Fine Mapping of a New Major QTL-qGLS8 for Gray Leaf Spot Resistance in Maize

QTL mapping and genome-wide association analysis reveal genetic loci and candidate gene for resistance to gray leaf spot in tropical and subtropical maize germplasm

KEY MESSAGE

Using QTL mapping and GWAS, two candidate genes (Zm00001d051039 and Zm00001d051147) were consistently identified across the three different environments and BLUP values. GWAS analysis identified the candidate gene, Zm00001d044845. These genes were subsequently validated to exhibit a significant association with maize gray leaf spot (GLS) resistance. Gray leaf spot (GLS) is a major foliar disease of maize (Zea mays L.) that causes significant yield losses worldwide. Understanding the genetic mechanisms underlying gray leaf spot resistance is crucial for breeding high-yielding and disease-resistant varieties. In this study, eight tropical and subtropical germplasms were crossed with the temperate germplasm Ye107 to develop a nested association mapping (NAM) population comprising 1,653 F2:8 RILs, consisting of eight recombinant inbred line (RIL) subpopulations, using the single-seed descent method. The NAM population was evaluated for GLS resistance in three different environments, and genotyping by sequencing of the NAM population generated 593,719 high-quality single-nucleotide polymorphisms (SNPs). Linkage analysis and genome-wide association studies (GWASs) were conducted to identify candidate genes regulating GLS resistance in maize. Both analyses identified 25 QTLs and 149 SNPs that were significantly associated with GLS resistance. Candidate genes were screened 20 Kb upstream and downstream of the significant SNPs, and three novel candidate genes (Zm00001d051039, Zm00001d051147, and Zm00001d044845) were identified. Zm00001d051039 and Zm00001d051147 were located on chromosome 4 and co-localized in both linkage (qGLS4-1 and qGLS4-2) and GWAS analyses. SNP-138,153,206 was located 0.499 kb downstream of the candidate gene Zm00001d051039, which encodes the protein IN2-1 homolog B, a homolog of glutathione S-transferase (GST). GSTs and protein IN2-1 homolog B scavenge reactive oxygen species under various stress conditions, and GSTs are believed to protect plants from a wide range of biotic and abiotic stresses by detoxifying reactive electrophilic compounds. Zm00001d051147 encodes a probable beta-1,4-xylosyltransferase involved in the biosynthesis of xylan in the cell wall, enhancing resistance. SNP-145,813,215 was located 2.69 kb downstream of the candidate gene. SNP-5,043,412 was consistently identified in three different environments and BLUP values and was located 8.788 kb downstream of the candidate gene Zm00001d044845 on chromosome 9. Zm00001d044845 encodes the U-box domain-containing protein 4 (PUB4), which is involved in regulating plant immunity. qRT-PCR analysis showed that the relative expression levels of the three candidate genes were significantly upregulated in the leaves of the TML139 (resistant) parent, indicating that these three candidate genes could be associated with resistance to GLS. The findings of this study are significant for marker-assisted breeding aimed at enhancing resistance to GLS in maize and lay the foundation for further elucidation of the genetic mechanisms underlying resistance to gray leaf spot in maize and breeding of new disease-resistant varieties.

Quantitative trait locus analysis of gray leaf spot resistance in the maize IBM Syn10 DH population

