimized for isthmus detection. MethodsPatients undergoing VT ablation were included if high-density maps in both VT and sinus or paced rhythms were available. Isochronal density was assessed at differing numbers of isochrones, and isthmus discrimination was assessed. Continuous metrics that mimicked ILAM by assessing the local distribution of LAT values—using interquartile range or the median absolute deviation—were also defined and assessed. ResultsEight electroanatomic maps (EAMs) were included. Isthmus discrimination improved progressively from a minimum area under the curve (AUC) of 0.600 when assessing the isochronal density of 8-isochrone EAMs to a maximum of 0.776 when assessing the density of 1000-isochrone EAMs (DeLong test, P < .0001). On logistic regression, the continuous metrics using interquartile range (AUC = 0.714) and median absolute deviation (AUC = 0.721) better discriminated isthmus identity than ILAM. ConclusionUsing more isochrones or using continuous ILAM analogues improves isthmus identification. By retaining more data, these metrics could increase the precision of VT ablation.

Powerful QTL mapping and favorable allele mining in an all-in-one population: a case study of heading date.

The multiparent advanced generation intercross (MAGIC) population is characterized with great potentials in power and resolution of quantitative trait locus (QTL) mapping, but single nucleotide polymorphism (SNP)-based GWAS does not fully reach its potential. In this study, a MAGIC population of 1021 lines was developed from four Xian and four Geng varieties from five subgroups of rice. A total of 44000 genes showed functional polymorphisms among eight parents, including frameshift variations or premature stop codon variations, which provides the potential to map almost all genes of the MAGIC population. Principal component analysis results showed that the MAGIC population had a weak population structure. A high-density bin map of 24414 bins was constructed. Segregation distortion occurred in the regions possessing the genes underlying genetic incompatibility and gamete development. SNP-based association analysis and bin-based linkage analysis identified 25 significant loci and 47 QTLs for heading date, including 14 known heading date genes. The mapping resolution of genes is dependent on genetic effects with offset distances of <55kb for major effect genes and <123kb for moderate effect genes. Four causal variants and noncoding structure variants were identified to be associated with heading date. Three to four types of alleles with strong, intermediate, weak, and no genetic effects were identified from eight parents, providing flexibility for the improvement of rice heading date. In most cases, japonica rice carries weak alleles, and indica rice carries strong alleles and nonfunctional alleles. These results confirm that the MAGIC population provides the exceptional opportunity to detect QTLs, and its use is encouraged for mapping genes and mining favorable alleles for breeding.

High-resolution mapping through whole-genome resequencing identifies two novel QTLs controlling oil content in peanut

Increasing oil content is a key objective in peanut breeding programs. Accurate identification of quantitative trait loci (QTLs) with linked markers for oil content can greatly aid in marker-assisted selection for high-oil breeding. In this study, a high-density bin map was constructed by resequencing a recombinant inbred line (RIL) population (ZH16×J11) consisting of 295 lines. The bin map contained 4,212 loci and had a total length of 1,162.3 cM. Ten QTLs for oil content were identified in six linkage groups. Notably, two of these QTLs, qOCB03.1 and qOCB06.1, were consistently detected in a minimum of three environments and explained up to 13.62% of phenotypic variation. They have not been reported in previous studies and thus are novel QTLs. The combination of favorable alleles from the qOCB03.1 and qOCB06 in the RIL population could increase oil content across multiple environments from 1.50 to 2.46%. Two InDel markers linked to qOCB03.1 and qOCB06.1 were developed and validated to be associated with oil content in another RIL population (ZH10×ICG12625) with diverse phenotypes. Additionally, the high-resolution map allowed for the precise positioning of qOCB03.1 and qOCB06.1 within a 1.77 Mb-interval on chromosome B03 and a 1.51 Mb- interval on chromosome B06, respectively. Annotation of genomic variants, analysis of transcriptome sequencing, and evaluation of the allelic effects in 292 peanut varieties revealed two candidate genes associated with oil content for each of the two QTLs. The identification of candidate genes in this study can enable the map-based cloning of key genes controlling oil content in peanut. Furthermore, these novel and stable QTLs and their tightly linked markers are valuable for marker-assisted breeding for increased oil content in peanut.

