ABSTRACT Sorghum [ Sorghum bicolor (L.) Moench] is a vital cereal crop in dry regions worldwide. However, in sub‐Saharan Africa (SSA), grain yields from currently grown varieties remain low (< 1 ton/ha) and exhibit variable nutrient composition. Therefore, the objective of this study was to undertake a genetic analysis of selected East African‐adapted sorghum genotypes for grain yield and its components, and for iron (Fe) and zinc (Zn) composition, to identify better performing parents and develop new families for pipeline breeding. Ten preselected female and four male parents were crossed using the North Carolina Mating Design II to derive 34 families. The new families and parents were field‐evaluated using a 6 × 8 alpha lattice design with three replications across three sites during the 2022 growing season. Data on grain yield and associated agronomic traits, and Zn and Fe content, were recorded and subjected to combining ability and genetic analysis. General combining ability (GCA) and specific combining ability (SCA) effects were highly significant ( p ≤ 0.001) for the assessed traits. Nonadditive gene action predominantly determined trait inheritance, with Baker's ratios < 0.5, suggesting that heterosis breeding can enhance genetic gains, including for micronutrients. Parents NAROSorg1, Sila and TanzaniaAcc#42 showed desirable GCA effects for grain yield, making them ideal selections for breeding. Positive and significant ( p ≤ 0.05) GCA effects for Fe content were recorded for IS30310, Sila, NAROSorg1 and SudanColl#41Lodudu, whereas Sekedo, Sila and IS12750 recorded a similar genetic trend for Zn. Hence, these parents are suitable for biofortifying sorghum with Zn and Fe. The families, namely, NAROSorg1 × IS30310, NAROSorg1 × IS12750, SesoI × TanzaniaAcc#42, Sekedo × TanzaniaAcc#42, NAROSorg3 × SudanColl#7Lodoka and Seredo × IS12750 recorded desirable SCA effects for grain yield. The identified parents and families are recommended for breeding and genetic advancement for cultivar development.
ABSTRACT Genomic prediction is widely used in plant breeding, but feature‐attribution scores from predictive models are sometimes interpreted as evidence for trait‐associated or causal loci. We evaluated whether global SHapley Additive exPlanations (SHAP) from XGBoost and LightGBM prioritize markers or genomic windows enriched for signals from mixed‐model genome‐wide association studies (GWAS). Three public datasets were analysed: flowering time at 16°C in 970 Arabidopsis thaliana accessions, standardized grain yield in 599 wheat lines and flowering time at Arkansas in 374 rice accessions. Within each dataset, prediction, out‐of‐fold SHAP and GWAS used harmonized marker panels. SHAP values were calculated on the held‐out samples of the same five cross‐validation models used to estimate predictive performance. Arabidopsis and rice were compared using physical windows, whereas wheat was analysed at marker level because reliable genomic coordinates were unavailable for its dominant DArT markers. Fivefold cross‐validation produced Pearson correlations of 0.759–0.799 in Arabidopsis , 0.373–0.565 in wheat and 0.632–0.685 in rice. The top 50 SHAP‐ranked features were enriched for the top 5% of GWAS‐ranked signals after controlling for genomic structure and marker density or frequency. In Arabidopsis , XGBoost and LightGBM recovered 7 and 8 GWAS‐ranked windows, compared with 3.31 and 3.64 conditionally expected ( and 0.0031). In rice, the corresponding overlaps were 11 and 12, compared with 4.03 and 4.59 expected ( for both). In wheat, 18 and 23 of the top 50 SHAP‐ranked markers belonged to the top 5% of mixed‐model association results; minor‐frequency‐stratified permutation tests gave for both models. Global XGBoost–LightGBM rank correlations were 0.904, 0.806 and 0.836 in Arabidopsis , rice and wheat, respectively, although overlap among the highest‐ranked subsets remained incomplete. Tree‐based SHAP therefore captures reproducible, association‐enriched predictive structure, but it is not equivalent to GWAS and should not be used as a standalone proxy for causal loci. Its most defensible role is complementary model diagnosis and candidate prioritization combined with association evidence, biological annotation and independent validation.
