Single Marker Analysis Research Articles

Quality Assessment of Corydalis saxicola Bunting Using Quantitative Analysis of Multi-Components by Single Marker and Fingerprint Analysis.

Yan Huanglian is the whole grass and rhizome of Corydalis saxicola Bunting (CSB) of the Papaveraceae family. CSB has various pharmacological effects and is a promising ethnopharmaceutical. The chromatographic fingerprint of 16 batches of CSB samples was established in this study. Quantitative analysis of multi-components by single marker and the external standard method (ESM) was used to quantitatively assess seven constituents of CSB. Because of its high stability and availability, dehydrocavidine was used as a reference to determine the relative correction factors (RCFs) of columbamine, epiberberine, coptisine hydrochloride, palmatine chloride, berberine hydrochloride, and chelerythrine based on high-performance liquid chromatography. The calculated quantitative analysis of multi-components by single marker values is consistent with those obtained from the ESM, and the repeatability of the RCFs was demonstrated. For the first time, the quantitative analysis of multi-components by the single marker method has been established for the simultaneous determination of seven components, and it is demonstrated to be feasible and accurate for the quality evaluation of CSB combined with chromatographic fingerprint analysis. The combination of these methods could be used as a reference for quality control in Chinese medicine.

Solanum pimpinellifolium exhibits complex genetic resistance to Pseudomonas syringae pv. tomato.

Pseudomonas syringae pv. tomato (Pst) is the causal agent of bacterial speck disease in tomatoes. The Pto/Prf gene cluster from Solanum pimpinellifolium was introgressed into several modern tomato cultivars and provided protection against Pst race 0 strains for many decades. However, virulent Pst race 1 strains that evade Pto-mediated immunity now predominate in tomato-growing regions worldwide. Here we report the identification of resistance to a Pst race 1 strain (Pst19) in the wild tomato accession S. pimpinellifolium LA1589 (hereafter LA1589), using our rapid high-throughput seedling screen. LA1589 supports less bacterial growth than cultivars, and does not exhibit a hypersensitive response to Pst19. We tested an existing set of 87 Inbred Backcross Lines (IBLs) derived from a cross between susceptible Solanum lycopersicum E-6203 and Solanum pimpinellifolium LA1589 for resistance to Pst19. Using single-marker analysis, we identified three genomic regions associated with resistance. Bacterial growth assays on IBLs confirmed that these regions contribute to resistance in planta. We also mapped candidate genes associated with resistance in a cross between the Solanum lycopersicum var. lycopersicum cultivar Heinz BG-1706 and S. pimpinellifolium LA1589. By comparing candidates from the two mapping approaches, we were able to identify 3 QTL and 5 candidate genes in LA1589 for a role in resistance to Pst19. This work will assist in molecular marker-assisted breeding to protect tomato from bacterial speck disease.

Identification and Validation of Blast Resistance Loci from the Durable Resistance Cultivar Hahng Yi 71

One of the effective strategies for developing blast disease-resistant cultivars to mitigate the yield losses caused by Pyricularia oryzae is the discovery of new genetic resources containing resistance genes. In the present study, a Thai landrace glutinous rice cultivar Hahng Yi 71 (HY71) was used as a durable, broad resistance source to identify QTLs against blast fungus and crossed with a susceptible recurrent parent cultivar RD6, generating 56 BC4F5 lines. The BC4F5 population was tested with six blast isolates, including THL54, THL583, THL658, THL690, THL795, and THL1119, and evaluated with 161 SSR markers to identify resistance regions using modified bulk segregation analysis. Single marker analysis showed 7 markers linked to a resistance reaction located on chromosomes 2, 4, and 5, then tentatively designated as qBL2-RD6, qBL4-HY71, and qBL5-HY71, respectively. Two introgressed lines from the mapping population, KKN97057-7-1-1-2-5-NKI-4-1 and KKN97057-7-1-1-2-5-NKI-5-1, were the qBL5-HY71 donor for introgressing into two rice lines, RGD07123-MS12-MS22-MS1, and RGD07123-MS12-MS22-MS9, which generated two single crosses and a backcross population by marker-assisted selection (MAS) using the linked markers RM39 and RM164. Three improved lines, RGD10021-MS18-B-MS8-MS40, RGD10031-MS-MS3-B-MS9-MS42 (single cross), and RGD11086-MS-MS15-MS10-MS19 (backcross), carrying qBL5-HY71, were tested for their resistance against leaf and neck blast disease by 62 and 8 blast isolates, respectively. The disease screening results showed that qBL5-HY71 was very effective in controlling leaf and neck blast. This study demonstrates the effectiveness of resistance loci qBL5-HY71 from HY71 on chromosome 5 and their linked markers in improving durable blast resistance in rice breeding programs.

