Search Results (311)

Wheat (Triticum aestivum L.) is a crucial global food crop that plays a central role in agricultural production and food security. The spike number per unit area (SN) is one of the three component factors of grain yield. In this study, we combined the UG-Map with 27 environments of a recombinant inbred line (RIL) population, and mapped a quantitative trait locus (QTL) for SN, QSn-7A-9048, in which the meta-QTL interval contains only one candidate gene, TraesCS7A02G-364700 (TaKMT-7A). Using the CRISPR/Cas9 system, we generated two homozygous mutant lines, aa-1 and aa-2 of TaKMT-7A, which resulted in frameshift mutations, leading to the premature termination of the translation process. The SN values for the wild type (WT), aa-1, and aa-2 were 4.48, 3.43, and 3.48, respectively. Compared with the WT, the SN of the two mutant lines significantly decreased, and no significant differences for grain number per spike (GNS) and thousand-grain weight (TGW) were detected. We also obtained two overexpression (OE) lines of TaKMT-7A, OE-1 and OE-2. The SN values for the negative control (NC), OE-1, and OE-2 were 2.31, 3.33, and 3.00, respectively. Compared with NC, the SN values in the OE lines significantly increased. The phenotypes of the knockout (KO) lines and OE lines demonstrate that TaKMT-7A acts as a positive regulator of SN in wheat. We performed RNA-Seq analysis using young tiller buds from the WT and aa-1 mutant lines at the tillering stage, and a total of 2315 differentially expressed genes (DEGs) were identified. We screened 22 wheat genes, of which 18 orthologous genes have previously been cloned and are associated with branching in rice and Arabidopsis. These genes included nitrogen transporter, amino metabolism, auxin transporter, auxin homeostasis, auxin response, auxin biosynthesis, strigolactone biosynthesis, and repress gibberellin responses. These genes may represent potential downstream targets of TaKMT-7A. Full article

Plant height is a key agronomic trait that influences plant architecture and mechanical harvesting suitability in cotton; however, the molecular mechanisms underlying its dynamic development remain unclear. In this study, two recombinant inbred line (RIL) populations sharing CCRI127 as a common paternal parent (RIL-GH07, n = 150; RIL-2358B, n = 276) were developed. Based on stable plant-height performance across multiple environments, tall and short extreme lines were selected from the two RIL populations for transcriptome sequencing. By integrating differential expression analysis with weighted gene co-expression network analysis (WGCNA), we identified hub genes associated with cotton plant height development, characterized the molecular features and core pathways governing dynamic stem elongation at different growth stages, thereby providing insights into the transcriptional regulation of plant height development in cotton. The two RIL populations showed broadly similar plant-height growth patterns, with slow elongation at 15 DOS, rapid elongation during 30–60 DOS, and reduced growth after 70 DOS. Transcriptome differential expression analysis identified 15,052 non-redundant DEGs, which exhibited clear population- and stage-specific expression patterns. In the GH07 population, the largest number of DEGs was detected at 15 DOS (7193), whereas in the 2358B population relatively large numbers of DEGs were maintained at both 30 DOS (3839) and 70 DOS (3118). Analysis of DEGs shared by the two populations across four developmental stages showed that, in addition to genes with consistent expression trends, each stage also contained a substantial number of DEGs with opposite expression directions. WGCNA identified 25 gene expression modules, among which the green and yellow modules were significantly positively correlated with plant height. Functional enrichment analysis indicated that genes in these two modules were mainly enriched in hormone regulation and signal transduction, protein modification and degradation, and intracellular transport. Seven hub genes were identified by integrating intramodular connectivity and kME values. Functional prediction suggested that these genes may play important roles in cotton plant height development. This study provides genetic resources and a theoretical basis for subsequent functional validation of cotton plant height-related genes and the improvement of plant architecture in cotton. Full article