Novel cryoballoon technology for atrial fibrillation ablation: Impact of pulmonary vein variant anatomy, cooling characteristics, and 1-year outcome from the CHARISMA registry

BackgroundNo data have been reported on cooling characteristics and the impact of variant pulmonary vein (PV) anatomy on atrial fibrillation (AF) recurrences after POLARx cryoballoon (CB) ablation. ObjectiveThe purpose of this study was to analyze the impact of PV anatomy variants and cooling characteristics after CB ablation from a large multicenter prospective registry. MethodsThe primary end point was defined as 1-year absence of any atrial tachyarrhythmias (ATAs: AF/atrial flutter/atrial tachycardia). Correlation between ATA recurrences and anatomy variants/cooling characteristics were evaluated. The secondary outcome was the rate of major periprocedural complications. ResultsA total of 429 consecutive patients diagnosed with paroxysmal AF (83.4%) or persistent AF (peAF; 16.6%) were enrolled. Twenty-eight patients (6.6%) exhibited an anatomical variant (common ostium: 4.0%; adjunctive PV: 2.6%). Nadir temperature, thaw time, and total deflation time were different between standard PVs and PV variants. After the blanking period, over a mean of 431 ± 99 days of follow-up, 63 patients (14.7%) suffered an ATA recurrence. Patients with recurrences had both a shorter thaw time (18.5 ± 7 seconds vs 19.8 ± 7 seconds; P = .0012) and a shorter total deflation time, whereas time to isolation was longer (57.4 ± 42 seconds vs 49.1 ± 33 seconds; P = .04). Patients with anatomy variants showed a similar ATA recurrence rate (5 of 28 [17.9%]) to the standard PV anatomy group (58 of 401 [14.5%]) (P = .584), with a hazard ratio (HR) of 1.43 (95% confidence interval [CI] 0.49–4.13; log-rank, P = .4384). After adjusting for confounders, heart failure (HR 4.12; 95% CI 1.75–9.73; P = .0013) and peAF (HR 1.81; 95% CI 1.03–3.18; P = .0433) remained associated with ATA recurrence during follow-up. ConclusionThe POLARx CB system demonstrated long-term efficacy, along with a safe profile, in both patients with paroxysmal AF and those with peAF, regardless of the presence PV variants. Time to isolation was longer in patients with ATA recurrences during follow-up. Clinical Trial RegistrationCatheter Ablation of Arrhythmias with a High-Density Mapping System in Real-World Practice (CHARISMA). ClinicalTrials.gov identifier: NCT03793998. Registration date: January 4, 2019.

Somatosensory temporal sensitivity in adults on the autism spectrum: A high-density electrophysiological mapping study using the mismatch negativity (MMN) sensory memory paradigm.

Atypical reactivity to somatosensory inputs is common in autism spectrum disorder and carries considerable impact on downstream social communication and quality of life. While behavioral and survey work have established differences in the perception of somatosensory information, little has been done to elucidate the underlying neurophysiological processes that drive these characteristics. Here, we implemented a duration-based somatosensory mismatch negativity (MMN) paradigm to examine the role of temporal sensitivity and sensory memory in the processing of vibrotactile information in autistic (n = 30) and neurotypical (n = 30) adults. To capture the variability in responses between groups across a range of duration discrepancies, we compared the electrophysiological responses to frequent standard vibrations (100 ms) and four infrequent deviant vibrations (115, 130, 145, and 160 ms). The same stimuli were used in a follow-up behavioral task to determine active detection of the infrequent vibrations. We found no differences between the two groups with regard to discrimination between standard and deviant vibrations, demonstrating comparable neurologic and behavioral temporal somatosensory perception. However, exploratory analyses yielded subtle differences in amplitude at the N1 and P220 time points. Together, these results indicate that the temporal mechanisms of somatosensory discrimination are conserved in adults on the autism spectrum, though more general somatosensory processing may be affected. We discuss these findings in the broader context of the MMN literature in autism, as well as the potential role of cortical maturity in somatosensory mechanisms.

