Root system architecture at the seedling stage plays a critical role in early vigor and stress resilience in wheat (Triticum aestivum L.). Chinese wheat landraces, shaped by long-term regional adaptation and largely underutilized in modern breeding, represent a valuable reservoir of genetic variation for root trait improvement. Here, we conducted a genome-wide association study for eight seedling root traits in 272 Chinese wheat landraces evaluated across three independent experiments and genotyped with a 660 K SNP array. A total of 289 significant SNPs were identified and consolidated into 36 stable quantitative trait loci (QTL). Individual QTL explained 4.0–7.9
Stay-green (SG) is an agriculturally important trait in all field crops, enabling plants to maintain green leaves and photosynthetic capacity for a longer period. Especially, SG plants often withstand adverse environmental conditions more effectively. This trait has become an important target in wheat breeding programs due to its potential contributions to yield stability and resilience to environmental challenges. In this study, 13 putative SG genes were identified in wheat using the Basic Local Alignment Search Tool (BLAST) and the Phytozome database, followed by determining their precise genomic positions. Among these SG genes, six proteins were predicted by subcellular localization software to be localized in the thylakoid membrane of chloroplast, suggesting a role in photosynthesis. Gene Ontology (GO) analysis indicated that the other putative SG genes are involved in porphyrin metabolism (related to chlorophyll degradation), glucose metabolism, and autophagy. Furthermore, RNA-seq data revealed that the putative SG genes were highly expressed during post-anthesis heat stress and showed increased expression under cold and phosphorus stress, indicating multifunctional roles in abiotic stress adaptation. The functional relevance of these genes to the SG trait was supported by marker-trait association analysis, which highlighted two candidate genes, TaNYC3-7A and TaUDP-5B, suggesting their potential role in regulating SG phenotypes in wheat.
Soil salinity is a major problem that reduces the growth and yield of rice, particularly in coastal rice-growing regions such as certain provinces of Cambodia. This study evaluated salinity tolerance in 60 Cambodian rice varieties at germination and seedling stages and combined physiological analyses with genome-wide association study (GWAS) to identify traits and genomic regions associated with salinity tolerance. The screening at the seedling stage showed CAR 11 was a highly salt-tolerant variety in response to salt stress, suggesting this variety could be used in actual salt-affected fields using the transplanting method and may also serve as a valuable genetic resource for salt-tolerance breeding. K+ concentration and Na+/K+ ratios in roots and shoots were identified as physiological traits determining salt tolerance of Cambodian rice varieties. Several varieties also exhibited high tolerance during germination under salt stress, suggesting their potential value as genetic resources for salt-tolerance breeding. GWAS identified some marker-trait associations and putative candidate genes associated with salinity tolerance-related traits under salt stress. These findings provide fundamental knowledge regarding salt tolerance and putative genes associated with traits in Cambodian rice varieties, and this knowledge is essential for developing salt-tolerant varieties via breeding programs and extending rice production in salt-affected areas.