Background: Internode length (IL), a key component of plant height (PH), plays an important role in achieving the optimal architecture in wheat. However, the genetic mechanisms underlying internode elongation are not well understood. Methods: In this study, a recombinant inbred line (RIL) population derived from a cross between Bainong 4199 (BN4199) and Zhengyinmai 2 (ZYM2) was evaluated for PH and five ILs across two field locations over two years and genotyped using a 120 K liquid-phase chip. Results: A total of 141 quantitative trait loci (QTL) associated with PH and the five ILs were mapped onto 20 chromosomes, except for chromosome 5D. Among these, 37 stable QTL were identified on chromosomes 1B, 2B, 2D, 4B, 5A, 7A, 7B and 7D, accounting for 3.86–25.97% of the phenotypic variation. Meanwhile, 23 co-localized QTL associated with at least two traits were detected, with QTL cluster regions on chromosomes 2D, 4B, 5A, 7A, and 7B. Moreover, the total additive effects of the QTL combinations increased with the number of QTL, which indicates the effectiveness of pyramid breeding. Additionally, based on gene function annotation, the cloning and characterization of rice orthologs, and analysis via the QTG miner module of the wheat integrative gene regulatory network (wGRN) platform, 63 candidate genes (e.g., Rht1, Rht8, TB1 and ZnF-B) were prioritized within the stable QTL intervals, and their tissue expression patterns were analyzed. Conclusions: Collectively, these findings not only deepen our understanding of the genetic basis of PH and ILs in wheat but also lay a foundation for the further validation and functional characterization of candidate genes, enabling the optimization of plant architecture through marker-assisted selection (MAS) to ultimately improve agronomic performance and yield potential. Full article

Pre-harvest sprouting (PHS) in wheat is a significant global challenge influenced by climate. This study aimed to decipher the genetic underpinnings of PHS and identify resistance genes using 309 recombinant inbred lines (RILs) derived from the “Berkut” × “Worrakatta” cross. Methods: Phenotypic assessment of PHS traits was performed using the whole-spike sprouting method across various environments, complemented by quantitative trait loci (QTL) analysis employing a wheat 50 K SNP chip. Results showed high PHS rates in both parental lines across multiple environments. Progeny exhibited substantial variation in PHS rates, with coefficients of variation ranging from 0.16 to 0.19 and phenotypic variation ranging from 23.92% to 100%, suggesting pronounced transgressive segregation. Nine QTLs associated with PHS were identified on chromosomes 1AL, 1DL, 2AL, 2AS, 2BS, 3DS, 4BL, and 7BL. These loci accounted for 2.67% to 6.39% of the phenotypic variation. Notably, the enhancer alleles at four loci—1DL, 2BS, 4BL, and 7BL—originated from “Worrakatta”, and “Berkut” contributed the enhancer alleles at the remaining five loci. Two QTLs, QPHS.xjau-1AL.1 and QPHS.xjau-1AL.2, were stable across multiple environments. Specifically, QPHS.xjau-1AL.1 was present in three environments and explained 3.86% to 6.39% of the phenotypic variation, while QPHS.xjau-1AL.2 appeared in one environment under average conditions, explaining 2.67% to 4.87% of the variation. Our study also identified eight candidate genes associated with wheat PHS, including those encoding Myb transcription factors that influence flavonoid biosynthesis and grain color, as well as genes involved in stress response and gibberellin biosynthesis, which are crucial for plant growth and development. These genes represent vital targets for enhancing wheat PHS resistance. Full article

Background: Improving grain yield in wheat remains a top priority, requiring integrated breeding and genetic strategies. This complexity poses a major challenge, driven by quantitative polygenic inheritance, environmental influence, and intricate genetic interactions. We investigated genetic factors and their interactions for agronomic and yield traits in two high-yielding winter wheat cultivars adapted to the US Southern Great Plains. Methods: A bi-parental mapping population consisting of 221 F₇ recombinant inbred lines (RIL) derived from ‘TAM 204’ and ‘Iba’ was evaluated for three years in 11 Texas environments. Both parents and RIL population were genotyped on Illumina NovaSeq 6000 and sequences were aligned to IWGSC RefSeq v1.0 using Bowtie2 for SNP calling. For QTL analyses, each trait was analyzed by individual environment, across multiple environments and mega-environments. Results: A total of 86 QTL were mapped for five traits and among them 32 were consistent in more than one environment or analysis. Among consistent QTL, four were pleiotropic to more than one agronomic or yield traits mapped on chromosomes 2B (57.18, 59.47 Mb) and 2D (29.34, 40.64 Mb). The consistent QTL on chromosome 2D (29.34 Mb) was pleiotropic to GYLD, DTH, TW, TKW and explained maximum phenotypic variation for all traits, representing photoperiod gene (Ppd-D1). Another QTL on chromosome 2D (40.64 Mb) was pleiotropic to GYLD and TW and based on the physical position comparisons it likely reflects a unique locus in Iba. The pleiotropic consistent QTL Qgyld.tamu.2B.59 from TAM 204 represents Ppd-B1 gene. Moreover, it is more likely that Qdth.tamu.5B.575 represents the Vrn-B1 gene in Iba. A total of 23 digenic epistatic interactions involved consistent QTL for all traits. Amongst these, epistatic interactions between the consistent QTL on 2B (57.18 Mb) and 2D (29.34 Mb) were observed for GYLD, DTH and TKW. Conclusions: Our findings revealed key allelic diversity and interaction effects in elite wheat cultivars, paving the way for marker development for identified pleiotropic loci and implementation in marker-assisted selection and recombination breeding. Full article

