Search

Lead (Pb) is one of the most toxic heavy metal pollutants, which can penetrate to plant cells via root absorption and thus cause irreversible damages to the human body through the food chain. To identify the hub gene responsible for Pb tolerance in maize, we performed a trait-associated co-expression network analysis at a genome-wide level, using two maize lines with contrasting Pb tolerances. Finally, ZmNRAMP6 that encodes a metal transporter was identified as the hub gene among the Pb tolerance-associated co-expression module. Heterologous expression of ZmNRAMP6 in yeast verified its role in Pb transport. Combined Arabidopsis overexpression and maize mutant analysis suggested that ZmNRAMP6 conferred plant sensitivity to Pb stress by transporting Pb ion from the roots to shoots. Knockout of ZmNRAMP6 caused Pb retention in the roots and activation of the antioxidant enzyme system, resulting in an increased Pb tolerance in maize. An integration of yeast one-hybrid and dual-luciferase reporter assay uncovered that ZmNRAMP6 was negatively regulated by a known Pb tolerance-related transcript factor ZmbZIP54. Different from the other known NRAMP genes, ZmNRAMP6 acted as a Pb transporter from the roots to shoots and environment. Collectively, knockout of ZmNRAMP6 will aid in the bioremediation of contaminated soil and food safety guarantee of forage and grain corn.

The study of yield traits can reveal the genetic architecture of grain yield for improving maize production. In this study, an association panel comprising 362 inbred lines and a recombinant inbred line population derived from X178 × 9782 were used to identify candidate genes for nine yield traits. High-priority overlap (HPO) genes, which are genes prioritized in a genome-wide association study (GWAS), were investigated using coexpression networks. The GWAS identified 51 environmentally stable SNPs in two environments and 36 pleiotropic SNPs, including three SNPs with both attributes. Seven hotspots containing 41 trait-associated SNPs were identified on six chromosomes by permutation. Pyramiding of superior alleles showed a highly positive effect on all traits, and the phenotypic values of ear diameter and ear weight consistently corresponded with the number of superior alleles in tropical and temperate germplasm. A total of 61 HPO genes were detected after trait-associated SNPs were combined with the coexpression networks. Linkage mapping identified 16 environmentally stable and 16 pleiotropic QTL. Seven SNPs that were located in QTL intervals were assigned as consensus SNPs for the yield traits. Among the candidate genes predicted by our study, some genes were confirmed to function in seed development. The gene Zm00001d016656 encoding a serine/threonine protein kinase was associated with five different traits across multiple environments. Some genes were uniquely expressed in specific tissues and at certain stages of seed development. These findings will provide genetic information and resources for molecular breeding of maize grain yield.

MADS26 affecting maize seed germination was identified by GWAS and transcriptomics. Gene-based association analyses revealed three variations within MADS26 regulating seed germination traits. Overexpressed MADS26 in Arabidopsis improved seed germination. Seed germination ability is extremely important for maize production. Exploring the genetic control of seed germination ability is useful for improving maize yield. In this study, a genome-wide association study (GWAS) was conducted to excavate the significant SNPs involved in seed germination ability based on an association panel consisting of 300 lines. A total of 11 SNPs and 75 candidate genes were significantly associated with the seed germination traits. In addition, we constructed 24 transcriptome libraries from maize seeds at four germination stages using two inbred lines with contrasting germination rates. In total, 15,865 differentially expressed genes were induced during seed germination. Integrating the results of GWAS and transcriptome analysis uncovered four prioritized genes underlying maize seed germination. The variations located in the promoter of Zm00001d017932, a MADS-transcription factor 26 (MADS26), were verified to affect the seed germination, and the haplotype TAT was determined as a favorable haplotype for high-germination capability. MADS26 was induced to express by ethylene during seed germination in maize and overexpressing MADS26 increased the seed germination ability in Arabidopsis. These findings will contribute to understanding of the genetic and molecular mechanisms on seed germination and the genetic modification of seed germination ability in maize.

The ability of immature maize (Zea mays) embryos to form embryonic calluses (ECs) is highly genotype dependent, which limits transgenic breeding development in maize. Here, we report the association map-based cloning of ZmSAUR15 using an association panel (AP) consisting of 309 inbred lines with diverse formation abilities for ECs. We demonstrated that ZmSAUR15, which encodes a small auxin-upregulated RNA, acts as a negative effector in maize EC induction. Polymorphisms in the ZmSAUR15 promoter that influence the expression of ZmSAUR15 transcripts modulate the EC induction capacity in maize. ZmSAUR15 is involved in indole-3-acetic acid biosynthesis and cell division in immature embryo-derived callus. The ability of immature embryos to induce EC formation can be improved by the knockout of ZmSAUR15, which consequently increases the callus regeneration efficiency. Our study provides new insights into overcoming the genotypic limitations associated with EC formation and improving genetic transformation in maize.

The heavy metals lead and cadmium have become important pollutants in the environment, which exert negative effects on plant morphology, growth and photosynthesis. It is particularly significant to uncover the genetic loci and the causal genes for lead and cadmium tolerance in plants. This study used an IBM Syn10 DH population to identify the quantitative trait loci (QTL) controlling maize seedling tolerance to lead and cadmium by linkage mapping. The broad-sense heritability of these seedling traits ranged from 65.8–97.3% and 32.0–98.8% under control (CK) and treatment (T) conditions, respectively. A total of 53 and 64 QTL were detected under CK and T conditions, respectively. Moreover, 42 QTL were identified using lead and cadmium tolerance coefficient (LCTC). Among these QTL, five and two major QTL that explained > 10% of phenotypic variation were identified under T condition and using LCTC, respectively. Furthermore, eight QTL were simultaneously identified by T and LCTC, explaining 5.23% to 9.21% of the phenotypic variations. Within these major and common QTL responsible for the combined heavy metal tolerance, four candidate genes (Zm00001d048759, Zm00001d004689, Zm00001d004843, Zm00001d033527) were previously reported to correlate with heavy metal transport and tolerance. These findings will contribute to functional gene identification and molecular marker-assisted breeding for improving heavy metal tolerance in maize.