ABSTRACT Peanut ( Arachis hypogaea L., 2 n = 4 x = 40, AABB) is an important legume crop worldwide. Wild peanuts ( Arachis spp.) represent a valuable secondary gene pool with diverse disease resistances. However, most wild peanut species are diploid (2 n = 2 x = 20) and this ploidy barrier is a major obstacle to hybridization and gene introgression. Ploidy manipulation has been used to overcome this problem but requires a rapid, efficient chromosome doubling method to facilitate gene introgressions. Our previously reported colchicine buffer submergence method successfully induced tetraploidy in diploid peanut. However, induction efficiency was low and seedling mortality was high. In this study, four modified colchicine‐buffer‐submergence methods were evaluated, including three substrate‐based and one semi‐suspension colchicine application methods. Pre‐germinated seeds of four wild peanut species, A . duranensis (A‐genome) , A. stenosperma (A‐genome), A. magna (B‐genome), and A . batizocoi (K‐genome)—were used in this study. To obtain optimal results, the treatment period for A. magna and the colchicine concentration for A. stenosperma were further adjusted. Ploidy of surviving treated plants was validated by flow cytometry. With the optimal treatment of each species, the highest tetraploid conversion rates were 57%, 14%, 60%, and 50% among surviving A. batizocoi , A. duranensis , A. magna , and A. stenosperma seedlings, respectively. The stomatal size and density results show that all diploids have smaller stomata and higher stomatal density than the tetraploids. These results provide an improved protocol for chromosome doubling in wild peanut species and will facilitate gene introgressions for future peanut breeding.
ABSTRACT Doubled haploid technology accelerates the development of fully homozygous maize lines compared with conventional selfing. However, specific protocols for supersweet corn ( Zea mays L . var. saccharata ), particularly regarding immersion time in antimitotic solutions and temperature during chromosome doubling, remain poorly defined. This study investigated haploid induction rates in supersweet corn with a tropicalised haploid inducer hybrid and evaluated the effects of temperature and immersion time across three antimitotic solutions in an adapted newly germinated seeds method for chromosome doubling. Survival rate was assessed in diploid seeds immersed in water at 0°C, 17°C and 25°C and in haploid seeds treated with water at 0°C and 17°C, as well as with colchicine, pronamide and amiprophos‐methyl combined with pronamide, at 17°C under different immersion durations. Chromosome doubling efficiency of putative haploid was compared among the newly germinated seed treatments and with the root immersion method in colchicine. The tropical inducer hybrid showed an average haploid induction rate of 14.6%. Temperature and exposure time strongly affected survival and overall protocol feasibility, and 17°C emerged as the most suitable temperature by enabling longer exposure to antimitotic agents while maintaining higher survival. Treatments with 10 h in pronamide and 12 h in amiprophos‐methyl plus pronamide increased chromosome doubling but caused high mortality, indicating that shorter exposures are more suitable. Water treatment at 0°C did not improve chromosome doubling efficiency. These results demonstrate that herbicide‐based immersion of newly germinated seeds at 17°C is a promising alternative for chromosome doubling in tropical supersweet corn.
ABSTRACT Precision genome editing has long been a primary goal for plant breeders seeking to modify specific genes without inducing off‐target effects. This pursuit has led to the development of sophisticated tools such as zinc finger nucleases (ZFNs), transcription activator‐like effector nucleases (TALENs) and the widely adopted clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR‐associated protein 9 (Cas9) system, which has recently been augmented by Cas12 and Cas13 variants. In crop science, these technologies are leveraged for functional genomics—to elucidate gene roles in biological mechanisms—and for practical improvements such as herbicide resistance, male sterility and fatty acid modification. Palm crops represent vital sources of food and industrial raw materials; however, further genetic improvements are essential to boost productivity and enhance stress tolerance. Recent literature demonstrates that CRISPR/Cas9 has been successfully employed in palm species to knock out targets such as EgPDS , EgPTE , EgFAD2 and EgPATb , thereby highlighting its transformative potential. To fully capitalize on these advancements, rigorous efforts are required to optimize genome editing protocols and expand the application of Cas12 and base editing technologies to neglected species, such as the areca nut.
