The ZmNAC100-ZmWAK3 transcriptional module enhances maize cold tolerance by coordinately enhancing antioxidant defense and improving photosynthetic efficiency. Low temperature is a major abiotic stress that constrains agricultural productivity by severely inhibiting crop growth and development, leading to substantial yield losses. As a chilling-sensitive crop, maize is particularly vulnerable to cold stress. Cold conditions induce excessive accumulation of reactive oxygen species in plants, disrupting photosynthetic performance, compromising antioxidant defense systems, and disturbing cellular ion homeostasis. In this study, we demonstrated that the maize wall-associated receptor kinase gene ZmWAK3 positively regulates the response to low temperature. Using overexpression and mutant lines, we found that ZmWAK3 overexpression enhanced chilling tolerance by improving ROS scavenging capacity and photosynthetic efficiency. In contrast, zmwak3 mutant exhibited a cold-sensitive phenotype. At the molecular level, combined evidence from yeast one-hybrid, dual-luciferase reporter, and chromatin immunoprecipitation assays confirmed that the transcription factor ZmNAC100 directly binds to the ZmWAK3 promoter and activates its transcription. Furthermore, silencing ZmNAC100 in maize not only reduced cold tolerance but also downregulated ZmWAK3 expression. Collectively, our results elucidate a low-temperature response pathway in maize mediated by the ZmNAC100-ZmWAK3 module, which enhances cold tolerance by increasing antioxidant enzyme activities, alleviating oxidative damage, and improving photosynthetic performance.

Temperate and tropical maize inbred lines achieve high-level resistance to southern corn rust through distinct ETI associated and PTI associated signaling networks, with the peroxidase gene PER1 functioning as a common positive regulator across both resistance types. Southern corn rust (SCR), caused by the fungus Puccinia polysora, is a devastating fungal disease that leads to significant yield losses in maize worldwide. This study employs an integrated multi-omics approach, combining phenotyping, transcriptomics, metabolomics, weighted gene co-expression network analysis (WGCNA), and gene silencing, to delineate the molecular mechanisms of SCR resistance in temperate (Temp_R, R241) and tropical (Tr_R, Nei50205) maize inbred lines. Both lines displayed stable, high-level resistance, with Tr_R exhibiting more rapid callose deposition and cell wall fortification. Multi-omics analysis revealed that both resistant lines share activation of jasmonic acid (JA) signaling as a common defense foundation. Temp_R showed a stronger reliance on JA signaling and an intracellular defense cascade mediated by ncRNA-EDR1-RPP13L3. In addition to the common JA foundation, Tr_R also activates pattern-triggered immunity (PTI) associated signatures via LRR-RLK/CRK40 kinases, which further potentiates cell wall reinforcement through phenylpropanoid metabolism. Furthermore, we identified the peroxidase gene PER1 as a common positive regulator of resistance in both lines. Our findings unveil both shared and distinct genetic pathways underlying SCR resistance and underscore the value of tropical germplasm in breeding for durable resistance.

As an important food crop worldwide, maize is frequently impacted by drought stress. It is of great significance to study its drought resistance genes and mechanisms, in which DNA methylation modification in the promoter region plays a key role in regulating gene expression and stress resistance. In this study, using PEG6000 and 5-azadC to treat different drought-tolerant maize inbred lines (drought-tolerant R99 and drought-sensitive Mo17), combined with transcriptomic analysis, identified the gene ZmGST2 as being related to drought resistance. Subsequently, the methylation changes in its promoter region were further analyzed. The results indicated that the expression level of ZmGST2 was closely related to the methylation status of its promoter region under drought stress. Specifically, in drought-resistant R99, a decrease in methylation (demethylation) occurred within the CpG island of the ZmGST2 promoter region after drought treatment, which facilitated the expression of this gene and thereby enhanced drought resistance in maize. However, in the drought-sensitive Mo17, this demethylation change did not occur, resulting in reduced drought resistance. Further phenotypic analysis revealed that overexpression of ZmGST2 could enhance the reactive oxygen species scavenging ability in maize roots, improve root growth, and significantly enhance drought resistance. Overall, this study provides both a new candidate gene and a novel approach for molecular breeding aimed at enhancing maize drought resistance.