Contact-force local impedance algorithm to guide effective pulmonary vein isolation in AF patients: 1-year outcome from an international multicenter clinical setting.

The combination of highly localized impedance (LI) and contact force (CF) may improve tissue characterization and lesion prediction during radiofrequency (RF) pulmonary vein isolation (PVI) in patients with atrial fibrillation (AF). We report the outcomes of our acute and long-term clinical evaluation of CF-LI-guided PVI in consecutive AF ablation cases from an international multicenter clinical setting. Three hundred twenty-four consecutive patients from 20 European centers undergoing RF catheter ablation with the Stablepoint™ catheter were enrolled in the CHARISMA registry. Of these, 275 had a minimum follow-up of 1year and were included in the primary analysis. The mean procedure duration was 115 ± 47min, and the mean fluoroscopy time was 9.9 ± 6min. At the end of the procedures, all PVs had been successfully isolated in all study patients. Minor complications were reported in 12 patients (4.4%). At 1year, 36 (13.1%) patients had had an AF recurrence, and freedom from antiarrhythmic drugs and AF recurrence was achieved in 228 (82.9%) patients. The recurrence rate was higher in patients with persistent AF (21/116, 18.1%) than in those with paroxysmal AF (15/159, 9.4%; p = 0.0459). On multivariate logistic analysis adjusted for baseline confounders, only time > 6months from first diagnosis of AF to ablation (HR = 2.93, 95%CI 1.03 to 8.36, p = 0.0459) was independently associated with recurrences. An ablation strategy for PVI guided by CF-LI technology proved safe and effective and resulted in a low recurrence rate of AF over 1-year follow-up, irrespective of the underlying AF type. Catheter Ablation of Arrhythmias with a High-Density Mapping System in Real-World Practice. (CHARISMA). URL: http://clinicaltrials.gov/ Identifier: NCT03793998.

Association between high-density mapping of atypical atrial flutter, clinical outcomes and healthcare utilization.

Success of atypical atrial flutter (AAFL) ablation has historically been limited by difficulty mapping the complex re-entrant circuits involved. While high-density (HD) mapping has become commonplace in clinical practice, there are limited data on outcomes of HD versus non-HD mapping for AAFL ablation. To compare clinical outcomes and healthcare utilization using HD mapping versus non-HD mapping for AAFL ablation. Retrospective analysis of all AAFL procedures between 2005 and 2022 at an academic medical center was conducted. Procedures utilizing a 16-electrode HD Grid catheter and Precision mapping system were compared to procedures using prior generation 10-20 electrode spiral catheters and the Velocity system (Abbott, IL). Cox regression models and Poisson regression models were utilized to examine procedural and healthcare utilization outcomes. Models were adjusted for left ventricular ejection fraction, CHA2DS2-VASc, and history of prior ablation. There were 108 patients (62% HD mapping) included in the analysis. Baseline clinical characteristics were similar between groups. Use of HD mapping was associated with a higher rate of AAFL circuit delineation (92.5% vs. 76%; p = .014) and a greater adjusted procedure success rate, defined as non-inducibility at procedure end, (aRR (95% CI) 1.26 (1.02-1.55) p = .035) than non-HD mapping. HD mapping was also associated with a lower rate of ED visits (aIRR (95% CI) 0.32 (0.14-0.71); p = .007) and hospitalizations (aIRR (95% CI) 0.32 (0.14-0.68); p = .004) for AF/AFL/HF through 1 year. While there was a lower rate of recurrent AFL through 1 year among HD mapping cases (aHR (95% CI) 0.60 (0.31-1.16) p = .13), statistical significance was not met likely due to the low sample size and higher rate of ambulatory rhythm monitoring in the HD group (61% vs. 39%, p = .025). Compared to non-HD mapping, AAFL ablation with HD mapping is associated with improvements in the ability to define the AAFL circuit, greater procedural success, and a reduction in the number of ED visits and hospitalization for AF/AFL/HF.