ABSTRACT Erucic acid (EA; 22:1) lies at the intersection of food safety, industrial chemistry and plant breeding, because regulations continue to restrict its concentration in edible oils while demand remains strong for renewable long‐chain fatty acids in lubricants, polymers and related specialty products. In oilseed crops, EA accumulation depends on the efficiency of fatty‐acid elongation from oleic acid, the strength of competing desaturation pathways and the broader metabolic context of developing seeds. These processes are further influenced by environmental conditions, particularly temperature and water availability during seed filling, which can generate substantial genotype × environment effects on final EA content. From a breeding perspective, low‐erucic cultivars represent a major historical success in quality improvement, whereas the development and stabilization of high‐erucic genotypes remain a more demanding challenge because industrial use requires consistently high EA levels together with acceptable oil content and agronomic performance. Here, we review the molecular, genetic and agronomic control of EA in oilseed crops and show how this knowledge can support more effective breeding strategies. The interest of this review lies in bringing together evidence that is often dispersed across biochemistry, genomics, physiology and applied breeding, thereby providing a clearer framework for the improvement of both established low‐erucic backgrounds and, more importantly, high‐erucic industrial materials. The major points are that EA accumulation is primarily determined by the FAE1‐encoded elongase, that transcriptional regulation and metabolic flux further shape substrate allocation to very‐long‐chain fatty acids, that environmental modulation is especially important for the stable expression of HEAR phenotypes and that QTL analysis, marker‐assisted selection, gene editing and emerging predictive approaches now offer improved tools for the targeted breeding of oilseed ideotypes with contrasting end uses.
ABSTRACT Historically cultivated for medicinal and dyeing purposes, safflower ( Carthamus tinctorius L.) saw a shift towards widespread oilseed production after the 1920s due to the growing importance of oils. However, there is a renewed interest in its medicinal and dyeing properties today. Consequently, there is a critical need to develop new safflower lines with enhanced pigment content to meet the increasing industrial and pharmaceutical demand. This study aims to investigate the effect of chemical mutagens (ethyl methanesulfonate and sodium azide) on pigment (hydroxysafflor yellow A (HSYA) and carthamin) formation in safflower in M 1 and M 2 generations. The flower (intact and powder) colour values of HSYA and carthamin contents were analysed by comparing HSYA and carthamin values across generations. The correlation between HSYA and carthamin content and flower colour value was investigated by comparing HSYA and carthamin values across generations. The highest HSYA content was achieved in both generations with a 0.2% EMS treatment for 6 h, reaching 20.99 mg/g in the M 1 and 17.28 mg/g in the M 2 generation. The change in carthamin content of M 1 generation safflower flowers was not statistically significant. In contrast, the highest carthamin content in M 2 generation flowers was observed with SA 0.3% 4 h mutagen treatment (0.1 mg/g). Lightness (L) values were significantly positively correlated with HSYA concentration ( p < 0.01). Increased HSYA content in safflower flowers is typically associated with higher L and b values, corresponding to a yellower and brighter appearance.
ABSTRACT Sweet potatoes ( Ipomoea batatas Lam.), a staple crop of global importance, are vital for food and nutritional security, especially in developing nations. But their continued production is threatened by unpredictable environmental variability, such as the increasing effects of climate change and rising soil salinity. This review highlights the urgent need to create better genotypes that exhibit consistent yield and nutritional quality under a range of stressful conditions and provides an overview of existing information regarding the challenges facing sweet potato production. We explore the complications of the genotype × environment (G × E) interaction, explaining its significant influence on yield stability, and describe sophisticated statistical techniques such as AMMI and GGE biplot analyses for evaluating it. The review highlights the significance of sweet potatoes for biofortification by thoroughly analysing their nutritional value and focusing on important bioactive substances like anthocyanins and β‐carotene (provitamin A). It also investigates how stable these chemicals are in different conditions. Furthermore, we address the emerging problems of soil salinity, detailing the physiological and molecular mechanisms of salt stress tolerance in sweet potato, and emphasizing the benefits and recent findings from controlled hydroponic screening approaches in identifying resilient genotypes. Lastly, this review combines three important characteristics—salt tolerance, nutritional stability and environmental adaptability—to provide a comprehensive strategy for creating sweet potato cultivars that are both nutritionally rich and adaptable to stress. We wrap up by highlighting future research directions for sweet potato breeding, such as the use of cutting‐edge phenomic, metabolomic and genomic tools, as well as the significance of climate‐smart agricultural practices and participatory breeding for sustainable sweet potato production.