Heat Shock Protein plays a vital role in maintaining protein homeostasis and protecting cells from stress stimulation. As one of the HSP40 proteins, DnaJ is a stress response protein widely existing in plant cells. The function and regulatory mechanism of ZmDnaJ, a novel chloroplast-localized type-III HSP40, in maize drought tolerance were characterized. Tissue-specific expression analysis showed that ZmDnaJ is highly expressed in the leaves, and is strongly drought-induced in maize seedlings. Overexpression of ZmDnaJ improved maize drought tolerance by enhancing stomatal closure and increasing ABA content to mediate photosynthesis. In contrast, the CRISPR-Cas9 knockout zmdnaj mutant showed lower relative water content and high sensitivity to drought stress. Moreover, Y2H, BiFC and Co-IP analyses revealed that ZmDnaJ interacts with an ABA synthesis-related protein ZmNCED6 to regulate drought tolerance. Similarly, ZmNCED6 overexpressed lines showed stronger oxidation resistance, enhanced photosynthetic rate, stomatal closure and ABA content, whilst the CRISPR-Cas9 knockout mutant showed sensitive to drought stress. More importantly, ZmDnaJ could regulate key drought tolerance genes (ZmPYL10, ZmPP2C44, ZmEREB65, ZmNCED4, ZmNCED6 and ZmABI5), involved in ABA signal transduction pathways. Taken together, our findings suggest that ZmDnaJ-ZmNCED6 module improves drought tolerance in maize.

Southern corn rust (SCR) caused by Puccinia polysora Underw. (P. polysora) poses a serious threat to global maize (Zea mays L.) production. This study used six maize inbred lines (DTMA-45, DTMA-50, R99, N110, P767 and 15B020F3) as materials to systematically explore the response mechanism of maize to southern corn rust through phenotype identification, transcriptome sequencing, functional enrichment analysis, gene co-expression network analysis, and quantitative RT-PCR experiments. Phenotypic analysis shows that DTMA-50, R99 and P767 have strong resistance, while DTMA-45, N110 and 15B020F3 are more sensitive. Transcriptome analysis identified a large number of differentially expressed genes (DEGs), whereas gene ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed that these genes are involved in multiple biological processes and metabolic pathways such as defense response, cytoskeleton organization, and plant hormone signaling transduction. Weighted gene co-expression network analysis (WGCNA) identified modules and key genes related to resistance, such as cell wall tissue related genes in the coral2 module and some genes in the ABC transporter and plant pathogen interaction pathways up-regulated in the resistant strain. Quantitative real-time PCR showed that ABCG11 (LOC100281487) and CCR1 (LOC103649447) genes are continuously up-regulated in the early stages of infection in the resistant line R99, which may play an important role in resisting fungal invasion. This study reveals the complex molecular mechanisms underlying maize’s response to southern corn rust, offering important theoretical support and potential targets for maize disease resistance breeding.

The drought stress-responsive transcription factor ZmbZIP38 interacts with ZmDnaJ to regulate maize drought tolerance through modulating ABA biosynthesis and signaling, stomatal closure and root growth under stress. Basic leucine zipper (bZIP) transcription factors (TFs) crucially regulate plant drought stress response. However, how bZIP TFs regulate maize drought tolerance remains elusive. Previously, we demonstrated that ZmDnaJ enhances maize drought tolerance by promoting ABA biosynthesis and stomatal closure. In this study, we have fished out ZmbZIP38 (by yeast one-hybrid analysis) as key interacting partner of ZmDnaJ, and elucidate its function in ZmDnaJ-mediated drought tolerance in maize. ZmDnaJ promoter analysis results showed that ZmbZIP38 directly targets ZmDnaJ by binding to ABRE motifs in the corresponding gene promoters. Overexpression of ZmbZIP38 significantly enhanced maize survival rate under drought stress, which was accompanied by expanded leaf area and higher stomatal closure. ZmbZIP38-overexpressing maize lines also showed enhanced ROS scavenging, reduced H2O2 and MDA accumulation, and up-regulated expression of antioxidant enzymes-associated genes. Moreover, ZmbZIP38-OE maize lines exhibited elevated ABA levels under drought stress, correlating with the up-regulated expression of ABA biosynthetic genes. Conversely, zmbzip38 knockdown mutants displayed reduced drought tolerance, evidenced by increased cell damage and decreased leaf area. Collectively, our findings demonstrate that ZmbZIP38 regulates maize seedling drought tolerance by modulating ABA biosynthesis and signaling, ROS scavenging and root growth, highlighting its potential role in abiotic stress response, and particularly enhancing maize drought tolerance.