Background/Objectives: Plant architecture is a critical determinant of high-density tolerance and yield potential in maize (Zea mays L.), yet the genetic networks orchestrating these complex traits require deeper elucidation. Methods: In this study, we utilized a Multi-parent Advanced Generation Inter-cross (MAGIC) population comprising 935 recombinant inbred lines (RILs) derived from 16 diverse elite founders. A comprehensive phenotypic characterization of six pivotal architectural traits—plant height (PH), ear height (EH), ear leaf length (LL), ear leaf width (LW), tassel main axis length (TL), and tassel branch number (TBN)—was conducted across three distinct agro-ecological environments. Results: Phenotypic analysis revealed substantial natural variation and high broad-sense heritability (H² ranging from 60% to 86%), with TBN exhibiting the most pronounced variability. Correlation architecture demonstrated a strong coupling between vertical growth traits (PH and EH, r = 0.73), while lateral leaf expansion (LW) and tassel complexity (TBN) showed significant genetic independence. Using a mixed linear model (MLM) for genome-wide association studies (GWAS), we identified 21 significant SNP–trait associations, including distinct chromosomal clusters on chromosome 8 for EH and chromosome 7 for TBN. By integrating genomic intervals with tissue-specific expression profiling, 23 core candidate genes were prioritized. Notably, Zm00001d042528 (FAS1), involved in chromatin assembly, was implicated in modulating meristematic cell division for plant stature. Other key regulators included Zm00001d020537 (O5) and Zm00001d025360 (F-box protein), which were associated with reproductive organ development and leaf elongation, respectively. Conclusions: These results indicate that maize plant architecture is regulated by a modular genetic framework, with specific loci independently regulating canopy structure and source–sink components. It should be noted that the findings of this study are based solely on statistical models identifying significant associations between genetic loci and phenotypes; the biological regulatory functions of the candidate genes have not yet been experimentally validated. Nevertheless, this study provides new insights into the molecular mechanisms underlying maize morphogenesis and lays a solid theoretical foundation for molecular design breeding aimed at developing high-yielding varieties tolerant of high planting densities. Full article

Fusarium ear rot (FER) caused by Fusarium verticillioides is a major constraint on global maize production. The genetic basis of FER resistance is not yet fully understood, and the development of effective breeding strategies for improving FER resistance is still a critical priority. In the present study, a collection of 254 CIMMYT tropical maize lines genotyped with 955,690 high-quality SNPs was used to conduct genome-wide association studies (GWAS), complemented by QTL (quantitative trait locus) mapping in two recombinant inbred line populations. Additionally, genomic prediction (GP) exploring various statistical models and SNP selection schemes was implemented to optimize predictive accuracy for improving FER resistance. The broad-sense heritability estimates of FER resistance were 0.69–0.86 in the CML panel across six environments and 0.39–0.69 in the two RIL populations. At a p-value threshold of 2.61 × 10⁻⁷, GWAS identified 18 SNPs significantly associated with FER resistance across six environments, and in single environment analyses, their phenotypic variance explained (PVE) values ranged from 0.68 to 13.75%, with 13 SNPs exceeding a PVE of 5%. At a p-value threshold of 1 × 10⁻⁵, an additional 37 SNPs were detected, clustering within seven environmentally stable regions identified in at least two environments. Furthermore, 13 haplotype blocks exhibiting significant phenotypic differences were identified within these stable regions, with PVE values ranging from 2.39 to 15.24%, 9 of which exceeded 5%. QTL mapping in the two RIL populations revealed 27 moderate-effect QTLs at a LOD threshold of 2.5, including four detected repeatedly across environments, though only one QTL overlapped with the GWAS-identified region. Moderate genomic prediction accuracies of FER severity were achieved across models, with GBLUP and BayesB outperforming other models, and the prediction accuracies of these two models in the three populations were all around 0.5. Integrating the significant SNP set from genetic mapping results with a 100-SNP background set enhanced the stability of cross-population predictions. These results implied that FER resistance in tropical maize is controlled by multiple genomic regions with small-to-moderate genetic effects, whereas the consistency of genomic regions detected by GWAS and QTL mapping is low. Genomic prediction incorporating regions identified across different genetic backgrounds emerges as a promising tool for accelerating FER resistance breeding. Full article