ABSTRACT This special issue was offered to provide a platform to the plant scientists working on development and/or evaluation of plant mutants facilitating climate‐resilient crop breeding. A total of 13 research and review articles were accepted for publication. These research and review papers focused on the development and evaluation of the novel mutants for their adaptation to various climates including both biotic and abiotic stresses using emerging tools of molecular physiology and statistics. These also presented the use of different physical and chemical mutagens and advanced molecular tools to develop and detect mutations, respectively. Likewise, some novel approaches for crop improvement were presented, including targeted mutations, bioinformatics and functional genomics. Additionally, one study on precise gene editing in rice reported that tolerance to bacterial leaf blight can be achieved without yield penalty. Overall, this special issue highlights the role of mutation breeding and advanced crop improvement tools in ensuring global food security.
ABSTRACT Extending tomato shelf life is a major breeding priority to reduce postharvest losses. Among ripening mutants used in breeding programs, the alc allele remains understudied, and its inheritance and the factors underlying the variability in phenotypic expression are not fully understood. To address this, we developed and evaluated an F 2 population ( n = 137) derived from a normally ripening line and an alc ‐mutant Penjar landrace. Individual F 2 plants were evaluated for agronomic and fruit‐quality traits, and shelf life was evaluated individually on 20 fruits per plant, enabling estimation of intra‐ and inter‐plant variation. Transgressive segregation was observed for most quantitative traits. The long shelf life (LSL) phenotype co‐segregated tightly with alc , which showed partial recessivity (degree of dominance, d/a = −0.33 from parental/F 1 means; −0.29 from F 2 genotype classes). Mean shelf life was 18.2 ± 0.5 days in F 2 ‐WT plants, 25.8 ± 0.7 in F 2 ‐heterozygotes and 55.1 ± 2.1 in F 2 ‐ alc / alc mutants. Broad‐sense heritability decreased markedly from F 2 ‐WT class (0.85) to F 2 ‐ alc / alc class (0.46). Substantial inter‐plant variability, together with the wide variation observed among F 2 alc / alc individuals, suggests that the LSL phenotype is influenced not only by the major effect of alc but also by modifier loci and developmental environmental effects. Fruit‐to‐fruit variance indicated that shelf life phenotyping requires larger sample sizes for alc / alc mutants (244–303 fruits) than for WT (8–27) or Alc / alc genotypes (54–59). Agronomic performance did not differ among F 2 alc classes, whereas fruit quality was significantly affected, showing reduced redness, increased yellowness and lightness, higher soluble solids and greater firmness. These results support the targeted deployment of alc in tomato breeding while highlighting that its phenotypic expression depends on modifier effects and developmental environmental conditions, both of which should be considered when evaluating the stability of the LSL phenotype.
ABSTRACT The soil‐borne yellow mosaic virus disease, caused by infection of barley yellow mosaic virus (BaYMV) and barley mild mosaic virus (BaMMV), poses a persistent and serious threat to autumn‐sown barley ( Hordeum vulgare L.) in East Asia and Europe. Identifying and deploying resistance genes is crucial for protecting barley from viral infections, particularly against pathogenic isolates that have overcome existing resistance in commercial cultivars. In this study, we performed genetic mapping using a double haploid (DH) population generated via microspore culture from F 1 hybrids of two parental lines, ‘Mihori Hadaka 3’, which carries the recessive resistance gene rym2 and the Chinese malting barley variety ‘Dan 2’. This population was genotyped using a complexity‐reduced target‐enrichment assay. Through QTL mapping and linkage analysis with newly developed KASP markers, we identified two resistant genes, rym2 , located within the physical interval 156.9–438.9 Mb spanning the peri‐centromeric region on chromosome 7H and a new resistant gene that was tentatively designated Rym19 from ‘Dan 2’ on chromosome 5H spanning the peri‐centromeric region as well, within the interval 33.3 to 437.4 Mb. The gene rym2 was known for conferring resistance to multiple BaMMV/BaYMV isolates, whereas the Rym19 conferred race‐specific resistance against BaYMV; however, it was less effective in mechanical inoculation. In summary, this work reports the genetic mapping of both the broad‐spectrum resistance gene rym2 on chromosome 7H and a BaYMV‐specific resistance gene Rym19 on chromosome 5H, establishing a foundation for future fine mapping and cloning of these genes, as well as marker‐assisted selection from their respective donor accessions for barley resistance breeding.