Using GWAS and QTL mapping identified 100 QTL and 138 SNPs, which control yield-related traits in maize. The candidate gene GRMZM2G098557 was further validated to regulate ear row number by using a segregation population. Understanding the genetic basis of yield-related traits contributes to the improvement of grain yield in maize. This study used an inter-mated B73 × Mo17 (IBM) Syn10 doubled-haploid (DH) population and an association panel to identify the genetic loci responsible for nine yield-related traits in maize. Using quantitative trait loci (QTL) mapping, 100 QTL influencing these traits were detected across different environments in the IBM Syn10 DH population, with 25 co-detected in multiple environments. Using a genome-wide association study (GWAS), 138 single-nucleotide polymorphisms (SNPs) were identified as correlated with these traits (P

Root system architecture (RSA) contributes to nitrogen (N) uptake and utilization in maize. In this study, a germplasm enhancement of maize double haploid population of 226 lines genotyped with 61,634 SNPs was used to investigate the genetic basis of RSA under two N levels using a genome-wide association study (GWAS). GLM + PCA, FarmCPU, and MLM models were utilized to balance false positives and false negatives. In total, 33 and 51 significant SNP-trait associations were detected under high and low N conditions, respectively. Under high N, SNP S9_2483543 was detected by all models. Linkage disequilibrium (LD) regions of some SNPs overlapped with the intervals of QTL for RSA and N response that were detected in previous studies. In particular, several known genes, Rtcs, Rtcl, Rtcl, and Ms44, were located in the LD regions of S1_9992325, S9_151726472, S9_154381179, and S4_197073985, respectively. Among the candidate genes identified by this study, GRMZM2G139811, GRMZM2G314898, GRMZM2G054050, GRMZM2G173682, GRMZM2G470914, GRMZM2G462325, GRMZM2G416184, and GRMZM2G064302 were involved in seedling, seed, and root system development or N metabolism in Arabidopsis or rice. The markers identified in this study can be used for marker-assisted selection of RSA traits to improve nitrogen use efficiency in maize breeding, and the candidate genes will contribute to further understanding of the genetic basis of RSA under diverse N conditions. Keywords: Maize, Root system architecture, Different nitrogen conditions, Genome-wide association study, Genetic basis

Soil salinization is an important factor threatening the yield and quality of maize. Ca2+ plays a considerable role in regulating plant growth under salt stress. Herein, we examined the shoot Ca2+ concentrations, root Ca2+ concentrations, and transport coefficients of seedlings in an association panel composed of 305 maize inbred lines under normal and salt conditions. A genome-wide association study was conducted by using the investigated phenotypes and 46,408 single-nucleotide polymorphisms of the panel. As a result, 53 significant SNPs were specifically detected under salt treatment, and 544 genes were identified in the linkage disequilibrium regions of these SNPs. According to the expression data of the 544 genes, we carried out a weighted coexpression network analysis. Combining the enrichment analyses and functional annotations, four hub genes (GRMZM2G051032, GRMZM2G004314, GRMZM2G421669, and GRMZM2G123314) were finally determined, which were then used to evaluate the genetic variation effects by gene-based association analysis. Only GRMZM2G123314, which encodes a pentatricopeptide repeat protein, was significantly associated with Ca2+ transport and the haplotype G-CT was identified as the superior haplotype. Our study brings novel insights into the genetic and molecular mechanisms of salt stress response and contributes to the development of salt-tolerant varieties in maize. This article is protected by copyright. All rights reserved.

As one of the major crops, maize (Zea mays L.) is mainly distributed in tropical and temperate regions. However, with the changes of the environments, chilling stress has become a significantly abiotic stress affecting seed germination and thus the reproductive and biomass accumulation of maize. Herein, we investigated five seed germination-related phenotypes among 300 inbred lines under low-temperature condition (10 °C). By combining 43,943 single nucleotide polymorphisms (SNPs), a total of 15 significant (P -6) SNPs were identified to correlate with seed germination under cold stress based on the FarmCPU model in GWAS, among which three loci were repeatedly associated with multiple traits. Ten gene models were closely linked to these three variations, among which Zm00001d010454, Zm00001d010458, Zm00001d010459, and Zm00001d050021 were further verified by candidate gene association study and expression pattern analysis. Importantly, these candidate genes were previously reported to involve plant tolerance to chilling stress and other abiotic stress. Our findings contribute to the understanding of the genetic and molecular mechanisms underlying chilling germination in maize.

Microelements are necessary for plant growth and development, they control key processes of physiological metabolism. Herein, we evaluated three accumulation-related performances for each of the four microelements (Fe, Zn, Cu, and Mn) among 305 inbred maize lines. Quantification of these microelements in maize roots and shoots revealed abundant phenotypic variations in the association panel, with the variation coefficients ranging from 0.31 to 0.76. Principal component analysis (PCA) of the three related traits (concentration in root, concentration in shoot, and transport coefficient) showed that PC1 and PC2 explained >95% of phenotypic variations for each element. The scores of PC1 and PC2 were thereby used for a genome-wide association study by combining 44,134 SNPs of this panel. A total of 27, 1, 5, and 3 SNPs were significantly (P 0.8) to these SNPs. Of them, GRMZM2G142870, GRMZM2G045531, and GRMZM2G143512 were individually annotated as ABC transporter C family member 14, zinc transporter 3, and heavy metal ATPase10. A candidate gene association analysis further verified that GRMZM2G142870 and GRMZM2G045531 affect Zn and Mn accumulations, respectively. Evaluation of contrasting allele ratios in elite lines indicated that the majority of the alleles correlating with higher Zn or Cu had not been utilized in maize breeding. Integration of more "higher-accumulation" alleles in the elite lines will be practical for improving Zn and Cu accumulations in maize. Our findings contribute to genetic revelation and molecular marker-assisted selection of microelement accumulations in maize.

