Unravelling the genetic framework associated with grain quality and yield-related traits in maize (Zea mays L.)

Abstract

Maize serves as a crucial nutrient reservoir for a significant portion of the global population. However, to effectively address the growing world population's hidden hunger, it is essential to focus on two key aspects: biofortification of maize and improving its yield potential through advanced breeding techniques. Moreover, the coordination of multiple targets within a single breeding program poses a complex challenge. This study compiled mapping studies conducted over the past decade, identifying quantitative trait loci associated with grain quality and yield related traits in maize. Meta-QTL analysis of 2,974 QTLs for 169 component traits (associated with quality and yield related traits) revealed 68 MQTLs across different genetic backgrounds and environments. Most of these MQTLs were further validated using the data from genome-wide association studies (GWAS). Further, ten MQTLs, referred to as breeding-friendly MQTLs (BF-MQTLs), with a significant phenotypic variation explained over 10% and confidence interval less than 2 Mb, were shortlisted. BF-MQTLs were further used to identify potential candidate genes, including 59 genes encoding important proteins/products involved in essential metabolic pathways. Five BF-MQTLs associated with both quality and yield traits were also recommended to be utilized in future breeding programs. Synteny analysis with wheat and rice genomes revealed conserved regions across the genomes, indicating these hotspot regions as validated targets for developing biofortified, high-yielding maize varieties in future breeding programs. After validation, the identified candidate genes can also be utilized to effectively model the plant architecture and enhance desirable quality traits through various approaches such as marker-assisted breeding, genetic engineering, and genome editing.

Keywords: breeder-friendly; candidate genes; maize; meta-QTLs; quality; yield.

FIGURE 1

Distribution of QTLs associated with quality and yield related traits.

FIGURE 2

Some characteristic features of QTLs and MQTLs (A) Distribution of MQTLs on different maize chromosomes; (B) Number of QTLs under each MQTL; (C) Average CI of QTLs and MQTLs available on different maize chromosomes.

FIGURE 3

Distribution of MQTLs on different maize chromosomes. Common: MQTLs associated with both quality and yield-associated traits, BFQ: breeder-friendly quality trait MQTLs, BFY: breeder-friendly yield trait MQTLs, BFC: breeder-friendly common MQTLs (involving both quality and yield-related traits).

FIGURE 4

Diagram deciphering the salient characteristics of MQTLs, BF-MQTLs, candidate genes. Outermost circle represents the location of MQTLs predicted during the present study. Second circle (blue) provides an overview of density of MQTLs on different chromosomes. Third circle represents locations and densities of BF-MQTL along with putative gene density. Lines within innermost circle represents phylogenetic relationships between identified genes.

FIGURE 5

Biological functions of various classes of genes annotated under BF-MQTLs region.

FIGURE 6

Tissue-specific expression of different genes available from MQTL regions (A: anther, IN: internode, L: leaf, RP: reproductive, R: root, S: shoot, SA: shoot axis internode, SSAM: stem and shoot apical meristem).

FIGURE 7

Syntenic relationships of genes available from the maize MQTL regions with the (A) rice and (B) wheat genomes. The physical lengths of the chromosomes are indicated by the rulers drawn above on each chromosome.