ZmWAK3 negatively regulates drought tolerance in maize seedlings by modulating cell wall remodeling and stomatal dynamics, and is directly regulated by the ZmWRKY44 transcription factor. Drought, a significant abiotic stress affecting maize production in key growing regions, necessitates a deeper understanding of its regulatory mechanisms to develop drought-resistant varieties and ensure yield stability. WAKs are pivotal receptor kinases in cell wall signaling, mediating extracellular-to-intracellular communication and participating in diverse processes, including cell expansion, stress adaptation, and pathogen defense. However, the role of WAKs in the drought response remains poorly elucidated. Functional analysis of ZmWAK3 through overexpression and mutant lines has revealed its negative regulatory role in maize drought tolerance. It was found that ZmWAK3 reduces pectin content by increasing polygalacturonase activity, thereby promoting cell wall relaxation. Furthermore, ZmWAK3 was observed to regulate stomatal aperture. Additionally, we demonstrated that the transcription factor ZmWRKY44 directly activates ZmWAK3 expression by binding to a W-box cis-element within its promoter. Crucially, we identified a drought-associated InDel locus within ZmWAK3 and developed the functional marker ZmWAK3-177, which effectively distinguishes drought-tolerant alleles and serves as a practical tool for marker-assisted selection in breeding programs. Collectively, these results reveal a novel mechanism of ZmWAK3 in drought stress response and provide actionable genetic resources for improving maize drought resilience.

Map-based cloning of Zmccr3 for regulate SG and its molecular regulatory pathway was performed and validated. WGCNA, target genes/pathways during the process of seed dormancy formation were obtained. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect the grain yield and quality of grain in cereal and hybrid seed production. Although the benefits of studying SD and seed germination (SG) during seed development are well established, research into the genetic variation and molecular regulation of SD, particularly during the transition from SD to SG, remains very limited. In this study, bulked segregant analysis (BSA) and linkage analysis were used to map the QTL for the maize vp16 mutant of PHS. Using genetic and biological methods, the candidate gene was identified as Zmccr3, encoding cinnamoyl-CoA reductase 3 (ccr3), which is involved in the phenylalanine pathway of lignin metabolism and affects SG. Based on RNA-seq (RNA sequencing) at two stages of grain development with extreme PHS traits, a weighted gene coexpression network analysis (WGCNA) related to SD and SG formation was constructed, and ten target genes and three pathways during the transition from SD to SG were identified. Simultaneously, the Zmccr3 pathway was established and validated, involving upstream lipid metabolism, redox modification and degradation of cell wall oligosaccharides (as electrophilic compounds), regulation of GA signaling and intracellular ROS homeostasis, and downstream oxidation of cell wall lignin units and synthesis of phenolic compounds that affect endosperm weakening and cell wall loosening, ultimately regulating SG or SD. Therefore, we propose the Zmccr3 hypothesis to elucidate its possible functions. These findings have important theoretical and practical implications for understanding the genetic basis of PHS and SD in maize, increasing genetic resources and improving traits.

Plant-specific homeodomain-leucine zipper I (HD-Zip I) transcription factors (TFs) crucially regulate plant drought tolerance. However, their specific roles in maize (Zea mays L.) regulating drought tolerance remain largely unreported. Here, we screened a maize HD-Zip I TF family gene, ZmHB53, and clarified its role in drought stress. ZmHB53 overexpression maize plants exhibited sensitivity to abscisic acid (ABA), tolerant to polyethylene glycol (PEG 6000)-induced stress during germination, along with improved seedling drought resistance. Compared to the wild-type, ZmHB53 overexpression lines show higher water retention, biomass, and survival rates, and reduced water loss and stomatal size under drought, suggesting ZmHB53's role in drought adaptation. DNA affinity purification sequencing (DAP-Seq), yeast one hybrid, electrophoretic mobility shift assay (EMSA), and dual luciferase showed that ZmHB53 directly bound to and upregulated the expression of ABA receptor ZmPYL4. Meanwhile, transgenic plants overexpressing ZmPYL4 also exhibit ABA sensitivity and drought tolerance. The research results provide novel insights into the regulatory role of ZmHB53 and ZmPYL4 in enhancing maize's drought tolerance, establishing a foundation for future validation and potential application of ZmHB53 in strategies to improve maize resistance to drought.