Maize tassel architecture is a complex quantitative trait that is significantly correlated with biomass yield and grain yield. The present study evaluated the major trait of maize tassel architecture, namely, tassel branch number (TBN), in an association population of 359 inbred lines and an IBM Syn 10 population of 273 doubled haploid lines across three environments. Approximately 43,958 high-quality single nucleotide polymorphisms were utilized to detect significant QTNs associated with TBN based on new multi-locus genome-wide association study methods. There were 30, 38, 73, 40, 47, and 53 QTNs associated with tassel architecture that were detected using the FastmrEMMA, FastmrMLM, EM-BLASSO, mrMLM, pkWMEB, and pLARmEB models, respectively. Among these QTNs, 51 were co-identified by at least two of these methods. In addition, 12 QTNs were consistently detected across multiple environments. Furthermore, 19 QTLs distributed on chromosomes 1, 2, 3, 4, 6, and 7 were detected in 3 environments and the BLUP model based on 6618 bin markers, which explained 3.64-10.96% of the observed phenotypic variations in TBN. Of these, three QTLs were co-detected in two environments. One QTN associated with TBN was localized to one QTL. Approximately 55 candidate genes were detected by common QTNs and LD criteria. One candidate gene, Zm00001d016615, was identified as a putative target of the RA1 gene. Meanwhile, RA1 was previously validated to plays an important role in tassel development. In addition, the newly identified candidate genes Zm00001d003939, Zm00001d030212, Zm00001d011189, and Zm00001d042794 have been reported to involve in a spikelet meristem identity module. The findings of the present study improve our understanding of the genetic basis of tassel architecture in maize.

Background Maize is one of the primary crops of genetic manipulation, which provides an excellent means of promoting stress resistance and increasing yield. However, the differences in induction and regeneration capacity of embryonic callus (EC) among various genotypes result in genotypic dependence in genetic transformation. Results In this study, embryonic calli of two maize inbred lines with strong redifferentiation capacity and two lines with weak redifferentiation capability were separately subjected to transcriptome sequencing analysis during the early redifferentiation stages (stage I, 1–3 d; stage II, 4–6 d; stage III, 7–9 d) along with their corresponding controls. A total of ~ 654.72 million cDNA clean reads were yielded, and 62.64%~ 69.21% clean reads were mapped to the reference genome for each library. In comparison with the control, the numbers of differentially expressed genes (DEGs) for the four inbred lines identified in the three stages ranged from 1694 to 7193. By analyzing the common and specific DEGs of the four materials, we found that there were 321 upregulated genes and 386 downregulated genes identified in the high-regeneration lines (141 and DH40), whereas 611 upregulated genes and 500 downregulated genes were specifically expressed in the low-regeneration lines (ZYDH381–1 and DH3732). Analysis of the DEG expression patterns indicated a sharp change at stage I in both the high- and low-regeneration lines, which suggested that stage I constitutes a crucial period for EC regeneration. Notably, the specific common DEGs of 141 and DH40 were mainly associated with photosynthesis, porphyrin and chlorophyll metabolism, ribosomes, and plant hormone signal transduction. In contrast, the DEGs in ZYDH381–1 and DH3732 were mainly related to taurine and hypotaurine metabolism, nitrogen metabolism, fatty acid elongation, starch and sucrose metabolism, phenylpropanoid biosynthesis, and plant circadian rhythm. More importantly, WOX genes, which have an ancestral role in embryo development in seed plants and promote the regeneration of transformed calli, were specifically upregulated in the two high-regeneration lines. Conclusions Our research contributes to the elucidation of molecular regulation during early redifferentiation in the maize embryonic callus.

SUMMARY Inorganic phosphorus (Pi) is an essential element in numerous metabolic reactions and signaling pathways, but the molecular details of these pathways remain largely unknown. In this study, metabolite profiles of maize (Zea mays L.) leaves and roots were compared between six low‐Pi‐sensitive lines and six low‐Pi‐tolerant lines under Pi‐sufficient and Pi‐deficient conditions to identify pathways and genes associated with the low‐Pi stress response. Results showed that under Pi deprivation the concentrations of nucleic acids, organic acids and sugars were increased, but that the concentrations of phosphorylated metabolites, certain amino acids, lipid metabolites and nitrogenous compounds were decreased. The levels of secondary metabolites involved in plant immune reactions, including benzoxazinoids and flavonoids, were significantly different in plants grown under Pi‐deficient conditions. Among them, the 11 most stable metabolites showed significant differences under low‐ and normal‐Pi conditions based on the coefficient of variation (CV). Isoleucine and alanine were the most stable metabolites for the identification of Pi‐sensitive and Pi‐resistant maize inbred lines. With the significant correlation between morphological traits and metabolites, five low‐Pi‐responding consensus genes associated with morphological traits and simultaneously involved in metabolic pathways were mined by combining metabolites profiles and genome‐wide association study (GWAS). The consensus genes induced by Pi deficiency in maize seedlings were also validated by reverse‐transcription quantitative polymerase chain reaction (RT‐qPCR). Moreover, these genes were further validated in a recombinant inbred line (RIL) population, in which the glucose‐6‐phosphate‐1‐epimerase encoding gene mediated yield and correlated traits to phosphorus availability. Together, our results provide a framework for understanding the metabolic processes underlying Pi‐deficient responses and give multiple insights into improving the efficiency of Pi use in maize., Significance statement Metabolite profiling and GWAS were applied to reveal maize low‐Pi response mechanisms.

Heretofore, little is known about the mechanism underlying the genotype-dependence of embryonic callus (EC) induction, which has severely inhibited the development of maize genetic engineering. Here, we report the genome sequence and annotation of a maize inbred line with high EC induction ratio, A188, which is assembled from single-molecule sequencing and optical genome mapping. We assembled a 2,210 Mb genome with a scaffold N50 size of 11.61 million bases (Mb), compared to those of 9.73 Mb for B73 and 10.2 Mb for Mo17. Comparative analysis revealed that ∼30% of the predicted A188 genes had large structural variations to B73, Mo17 and W22 genomes, which caused considerable protein divergence and might lead to phenotypic variations between the four inbred lines. Combining our new A188 genome, previously reported QTLs and RNA sequencing data, we reveal 8 large structural variation genes and 4 differentially expressed genes playing potential roles in EC induction.HighlightOur manuscript presents a high-quality reference genome of the inbred line A188, and provides new insights into candidate genes underlying maize embryonic callus induction and other maize agronomic traits.