RNA interference technology is a key genetic engineering tool enabling regulation of genes involved in a wide range of metabolic processes, including the composition of seed storage proteins. This approach is of significant importance for sorghum, a high-yielding drought-tolerant cereal crop characterized by resistance of its grain storage proteins, kafirins, to proteolytic digestion. To suppress γ-kafirin synthesis in the commercial grain sorghum cultivar Avans, we obtained a transgenic plant carrying a construct for RNA silencing of the γ-kafirin gene (gKAF1). This paper presents the results of an analysis of the inheritance of the copy number of the introduced genetic construct in the lines created by self-pollination of original T0 plant, and effects of the RNAi genetic construct on the γ-kafirin mRNA level, grain protein content and protein digestibility, and the manifestation of agronomically important traits in a series of generations (T3-T6). qPCR showed that in plants from early generations (T2, T3), the copy number of the construct varied from one to three (2–5 haplotypes); after self-pollination of plants with 2 and 3 copies of the construct, the copy number in their progeny decreased to 1–2. Real-time RT-PCR revealed that γ-kafirin mRNA level in plants with the RNAi construct was reduced by 140 times compared to the donor cv. Avans, one copy was sufficient for almost complete degradation of γ-kafirin mRNA. All plants from the studied lines were distinguished by high in vitro grain protein digestibility (up to 88–92
Genomic selection (GS) in self-pollinated crops such as rice requires the advancement and evaluation of very large populations, which can strain land, labour, and financial resources in breeding programs. We evaluated a “panicle-to-hill” method, a refinement of hill-plot planting, as a cost-effective alternative to conventional panicle-to-row progeny advancement for Basmati rice populations targeted for GS. Thirty-eight founder lines were inter-crossed to generate 63 F1 combinations, which were advanced to 63 F2 populations comprising 17,988 progenies. From F3 onward, generations were advanced by sowing seed from a single panicle per progeny as a hill, with each hill representing an individual progeny. The F3 and F4 generation were advanced through panicle-to-hill method, through shuttle breeding between ICAR–IARI, New Delhi, and ICAR–IARI, Rice Breeding and Genetics Research Centre, Aduthurai, to achieve two generations per year. Direct hill seeding at 30 cm × 30 cm spacing reduced land use from approximately 0.44 to 0.10 m2 per progeny and eliminated nursery and transplanting operations. Aggregated field operation and post-harvest records indicated that the panicle-to-hill method was approximately six times cheaper per progeny per generation than the panicle-to-row method, corresponding to about Indian Rupee (INR) 4.46 per progeny per generation under our conditions. Progeny losses were minimal, which offers a practical, scalable, and cost-effective strategy for advancing very large rice populations in breeding programs operating under land and budget constraints.
Sustaining rice productivity under increasing climate change requires breeding strategies that extend beyond traditional shoot-focused traits. Root system architecture (RSA) plays a crucial role in plant adaptation because it determines how efficiently roots explore soil for water, nutrients, and oxygen under stress conditions. This review synthesizes the current understanding of RSA in rice as a dynamic trait complex that integrates root spatial configuration, developmental processes, anatomical features, and physiological functions, collectively influencing abiotic stress tolerance. Evidence across drought, salinity, flooding, and nutrient-deficient environments indicates that adaptive RSA traits can improve resource acquisition efficiency and stabilize yield in stress-prone ecosystems. Key genes and quantitative trait loci have been identified that regulate major RSA components, including DRO1, which controls root growth angle and deep rooting for drought avoidance; PSTOL1, from the Pup1 locus, which enhances root growth and phosphorus acquisition under low-P soils; qSOR1, which influences shallow root architecture; and weg1 and our1 mutation genes have been shown to alter root development and branching architecture. These discoveries highlight the genetic basis of RSA and its potential for crop improvement. However, the effectiveness of specific root traits is highly dependent on environmental conditions, and their benefits are often associated with trade-offs in carbon allocation and resource use. Integrating genomic insights, advances in phenotyping, and RSA-based breeding strategies may therefore enable the development of climate-resilient rice varieties that maintain productivity under diverse abiotic stresses.
Waxy maize landraces in Yunnan possess complex genetic backgrounds hindering breeding. To address this, we engineered novel waxy germplasm with a defined genetic background using CRISPR/Cas9-mediated targeted mutagenesis of the waxy gene encoding granule-bound starch synthase I (GBSSI) in the maize inbred line B104. A 20-bp target site (Wx-T4) within exon 4 was designed and validated for specificity. Agrobacterium tumefaciens-mediated transformation of B104 embryos, followed by Basta selection and sequencing, yielded stable T2 homozygous mutants (waxy-1: 18 bp deletion; waxy-2: 4 bp deletion). Iodine staining confirmed the waxy phenotype reduced amylose with increased amylopectin, and Western blot showed near-complete (waxy-1) or complete (waxy-2) loss of GBSSI protein. Critically, metabolic analysis revealed significant shifts beyond starch: DNS assay and GC–MS quantification demonstrated a dramatic increase in total soluble sugars in mutant kernels. Specifically, glucose and fructose levels surged, respectively, while sucrose content decreased compared to wild-type B104. This indicates waxy mutation triggers metabolic reprogramming, diverting carbon flux from starch towards soluble sugar accumulation, and particularly reducing sugars.