Deciphering the genetic architecture of β-glucan content in oats (Avena sativa L.) through QTL mapping

Oat is a cereal grain grown for human and animal nutrition. It is known for its high dietary fibre content, phytochemicals, and nutritional value. The primary component of oat fibre is β-glucan, a group of polysaccharides comprising mixed-linkage (1,3) (1,4)-D-glucose units. The β-glucan concentrations of oat cultivars usually range from 3 to 6% and are considered a polygenic trait controlled by multiple genes with additive effects. The primary goal of this study was to identify quantitative trait loci (QTLs) for β-glucan content. Two contrasting parents for β-glucan content, OL10 (5.8%) and OL11 (0.8%), were selected from 91 germplasm lines, and an F2:4 mapping population was generated for QTL mapping. Five genotypes with the highest levels of β-glucan content were observed. The QTLs affecting β-glucan content were identified using QTL cartographer, employing single marker analysis (SMA) and composite interval mapping (CIM). Two putative QTL regions were identified, one on linkage group (LG) 1 and the other on LG 4, with LOD (logarithm of the odds) scores of 3.7 and 4.3, respectively, explaining 31 and 33% of the phenotypic variation. The information generated is important in identifying the genomic regions responsible for β-glucan content in oats.

Validation and identification of promising gene specific markers governing foliar disease resistance in groundnut (Arachis hypogaea L.).

Groundnut is vulnerable to the major foliar fungal disease viz., late leaf spot (LLS) and rust in kharif season, which results in severe yield losses. Until now, LLS and rust resistance linked markers were developed based on GPBD 4 as a major donor source and were validated in its derivatives only, which restricted their use in marker assisted selection (MAS) involving other donors. The current study focused to validate LLS and rust resistance linked markers employing advanced breeding lines of F6 generation, derived from nine different crosses involving nine diverse parents, to identify potential markers for marker-assisted breeding of LLS and rust resistance in groundnut. Out of 28-trait linked markers used for validation, 8 were polymorphic (28.57%). Marker-trait association (MTA) and Single Marker Analysis (SMA) revealed that the SSR marker pPGPseq5D05 is significantly associated with both LLS (15.8% PVE) and rust (17.5% PVE) resistance, whereas, the marker IPAHM103 is tightly linked with rust resistance (26.8% PVE) alone. In silico analysis revealed that the marker gene for IPAHM103 is a zinc finger protein and the marker gene for pPGPseq5D05 is an ADP-ribosylation factor GTPase-activating protein. Both these protein products impart resistance or tolerance to biotic stress in crop plants. Two other markers namely, GMLQ975 and pPGPseq13A10 were also found to be associated with LLS resistance explaining MTA up to 60%. These gene specific markers will enable us to screen more number of germplasm lines or newly developed lines in MAS schemes for LLS and rust resistance using a wide range of resistant sources.

Blood-Based DNA Methylation Analysis by Multiplexed OBBPA-ddPCR to Verify Indications for Prostate Biopsies in Suspected Prostate Cancer Patients.

Current prostate carcinoma (PCa) biomarkers, including total prostate-specific antigen (tPSA), have unsatisfactory diagnostic sensitivity and specificity resulting in overdiagnosis and overtreatment. Previously, we described an optimised bias-based preamplification-digital droplet PCR (OBBPA-ddPCR) technique, which detects tumour DNA in blood-derived cell-free DNA (cfDNA) of cancer patients. The current study investigated the performance of newly developed OBBPA-ddPCR-based biomarkers. Blood plasma samples from healthy individuals (n = 90, controls) and PCa (n = 39) and benign prostatic hyperplasia patients (BPH, n = 40) were analysed. PCa and BPH patients had tPSA values within a diagnostic grey area of 2-15 ng/mL, for whom further diagnostic validation is most crucial. Methylation levels of biomarkers RASSF1A, MIR129-2, NRIP3, and SOX8 were found significantly increased in PCa patients compared to controls. By combining classical PCa risk factors (percentage of free PSA compared to tPSA (QfPSA) and patient's age) with cfDNA-based biomarkers, we developed PCa risk scores with improved sensitivity and specificity compared to established tPSA and QfPSA single-marker analyses. The diagnostic specificity was increased to 70% with 100% sensitivity for clinically significant PCa patients. Thus, prostate biopsies could be avoided for 28 out of 40 BPH patients. In conclusion, the newly developed risk scores may help to confirm the clinical decision and prevent unnecessary prostate biopsy.