Two hub genes GRMZM2G075104 and GRMZM2G333183 involved in salt tolerance were identified by GWAS and WGCNA. Furthermore, they were verified to affect salt tolerance by candidate gene association analysis. Salt stress influences maize growth and development. To decode the genetic basis and hub genes controlling salt tolerance is a meaningful exploration for cultivating salt-tolerant maize varieties. Herein, we used an association panel consisting of 305 lines to identify the genetic loci responsible for Na+- and K+-related traits in maize seedlings. Under the salt stress, seven significant single nucleotide polymorphisms were identified using a genome-wide association study, and 120 genes were obtained by scanning the linkage disequilibrium regions of these loci. According to the transcriptome data of the above 120 genes under salinity treatment, we conducted a weighted gene co-expression network analysis. Combined the gene annotations, two SNaC/SKC (shoot Na+ content/shoot K+ content)-associated genes GRMZM2G075104 and GRMZM2G333183 were finally identified as the hub genes involved in salt tolerance. Subsequently, these two genes were verified to affect salt tolerance of maize seedlings by candidate gene association analysis. Haplotypes TTGTCCG-CT and CTT were determined as favorable/salt-tolerance haplotypes for GRMZM2G075104 and GRMZM2G333183, respectively. These findings provide novel insights into genetic architectures underlying maize salt tolerance and contribute to the cultivation of salt-tolerant varieties in maize.

Ear tip-barrenness (ETB) phenotype threatens crop yield, because it reduces the kernel number per ear. The genetic basis of ETB in maize remains largely unknown. Herein, a genome-wide association study (GWAS) and quantitative trait loci (QTL) mapping were jointly applied to identify the significant genetic loci interrelated with ETB. Six significant SNPs were detected at a stringent P-value threshold (1.95 × 10-6 ). Additionally, four environment-stable SNPs were co-detected across a single environment and best linear unbiased prediction (BLUP) model at a less stringent P-value threshold (1 × 10-4 ). The above 10 SNPs were closely linked to 6 candidate genes, which mainly involved seed development, photosynthesis and ethylene response. Moreover, the ratio of superior allele at each significant SNP ranged from 0 to 83.33% in 30 investigated maize elite lines. QTL mapping identified 14 QTL with phenotypic variation explained (PVE) ranging from 3.64 to 7.09%, of which one QTL (qETB2-1) was repeatedly identified in two environments. Combined analysis of GWAS and QTL mapping showed that one SNP (PZE-102175229, chromosome 2: 217 66 Mb) was located in the QTL (qETB2-2, chromosome 2: 215 90-217 82 Mb). Eighteen gene models situated in the linkage disequilibrium (LD) region of the co-localized SNP were further used to evaluate their correlation with ETB by candidate gene association analysis. Two superior haplotypes and two superior alleles were detected among 74 lines for Zm00001d007195, Zm00001d007197 and Zm00001d007201. These results provide more information for clarifying the molecular mechanism of ETB and for speeding up the genetic improvement of maize varieties.

Large phenotypic variations in the lead (Pb) concentration were observed in grains and leaves of maize plants. A further understanding of inheritance of Pb accumulation may facilitate improvement of low-Pb-accumulating cultivars in maize. A genome-wide association study was conducted in a population of 269 maize accessions with 43,737 single-nucleotide polymorphisms (SNPs). The Pb concentrations in leaves and kernels of 269 accessions were collected in pot-culture and field experiments in years of 2015 and 2016. Significant differences in Pb accumulation were found among individuals under different environments. Using the structure and kinship model, a total of 21 SNPs significantly associated with the Pb accumulation were identified with P

P1B-type ATPases, known as heavy metal ATPases (HMAs), play an important role in the control of cadmium (Cd) accumulation in plants. In this study, a total of 12 ZmHMA genes were identified in the maize genome and particularly classified into six clusters based on their phylogenetic relationship and motif compositions. Furthermore, the expression patterns of different ZmHMA genes varied with developmental stages, and were tissue specific under normal conditions. ZmHMA2 and ZmHMA3 genes exhibited significant up-regulation under Cd treatment. Eventually, the association analysis between 103 inbred lines and alleles in ZmHMA2 and ZmHMA3 revealed that one insertion–deletion (InDel) in the intron from ZmHMA2 was associated with leaf Cd concentration under low Cd condition at the seedling stage. Twenty polymorphisms in ZmHMA3 were significantly associated with leaf Cd concentration under various Cd levels at seedling and maturing stages. Five single nucleotide polymorphisms (SNPs) and two InDels of these significantly associated polymorphic loci from ZmHMA3 caused the amino acid substitutions and insertion or deletion events. Importantly, the proteins encoded by ZmHMA2 and ZmHMA3 genes were located in the plasma membrane. This comprehensive analysis will provide an important theoretical basis for future functional verification of ZmHMA genes to unravel the mechanisms of Cd accumulation in leaves of maize. Additionally, the favorable alleles in ZmHMA3 will lay a foundation for the marker-assisted selection of low Cd accumulation in maize.

Kernel weight in a unit volume is referred to as kernel test weight (KTW) that directly reflects maize (Zea mays L.) grain quality. In this study, an inter-mated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population and an association panel were used to identify loci responsible for KTW of maize across multiple environments. A total of 18 significant KTW-related single-nucleotide polymorphisms (SNPs) were identified using genome-wide association study (GWAS); they were closely linked to 12 candidate genes. In the IBM Syn10 DH population, linkage analysis detected 19 common quantitative trait loci (QTL), five of which were repeatedly detected among multiple environments. Several verified genes that regulate maize seed development were found in the confidence intervals of the mapped QTL and the LD regions of GWAS, such as ZmYUC1, BAP2, ZmTCRR-1, dek36 and ZmSWEET4c. Combined QTL mapping and GWAS identified one significant SNP that was co-identified in the both populations. Based on the co-localized SNP across the both populations, 17 candidate genes were identified. Of them, Zm00001d044075, Zm00001d044086, and Zm00001d044081 were further identified by candidate gene association study for KTW. Zm00001d044081 encodes homeobox-leucine zipper protein ATHB-4, which has been demonstrated to control apical embryo development in Arabidopsis. Our findings provided insights into the mechanism underlying maize KTW and contributed to the application of molecular-assisted selection of high KTW breeding in maize.

