The oil content of maize kernels is essential to determine its nutritional and economic value. A multiparent population (MPP) consisting of five recombinant inbred line (RIL) subpopulations was developed to elucidate the genetic basis of the total oil content (TOC) in maize. The MPP used the subtropical maize inbred lines CML312 and CML384, along with the tropical maize inbred lines CML395, YML46, and YML32 as the female parents, and Ye107 as the male parent. A genome-wide association study (GWAS) was performed using 429 RILs of the multiparent population across three environments, employing 584,847 high-quality single nucleotide polymorphisms (SNPs). Furthermore, linkage analysis was performed in the five subpopulations to identify quantitative trait loci (QTL) linked to TOC in maize. Through QTL mapping and GWAS, 18 QTLs and 60 SNPs that were significantly associated with TOC were identified. Two novel candidate genes, Zm00001d029550 and Zm00001d029551, related to TOC in maize and located on chromosome 1 were reported, which have not been previously reported. These genes are involved in biosynthesis, lipid signal transduction, plant development and metabolism, and stress responses, potentially influencing maize TOC. Haplotype analysis of Zm00001d029550 and Zm00001d029551 revealed that Hap3 could be considered a superior haplotype for increasing TOC in maize. A co-located SNP (SNP-75791466) on chromosome 1, located 5648 bp and 11,951 bp downstream of the candidate genes Zm00001d029550 and Zm00001d029551, respectively, was found to be expressed in various maize tissues. The highest expression was observed in embryos after pollination, indicating that embryos are the main tissue for oil accumulation in maize. This study provides a theoretical basis for understanding the genetic mechanisms underlying maize TOC and developing high-quality, high-oil maize varieties.

Kernel row number (KRN) is one of the key traits that significantly affect maize yield and productivity. Therefore, investigating the candidate genes and their functions in regulating KRN provides a theoretical basis and practical direction for genetic improvement in maize breeding, which is vital for increasing maize yield and understanding domestication. In this study, three recombinant inbred line (RIL) populations were developed using the parental lines AN20, YML1218, CM395, and Ye107, resulting in a multiparent population comprising a total of 490 F9 RILs. Phenotypic evaluation of the RILs for KRN was performed in three distinct environments. The heritability estimates of the RILs ranged from 81.40% to 84.16%. Genotyping-by-sequencing (GBS) of RILs identified 569,529 high-quality single nucleotide polymorphisms (SNPs). Combined genome-wide association study (GWAS) and linkage analyses revealed 120 SNPs and 22 quantitative trait loci (QTLs) which were significantly associated with KRN in maize. Furthermore, two novel candidate genes, Zm00001d042733 and Zm00001d042735, regulating KRN in maize were identified, which were located in close proximity to the significant SNP3-178,487,003 and overlapping the interval of QTL qKRN3-1. Zm00001d042733 encodes ubiquitin carboxyl-terminal hydrolase and Zm00001d042735 encodes the Arabidopsis Tóxicos en Levadura family of proteins. This study identified novel candidate loci and established a theoretical foundation for further functional validation of candidate genes. These findings deepen our comprehension of the genetic mechanisms that underpin KRN and offer potential applications of KRN-related strategies in developing maize varieties with higher yield.

Common rust (CR), caused by Puccina sorghi, is a major foliar disease in maize that leads to quality deterioration and yield losses. To dissect the genetic architecture of CR resistance in maize, this study utilized the susceptible temperate inbred line Ye107 as the male parent crossed with three resistant tropical maize inbred lines (CML312, D39, and Y32) to generate 627 F₇ recombinant inbred lines (RILs), with the aim of identifying maize disease-resistant loci and candidate genes for common rust. Phenotypic data showed good segregation between resistance and susceptibility, with varying degrees of resistance observed across different subpopulations. Significant genotype effects and genotype × environment interactions were observed, with heritability ranging from 85.7% to 92.2%. Linkage and genome-wide association analyses across the three environments identified 20 QTLs and 62 significant SNPs. Among these, seven major QTLs explained 66% of the phenotypic variance. Comparison with six SNPs repeatedly identified across different environments revealed overlap between qRUST3-3 and Snp-203,116,453, and Snp-204,202,469. Haplotype analysis indicated two different haplotypes for CR resistance for both the SNPs. Based on LD decay plots, three co-located candidate genes, Zm00001d043536, Zm00001d043566, and Zm00001d043569, were identified within 20 kb upstream and downstream of these two SNPs. Zm00001d043536 regulates hormone regulation, Zm00001d043566 controls stomatal opening and closure, related to trichome, and Zm00001d043569 is associated with plant disease immune responses. Additionally, we performed candidate gene screening for five additional SNPs that were repeatedly detected across different environments, resulting in the identification of five candidate genes. These findings contribute to the development of genetic resources for common rust resistance in maize breeding programs.

Ear diameter (ED) is a key agronomic trait that significantly influences maize yield and is regulated by both genetic and environmental factors. We systema

Common rust (CR), caused by Puccina sorghi, is one of the major foliar diseases in maize, leading to quality deterioration and yield losses. To dissect the genetic architecture of CR resistance in maize, this study utilized the susceptible temperate inbred line Ye107 as the male parent crossed with three resistant tropical maize inbred lines (CML312, D39, and Y32) to generate 627 F7 recombinant inbred lines (RILs), aiming to identify maize disease-resistant loci and candidate genes for common rust. Phenotypic data exhibited good segregation between resistance and susceptibility, with varying degrees of resistance observed across different subpopulations. Significant genotype effects and genotype × environment interactions were noted with heritability ranging from 85.7% to 92.2%. Linkage analysis and genome-wide association analysis across three environments identified 20 QTLs and 62 significant SNPs. Among them, seven major QTLs explained 66% of the phenotypic variance. Comparison with six SNPs repeatedly identified across different environments revealed overlap between qRUST3-3 and Snp-203,116,453, and Snp-204,202,469. Haplotype analysis indicated two significantly different haplotypes for CR resistance for both of these SNPs. Based on LD decay plots, three co-located candidate genes, namely Zm00001d043536, Zm00001d043566, and Zm00001d043569, were identified within 20 kb up-stream and downstream of these two SNPs. Zm00001d043536 regulates hormone regulation, Zm00001d043566 controls stomatal opening and closure, related to trichome, and Zm00001d043569 is associated with plant disease immune responses. Additionally, we performed candidate gene screening for five additional SNPs repeatedly detected across different environments, resulting in the identification of five candidate genes. These findings contribute to the development of genetic resources for common rust resistance in maize breeding programs.