Microfluidic device featuring micro-constrained channels for multi-parametric assessment of cellular biomechanics and high-precision mechanical phenotyping of gastric cells

BackgroundCellular biomechanics plays a significant role in the regulation of cellular physiological and pathological processes. In recent years, multiple methods have been developed to evaluate cellular biomechanics, such as atomic force microscopy (AFM), micropipette aspiration, and magnetic tweezers. However, most of these methods only focus on a single parameter and cannot automate the process at a high-efficiency level. A novel microfluidic method is necessary to achieve the simultaneous multi-parametric measurement of cellular biomechanics and high-precision cellular mechanical phenotyping at high throughput. ResultsTo tackle the issue concerning the low-throughput and cellular single-parameter evaluation, we designed and fabricated a microfluidic chip featuring multiple micro-constrained channels structure, providing a simultaneous multi-parametric assessment of cellular biomechanics, including elastic modulus, recovery capability, and deformability. We compared the biomechanical properties of normal human gastric mucosal epithelial cells (GES-1) and human gastric cancer cells (AGS and MKN-45) by the chip. Results demonstrated that the elastic modulus of GES-1, AGS, and MKN-45 cells decreased sequentially, which was the opposite of their invasiveness and metastasis potential, suggesting the inverse correlation between cellular elastic modulus and malignancy. Meanwhile, the recovery capability and deformability of GES-1, AGS, and MKN-45 cells increased sequentially, demonstrating the positive correlation between cellular deformability and malignancy. Furthermore, multiple parameters were used to distinguish gastric cancer cells from normal gastric cells via machine learning. An accuracy of over 94.8% for identifying gastric cancer cells was achieved. SignificanceThis study provides a deep insight into the biophysical mechanism of gastric cancer metastasis at the single-cell level and possesses great potential to function as a valuable tool for single-cell analysis, thereby facilitating high-precision and high-throughput discrimination of cellular phenotypes that are not easily discernible through single-marker analysis.

Soybean Variety Saedanbaek Confers a New Resistance Allele to Phytophthora sojae

Phytophthora root and stem rot (PRSR) disease results in substantial losses in soybean production worldwide. The occurrence of PRSR caused by Phytophthora sojae Kaufmann & Gerdemann has become increasingly important for soybean production in the Republic of Korea, but domestic soybean–P. sojae interaction has been less studied. The disease has been managed by developing varieties harboring resistance to the Phytophthora sojae (Rps) gene. The present study aimed to identify a major gene locus conferring resistance to new P. sojae isolate 2858 in the recombinant inbred line population derived from a cross between parental lines ‘Daepung’ (susceptible) and ‘Saedanbaek’ (resistant). Seventy-three recombination inbred lines (RILs) were evaluated for resistance to P. sojae isolate 2858. A resistance locus was identified in the approximate 3.3–4.3 megabase pair region on chromosome 3 using both single-marker and linkage analyses. The Rps of Saedanbaek (RpsSDB) was located on the well-known Rps gene/allele cluster region, which also partially overlapped with a locus previously identified in the Korean soybean variety, ‘Daewon’, resistant to another P. sojae isolate 2457 (RpsDW). Approximately 402 kilobase pairs of the interval region overlapped, including six nucleotide-binding site-leucine-rich repeat (NBS-LRR)-coding genes. Additional phenotypic assays revealed that Saedanbaek was susceptible to isolate 2457 and that Daewon was susceptible to isolate 2858, indicating that RpsSDB and RpsDW are different genes or alleles that confer race-specific resistance to the two P. sojae isolates. These results provide information that will be helpful for breeders developing P. sojae-resistant cultivars.

Genetic Mapping of a Novel Gene PmAege7M from Aegilops geniculata Conferring Resistance to Wheat Powdery Mildew.