Summary Kernel size‐related traits are the most direct traits correlating with grain yield. The genetic basis of three kernel traits of maize, kernel length (KL), kernel width (KW) and kernel thickness (KT), was investigated in an association panel and a biparental population. A total of 21 single nucleotide polymorphisms (SNPs) were detected to be most significantly (P

Stalk lodging severely limits the grain yield of maize (Zea mays L.). Mechanical stalk strength can be reflected by the traits of stalk diameter (SD), stalk bending strength (SBS), and lodging rind penetrometer resistance (RPR). To determine the genetic basis of maize stalk lodging, quantitative trait loci (QTLs) were mapped for these three traits using the IBM Syn10 DH population in three environments. The results indicated that there were strong genetic correlations among the three traits, and the analyses of phenotypic variations for SD, SBS, and RPR across the three environments showed high broad-sense heritability (0.6843, 0.5175, and 0.7379, respectively). In total, 44 significant QTLs were identified control the above traits across the 3 environments. A total of 14, 14, and 16 QTLs were identified for SD, SBS, and RPR across single-environment mapping, respectively. Notably, ten QTLs were stably expressed across multiple-environments, including two QTLs for SD, three for SBS, and five for RPR. Three major QTLs each accounting for over 10% of the phenotypic variation were qSD6-2 (10.03%), qSD8-2 (13.73%), and qSBS1-2 (11.89%). Comprehensive analysis of all QTLs in this study revealed that 5 QTL clusters including 12 QTLs were located on chromosomes 1, 3, 7, and 8, respectively. Among these 44 QTLs, 9 harbored 13 stalk lodging-associated SNPs that were detected by our recently published work, with 1 SNP successfully validated in the IBM Syn10 DH population. These chromosomal regions will be useful for marker-assisted selection and fine mapping of stalk lodging-related traits in maize.

Salt stress affects crop yield by limiting growth and delaying development. In this study, we constructed 16 transcriptome libraries from maize seedling roots using two maize lines, with contrasting salt tolerance, that were exposed to salt stress for 0, 6, 18 and 36 h. In total, 6,584 differential expression genes (DEGs; 3,669 upregulated, 2,915 downregulated) were induced in the salt-sensitive line and 6,419 DEGs (3,876 upregulated, 2,543 downregulated) were induced in the salt-tolerant line. Several DEGs common to both lines were enriched in the ABA signaling pathway, which was presumed to coordinate the process of maize salt response. A total of 459 DEGs were specifically induced in the salt-tolerant line and represented candidate genes responsible for high salt-tolerance. Expression pattern analysis for these DEGs indicated that the period between 0 and 6 h was a crucial period for the rapid response of the tolerant genes under salt stress. Among these DEGs, several genes, Aux/IAA, SAUR, and CBL-interacting kinase have been reported to regulate salt tolerance. In addition, the transcription factors WRKY, bZIP and MYB acted as regulators in the salt-responsive regulatory network of maize roots. Our findings will contribute to understanding of the mechanism on salt response and provide references for functional gene revelation in plants.

In this study, a maize inbred line with a strong capacity to induce embryonic callus, 18-599R, was used to analyze the transcription factors expressed during embryonic callus formation. A total of 1180 transcription factors were found to be expressed during three key stages of callus induction. Of these, compared with control, 361, 346 and 328 transcription factors were significantly downregulated during stages I, II and III, respectively. In contrast, 355, 372 and 401 transcription factors (TFs) were upregulated during the respective stages. We constructed a transcription factor-mediated regulatory network and found that plant hormone signal transduction was the pathway most significantly enriched among TFs. This pathway includes 48 TFs regulating cell enlargement, cell differentiation, cell division and cell dedifferentiation via the response to plant hormones. Through real-time polymerase chain reaction (PCR) and degradome sequencing, we identified 23 transcription factors that are regulated by miRNA. Through further analysis, ZmMYB138, a member of the MYB transcription factor family localized in the nucleus, was verified to promote embryonic callus formation in the maize embryo through GA signal transduction.

The regenerative capacity of the embryonic callus, a complex quantitative trait, is one of the main limiting factors for maize transformation. This trait was decomposed into five traits, namely, green callus rate (GCR), callus differentiating rate (CDR), callus plantlet number (CPN), callus rooting rate (CRR), and callus browning rate (CBR). To dissect the genetic foundation of maize transformation, in this study multi-locus genome-wide association studies (GWAS) for the five traits were performed in a population of 144 inbred lines genotyped with 43,427 SNPs. Using the phenotypic values in three environments and best linear unbiased prediction (BLUP) values, as a result, a total of 127, 56, 160, and 130 significant quantitative trait nucleotides (QTNs) were identified by mrMLM, FASTmrEMMA, ISIS EM-BLASSO, and pLARmEB, respectively. Of these QTNs, 63 QTNs were commonly detected, including 15 across multiple environments and 58 across multiple methods. Allele distribution analysis showed that the proportion of superior alleles for 36 QTNs was

Stalk lodging resistance, which is mainly measured by stem diameter (SD), stalk bending strength (SBS), and rind penetrometer resistance (RPR) in maize, seriously affects the yield and quality of maize (Zea mays L.). To dissect its genetic architecture, in this study multi-locus genome-wide association studies for stalk lodging resistance-related traits were conducted in a population of 257 inbred lines, with tropical, subtropical, and temperate backgrounds, genotyped with 48,193 high-quality single nucleotide polymorphisms. The analyses of phenotypic variations for the above traits in three environments showed high broad-sense heritability (0.679, 0.720, and 0.854, respectively). In total, 423 significant Quantitative Trait Nucleotides (QTNs) were identified by mrMLM, FASTmrEMMA, ISIS EM-BLASSO, and pLARmEB methods to be associated with the above traits. Among these QTNs, 29, 34, and 48 were commonly detected by multiple methods or across multiple environments to be related to SD, SBS, and RPR, respectively. The superior allele analyses in 30 elite lines showed that only eight lines contained more than 50% of the superior alleles, indicating that stalk lodging resistance can be improved by the integration of more superior alleles. Among sixty-three candidate genes of the consistently expressed QTNs, GRMZM5G856734 and GRMZM2G116885, encoding membrane steroid-binding protein 1 and cyclin-dependent kinase inhibitor 1, respectively, possibly inhibit cell elongation and division, which regulates lodging resistance. Our results provide the further understanding of the genetic foundation of maize lodging resistance.