Mixograph properties represent important quantitative traits that are controlled by multiple genes and influenced by environmental factors. In this study, we conducted quantitative trait locus (QTL) mapping for key Mixograph paraments using a recombinant inbred line (RIL) population derived from a cross between Yangxiaomai and Zhongyou 9507. Based on a high-density genetic map, six stable QTLs were identified on chromosomes 1A, 1B, and 1D across four environments, with individual phenotypic variation explained, ranging from 2.26 to 28.70%. Among these, QTh.ahau-1A, QMt/QPa.ahau-1B, and QTw.ahau-1D.1 are potentially novel loci. Furthermore, four functional Kompetitive Allele-Specific PCR (KASP) markers were developed based on tightly linked SNPs and validated in 110 advanced breeding lines, confirming their significant association with the target traits and utility for marker-assisted selection (MAS). Additionally, six candidate genes were predicted, which encoded proteins such as a hydroxyproline-rich glycoprotein, a CCCH-type zinc finger protein, protease, kinase, a phosphoglucan water dikinase, and a TRP-like family protein. Collectively, these findings provide valuable genetic loci, functional molecular markers, and candidate gene resources for improving wheat processing quality through MAS-based breeding. Full article

Severe southern soybean crinkle leaf disease (SSCLD) reduces soybean seed yield by approximately 40%. Identifying the genes that control SSCLD is crucial for breeding resistant varieties and elucidating the molecular mechanisms underlying SSCLD infection. In this study, recombinant inbred lines (RILs, n = 236) derived from a cross between Nannong1138-2 (NN1138-2) and Zhengxiaodou (ZXD) were used as experimental materials. A field trial employing a randomized block design was conducted in four environments across two locations, Nanning (2019–2021) and Du’an (2020) in Guangxi, to identify the disease severity grades of SSCLD in the field. QTLs controlling SSCLD were detected via a genetic map constructed using 3255 SLAF (specific locus amplified fragment) markers from the recombinant inbred lines. RT–qPCR was used to analyze candidate gene expression at major effect loci. The results revealed that eight SSCLD-associated QTLs were identified on chromosomes 3, 6, 12, and 17. Notably, the qw12-1 locus on chromosome 12 was detected across three developmental stages in three of the four environments, explaining 10.18–58.20% of the phenotypic variation. RT–qPCR analysis of 12 disease resistance-related genes within the qw12-1 interval revealed that GLYMA_12G233000 and GLYMA_12G239200 presented significantly higher expression in crinkled leaf lines than in normal leaf lines during the V5 (fifth trifoliolate stage), R2 (full bloom stage), and R6 (full seed stage) stages. These genes were prioritized as potential prime candidates for SSCLD resistance genes. This research provides foundational data for the fine mapping of qw12-1 and cloning SSCLD-related genes, advancing our understanding of the molecular mechanisms underlying SSCLD. Full article

