In this study, hotspot regions, QTL clusters, and candidate genes for eight ear-related traits of maize (ear length, ear diameter, kernel row number, kernel number per row, kernel length, kernel width, kernel thickness, and 100-kernel weight) were summarized and analyzed over the past three decades. This review aims to (1) comprehensively summarize and analyze previous studies on QTLs associated with these eight ear-related traits and identify hotspot bin regions located on maize chromosomes and key candidate genes associated with the ear-related traits and (2) compile major and stable QTLs and QTL clusters from various mapping populations and mapping methods and techniques providing valuable insights for fine mapping, gene cloning, and breeding for high-yield and high-quality maize. Previous research has demonstrated that QTLs for ear-related traits are distributed across all ten chromosomes in maize, and the phenotypic variation explained by a single QTL ranged from 0.40% to 36.76%. In total, 23 QTL hotspot bins for ear-related traits were identified across all ten chromosomes. The most prominent hotspot region is bin 4.08 on chromosome 4 with 15 QTLs related to eight ear-related traits. Additionally, this study identified 48 candidate genes associated with ear-related traits. Out of these, five have been cloned and validated, while twenty-eight candidate genes located in the QTL hotspots were defined by this study. This review offers a deeper understanding of the advancements in QTL mapping and the identification of key candidates associated with eight ear-related traits. These insights will undoubtedly assist maize breeders in formulating strategies to develop higher-yield maize varieties, contributing to global food security.

Kernel number per row (KNR) is an essential component of maize (Zea mays L.) grain yield (GY), and understanding its genetic mechanism is crucial to improve GY. In this study, two F₇ recombinant inbred line (RIL) populations were created using a temperate–tropical introgression line TML418 and a tropical inbred line CML312 as female parents and a backbone maize inbred line Ye107 as the common male parent. Bi-parental quantitative trait locus (QTL) mapping and genome-wide association analysis (GWAS) were then performed on 399 lines of the two maize RIL populations for KNR in two different environments using 4118 validated single nucleotide polymorphism (SNP) markers. This study aimed to: (1) detect molecular markers and/or the genomic regions associated with KNR; (2) identify the candidate genes controlling KNR; and (3) analyze whether the candidate genes are useful in improving GY. The authors reported a total of 7 QTLs tightly linked to KNR through bi-parental QTL mapping and identified 21 SNPs significantly associated with KNR through GWAS. Among these, a highly confident locus qKNR7-1 was detected at two locations, Dehong and Baoshan, with both mapping approaches. At this locus, three novel candidate genes (Zm00001d022202, Zm00001d022168, Zm00001d022169) were identified to be associated with KNR. These candidate genes were primarily involved in the processes related to compound metabolism, biosynthesis, protein modification, degradation, and denaturation, all of which were related to the inflorescence development affecting KNR. These three candidate genes were not reported previously and are considered new candidate genes for KNR. The progeny of the hybrid Ye107 × TML418 exhibited strong heterosis for KNR, which the authors believe might be related to qKNR7-1. This study provides a theoretical foundation for future research on the genetic mechanism underlying KNR in maize and the use of heterotic patterns to develop high-yielding hybrids.

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.

Background: Maize white spot (MWS) is a highly destructive leaf disease and has become a major threat to global maize production in recent years. This indicates that identifying new anti-MWS genes is of vital importance. In this study, two recombinant inbred line (RIL) subpopulations derived from Suwan germplasms with MWS resistance were used. Results: By integrating quantitative trait loci (QTL) mapping and genome-wide association study (GWAS) strategies, resistance-related loci were successfully identified. The analysis results consistently indicated that there was a major resistance region on chromosome 3, where the major QTL locus qMWS3-2 , consistently identified across three environments and BLUP values, could explain up to 10.81% of the phenotypic variation and co-localized with two significant single nucleotide polymorphisms (SNPs). Within this region, two candidate genes were identified: Zm00001eb155730 encoding mitogen-activated protein kinase and Zm00001eb155910 involved in sulfur metabolism. Haplotype analysis showed that the favorable haplotypes of these two genes were both associated with significantly enhanced resistance to MWS and were only present in the subpopulation derived from the highly resistant parent D39. Expression analysis further revealed a unique defense mechanism of D39. This parent strongly suppressed the candidate gene Zm00001eb155730 , which was significantly upregulated in the highly susceptible parent. As for the defense-related gene Zm00001eb155910 , its expression pattern is different from the induced expression of the susceptible parents Ye107 and the parent YML32. Conclusions: The candidate genes and favorable haplotypes identified in this study provide valuable resources for molecular breeding of maize and will promote the breeding process of high-resistance MWS varieties.