Background Accumulation of cadmium (Cd) in maize (Zea mays L.) poses a significant risk to human health as it is ingested via the food chain. A genome-wide association study (GWAS) was conducted in a population of 269 maize accessions with 43,737 single nucleotide polymorphisms (SNPs) to identify candidate genes and favorable alleles for controlling Cd accumulation in maize. Results When grown in contaminated soil, accessions varied significantly in leaf Cd concentration at both the seeding and maturing stages with phenotypic variation and the coefficient of variation all above 48%. The co-localized region between SYN27837 (147,034,650 bp) and SYN36598 (168,551,327 bp) on chromosome 2 was associated with leaf Cd under three soil conditions varying in Cd content in 2015 and 2016. The significant SNP (SYN25051) at position 161,275,547 could explained 27.1% of the phenotype variation. Through QTL mapping using the IBMSyn10 double haploid (DH) population, we validated the existence of a major QTL identified by GWAS; qLCd2 could explain the 39.8% average phenotype variation across the experiments. Expression of GRMZM2G175576 encoding a cadmium/zinc-transporting ATPase underlying the QTL was significantly increased in roots, stems and leaves of B73, a low Cd accumulation line in response to Cd stress. Conclusions Our findings provide new insights into the genetic control of Cd accumulation and could aid rapid development of maize genotypes with low-Cd accumulation by manipulation of the favorable alleles. Electronic supplementary material The online version of this article (doi: 10.1186/s12864-017-4395-x) contains supplementary material, which is available to authorized users.

The heavy metal cadmium (Cd), acts as a widespread environmental contaminant, which has shown to adversely affect human health, food safety and ecosystem safety in recent years. However, research on how plant respond to various kinds of heavy metal stress is scarcely reported, especially for understanding of complex molecular regulatory mechanisms and elucidating the gene networks of plant respond to Cd stress. Here, transcriptomic changes during Mo17 and B73 seedlings development responsive to Cd pollution were investigated and comparative RNAseq-based approach in both genotypes were performed. 115 differential expression genes (DEGs) with significant alteration in expression were found co-modulated in both genotypes during the maize seedling development; of those, most of DGEs were found comprised of stress and defense responses proteins, transporters, as well as transcription factors, such as thaumatin-like protein, ZmOPR2 and ZmOPR5. More interestingly, genotype-specific transcriptional factors changes induced by Cd stress were found contributed to the regulatory mechanism of Cd sensitivity in both different genotypes. Moreover, 12 co-expression modules associated with specific biological processes or pathways (M1 to M12) were identified by consensus co-expression network. These results will expand our understanding of complex molecular mechanism of response and defense to Cd exposure in maize seedling roots.

MicroRNAs (miRNAs) are a family of small non-coding RNAs that, in most cases, negatively regulate gene expression at the post-transcriptional level. Plant miRNAs have been implicated in developmental processes and adaptation to environmental stress including biotic and abiotic stresses. Here, we report a comprehensive analysis of miRNAs and associated target genes under banded leaf and sheath blight (BLSB) stress caused by R. solani in maize. Eight differentially expressed miRNAs were randomly selected from deep sequencing results and validated by qRT-PCR together with their putative target genes, most of which are transcription factors as well as metabolic genes involved in auxin signaling. The results revealed that majorities of the analyzed miRNAs show an inverse correlation with their corresponding predicted target genes. In addition, a putative regulatory network of miRNAs-mRNAs responsive to R. solani was constructed. This study provides insight into the regulatory functions of miRNAs, thereby expanding our knowledge of the molecular mechanisms of pathogen resistance.

The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutant analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development.

Pb can damage the physiological function of human organs by entering the human body via food-chain enrichment. Revealing the mechanisms of maize tolerance to Pb is critical for preventing this. In this study, a Pb-tolerant maize inbred line, 178, was used to analyse transcription factors (TFs) expressed under Pb stress based on RNA sequencing data. A total of 464 genes expressed in control check (CK) or Pb treatment samples were annotated as TFs. Among them, 262 differentially expressed transcription factors (DETs) were identified that responded to Pb treatment. Furthermore, the DETs were classified into 4 classes according to their expression patterns, and 17, 12 and 2 DETs were significantly annotated to plant hormone signal transduction, basal transcription factors and base excision repair, respectively. Seventeen DETs were found to participate in the plant hormone signal transduction pathway, where basic leucine zippers (bZIPs) were the most significantly enriched TFs, with 12 members involved. We further obtained 5 Arabidopsis transfer DNA (T-DNA) mutants for 6 of the maize bZIPs, among which the mutants atbzip20 and atbzip47, representing ZmbZIP54 and ZmbZIP107, showed obviously inhibited growth of roots and above-ground parts, compared with wild type. Five highly Pb-tolerant and 5 highly Pb-sensitive in maize lines were subjected to DNA polymorphism and expression level analysis of ZmbZIP54 and ZmbZIP107. The results suggested that differences in bZIPs expression partially accounted for the differences in Pb-tolerance among the maize lines. Our results contribute to the understanding of the molecular regulation mechanisms of TFs in maize under Pb stress.

Background Maize (Zea mays) is an important model crop for transgenic studies. However, genetic transformation of maize requires embryonic calli derived from immature embryo, and the impact of utilizing tissue culture methods on the maize epigenome is poorly understood. Here, we generated whole-genome MeDIP-seq data examining DNA methylation in dedifferentiated and normal immature maize embryos. Results We observed that most of the dedifferentiated embryos exhibited a methylation increase compared to normal embryos. Increased methylation at promoters was associated with down-regulated protein-coding gene expression; however, the correlation was not strong. Analysis of the callus and immature embryos indicated that the methylation increase was induced during induction of embryonic callus, suggesting phenotypic consequences may be caused by perturbations in genomic DNA methylation levels. The correlation between the 21-24nt small RNAs and DNA methylation regions were investigated but only a statistically significant correlation for 24nt small RNAs was observed. Conclusions These data extend the significance of epigenetic changes during maize embryo callus formation, and the methylation changes might explain some of the observed embryonic callus variation in callus formation. Electronic supplementary material The online version of this article (doi:10.1186/s12870-017-1055-x) contains supplementary material, which is available to authorized users.

The induction efficiency of maize embryonic callus is highly dependent on the genotype, and only a few lines possess a high capacity for callus formation. Although certain genes and pathways have been reported to contribute to the regulation of callus induction, to the best of our knowledge, the functions of the small interfering RNAs (siRNAs) involved in this process remain unknown. In this study, we identified 861 differentially expressed siRNAs and 576 target genes in the callus induction process. These target genes were classified into 3 clusters, and their functions involve controlling metalloexopeptidase activity, catalase activity, transcription regulation, and O-methyltransferase activity. In addition, certain genes related to auxin transport and stem cell or meristem development (e.g., PLT5-like, ARF15, SAUR-like, FAS1-like, Fea3, SCL5, and Zmwox2A) were regulated by the differentially expressed siRNAs. Moreover, zma-siR004119-2 directly cleaves the 5' UTR of Homeobox-transcription factor 25, which further leads to the down-regulation of its expression. Twelve 24-nt-siRNAs led to the hyper-methylation of GRMZM2G013465, which further decreases its expression. These results suggest that differentially expressed siRNAs regulate callus formation by controlling the expression of their target genes.