Sex-related differences in left atrial substrate among patients with atrial fibrillation: evidence from high-density voltage mapping

BackgroundThere is sufficient evidence that women with atrial fibrillation (AF) have a greater symptom burden than men with AF and are more likely to experience recurrence after catheter ablation. However, the mechanisms underlying these sex differences are unclear.MethodsWe prospectively enrolled 125 consecutive patients, including 40 non-AF patients and 85 AF patients, who underwent high-density voltage mapping during sinus rhythm and AF patients who underwent first ablation.ResultsOverall, 37 (44%) female patients with AF and 24 (60%) female non-AF patients with a mean age of 61.7 ± 11.6 years and 53.6 ± 16.7 years, respectively, were enrolled in this study. The results showed that the atrial voltage of female AF patients was significantly lower than that of male AF patients (1.11 ± 0.58 mV vs. 1.53 ± 0.65 mV; P = 0.003), while there were no significant sex differences in non-AF patients (3.02 ± 0.86 mV vs. 3.21 ± 0.84 mV; P = 0.498). Multiple linear regression analysis revealed that female sex (− 0.29, 95% confidence interval [CI] − 0.64 to − 0.13, P = 0.004) and AF type (− 0.32, 95% CI − 0.69 to − 0.13, P = 0.004) were the only factors independently associated with voltage. Compared with men, women in the paroxysmal AF group had a 3.5-fold greater incidence of recurrence (adjusted hazard ratio 4.49; 95% CI 1.101–18.332, P = 0.036). Both globally and regionally, the results showed that sex-related differences in voltage values occurred prominently in paroxysmal AF patients but not in nonparoxysmal AF patients.ConclusionSex-related differences in atrial substrates and arrhythmia-free survival were found in paroxysmal AF patients, suggesting the existence of sex-related pathophysiological factors.

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.

Mapping the genetic basis for sex determination and growth in hybrid tilapia (Oreochromis mossambicus × O. niloticus)

Tilapia growth and sex are key traits for aquaculture. Elucidating their molecular mechanisms can enable molecular breeding and accelerate genetic gain. To uncover the genetic basis underlying these traits for molecular breeding, we generated an F2 family by crossing Mozambique and Nile tilapia. The growth and sex traits of 284 F2 fish were recorded at 150 days post hatch. These F2 individuals exhibited sexual dimorphism in weight, body shape, and lip thickness, and were genotyped with RAD-sequencing. A high-density linkage map, consisting of 22 linkage groups with 38,102 SNPs was constructed. Association mapping revealed that QTL containing the amhy gene from male Nile tilapia largely determined sex, modulated by minor-effect loci. For growth-related traits, QTL and association analyses discovered that body weight or total length was predominantly controlled by a large-effect locus, while body shape was determined by several minor-effect loci. Analysis of transcriptomics in the liver and muscle identified novel candidate genes, including dusp2, rtn4r, bhmt1, adamts12 and s100p, for growth. These findings provide tools for sex-specific molecular breeding and valuable information for understanding the genomic architecture of growth and body shape variation. Assessing the sex-specific effects on growth can further refine selective breeding in aquaculture.

QTL mapping of downy mildew resistance in foxtail millet by SLAF‑seq and BSR-seq analysis.