Introduction of dwarfism to cereals has set a new paradigm in crop improvement programmes. To date, very little progress has been made in the development of high-yielding dwarf/semi-dwarf genotypes in oilseed Brassica. Previous attempts using induced mutagenesis employed in the induction of dwarfism in Brassica crops yielded limited success, and many mutants had markedly unfavourable modifications in the plant. In the present study, we characterised a gamma radiation-induced dwarf and early mutant, Trombay juncea dwarf-1 (tjd1), in Indian mustard, Brassica juncea cv. Varuna, that showed improved yield-contributing traits like total siliquae number and number of branches. This mutant offers a prominent source of dwarfism and earliness for crop improvement in Indian mustard, B. juncea. Nature of dwarfism in tjd1 was assessed in terms of major components of plant architecture contributing to plant height. The mutant showed about 45.09% reduction in plant height compared to the parent cultivar due to the reduction in the height of the first branch, length of main fruiting axis and number and length of the internodes. At anatomical level, mutant tjd1 showed reduction in both cell size and number of cells/mm. The genetic analysis using F1, F2 and BC1F1 populations indicate that the dwarf plant height is controlled by a single recessive gene with incomplete dominance. The mutant responded towards auxin treatment at both seedling and late vegetative phase and also showed significant downregulation of the key genes involved in phytohormone pathways. Overall, the B. juncea mutant tjd1 will be very useful as a source for ideotype breeding to develop early and dwarf/semi-dwarf high-yielding genotypes.
Chickpea (Cicer arietinum L.) is a legume that is widely consumed around the world due to its nutritional content. Fusarium oxysporum f. sp. ciceris is a serious, destructive pathogen that causes fusarium wilt disease and affects chickpea production. The development of chickpea varieties resistant to this pathogen is the most effective way to control fusarium wilt. This study aims to determine the population structure of chickpea and to identify markers associated with resistance to the Foc0 race. A total of 201 C. arietinum and 116 C. reticulatum genotypes were collected and used as a plant material. Following DNA isolation, GBS was performed on all 317 Cicer genotypes. The resulting GBS-derived SNPs were used as the genotypic dataset, whereas the disease severity scores of the isolates on chickpea genotypes served as phenotypic data. The associations between the SNPs and Foc0 resistance genes were detected according to the MLM (Q + K) model using TASSEL Software 3.0, and the population structure was analysed using STRUCTURE software (v.2.2). Population is divided into two subpopulations (K = 2): wild and cultivated. The population consisting of wild-type genotypes was further divided into two subpopulations (K = 2), whereas the cultivated genotypes were divided into four subpopulations (K = 4). Among them, TR83102 exhibited the highest resistance phenotyping score (35.71). Heritability was calculated as 0.78 for wild and 0.86 for cultivated species. A total of 37,123 SNPs were analysed, and FDR and Bonferroni thresholds were determined. As a result, 56 important markers were identified. These important markers can be used in breeding studies to develop Foc0-resistant varieties and to understand the resistance mechanisms against FW.
Fall armyworm (FAW) is a major constraint to maize (Zea mays L.) production and nutritional quality in sub-Saharan Africa, necessitating the development of extra-early cultivars with stable grain yield, pest tolerance and enhanced nutritional quality. This study evaluated genetic variability and selection efficiency among 20 extra-early provitamin A-quality protein maize (PVA-QPM) inbreds under natural FAW infestation across two cropping seasons (2023 and 2024) at Oke-Oyi, Nigeria. Significant (p < 0.01) genotypic, environmental and genotype & times; environment interaction effects were observed for grain yield, FAW severity, yield stability index and nutritional quality traits. Superior inbreds, including TZEEIORQ 43, TZEEIORQ 490 and TZEEIORQ 29, combined high grain yield (2720-2750 kg ha(-1)) with low FAW severity (3.2-3.4) and high yield stability (0.92-0.93). These genotypes exhibited elevated beta-carotene (8.1-8.3 mu g g(-1)), tryptophan (0.86-0.87 g 100 g(-1)), iron (39-40 mg kg(-1)) and zinc (27-28 mg kg(-1)). Genotypic variation for these traits was consistent across both seasons. Untargeted LC-MS metabolomic profiling identified accumulation of chlorogenic acid, ferulic acid, beta-carotene, tryptophan, glutathione, malic acid and linolenic acid. These metabolites were associated with phenylpropanoid, flavonoid, amino acid and jasmonate-linked pathways. Multivariate analyses revealed structured associations among metabolite profiles, FAW infestation response, grain yield and nutrient composition. Results demonstrate genetic variability among inbreds for agronomic, nutritional and metabolic traits under FAW pressure, supporting improvement of FAW tolerance, yield stability and nutritional quality in extra-early PVA-QPM for resilient sub-Saharan Africa.