Vanilla planifolia suffers major losses from root and stem rot (RSR) caused by Fusarium oxysporum f. sp. radicis-vanillae (Forv), amplified by low genetic diversity. We dissected quantitative resistance by phenotyping a selfed population AF_CR0040 (n = 115) inoculated with three Forv isolates (Fo166, Fo254, Fo297). Five traits were scored: symptoms at 5, 10 and 15 days post-inoculation (dpi), the area under the disease progress curve (AUDPC) and the day of mycelium appearance (d.myc). Multiple quantitative trait locus (QTL) mapping (MQM) was realized on a high-density genotyping-by-sequencing (GBS) map. QTL were anchored to the CR0040 genome to identify candidates. We detected 121 QTL across isolates and traits, explaining 2.5 to 21.8
Direct-seeded rice (DSR) requires rapid seedling establishment, tolerance to early submergence, and structural resilience to prevent lodging. Dissecting the genetic and molecular basis of these traits is essential for breeding high-performing, resilient cultivars. A panel of 100 diverse rice germplasms was evaluated for early seedling vigor (ESV), anaerobic germination (AG) tolerance and lodging resistance (LR). Comprehensive correlation and multivariate analyses revealed strong interrelationships among seedling vigor indices, germination traits, seedling biomass and morphological features. Key traits such as anaerobic vigor index (AVI), shoot length and coleoptile length were identified as major contributors to AG tolerance, whereas the bending moment, section modulus and panicle weight were critical for lodging resistance and yield. Principal component analysis separated promising genotypes for seedling vigor, anaerobic germination tolerance, and structural robustness. Association analysis using SSR and InDel markers identified several marker–trait associations, including markers linked with vigor, anaerobic germination tolerance, lodging resistance, and yield-related traits. These results identify promising germplasm and candidate marker–trait associations that may support future validation and breeding efforts in direct-seeded rice.
Genetic gain in crop breeding programmes is inversely proportional to the duration of the breeding cycle. Therefore, breeders utilize different generation enhancement strategies especially in annual crops to achieve high genetic gains. Onion is a biennial plant, forms a bulb in the first year and bolts (flowers) in the second year as a result conventionally developing a new cultivar can take 16–20 years. Therefore, the objective of this study was to reduce the generation time in short-day onion cultivars using different speed-breeding approaches under low-cost polyhouse and field conditions. Under a polyhouse with 16 h (h) photoperiod, bulbs matured early, with PRO-7, Punjab Naroya, and PWO-2 were harvested in 75, 100, and 100 days during early season planting, and 57.7, 72.0, and 75.0 days in main season planting, respectively. Under natural field conditions, PRO-7, Punjab Naroya, and PWO-2 were harvested in 140.0, 153.7, and 167.7 days during the early season, and in 121.0, 146.0, and 141.7 days during the main season, respectively. In the field-based low-cost speed breeding, Punjab Naroya matured in 96 days compared to 150 days under natural field conditions in the main season. Bulb size was significantly reduced under extended photoperiod in polyhouse in comparison to natural field conditions. Therefore, we used different mulches and found that black mulch improved bulb size under extended photoperiod in field-based speed breeding. After bulb harvesting, bulb dormancy was broken by using hydrogen peroxide (H2O2) treatments. To fulfil the vernalization requirement, hydrogen peroxide treated bulbs were planted at Keylong (Himachal Pradesh, India), and 10
Parthenocarpy, the development of fruits without fertilization is an important trait in vegetable crops for ensuring stable yield and fruit quality under environmental conditions that adversely affect pollination and fertilization. It has been extensively studied in solanaceous (Tomato and eggplant) and cucurbitaceous (Cucumber and watermelon) crops. This review synthesizes current knowledge on the physiological, hormonal and molecular mechanisms underlying parthenocarpic fruit development in vegetable crops. Available evidence indicates that auxin acts as the primary trigger of fertilization-independent fruit set by stimulating ovary growth, cell division and fruit development through downstream signaling pathways. Gibberellins and cytokinins function as key cooperators through extensive crosstalk with auxin pathways, whereas ethylene predominantly suppresses fruit initiation. Recent advances in QTL mapping, transcriptomics and functional genomics studies have identified diverse hormone biosynthesis genes, signaling components and transcription factors that are involved in parthenocarpy regulation, revealing both conserved and crop-specific regulatory mechanisms. Emerging evidence further highlights the contribution of sugar signaling to ovary sink establishment and its interaction with hormone-responsive pathways during fruit set. Comparative analyses suggest that, while common hormonal modules regulate parthenocarpic development across species, substantial variation exists in downstream regulatory networks among crops. Recent advances in genome editing and multi-omics approaches provide new opportunities to dissect regulatory pathways and accelerate the development of climate-resilient parthenocarpic vegetable cultivars.