Key message Three major QTLs for resistance to downy mildew were located within an 0.78 Mb interval on chromosome 8 in foxtail millet. Downy mildew, a disease caused by Sclerospora graminicola, is a serious problem that jeopardizes the yield and quality of foxtail millet. Breeding resistant varieties represents one of the most economical and effective solutions, yet there is a lack of molecular markers related to the resistance. Here, a mapping population comprising of 158 F6:7 recombinant inbred lines (RILs) was constructed from the crossing of G1 and JG21. Based on the specific locus amplified fragment sequencing results, a high-density linkage map of foxtail millet with 1031 bin markers, spanning 1041.66 cM was constructed. Based on the high-density linkage map and the phenotype data in four environments, a total of nine quantitative trait loci (QTL) associated with resistance to downy mildew were identified. Further BSR-seq confirmed the genomic regions containing the potential candidate genes related to downy mildew resistance. Interestingly, a 0.78-Mb interval between C8M257 and C8M268 on chromosome 8 was highlighted because of its presence in three major QTL, qDM8_1, qDM8_2, and qDM8_4, which contains 10 NBS-LRR genes. Haplotype analysis in RILs and natural population suggest that 9 SNP loci on Seita8G.199800, Seita8G.195900, Seita8G.198300, and Seita.8G199300 genes were significantly correlated with disease resistance. Furthermore, we found that those genes were taxon-specific by collinearity analysis of pearl millet and foxtail millet genomes. The identification of these new resistance QTL and the prediction of resistance genes against downy mildew will be useful in breeding for resistant varieties and the study of genetic mechanisms of downy mildew disease resistance in foxtail millet.

Genetic analysis of agronomic and physiological traits associated with latex yield revealed complex genetic bases in Hevea brasiliensis

Hevea brasiliensis, a natural rubber producing species, is widely cultivated due to its high rubber yield potential. Natural rubber is synthesised in the rubber particles of laticifers. Latex diagnosis (LD) was established to characterise the physiological state of the laticiferous system by measuring its physiological parameters, i.e., sucrose, inorganic phosphorous (Pi), thiols and total solid content (TSC). Rubber clones are often classified in three groups i.e., quick starters, medium starters and slow starters. To better understand the genetic bases of latex yield, a biparental population was generated from a cross between the quick-starter clone PB 260 and the medium-starter clone SP 217. LD was performed during the peak latex production season and used to calculate sucrose loading. The agronomic and physiological parameters associated with latex yield led to the classification of genotypes according to the rubber clonal typology and to the identification of quantitative trait loci (QTL) using a high-density map. Inorganic phosphorous content was positively associated with yield during the first year of production thus enabling identification of quick-starter clones. In addition, the LD-based clonal typology led to determine the long-term yield potential and the use of appropriate ethephon stimulation. QTL analysis successfully identified several QTLs related to yield, sucrose, Pi and TSC. One QTL related to sucrose loading was identified in the same position as the QTL for sucrose on linkage group 1. To our knowledge, this is the first study to report QTL analysis for this trait. The use of a high-density map enables the identification of genes underlying QTLs. Several putative genes underlying QTLs related to yield, sucrose and TSC were identified.

High-density mapping of durable and broad-spectrum stripe rust resistance gene Yr30 in wheat.

The durable stripe rust resistance gene Yr30 was fine-mapped to a 610-kb region in which five candidate genes were identified by expression analysis and sequence polymorphisms. The emergence of genetically diverse and more aggressive races of Puccinia striiformis f. sp. tritici (Pst) in the past twenty years has resulted in global stripe rust outbreaks and the rapid breakdown of resistance genes. Yr30 is an adult plant resistance (APR) gene with broad-spectrum effectiveness and its durability. Here, we fine-mapped the YR30 locus to a 0.52-cM interval using 1629 individuals derived from residual heterozygous F5:6 plants in a Yaco"S"/Mingxian169 recombinant inbred line population. This interval corresponded to a 610-kb region in the International Wheat Genome Sequencing Consortium (IWGSC) RefSeq version 2.1 on chromosome arm 3BS harboring 30 high-confidence genes. Five genes were identified as candidate genes based on functional annotation, expression analysis by RNA-seq and sequence polymorphisms between cultivars with and without Yr30 based on resequencing. Haplotype analysis of the target region identified six haplotypes (YR30_h1-YR30_h6) in a panel of 1215 wheat accessions based on the 660K feature genotyping array. Lines with YR30_h6 displayed more resistance to stripe rust than the other five haplotypes. Near-isogenic lines (NILs) with Yr30 showed a 32.94% higher grain yield than susceptible counterparts when grown in a stripe rust nursery, whereas there was no difference in grain yield under rust-free conditions. These results lay a foundation for map-based cloning Yr30.