In a study of DNA methylation changes in melatonin-deficient rice mutants, mutant plants showed premature leaf senescence during grain-filling and reduced grain yield. Melatonin deficiency led to transcriptional reprogramming, especially of genes involved in chlorophyll and carbon metabolism, redox regulation, and transcriptional regulation, during dark-induced leaf senescence. Hypomethylation of mCG and mCHG in the melatonin-deficient rice mutants was associated with the expression change of both protein-coding genes and transposable element-related genes. Changes in gene expression and DNA methylation in the melatonin-deficient mutants were compensated by exogenous application of melatonin. A decreased S-adenosyl-L-methionine level may have contributed to the DNA methylation variations in rice mutants of melatonin deficiency under dark conditions.

Stalk strength increases resistance to stalk lodging, which causes maize (Zea mays L.) production losses worldwide. The genetic mechanisms regulating stalk strength remain unclear. In this study, three stalk strength-related traits (rind penetrometer resistance, stalk crushing strength, and stalk bending strength) and four plant architecture traits (plant height, ear height, stem diameter, stem length) were measured in three field trials. Substantial phenotypic variation was detected for these traits. A genome-wide association study (GWAS) was conducted using general and mixed linear models and 372,331 single-nucleotide polymorphisms (SNPs). A total of 94 quantitative trait loci including 241 SNPs were detected. By combining the GWAS data with public gene expression data, 56 candidate genes within 50 kb of the significant SNPs were identified, including genes encoding flavonol synthase (GRMZM2G069298, ZmFLS2), nitrate reductase (GRMZM5G878558, ZmNR2), glucose-1-phosphate adenylyltransferase (GRMZM2G027955), and laccase (GRMZM2G447271). Resequencing GRMZM2G069298 and GRMZM5G878558 in all tested lines revealed respectively 47 and 2 variants associated with RPR. Comparison of the RPR of the zmnr2 EMS mutant and the wild-type plant under high- and low-nitrogen conditions verified the GRMZM5G878558 function. These findings may be useful for clarifying the genetic basis of stalk strength. The identified candidate genes and variants may be useful for the genetic improvement of maize lodging resistance.

Crown root traits, including crown root angle (CRA), diameter (CRD), and number (CRN), are major determining factors of root system architecture, which influences crop production. In maize, the genetic mechanisms determining crown root traits in the field are largely unknown. CRA, CRD, and CRN were evaluated in a recombinant inbred line population in three field trials. High phenotypic variation was observed for crown root traits, and all measured traits showed significant genotype–environment interactions. Single-environment (SEA) and multi-environment (MEA) quantitative trait locus (QTL) analyses were conducted for CRA, CRD, and CRN. Of 46 QTL detected by SEA, most explained less than 10% of the phenotypic variation, indicating that a large number of minor-effect QTL contributed to the genetic component of these traits. MEA detected 25 QTL associated with CRA, CRD, and CRN, and 2 and 1 QTL were identified with significant QTL-by-environment interaction effects for CRA and CRD, respectively. A total of 26.1% (12/46) of the QTL identified by SEA were also detected by MEA, with many being detected in more than one environment. These findings contribute to our understanding of the phenotypic and genotypic patterns of crown root traits in different environments. The identified environment-specific QTL and stable QTL may be used to improve root traits in maize breeding.

Seed moisture at harvest is a critical trait affecting maize quality and mechanized production, and is directly determined by the dehydration process after physiological maturity. However, the dynamic nature of seed dehydration leads to inaccurate evaluation of the dehydration process by conventional determination methods. Seed dry weight and fresh weight were recorded at 14 time points after pollination in a recombinant inbred line (RIL) population derived from two inbred lines with contrasting seed dehydration dynamics. The dehydration curves of RILs were determined by fitting trajectories of dry weight accumulation and dry weight/fresh weight ratio change based on a logistic model, allowing the estimation of eight characteristic parameters that can be used to describe dehydration features. Quantitative trait locus (QTL) mapping, taking these parameters as traits, was performed using multiple methods. Single-trait QTL mapping revealed 76 QTL associated with dehydration characteristic parameters, of which the phenotypic variation explained (PVE) was 1.03% to 15.24%. Multiple-environment QTL analysis revealed 21 related QTL with PVE ranging from 4.23% to 11.83%. Multiple-trait QTL analysis revealed 58 QTL, including 51 pleiotropic QTL. Combining these mapping results revealed 12 co-located QTL and the dehydration process of RILs was divided into three patterns with clear differences in dehydration features. These results not only deepen general understanding of the genetic characteristics of seed dehydration but also suggest that this approach can efficiently identify associated genetic loci in maize.