Drought stress severely compromises photosynthetic efficiency and yield stability in barley, yet the genetic and regulatory networks underlying drought-responsive chlorophyll fluorescence traits remain inadequately characterized. The current study was carried out to identify the hub genes and regulatory factors associated with major QTLs under drought stress in barley. Accordingly, a genome‒wide composite interval mapping approach was utilized under the framework of multi‒locus genome‒wide association studies. A total of 25 stable lines were identified using genotype by environment interactions. Furthermore, 34 and 63 stable and closely linked QTLs associated with OJIP (O, J, I, P phases of chlorophyll fluorescence induction) test parameters were traced in control and drought conditions, respectively. Common genomic regions across both environments were mapped on chromosomes 1H, 3H, 4H, 5H, and 7H. Bioinformatics analysis included gene ontology (GO) enrichment, protein–protein interaction (PPI) network construction, transcription factor (TF) and microRNA (miRNA) target prediction, and in silico expression validation using RNA-Seq data. Moreover, 214 candidate genes related to major QTLs were identified through bioinformatics analysis. Gene ontology analysis revealed that these candidate genes were enriched in biological processes including cytoskeleton organization, stress response, proteolysis, and lipid biosynthesis. The most significant molecular functions were related to peptidase inhibitor activity and endopeptidase regulator and inhibitor activities. In addition, eight hub genes were identified in protein–protein interaction networks. Among these, four genes (HORVU.MOREX.r3.5HG0446800, HORVU.MOREX.r3.5HG0447870, HORVU.MOREX.r3.3HG0246800, and HORVU.MOREX.r3.3HG0246580) were validated through in silico RNA‑Seq analysis. Finally, 11 transcription factors (e.g., the B3 family) and protein kinases (RLK/Pelle and CAMK) emerged as key regulators, whereas 69 microRNAs (e.g., hvu‒miR5049, hvu‒miR6192, and hvu‒miR6197) were implicated in gene regulatory networks. Collectively, the validated hub genes may serve as promising candidate targets for the development of functional markers in marker-assisted selection (MAS), potentially facilitating early-stage screening and pyramiding of drought-tolerant alleles in barley breeding programs, pending experimental validation. This study provides new insights into the molecular processes underlying drought tolerance in barley.