Southern corn rust (SCR), caused by Puccinia polysora Underw (P. polysora), is a catastrophic disease affecting maize, leading to significant global yield losses. The disease manifests primarily as pustules on the upper surface of corn leaves, obscuring our understanding of its cellular heterogeneity, the maize's response to its infection and the underlying gene expression regulatory mechanisms. In this study, we dissected the heterogeneity of maize's response to P. polysora infection using single-cell RNA sequencing. We delineated cell-type-specific gene expression alterations in six leaf cell types, creating the inaugural single-cell atlas of a maize leaf under fungal assault. Crucially, by reconstructing cellular trajectories in susceptible line N110 and resistant line R99 during infection, we identified diverse regulatory programs that fortify R99's resistance across different leaf cell types. This research uncovers an immune-like state in R99 leaves, characterized by the expression of various fungi-induced genes in the absence of fungal infection, particularly in guard and epidermal cells. Our findings also highlight the role of the fungi-induced glycoside hydrolase family 18 chitinase 7 protein (ZmChit7) in conferring resistance to P. polysora. Collectively, our results shed light on the mechanisms of maize resistance to fungal pathogens through comparative single-cell transcriptomics, offering a valuable resource for pinpointing novel genes that bolster resistance to P. polysora.

Drought stress, a major abiotic stress, significantly affects wheat (Triticum aestivum L.) production globally. To identify genes and metabolic pathways crucial for responding to short-term drought stress, we conducted transcriptomic and metabolomic analyses of winter wheat cultivar Jimai 418 at four developmental stages: jointing (GS31), booting (GS45), anthesis (GS65), and 8 days after anthesis (DAA8). Transcriptomic analysis identified 14,232 differentially expressed genes (DEGs) under drought stress compared to the control. Specifically, 1387, 4573, 7380, and 892 DEGs were identified at the four developmental stages, respectively. Enriched pathways associated with these DEGs included plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling, galactose metabolism, and starch and sucrose metabolism. Totals of 222, 633, 358, and 38 differentially accumulated metabolites (DAMs) were identified at the four stages, respectively. Correlation analysis of both datasets revealed DEGs and DAMs associated with plant hormone signal transduction, arginine and proline metabolism, ABC transporters, and amino acid biosynthesis. These findings offer significant insights into Jimai 418’s molecular response to short-term drought stress. The identified DEGs, DAMs, and enriched pathways contribute to our understanding of wheat drought tolerance. This research will facilitate further investigations into drought tolerance mechanisms and guide the breeding of wheat varieties with enhanced drought resistance.

Drought is a main abiotic stress factor hindering plant growth, development, and crop productivity. Therefore, it is crucial to understand the mechanisms by which plants cope with drought stress. Here, the function of the maize peroxidase gene ZmPRX1 in drought stress tolerance was investigated by measurement of its expression in response to drought treatment both in a ZmPRX1 overexpression line and a mutant line. The higher root lignin accumulation and seedling survival rate of the overexpression line than that of the wild type or mutant support a role for ZmPRX1 in maize drought tolerance by regulating root development and lignification. Additionally, yeast one-hybrid, Dule luciferase and ChIP-qPCR assays showed that ZmPRX1 is negatively regulated by a nuclear-localized ZmWRKY86 transcription factor. The gene could potentially be used for breeding of drought-tolerant cultivars.

干旱严重影响玉米的产量和品质.钙依赖性蛋白激酶(Calcium-dependent protein kinase,CPK)是一种Ca2+结合蛋白,在植物非生物胁迫应答方面发挥重要作用.本研究对玉米37个ZmCPKs的染色体定位、系统进化、基因结构、保守结构域和理化性质进行了分析.其中,36个ZmCPK基因不均匀的分布在9条染色体上;通过系统进化分析将其分为4个亚组,同一亚组成员具有相似的基因结构和保守结构域;ZmCPKs启动子分析表明,ZmCPKs启动子区含有大量的逆境响应元件,包括MBS、DRE和ABRE等;qTeller数据库和转录组数据分析表明,ZmCPKs基因家族成员在营养生长和生殖生长期均有表达,其中,26个基因在干旱胁迫下表达量发生变化.综合启动子元件及转录组数据,共筛选出9个基因作为干旱响应候选基因.进一步qRT-PCR验证显示,这9个基因均受PEG诱导表达.本研究可为玉米耐旱性的遗传改良提供优异的基因资源.