Soybean (Glycine max L. Merr.) is a globally significant oilseed crop. The number of four-seeded pods in the lower part (FSPL) serves as a critical yield component under high-density planting. To date, numerous crop-specific traits have been investigated in multiple breeding studies of soybean; however, little attention has been paid to studies on FSPL. Hence, in this study, we investigated the genetic basis of FSPL using a recombinant inbred line population (RIL3613) across four environments. The segregated genetic mapping population was cultivated during the field experiments, and the collected phenotypic dataset of FSPL exhibited quantitative genetics and high broad-sense heritability (0.724), indicating stable genetic control. Further, we performed quantitative trait locus (QTL) mapping using raw means in each environment and identified 10 QTL, explaining phenotypic variations (PVE) ranging from 0.10% to 2.94%. Among the identified environmentally stable QTL, qFSPL-15-1 was consistently detected across all environments. Two candidate genes [Glyma.15G034100 (encoding lysophosphatidic acid acyltransferase 2) and Glyma.15G034200 (encoding an RNA-binding protein)] were predicted within the flanking genomic interval. The allele frequencies of haplotype combinations of Hap1: Pro2 + CDS1 for Glyma.15G034100 and Hap3: Pro3 + CDS1 for Glyma.15G034200 in wild soybeans (26.6–30.0%) were larger than improved cultivars (52.6–53.4%). We believe that our current findings elucidate the molecular mechanisms regulating lower-pod formation and provide precise genetic targets for marker-assisted selection in high-yield soybean breeding. Full article

Rapid Visco Analyzer (RVA) profile characteristics are important indicators of rice (Oryza sativa L.) eating quality. In this study, based on the high-density genetic linkage map constructed under the genetic background of Yuexianghzan (YXZ) and Shengbasimiao (SBSM), combined with the RVA profile characteristic data of recombinant inbred lines (RILs) grown in two environments, QTL scanning was performed using the ridge regression analysis method. A total of 59 QTLs associated with RVA profile characteristics were detected across 11 chromosomes in the two environments, with individual QTLs explaining 0.12% to 85.16% of the phenotypic variation. Moreover, 11 QTLs were repeatedly detected in two environments with large effects. The QTL located in the 1.44–1.85 Mb interval on chromosome 6 simultaneously controlled eight RVA profile characteristics and contained the cloned waxy (Wx) gene. Additionally, the intervals 20.58–20.70 Mb on chromosome 5 and 24.96–25.42 Mb on chromosome 8 were repeatedly mapped and influenced multiple RVA characteristics. Based on gene annotation information, a total of nine candidate genes (LOC_Os05g34730, LOC_Os05g34830, LOC_Os05g34854, LOC_Os06g03910, LOC_Os06g04200, LOC_Os06g42720, LOC_Os08g39830, LOC_Os08g39850, and LOC_Os08g39860) that directly or indirectly influence the starch synthesis pathway were identified. The results of this study lay a foundation for further map-based cloning of genes related to rice RVA profile characteristics and molecular design breeding. Full article

Plants adapt to abiotic stresses by modulating morphological, physiological, and biochemical processes, which constitute the fundamental mechanisms of stress tolerance. Rice is highly susceptible to drought stress at all developmental stages, leading to substantial reductions in growth and yield, signifying the urgent need to develop drought-tolerant rice genotypes. In this study, recombinant inbred lines (RILs) in rice with enhanced drought tolerance were developed through a cross between the high-yielding rice variety BRRI-28 and the commercial variety BINA-7, followed by successive selfing and phenotypic selection. The resulting lines were evaluated using integrated morphological, physiological, biochemical, and anatomical analyses under well-watered (WW) and drought conditions (DC). BRRIdhan-56, a known drought-tolerant variety, was included as a check genotype. Among the tested lines, RIL-3 exhibited superior agronomic performance under DC, including a significantly higher tiller number, plant height, and seed dry weight, and improved root attributes compared with its parental lines and, for several traits, exceeding those of BRRIdhan-56. Leaf rolling was absent in RIL-3 and the check variety until the 23rd day of drought stress, whereas other genotypes exhibited varying degrees of stress symptoms. Panicle exertion under DC was observed exclusively in RIL-3 and the check. Although all genotypes showed reductions in biomass, relative water content, and chlorophyll levels under DC, RIL-3 consistently maintained higher values than its parental lines and comparable or superior levels to the check variety. Notably, RIL-3 exhibited a distinctive physiological response characterized by sustained chlorophyll retention and low proline accumulation under severe drought, in contrast to the high proline levels observed in sensitive lines. A root anatomical analysis further revealed well-developed aerenchyma formation in RIL-3 following drought treatment, supporting its drought tolerance. Together, these results demonstrate that RIL-3 combines an enhanced drought tolerance with a stable agronomic and yield-related performance and a unique physiological trait profile under drought stress, highlighting its potential value as a promising genotype for drought-tolerance breeding programs. Full article