Doubled haploid (DH) technology has become an important tool for accelerating maize breeding by enabling the rapid development of completely homozygous lines. However, breeding decisions depend not only on haploid induction rate or chromosome doubling success, but also on the cumulative efficiency of the entire DH pipeline. Despite its practical importance, information on material losses from induced seed to recovered DH line remains limited under routine breeding conditions. The aim of this study was to assess the efficiency of doubled haploid production in maize by quantifying material losses across successive stages of haploid induction, phenotypic selection, chromosome doubling, and final recovery of fertile DH lines. Fifty genetically diverse maize donor populations were pollinated with a maternal haploid inducer carrying the dominant phenotypic markers R1-nj and Pl1. Putative haploid seeds were initially identified using the R1-nj anthocyanin marker, followed by secondary validation using the Pl1 root pigmentation marker. A total of 38,916 seeds were evaluated, of which 5,870 putative haploids were identified at the first screening stage, corresponding to a putative haploid selection rate of 15.08
Growth habit is one of the most important domestication traits in dry bean (Phaseolus vulgaris L.). In the U.S. for example, Type II indeterminate upright plant varieties have allowed farmers to switch from historic two-pass harvest to one-pass direct harvest. Previous work suggested a stem diameter of 5.6 mm as threshold to select Type II architecture genotypes suitable for direct combining. This study aimed to validate the correlation between stem diameter and other agronomic traits using lines comprising various market classes from a public breeding program. It also assesses if stem diameter could be used to select genotypes that combine high seed yield and upright architecture. GWAS was also used to identify genomic regions related to plant height and stem diameter. Mean stem diameter among breeding lines was 7.7 mm, higher than the proposed threshold. Stem diameter showed no significant G × E interactions, with the highest broad-sense heritabilities observed for regular-darkening pinto (pinto) and slow darkening (SD) pinto. Plant height was the most relevant trait for seed yield variation in black, great northern, and navy beans. In contrast, both plant height and stem diameter are required to explain part of seed yield variability and selecting upright plants for pinto, red/pink, and SD-pinto. GWAS revealed significant regions located on chromosomes Pv03, Pv07, and Pv11 depending on trait and race used. A region near 40.7 Mb on Pv07 was associated with both plant height and stem diameter, suggesting further studies on indeterminate upright dry bean plant architecture should focus on this region.
The macaw palm (Acrocomia aculeata) is a native Neotropical palm with potential for vegetable oil production, particularly for biofuel generation. However, its domestication remains incipient, and information on long-term progeny performance is still limited. This study evaluated fruit yield and biennial bearing in a macaw palm progeny test to identify superior families for genetic improvement. Thirty-six half-sib progenies from two regions of Minas Gerais, Brazil, were assessed for fruit production from 2019 to 2024 at the Federal University of Viçosa, Minas Gerais. The experiment followed a randomized complete block design with three blocks and three plots per block. Genetic variances, parameters, and progeny performance were estimated using mixed linear models (REML/BLUP) implemented in the ASReml package in R. Biennial bearing was assessed based on multi-year yield patterns and phenotypic correlations between consecutive and alternate production cycles. Mean fruit production ranged from 1.34 kg plant−1 in 2019 to 26.32 kg plant−1 in 2022. Most of the genetic variability for yield was concentrated within progenies, as indicated by the broad-sense heritability estimate of 0.36, suggesting high intraprogeny heterogeneity. Four of the evaluated progenies stood out for their superior performance, year-to-year stability, and, in some cases, early production. Selection of eight individuals within these progenies increased the population mean yield by 30.12
Rice false smut, caused by Ustilaginoidea virens, is a major yield and quality limiting disease in humid rice ecologies. Breeding for durable resistance is constrained by limited stable genetic resistance sources, and is further complicated by pronounced genotype × environment interactions (GEI) and pathogen variability, which cause inconsistent field expression. We hypothesized that rigorous multi-environment evaluations using integrated multi-trait selection models could uncover stable resistance sources that do not compromise grain yield. To test this, an F₆ recombinant inbred line (RIL) population (n = 208) derived from crossing a high yielding susceptible variety (CO43) and a highly resistant donor (RG170) was systematically evaluated for agronomic performance and disease response. Initial screening revealed substantial genetic variability and high heritability (> 0.60). Consequently, 31 superior RILs were advanced to replicated multi-location trials across three distinct climatic environments. The evaluations revealed that GEI accounted for 53
Powdery mildew associated with Erysiphe pisi is one of the main sanitary constraints affecting pea (Pisum sativum L.) cultivation in southwestern Colombia. The objective of this study was to estimate the final severity of powdery mildew in stipules, pods, and tendrils of eight climbing pea genotypes carrying the Afila gene and the commercial check San Isidro, using an organ-specific scale based on digital image analysis, and to evaluate its relationship with green pod yield. The evaluated genotypes originated from the pea breeding program of the Universidad de Nariño and were obtained through crosses and backcrosses aimed at incorporating the Afila gene into adapted climbing materials. The disease was evaluated under field conditions, natural infection, and without fungicide application. Severity was quantified as the percentage of infected area in each organ, and yield was expressed in t ha⁻1. Highly significant differences among genotypes were detected for severity in stipules, pods, and tendrils, mean severity, and yield. Genotypes GR2, GR10, and GR29 showed lower final severity in the three evaluated organs and higher green pod yield, whereas San Isidro showed the highest mean severity and the lowest yield. Severity variables were positively correlated with each other and negatively correlated with yield. The results indicate that organ-specific digital quantification allows discrimination of the phenotypic response of genotypes carrying the Afila gene to powdery mildew, and that GR2, GR10, and GR29 constitute promising materials for advanced selection.