Maize (Zea mays L.) is one of the major staple crops providing human food, animal feed, and raw material support for biofuel production. For its growth and development, maize requires essential macronutrients. In particular, nitrogen (N) plays an important role in determining the final yield and quality of a maize crop. However, the excessive application of N fertilizer is causing serious pollution of land area and water bodies. Therefore, cultivating high-yield and low-N-tolerant maize varieties is crucial for minimizing the nitrate pollution of land and water bodies. Here, based on the analysis of the maize leaf transcriptome and proteome at the grain filling stage, we identified 3957 differentially expressed genes (DEGs) and 329 differentially abundant proteins (DAPs) from the two maize hybrids contrasting in N stress tolerance (low-N-tolerant XY335 and low-N-sensitive HN138) and screened four sets of low-N-responsive genes and proteins through Venn diagram analysis. We identified 761 DEGs (253 up- and 508 down-regulated) specific to XY335, whereas 259 DEGs (198 up- and 61 down-regulated) were specific to HN138, and 59 DEGs (41 up- and 18 down-regulated) were shared between the two cultivars under low-N-stress conditions. Meanwhile, among the low-N-responsive DAPs, thirty were unique to XY335, thirty were specific to HN138, and three DAPs were shared between the two cultivars under low-N treatment. Key among those genes/proteins were leucine-rich repeat protein, DEAD-box ATP-dependent RNA helicase family proteins, copper transport protein, and photosynthesis-related proteins. These genes/proteins were involved in the MAPK signaling pathway, regulating membrane lipid peroxidation, and photosynthesis. Our results may suggest that XY335 better tolerates low-N stress than HN138, possibly through robust low-N-stress sensing and signaling, amplified protein phosphorylation and stress response, and increased photosynthesis efficiency, as well as the down-regulation of 'lavish' or redundant proteins to minimize N demand. Additionally, we screened glutathione transferase 42 (ZmGST42) and performed physiological and biochemical characterizations of the wild-type (B73) and gst42 mutant at the seedling stage. Resultantly, the wild-type exhibited stronger tolerance to low N than the mutant line. Our findings provide a better understanding of the molecular mechanisms underlying low-N tolerance during the maize grain filling stage and reveal key candidate genes for low-N-tolerance breeding in maize.

Global crop production and food-and-nutrition security are severely threatened by climate change-induced effects, including compound environmental stresses and dwindling crop genetic diversity. Developing climate-resilient crops, despite saddled with its own challenges, is touted as the most effective and sustainable way to adapt agriculture to climate change and guarantee future food-and-nutrition security. In this review-cum-perspective, we highlight key bottlenecks to engineering crop climate resilience before synthesizing existing opportunities for attaining the same. We advance that achieving crop climate resilience hinges on our capacity to (i) uncover the fundamental underpinnings of plant responses to compound stresses, (ii) harness the wild-side of crop species, (iii) innovate with novel breeding methods, (iv) couple the latest genomics and biotechnological advances, (v) modify current agronomic practices, and (vi) foster multi-disciplinary collaborations. Priority targets/avenues for research include improving crop photosynthesis capacity, enhancing aquaporin activity and water-use efficiency, root system architecture adjustment, plant-associated microbiomes exploration, and metabolic pathway engineering.

探讨不同种类有机肥料对糯玉米鲜果穗产量与品质的影响,可为有机肥在糯玉米生产中的应用提供理论指导.本研究以斯达糯 41 为试验材料,研究了不同种类有机肥对糯玉米鲜果穗产量与品质的影响.结果表明:与全量施氮 T2 和减量施氮 T3 处理相比,减量施氮配施有机肥 T4、T5 和 T6 处理使得鲜果穗产量显著增加,T4、T5 和 T6 处理显著降低了籽粒内聚性,增加了籽粒咀嚼性;减量施氮配施蚯蚓粪有机肥 T5 处理下鲜食果穗品尝评分为 90.7 分,品质评定等级达到 1 级,减量施氮配施蚯蚓粪有机肥T5 处理下可以实现糯玉米鲜果穗产量和品质的协同提高.