MAIZE cultivation is widespread throughout the world under a diverse array of climates. These diverse growing habits pose myriad biotic and abiotic threats to successful maize production. Waterlogging (WL) stress, the second most important abiotic constraint after drought, leads to around 25%-30% of production losses each year. Effective identification of suitable donor lines with tolerance against WL and using it in breeding programmes is the main concern for the breeders. The present study focused on the effective and early identification of maize genotypes tolerant to WL based on root traits. For this, 120 maize inbred lines along with Zea mays ssp. parviglumis from different genetic origin were evaluated for WL tolerance both at pre-emergence as well as the seedling stage at different WL durations, namely, 3, 6 and 9 days to flooding. Results based on percentage germination at pre-emergence and percentage survival at the seedling stage reveal that germination tolerance is independent of seedling stage tolerance. The chlorophyll content exhibited that the tolerant lines had almost similar levels of chlorophyll at 3 days of flooding with control and subsequent decline recorded in 6 and 9 days. The least reduction in chlorophyll content at 9 days of flooding was found in EML 285. Waterlogging tolerance coefficient (WTC) based on root and shoot traits is higher in tolerant lines than in susceptible ones. Root traits are foremost affected by WL stress and plants cope with such stress by having adaptive mechanisms against it; therefore, the identified lines were further revalidated by the radial oxygen loss (ROL) barrier test, which is an adaptive response under WL stress, which confirmed the line identified under WTC based on root traits, namely, I 185, I 172, LM 16 and teosinte (check), having more than 90% barrier formation corresponds more to the formation of a ROL barrier. These identified lines can be used as parents in hybrid development or deriving the WL-tolerant lines.
Open-pollinated progeny tests are still widely interpreted as if all the individuals within a maternal family were true half-sibs. However, in species with mixed mating systems, this assumption is often biologically unrealistic and may bias the estimation of the additive variance, narrow-sense heritability and expected selection gains. It concerns crops, forages, perennial species and any breeding population where selfing and outcrossing coexist. Here, it is argued that the routine half-sib interpretation should no longer be treated as the default view of open-pollinated families in mixed-mating populations. Here, I build on the covariance framework of relatives under mixed selfing and random mating to interpret maternal progenies through the mean coancestry within families rather than through a fixed half-sib coefficient. The increasing availability of molecular markers now makes it feasible to infer mating systems, realized relatedness and pedigree structures, more accurately, allowing breeders to replace convenience-based assumptions with biologically informed genetic evaluations.
The breeding of pear (Pyrus communis) cultivars that meet market requirements and are at the same time resistant to fire blight is a challenging task beacuse appropriate resistance donors are scarce. To identify valuable resistance sources, phenotypic screening and genetic characterization are indispensable. We established an F1 population by crossing two moderately resistant pear cultivars, 'Petersbirne' and 'Harrow Sweet', to identify loci for resistance in 'Petersbirne' and to evaluate if the combination of two resistant cultivars will lead to a higher resistance level in the progeny compared with a cross with the susceptible 'Conference'. The 'Petersbirne' & times; 'Harrow Sweet' population had a lower average percent lesion length (PLL), 17.8, compared with 34.3 of the 'Harrow Sweet' & times; 'Conference' population. Mapping of the severity of fire blight in 'Petersbirne' revealed one resistance QTL on linkage group (LG) 02, which shares the same resistance haplotype as determined for 'Harrow Sweet'. Further, progenies homozygous for the resistance haplotype for the LG02 QTL had a significantly lower PLL value than the heterozygous progenies. Additionally, we identified a previously unidentified putative minor QTL on LG14 in 'Harrow Sweet' but could not confirm previously detected QTL on LGs other than LG02. Although a new resistance locus could not be identified in 'Petersbirne', the combination of two resistant cultivars seems to enhance the number of fire blight-resistant progenies and thus breeding success.