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), is one of the most damaging foliage diseases of wheat across the world. Aegilops geniculata Roth is a valuable gene resource for enhancing wheat resistance to powdery mildew. This study identified Ae. geniculata accession PI 487224 as immune and PI 487228 as susceptible to powdery mildew. Genetic analysis of the F1, F2, and F2:3 progeny derived from PI 487224 × PI 487228 showed that powdery mildew resistance in PI 487224 was controlled by two independent dominant genes located on two different nonhomologous chromosomes. By combing bulked segregant RNA-Seq, genetic linkage analysis of a single resistance gene segregation population, and marker analysis of a set of 14 wheat-Ae. geniculata chromosome addition lines, one of the resistance genes, temperately designated PmAege7M, was mapped to a 4.9-cM interval flanked by markers STS7-55926 and SNP7-45792/STS7-65911 on the long arm of chromosome 7 Mg of PI 487224, spanning 604.73 to 622.82 Mb on the 7D long arm based on the Ae. tauschii reference genome (Aet_v4.0). The map and closely linked markers of PmAege7M from Ae. geniculata in this study will facilitate the transfer of PmAege7M into common wheat and fine mapping of the gene.

Expression of Genes Involved in Anthracnose Resistance in Chili (Capsicum baccatum) 'PBC80'-Derived Recombinant Inbred Lines.

Chili anthracnose has long been a threat to chili production worldwide. Capsicum baccatum 'PBC80' has been identified as a source of resistance to anthracnose. Recently, a QTL for ripe fruit resistance from 'PBC80'-derived RILs was located on chromosome 4 (123 Mb) and contained over 80 defense-related genes. To identify the genes most related to anthracnose resistance, a fine map of the QTL region was developed using single-marker analysis. Nine genes were selected from the new QTL (1.12 Mb) to study their expression after being challenged with Colletotrichum scovillei 'MJ5' in two different RIL genotypes (Resistance/Resistance or R/R and Susceptible/Susceptible or S/S) at 0, 6 and 12 h. Of the nine genes, LYM2, CQW23_09597, CLF, NFXL1, and PR-14 were significantly up-regulated, compared to the control, in the R/R genotype. ERF was up-regulated in both chili genotypes. However, the expression was relatively and constantly low in the S/S genotype. Most up-regulated genes reached the highest peak (2.3-4.5 fold) at 6 h, except for ERF, which had the highest peak at 12 h (6.4 fold). The earliest and highest expressed gene was a pathogen receptor, LYM2.

BG2: Bayesian variable selection in generalized linear mixed models with nonlocal priors for non-Gaussian GWAS data

BackgroundGenome-wide association studies (GWASes) aim to identify single nucleotide polymorphisms (SNPs) associated with a given phenotype. A common approach for the analysis of GWAS is single marker analysis (SMA) based on linear mixed models (LMMs). However, LMM-based SMA usually yields a large number of false discoveries and cannot be directly applied to non-Gaussian phenotypes such as count data.ResultsWe present a novel Bayesian method to find SNPs associated with non-Gaussian phenotypes. To that end, we use generalized linear mixed models (GLMMs) and, thus, call our method Bayesian GLMMs for GWAS (BG2). To deal with the high dimensionality of GWAS analysis, we propose novel nonlocal priors specifically tailored for GLMMs. In addition, we develop related fast approximate Bayesian computations. BG2 uses a two-step procedure: first, BG2 screens for candidate SNPs; second, BG2 performs model selection that considers all screened candidate SNPs as possible regressors. A simulation study shows favorable performance of BG2 when compared to GLMM-based SMA. We illustrate the usefulness and flexibility of BG2 with three case studies on cocaine dependence (binary data), alcohol consumption (count data), and number of root-like structures in a model plant (count data).

Candidate genes controlling alkaline-saline tolerance in two different growing stages of wheat life cycle

BackgroundAlkaline-saline (AS) stress threats crop development and productivity. Understanding the genetic control of AS tolerance in wheat is important to produce wheat cultivars that outstand such a severe stress condition.MethodsA set of 48 cultivars were tested under controlled and AS stress conditions at seedling and maturity stages. The effect of AS on seedlings and kernel traits was measured to select tolerant and high-yielding genotypes. Single-marker-analysis (SMA) and gene enrichment were conducted to understand the genetic control of AS tolerance in both growth stages.ResultsAS stress decreased all kernel traits and most of the seedling traits. High correlations were found between the studied traits in each growth stage. The correlation between the traits related to both stages was non-significant. SMA identified a total of 292 and 52 markers significantly associated with the studied traits under controlled and AS stress conditions. Seven and 20 gene models were identified to control AS tolerance in each stage. Gene enrichment analysis identified one and six networks that control AS tolerance. Four genotypes were selected as superior genotypes.ConclusionThe genetic control of the studied traits differs under control and AS conditions. Two genetic systems control AS tolerance in each growth stage. This study is the first one that unlocked the genetic control of AS tolerance in seedling and mature growth stages and identified the biological process that lead to this tolerance. Four genotypes were selected for crossing in future breeding programs to improve AS tolerance in spring wheat.