Phosphorus (P) is one of the three primary macronutrients that are required in large amounts for plant growth and development. To better understand molecular mechanism of maize and identify relevant genes in response to phosphorus deficiency, we used Solexa/Illumina's digital gene expression (DGE) technology to investigate six genome-wide expression profiles of seedling roots of the low-P tolerant maize inbred line 178. DGE studies were conducted at 6, 24 and 72 h under both phosphorus deficient and sufficient conditions. Approximately 3.93 million raw reads for each sample were sequenced and 6 816 genes exhibited significant levels of differential expressions in at least one of three time points in response to P starvation. The number of genes with increased expression increased over time from 6 to 24 h, whereas genes with decreased expression were more abundant at 72 h, suggesting a gradual response process for P deficiency at different stages. Gene annotations illustrated that most of differentially expressed genes (DEGs) are involved in different cellular and molecular processes such as environmental adaptation and carbohydrate metabolism. The expression of some known genes identified in other plants, such as those involved in root architecture, P metabolism and transport were found to be altered at least two folds, indicating that the mechanisms of molecular and morphological adaptation to P starvation are conserved in plants. This study provides insight into the general molecular mechanisms underlying plant adaptation to low-P stress and thus may facilitate molecular breeding for improving P utilization in maize.

Given the important roles of miRNAs in post-transcriptional gene regulation, identification of differentially expressed miRNAs will facilitate the elucidation of molecular mechanisms underlying kernel development. In this study, we constructed a small RNA library to comprehensively represent the full complement of individual small RNAs and to characterize miRNA expression profiles in pooled ears of maize ( Zea mays L.) at 10, 15, 20, 22, 25 and 30 days after pollination (DAP). At least 21 miRNAs were differentially expressed. The differential expression of three of these miRNAs, i.e., miR528a, miR167a and miR160b, at each stage was verified by qRT-PCR. The results indicated that these miRNAs might be involved in kernel development. In addition, the predicted functions of target genes indicated that most of the target genes are involved in signal transduction and cell communication pathways, particularly the auxin signaling pathway. The expression of candidate germination-associated miRNAs was analyzed by hybridization to a maize genome microarray, and revealed differential expression of genes involved in plant hormone signaling pathways. This finding suggests that phytohormones play a critical role in the development of maize kernels. We found that in combination with other miRNAs, miR528a regulated a putative laccase, a Ring-H2 zinc finger protein and a MADS box-like protein, whereas miR167a and miR160b regulated multiple target genes, including ARF (auxin response factor), a member of the B3 transcription factor family. All three miRNAs are important for ear germination, development and physiology. The small RNA transcriptomes and mRNA obtained in this study will help us gain a better understanding of the expression and function of small RNAs in the development of maize kernel.

Ear rot, caused by Fusarium verticillioides (FV), is a destructive disease of maize as it reduces grain yield and increases risks of mycotoxin production, thus endangering livestock. To identify genes differentially expressed during FV infection, four cDNA libraries were constructed for suppression subtractive hybridization using RNA isolated from bracts of an FV-resistant inbred maize line, Bt-1, as well as an FV-susceptible maize inbred line, Ye478. A total of 145 clones were obtained following reverse dot-blot hybridization, and these were sequenced from these libraries. Similarity analysis revealed that of these genes, 93 were unique, including 68 of known function, 24 of unknown function, and a single novel gene. Most genes of known function were predominantly involved in plant defense such as cell defense, transcription regulation, signal transduction, and metabolism. Expression profiles of eight representative genes, using semiquantitative reverse transcription-polymerase chain reaction, confirmed that differential gene regulation during FV infection was involved. These findings suggested that these differentially expressed genes might be involved in FV defense responses in maize.

Lead (Pb) has become one of the most abundant heavy metal pollutants of the environment. With its large biomass, maize could be an important object for studying the phytoremediation of Pb-contaminated soil. In our previous research, we screened 19 inbred lines of maize for Pb concentration, and line 178 was identified to be a hyperaccumulator for Pb in both the roots and aboveground parts. To identify important genes and metabolic pathways related to Pb accumulation and tolerance, line 178 was underwent genome expression profile under Pb stress and a control (CK). A total of approximately 11 million cDNA tags were sequenced and 4 665 539 and 4 936 038 clean tags were obtained from the libraries of the test and CK, respectively. In comparison to CK, 2379 and 1832 genes were identified up- or downregulated, respectively, more than fivefolds under Pb stress. Interestingly, all the genes were related to cellular processes and signaling, information storage and processing or metabolism functions. Particularly, the genes involved in posttranslational modification, protein turnover and chaperones; signal transduction, carbohydrate transport and metabolism; and lipid transport and metabolism significantly changed under the treatment. In addition, seven pathways including ribosome, photosynthesis, and carbon fixation were affected significantly, with 118, 12, 34, 21, 18, 72 and 43 differentially expressed genes involved. The significant upregulation of the ribosome pathway may reveal an important secret for Pb tolerance of line 178. And the sharp increase of laccase transcripts and metal ion transporters were suggested to account in part for Pb hyperaccumulation in the line.