Elevated temperatures adversely affect the growth and productivity of Brassica juncea at various developmental stages. Breeding heat-tolerant varieties presents an economically viable strategy to reduce the impacts of heat stress. Therefore, a genome-wide association study was conducted, focusing on agro-morphological traits under late-sown conditions, exerting heat stress at the reproductive phase. A diverse panel of 142 genotypes was used for phenotyping and SNP genotyping. During late-sown conditions of 2020-2021, 2021-2022 and 2022-2023, a total of 59 significant marker-trait associations were identified. Among these, 11 SNPs were consistently associated with key traits across the seasons. These stable SNPs were further analysed through gene annotation and in silico expression profiling. The SNPs were linked to several important agro-morphological traits affected by heat stress. In silico analysis of SNPs revealed important candidate genes directly involved in stress response and trait regulation. Expression profiling confirmed predominant expression of these genes in corresponding tissues, indicating their functional relevance. The identified candidate genes will be subsequently used for the development of heat-tolerant B. juncea varieties through molecular breeding approaches.
Powdery mildew is one of the most significant fungal diseases affecting apple, both the tree and its fruits, causing considerable economic losses to apple growers. Controlling this disease can require the application of multiple fungicides. A more sustainable approach is to grow resistant cultivars. In this study, we investigated the genetic basis of powdery mildew resistance in the wild apple accession Malus orientalis MOR17/1. To conduct genetic mapping, a crossing population was established between 'Golden Delicious' and MOR17/1. A total of 172 progeny were phenotyped under greenhouse and field conditions. The correlation between greenhouse and field data is low. Genotyping was performed employing a set of 17 SSR markers and the Axiom JKI50KMd SNP-array. A high-density linkage map was calculated for MOR17/1. The greenhouse data were used for mapping as single locus with JoinMap5.0 and together with the field data as quantitative trait loci (QTL) using MapQTL5.0. Mapping of the greenhouse data revealed a locus on LG02 for both phenotyping time points, as well as for the mean and maximum values. The highest LOD, 45.7, was observed for the second phenotyping. QTL mapping of field data from 3 years of observations confirmed the resistance locus on LG02 at a lower LOD for the second phenotyping in 2023 and for both phenotypings in 2025, as well as for the mean and maximum values. An additional QTL was detected at the bottom of the LG02 only in the first phenotyping in 2025. In the first phenotyping in 2024, a QTL was detected on LG11. A new locus conferring resistance to powdery mildew was mapped on LG02 of MOR17/1. These findings expand the pool of known powdery mildew resistance genes available to the breeders and offer new possibilities for resistance pyramids.
Seed yield and composition are major targets in soybean (Glycine max (L.) Merr.) breeding programmes, but simultaneous improvement is constrained by unfavourable correlations among target traits. In this study, we evaluated the potential of different selection indices to simultaneously improve seed yield and quality traits in soybean. Indices were derived from seed yield, protein content, oil content, and combined protein and oil content. For each quality trait, we calculated both yield-based indices (protein yield, oil yield and protein-plus-oil yield) and deviation-type indices (grain protein deviation [GPD], grain oil deviation [GOD] and grain content deviation [GCD]). In addition, three different methods were used to derive the deviation-type indices: plot-based regression, regression based on genotype BLUEs and a bivariate mixed model approach. Our analysis utilized data from 467 soybean genotypes evaluated in advanced multi-environment yield trials. All quality traits and deviation-type indices exhibited high heritability (h(2) > 0.86), whereas yield and yield-based indices showed moderate heritability (h(2) > 0.68). Genome-wide association studies (GWASs) were performed for all traits and indices using genotypic data from 333 lines. Results showed that selection on deviation-type indices is primarily driven by the underlying quality trait, as indicated by very high correlations and overlapping significant marker-trait associations. In contrast, yield-based indices reflected the combined influence of seed yield and the corresponding quality trait. Notably, GWAS on the bivariate-derived GPD index identified additional significant loci on chromosome 18 that were not detected for the univariate traits, suggesting that the bivariate approach captured aspects of the covariance structure between protein content and seed yield. Overall, our results suggest that deviation-type indices in soybean offer little practical advantage over direct selection for corresponding quality traits in materials with weak or environment-dependent trait correlations. At the same time, comparing index derivation methods shows that constructing phenotypes influences the interpretation of genetics downstream and that modelling multiple traits can reveal additional loci relevant to yield-quality trade-offs.