KEY MESSAGE

The exploration and dissection of a set of QTLs and candidate genes for gray leaf spot disease resistance using two fully assembled parental genomes may help expedite maize resistance breeding. The fungal disease of maize known as gray leaf spot (GLS), caused by Cercospora zeae-maydis and Cercospora zeina, is a significant concern in China, Southern Africa, and the USA. Resistance to GLS is governed by multiple genes with an additive effect and is influenced by both genotype and environment. The most effective way to reduce the cost of production is to develop resistant hybrids. In this study, we utilized the IBM Syn 10 Doubled Haploid (IBM Syn10 DH) population to identify quantitative trait loci (QTLs) associated with resistance to gray leaf spot (GLS) in multiple locations. Analysis of seven distinct environments revealed a total of 58 QTLs, 49 of which formed 12 discrete clusters distributed across chromosomes 1, 2, 3, 4, 8 and 10. By comparing these findings with published research, we identified colocalized QTLs or GWAS loci within eleven clustering intervals. By integrating transcriptome data with genomic structural variations between parental individuals, we identified a total of 110 genes that exhibit both robust disparities in gene expression and structural alterations. Further analysis revealed 19 potential candidate genes encoding conserved resistance gene domains, including putative leucine-rich repeat receptors, NLP transcription factors, fucosyltransferases, and putative xyloglucan galactosyltransferases. Our results provide a valuable resource and linked loci for GLS marker resistance selection breeding in maize.

Genetic dissection of resistance to gray leaf spot by genome-wide association study in a multi-parent maize population

BACKGROUND

Understanding the genetic mechanisms underlying gray leaf spot (GLS) resistance in maize is crucial for breeding GLS-resistant inbred lines and commercial hybrids. Genome-wide association studies (GWAS) and gene functional annotation are valuable methods for identifying potential SNPs (single nucleotide polymorphism) and candidate genes associated with GLS resistance in maize.

RESULTS

In this study, a total of 757 lines from five recombinant inbred line (RIL) populations of maize at the F7 generation were used to construct an association mapping panel. SNPs obtained through genotyping-by-sequencing (GBS) were used to perform GWAS for GLS resistance using a linear mixture model in GEMMA. Candidate gene screening was performed by analyzing the 10 kb region upstream and downstream of the significantly associated SNPs linked to GLS resistance. Through GWAS analysis of multi-location phenotypic data, we identified ten candidate genes that were consistently detected in two locations or from one location along with best linear unbiased estimates (BLUE). One of these candidate genes, Zm00001d003257 that might impact GLS resistance by regulating gibberellin content, was further identified through haplotype-based association analysis, candidate gene expression analysis, and previous reports.

CONCLUSIONS

The discovery of the novel candidate gene provides valuable genomic resources for elucidating the genetic mechanisms underlying GLS resistance in maize. Additionally, these findings will contribute to the development of new genetic resources by utilizing molecular markers to facilitate the genetic improvement and breeding of maize for GLS resistance.

Association Mapping for Evaluation of Population Structure, Genetic Diversity, and Physiochemical Traits in Drought-Stressed Maize Germplasm Using SSR Markers

Globally, maize is one of the most consumed crops along with rice and wheat. However, maize is sensitive to different abiotic stress factors, such as drought, which have a significant impact on its production. The aims of this study were to investigate (1) genetic variation among 41 maize-inbred lines and the relationships among them and (2) significant marker-trait associations (SMTAs) between 7 selected physiochemical traits and 200 simple sequence repeat (SSR) markers to examine the genetics of these traits. A total of 1023 alleles were identified among the 41 maize-inbred lines using the 200 SSR loci, with a mean of 5.1 alleles per locus. The average major allele frequency, gene diversity, and polymorphism information content were 0.498, 0.627, and 0.579, respectively. The population structure analysis based on the 200 SSR loci divided the maize germplasm into two primary groups with an admixed group. Moreover, this study identified, respectively, 85 SMTAs and 31 SMTAs using a general linear model (Q GLM) and a mixed linear model (Q  + K MLM) with statistically significant (p < 0.05 and <0.01) associations with the seven physiochemical traits (caffeic acid content, chlorogenic acid content, gallic acid content, ferulic acid content, 2,2-diphenyl-1-picrylhydrazyl free radical scavenging activity, leaf relative moisture content, total phenolic content). These SSR markers were highly correlated with one or more of the seven physiochemical traits. This study provides insights into the genetics of the 41 maize-inbred lines and their seven physiochemical traits and will be of assistance to breeders in the marker-assisted selection of maize for breeding programs.