MicroRNAs (miRNAs) are a class of small, non-coding regulatory RNAs that regulate gene expression by guiding target mRNA cleavage or translational inhibition in plants and animals. In this study, a small RNA library was constructed to identify conserved miRNAs as well as novel miRNAs in maize seedling roots under low level phosphorus stress. Twelve miRNAs were identified by high throughput sequencing of the library and subsequent analysis, two belong to conserved miRNA families (miRNA399b and miRNA156), and the remaining ten are novel and one of latter is conserved in gramineous species. Based on sequence homology, we predicted 125 potential target genes of these miRNAs and then expression patterns of 7 miRNAs were validated by semi-RT-PCR analysis. MiRNA399b, Zma-miR3, and their target genes (Zmpt1 and Zmpt2) were analyzed by real-time PCR. It is shown that both miRNA399b and Zma-miR3 are induced by low phosphorus stress and regulated by their target genes (Zmpt1 and Zmpt2). Moreover, Zma-miR3, regulated by two maize inorganic phosphate transporters as a newly identified miRNAs, would likely be directly involved in phosphate homeostasis, so was miRNA399b in Arabidopsis and rice. These results indicate that both conserved and maize-specific miRNAs play important roles in stress responses and other physiological processes correlated with phosphate starvation, regulated by their target genes. Identification of these differentially expressed miRNAs will facilitate us to uncover the molecular mechanisms underlying the progression of maize seedling roots development under low level phosphorus stress. Electronic supplementary material The online version of this article (doi:10.1007/s11033-012-1661-5) contains supplementary material, which is available to authorized users.

Background To safeguard the food supply for the growing human population, it is important to understand and exploit the genetic basis of quantitative traits. Next-generation sequencing technology performs advantageously and effectively in genetic mapping and genome analysis of diverse genetic resources. Hence, we combined re-sequencing technology and a bin map strategy to construct an ultra-high-density bin map with thousands of bin markers to precisely map a quantitative trait locus. Results In this study, we generated a linkage map containing 1,151,856 high quality SNPs between Mo17 and B73, which were verified in the maize intermated B73 × Mo17 (IBM) Syn10 population. This resource is an excellent complement to existing maize genetic maps available in an online database (iPlant, http://data.maizecode.org/maize/qtl/syn10/). Moreover, in this population combined with the IBM Syn4 RIL population, we detected 135 QTLs for flowering time and plant height traits across the two populations. Eighteen known functional genes and twenty-five candidate genes for flowering time and plant height trait were fine-mapped into a 2.21–4.96 Mb interval. Map expansion and segregation distortion were also analyzed, and evidence for inadvertent selection of early flowering time in the process of mapping population development was observed. Furthermore, an updated integrated map with 1,151,856 high-quality SNPs, 2,916 traditional markers and 6,618 bin markers was constructed. The data were deposited into the iPlant Discovery Environment (DE), which provides a fundamental resource of genetic data for the maize genetic research community. Conclusions Our findings provide basic essential genetic data for the maize genetic research community. An updated IBM Syn10 population and a reliable, verified high-quality SNP set between Mo17 and B73 will aid in future molecular breeding efforts. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2242-5) contains supplementary material, which is available to authorized users.

As introns are vulnerable to changes such as insertions and deletions when exposed to various evolutionary forces, they constitute a repository for developing genetic markers based on intron length polymorphisms (ILP). This study developed a set of genetic markers that use the potential intron length polymorphism in resistance gene analogs (RGAs) in Zea mays. By searching the genome of Zea mays B73 for the homologs of 73 R genes which have already been identified in plants, we found 861 RGAs, 632 of which have at least one intron that can serve as putative markers targeting the intron length polymorphism in RGAs (RGA-ILP). We developed 1972 candidate markers via electronic PCR (e-PCR) with primer pairs designed in each pair of exonic regions that flank an intron. Furthermore, the performance of RGA-ILP among four maize inbred lines (Huangzao4, B73, Mo17, and Dan340) was evaluated with 69 pairs of randomly selected primers. Of them, 46.4% showed bands that had discriminating length polymorphism, and between any two of the inbred lines the proportion of polymorphism ranged from 23.2 to 31.9%. To make it convenient to use these markers for those interested in molecular breeding of disease-resistant maize, we provide all related information in a web-based database named MaizeRGA, which is available at http://www.sicau.edu.cn/web/yms/rga/maizeRGA.html.

MethyLight is a sodium-bisulfite-dependent, quantitative, fluorescence-based, real-time PCR strategy that is used to detect and quantify DNA methylation in genomic DNA. High-throughput MethyLight allows the rapid and sensitive detection of very low frequencies of hypermethylated alleles in populations of alternated individuals. The high sensitivity and specificity of MethyLight can be applied not only to make it uniquely suited disease clinical but also quantitatively assessed of these low-frequency methylation events. Owing to its full of advantages of simple procedure, high efficiency and high sensitivity, MethyLight provides a powerful approach for clinical examination, Gene expression analysis, SNP analysis and allele analysis. Coupled with other techniques, MethyLight can be used immediately in identifying allelic alterations in genes exhibiting expressions correlating with phenotypes, Locating an allelic series of induced point mutations in genes of interest. The development of this technique should considerably enhance our ability to rapidly and accurately generate epigenetic profiles of samples.

Different stressed conditions impair plant growth and further, cause great loss of crop yield and even lead to lose production completely. Increasing resistance/tolerance of crops under stressed conditions is a major goal of numerous plant breeders, and many elegant works are focusing on this area to uncover these complicated mechanisms underlying it. However, the traditional strategies including physiological and biochemical methods, as well as studies on a few genes, can not well understand the overall biological mechanism. Microarray analysis opens a door to uncover these cryptic mechanisms, and has the ability of detecting gene transcription and regulation at genomic level in different plant tissues. And works in association with related methods of proteomics and metabolomics. Therefore, it is possible to locate genes in certain key metabolism pathways. Through these procedures, it is also possible to look for critical genes in the pathway and to well understand the molecular mechanism of resistance/tolerance. These results can be as a guidance for increasing the resistance/tolerance of stressed conditions using biotechnology methods in future. This paper mainly focused on and discussed the advances of microarray analysis of stressed conditions-related genes in plants.

Biotic and abiotic stresses influence plant growth and cause great loss to crop yield. In the long course of evo-lution, plants have developed intricate biological mechanism to resist stressed conditions. Under various stressed conditions, not only the protein-coding genes, but also the non-protein-coding genes were induced for response. More and more re-searches showed that the transcripts of these non-protein-coding genes played important role in regulation of gene expres-sion. miRNA is one of the groups in these no-coding regulatory small RNAs. Recent findings showed that in order to resist the biotic and abiotic stresses, expression of microRNA (miRNA) genes will be induced and their transcripts (miRNAs) can regulate gene expression by guiding target mRNA cleavage or translation inhibition. This paper focused on the advances of plant miRNAs research in stressed conditions, especially induced expression of miRNA and target gene regulation and its role on adaptation under stressed conditions. Then, the methods of miRNA researches in stressed environments are dis-cussed.