Red clover (Trifolium pratense L.) is a key grassland legume, and tetraploid cultivars are commonly appreciated for their high productivity and persistence. However, some tetraploid genotypes are self-fertile, which can promote inbreeding, potentially reducing productivity. Despite its importance, the effects of inbreeding on forage and seed production in tetraploid red clover remain poorly characterized. In this study, we generated four successive inbred generations derived from four parental self-fertile genotypes. The impact of inbreeding on forage and seed production was assessed in a two-year field trial and the effects of inbreeding on productivity traits were modelled. Our results demonstrate that stable inbred lines can be developed in tetraploid red clover. Inbreeding reduced forage and seed yield following an exponential decay pattern. Dry matter yield exhibited a half-life value of 3.5 generations, while seed yield and the seed number per flower head declined more steeply with half-life values of 1.4 and 1.5 generations, respectively. Responses were broadly consistent across the four genetic backgrounds, although inbred lines derived from ‘Titus 15’ showed lower reductions in productivity, highlighting potential candidates for hybrid breeding. Given the widespread occurrence of self-fertility in modern-day tetraploid red clover cultivars, breeders should consider the implications for inbreeding, as losses of 1–2
Wheat sharp eyespot is a soil-borne fungal disease and causes severe yield reduction in wheat worldwide. Identifying candidate genes and enhancing the resistance to sharp eyespot in wheat varieties are effective ways to control the disease. In this study, we performed meta-analysis to identify 7 high potential MQTL by integrating 80 initial QTL related to wheat sharp eyespot resistance. The average confidence interval (CI) of these MQTL was refined to 7.29 cM, representing a 1.95-fold increase in resolution compared to the initial QTL. Notably, the genetic distance of MQTL5 was condensed to less than 1 cM. A total of 275 high confidence annotated genes were obtained as candidate genes within these 7 MQTL by bioinformatic interrogation. GO and KEGG analyses revealed that these genes enriched most significantly in the plant-pathogen interaction pathway. Based on the analysis of qRT-PCR, we further screened out 6 candidate genes showed differential expression between resistant (CI12633 and Niavt14) and susceptible (Yu49 and EM23) cultivars after pathogen inoculation. These candidates include genes encoding an endo-1,3-β-glucanase-like protein (TraesCS6B02G138300), a calmodulin-binding family protein (TraesCS6B02G137500), a short-chain dehydrogenase reductase (TraesCS2D02G058400), two NBS-LRR proteins (TraesCS7D02G106100 and TraesCS7D02G106200), and a kinase family protein (TraesCS2B02G537200). All candidate genes were upregulated in resistant cultivars after Rhizoctonia cerealis infection. Our findings provide a principled foundation for marker-assisted selection and the elucidation of molecular resistance mechanisms in wheat defense against R. cerealis.
Antioxidant traits in rice are quantitatively inherited and play an important role in improving nutritional quality. However, the genetic basis of antioxidant variation within Thai rice remains unexplored. In this study, we investigated the genetic basis of total phenolic content (TPC), total flavonoid content (TFC), and antioxidant capacity (AC, measured by ABTS) in a panel of 159 Thai rice cultivars using genome-wide association analysis. A total of 209,594 high-quality SNPs located in promoter and exonic regions were analyzed using a mixed linear model implemented in GEMMA. All three traits exhibited high broad-sense heritability (H2 = 77.23–86.02