探讨复合肥与微生物菌剂配施对糯玉米产量和品质的影响,为微生物菌剂在糯玉米生产中的应用提供理论指导.以京科糯 768 和农科糯 336 为试验材料,设单施复合肥(T1)、复合肥和微生物菌剂配施(T2)、复合肥减施 10%和微生物菌剂配施(T3)、复合肥减施 20%和微生物菌剂配施(T4)、复合肥减施 30%和微生物菌剂配施(T5)、单施微生物菌剂(T6)6 个处理,研究复合肥与微生物菌剂配施对糯玉米产量和品质的影响.结果表明,与T1 相比,京科糯 768 和农科糯 336 的鲜穗产量在T2 处理下分别提高 3%和 5%、T3 处理下分别提高 1.4%和 2%;T3 处理下 2 个品种外观和品尝品质评分均高于T1 处理;与T1 处理相比,T3 处理下京科糯 768 籽粒可溶性总糖和总淀粉含量分别提高 51.38%和 9.43%,农科糯 336 籽粒可溶性总糖和总淀粉含量分别提高 25.54%和 12.73%.综合考虑产量和品质,复合肥减施 10%和微生物菌剂配施处理(T3)是最佳的配施模式.

以 15 个糯玉米品种为试验材料,研究不同糯玉米品种在同一地区种植的产量、食味品质和营养品质的差异.结果表明,①产量各性状在品种间变幅差异较大,籽粒总淀粉含量在品质性状间变幅最大,其他籽粒品质性状的变幅较小,均处在 0.04～5.20 之间.②食味品质总分与外观、风味、柔嫩性呈显著正相关,蔗糖含量与可溶性糖含量、总淀粉含量呈显著正相关,总淀粉含量与可溶性糖含量呈显著正相关,与可溶性蛋白质含量呈显著负相关,其余性状间均表现为相关不显著;籽粒弹性与籽粒硬度 2 相关不显著,其余性状间均表现出显著相关或极显著相关.③京科糯 2000 的食味品质总分、籽粒总淀粉含量和籽粒弹性均最高,斯达糯 41 和京科糯 768 的食味品质总分、籽粒可溶性糖和蔗糖含量也较高.基于不同品种综合品质性状的表现,京科糯 2000、京科糯 768 和斯达糯 41可以推荐作为冀东地区的优选糯玉米品种.

气候变化导致的全球变暖和水资源短缺造成了紧迫的全球粮食安全挑战。据统计，全世界因干旱造成的作物减产是最严重的，超过其他因素造成减产的总和，是最为严重的灾害之一。玉米（Zea mays L.）作为世界上重要的粮食及经济作物，干旱是制约玉米产量的关键因素之一。所以，了解玉米的抗旱机制，挖掘玉米中的抗旱基因，进一步利用抗旱基因来稳定及增加玉米产量是非常重要的。本实验室前期通过RNA-seq挖掘到了一个响应干旱胁迫的愈创木酚过氧化物酶1（ZmPRX1）基因。ZmPRX1基因含有3个外显子和2个内含子、编码一条长为367个氨基酸的多肽，CDS长1104 bp，亚细胞定位结果显示该基因编码的蛋白定位于细胞壁。干旱条件下，ZmPRX1基因的过表达增加了拟南芥幼苗叶片中抗氧化酶（SOD和POD）的活性，降低了拟南芥细胞膜的损伤，从而减轻了干旱所带来的的伤害，提高了拟南芥的抗旱性。研究结果对进一步了解玉米的抗旱机制提供了遗传资源。

Seventeen PHS-QTLs and candidate genes were obtained, including eleven major loci, three under multiple environments and two with co-localization by the other mapping methods; The functions of three candidate genes were validated using mutants; nine target proteins and five networks were filtered by joint analysis of GWAS and WGCNA. Seed dormancy (SD) and pre-harvest sprouting (PHS) affect yield, as well as grain and hybrid quality in seed production. Therefore, identification of genetic and regulatory pathways underlying PHS and SD is key to gene function analysis, allelic variation mining and genetic improvement. In this study, 78,360 SNPs by SLAF-seq of 230 maize chromosome segment introgression lines (ILs), PHS under five environments were used to conduct GWAS (genome wide association study) (a threshold of 1/n), and seventeen unreported PHS QTLs were obtained, including eleven QTLs with PVE > 10