Background/Objectives: Sweetness is a key determinant of the eating quality of sweet corn, primarily governed by the soluble sugar content in kernels. The soluble sugar content decreases rapidly during the postharvest shelf life, which directly affects the flavor and quality. Relatively few studies have been conducted on the shelf life of sweet corn. Methods: An F₆ recombinant inbred line (RIL) population was constructed from two super sweet inbred lines with contrasting soluble sugar degradation rates: D174 (low degradation rate) and D179 (high degradation rate). Extreme phenotype pools were established using soluble sugar content as the target trait. Based on bulked segregant analysis sequencing, we identified chromosomal segments associated with postharvest soluble sugar reduction in sweet corn, annotated the gene information within these segments, and analyzed the functions of the annotated genes using the Gene Ontology and Genomes databases. Results: Results revealed three associated regions located at 44,205,775–45,290,843 bp on chromosome 4, 6,250,656–6,744,665 bp on chromosome 2, and 135,428,709–136,732,132 bp on chromosome 10. This interval contained 195 genes. Integrated analysis of gene expression, gene annotations, and quantitative real-time PCR indicated that Zm00001eb069070, which is highly expressed in kernels with a prolonged shelf life, might be a key candidate gene regulating soluble sugar degradation in sweet corn. Conclusions: This study provides valuable genetic resources for the improvement of favorable agronomic traits and the advancement of molecular breeding strategies for sweet corn. Full article

Drought is one of the major constraints to lentil production worldwide, making the development of drought-tolerant varieties essential for stable yields. Identifying genes and markers linked to drought tolerance is a crucial first step. We analyzed 90 recombinant inbred lines (RILs) derived from an interspecific cross between the drought-susceptible Lens culinaris cv. Alpo and the tolerant L. odemensis ILWL235 to investigate genomic regions associated with drought tolerance. Using 4163 high-quality SNP markers obtained through Genotyping-by-Sequencing (GBS), we constructed a linkage map showing seven groups corresponding to the lentil chromosomes. The map spans 786.82 cM and covers 3.46 G bp, representing approximately 88% of the lentil genome. To assess drought tolerance, RILs were subjected to water stress under greenhouse conditions by maintaining the soil moisture at a 40% field capacity (FC) in pots for 15 days, with the leaf relative water content (RWC) recorded every two days. Plants were phenotyped for yield, 100-seed weight, and seed number under both control and stress conditions. We identified 26 Quantitative Trait Loci (QTLs) strongly associated with drought tolerance traits and found putative candidate genes for most of them. Additional traits, including stem pigmentation, flower coloration, seed coat patterning, and seed ground color, were also mapped, and their genomic locations validated the accuracy of our linkage map. Full article

Carotenoid content is a key trait that defines the unique characteristics of foxtail millet varieties. Varieties with different levels of carotenoids often show distinct genetic features and nutritional profiles. However, the genetic basis of carotenoid content in foxtail millet remains mostly unknown. In this study, we explored the genetic basis of carotenoid content using a recombinant inbred line (RIL) population of 305 lines derived from two parental accessions, JG21 (high-carotenoid, 16.75 mg·kg⁻¹) and JG25 (low-carotenoid, 0.93 mg·kg⁻¹). The results showed that the RIL population exhibited continuous phenotypic variation and significant transgressive segregation for carotenoid components (lutein, zeaxanthin, β-cryptoxanthin) and kernel color (measured by b* value), with zeaxanthin reaching 8.47 mg·kg⁻¹, significantly surpassing the higher parent (3.44 mg·kg⁻¹) in 24DY. To ensure that enhancing this nutritional trait does not compromise grain yield, we analyzed its relationship with key agronomic traits, testing for pleiotropic trade-offs. Notably, carotenoid content showed no significant correlation with any of the 8 key agronomic traits (r ranged from −0.11 to 0.08, all p > 0.05), suggesting no apparent trade-off, although fine-mapping is needed to separate pleiotropy from tight linkage for concurrent improvement. Genetic modeling analysis revealed that carotenoid content is stably controlled by three major-gene pairs plus polygenes (MX3-AI-A model), with major-gene heritability of 96.65% and polygene heritability of 3.35%. Based on this framework, three elite RILs with >23% higher carotenoid and superior agronomic performance were identified and advanced to marker-assisted backcrossing. These results provide a clear genetic framework and immediate breeding resources for marker-assisted selection, enabling the development of high-yielding, carotenoid-enriched foxtail millet varieties without compromising agronomic value. Full article