Validation of yield associated molecular markers in a groundnut minicore collection

Groundnut is one of the world's most significant commercial oilseed crops. Previously, superior breeding lines and cultivars were primarily employed in most of the groundnut breeding programmes, resulting in a limited genetic base. A thorough evaluation of core collections makes it possible to access germplasm for crop development. A total of 184 mini core genotypes of groundnut were used for validating already reported 55 AhTE molecular markers (Arachis hypogaea transposable element) in the present study (6 AhTE markers for number of primary branches, 5 for plant height, 7 for pod yield per plant, 12 for number of pods per plant, 2 for shelling percentage, 12 for test weight, 9 for sound mature kernel weight percentage and 2 for oil content). Phenotyping was done during kharif 2018 (June to October) and twelve yield related parameters were recorded across 184 genotypes. Single marker analysis indicated a significant association of 40 markers (48 MTAs) at 5% probability level. Amongst these 48 MTAs, 39 MTAs exhibited utmost marker-trait associations with PVE estimate greater than 10%. Yield related AhTE markers validated in the present study might be used as viable tools for marker aided groundnut breeding for yield and yield-related parameters.

Identification of SSR Molecular Markers for Jassid Resistance in Cotton

Background: This study has focussed on identifying the Simple Sequence Repeat (SSR) markers associated with the sucking pests (more precisely on jassid) tolerance/resistance loci. The study was initiated with 4348 mapped SSR markers to differentiate between resistant (R-1) and susceptible (BS-1) genotypes. Out of 4348 markers (retrieved from cotton microsatellite database and cottongen.org) used,17 markers were showing polymorphism between the parental lines. Methods: The F1 population was generated by crossing Resistant line (R-1) and the elite Susceptible line (Bs-1). F1 progeny were selfed to obtain F2 population. Following the screening, to identify the SSR markers associated with trait, Single Marker Analysis was performed. Result: The results indicated that two of the seventeen polymorphic markers - BL1646 and DOW047 had significant LoD of 4.5 and 7.2 respectively and PVE% of 6.6 and 10.3 respectively. Hence, these were identified as the two markers associated with jassid resistance trait having the potential for their use in marker assisted selection (MAS).

Identification of candidate genes for soybean seed coat-related traits using QTL mapping and GWAS.

Seed coat color is a typical morphological trait that can be used to reveal the evolution of soybean. The study of seed coat color-related traits in soybeans is of great significance for both evolutionary theory and breeding practices. In this study, 180 F10 recombinant inbred lines (RILs) derived from the cross between the yellow-seed coat cultivar Jidou12 (ZDD23040, JD12) and the wild black-seed coat accession Y9 (ZYD02739) were used as materials. Three methods, single-marker analysis (SMA), interval mapping (IM), and inclusive composite interval mapping (ICIM), were used to identify quantitative trait loci (QTLs) controlling seed coat color and seed hilum color. Simultaneously, two genome-wide association study (GWAS) models, the generalized linear model (GLM) and mixed linear model (MLM), were used to jointly identify seed coat color and seed hilum color QTLs in 250 natural populations. By integrating the results from QTL mapping and GWAS analysis, we identified two stable QTLs (qSCC02 and qSCC08) associated with seed coat color and one stable QTL (qSHC08) related to seed hilum color. By combining the results of linkage analysis and association analysis, two stable QTLs (qSCC02, qSCC08) for seed coat color and one stable QTL (qSHC08) for seed hilum color were identified. Upon further investigation using Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, we validated the previous findings that two candidate genes (CHS3C and CHS4A) reside within the qSCC08 region and identified a new QTL, qSCC02. There were a total of 28 candidate genes in the interval, among which Glyma.02G024600, Glyma.02G024700, and Glyma.02G024800 were mapped to the glutathione metabolic pathway, which is related to the transport or accumulation of anthocyanin. We considered the three genes as potential candidate genes for soybean seed coat-related traits. The QTLs and candidate genes detected in this study provide a foundation for further understanding the genetic mechanisms underlying soybean seed coat color and seed hilum color and are of significant value in marker-assisted breeding.

The LASSIE MPS panel: Predicting externally visible traits in dogs for forensic purposes

Predicting the outward appearance of dogs via their DNA, also known as Canine DNA Phenotyping, is a young, emerging field of research in forensic genetics. The few previous studies published in this respect were restricted to the consecutive analysis of single DNA markers, a process that is time- and sample-consuming and therefore not a viable option for limited forensic specimens. Here, we report on the development and evaluation of a Massively Parallel Sequencing (MPS) based molecular genetic assay, the LASSIE MPS Panel. This panel aims to predict externally visible as well as skeletal traits, which include coat color, coat pattern, coat structure, tail morphology, skull shape, ear shape, eye color and body size from DNA using 44 genetic markers in a single molecular genetic assay. A biostatistical naïve Bayes classification approach was applied to identify the most informative marker combinations for predicting phenotypes. Overall, the predictive performance was characterized by a very high classification success for some of the trait categories, and high to moderate success for others. The performance of the developed predictive framework was further evaluated using blind samples from three randomly selected dog individuals, whose appearance was well predicted.

Simultaneous selection of multiple important single nucleotide polymorphisms in familial genome wide association studies data

We propose a resampling-based fast variable selection technique for detecting relevant single nucleotide polymorphisms (SNP) in a multi-marker mixed effect model. Due to computational complexity, current practice primarily involves testing the effect of one SNP at a time, commonly termed as ‘single SNP association analysis’. Joint modeling of genetic variants within a gene or pathway may have better power to detect associated genetic variants, especially the ones with weak effects. In this paper, we propose a computationally efficient model selection approach—based on the e-values framework—for single SNP detection in families while utilizing information on multiple SNPs simultaneously. To overcome computational bottleneck of traditional model selection methods, our method trains one single model, and utilizes a fast and scalable bootstrap procedure. We illustrate through numerical studies that our proposed method is more effective in detecting SNPs associated with a trait than either single-marker analysis using family data or model selection methods that ignore the familial dependency structure. Further, we perform gene-level analysis in Minnesota Center for Twin and Family Research (MCTFR) dataset using our method to detect several SNPs using this that have been implicated to be associated with alcohol consumption.

A genome-wide association study of antidepressant-induced mania

Antidepressant-induced mania (AIM) is a side effect of antidepressant treatment that is characterized by mania or hypomania after the start of medication. It is likely polygenic, but its genetic component remains largely unexplored. We aim to conduct the first genome-wide association study of AIM in 814 bipolar disorder patients of European ancestry. We report no significant findings from our single-marker or gene-based analyses. Our polygenic risk score analyses also did not yield significant results with bipolar disorder, antidepressant response, or lithium response. Our suggestive findings on the hypothalamic-pituitary-adrenal axis and the opioid system in AIM require independent replications.

Effectiveness of TaDreb-B1 and 1-FEH w3 KASP Markers in Spring and Winter Wheat Populations for Marker-Assisted Selection to Improve Drought Tolerance.

Due to the advances in DNA markers, kompetitive allele-specific PCR (KASP) markers could accelerate breeding programs and genetically improve drought tolerance. Two previously reported KASP markers, TaDreb-B1 and 1-FEH w3, were investigated in this study for the marker-assisted selection (MAS) of drought tolerance. Two highly diverse spring and winter wheat populations were genotyped using these two KASP markers. The same populations were evaluated for drought tolerance at seedling (drought stress) and reproductive (normal and drought stress) growth stages. The single-marker analysis revealed a high significant association between the target allele of 1-FEH w3 and drought susceptibility in the spring population, while the marker-trait association was not significant in the winter population. The TaDreb-B1 marker did not have any highly significant association with seedling traits, except the sum of leaf wilting in the spring population. For field experiments, SMA revealed very few negative and significant associations between the target allele of the two markers and yield traits under both conditions. The results of this study revealed that the use of TaDreb-B1 provided better consistency in improving drought tolerance than 1-FEH w3.

Cytological and genetic effects of rye chromosomes 1RS and 3R on the wheat-breeding founder parent Chuanmai 42 from southwestern China.

The online version contains supplementary material available at 10.1007/s11032-023-01386-0.