Combining linkage mapping and association analysis to dissect the genetic architecture of preventing-pollination-induced leaf senescence in maize (Zea mays L.)

Senescence is a pivotal developmental process in plants. A timely transition from the stay-green stage to senescence is crucial for optimizing crop quality and yield. In this study, we combined linkage mapping and association analysis to dissect the genetic architecture of preventing-pollination-induced leaf senescence in maize. Three senescence-related traits, including green days (GD), senescence days (SD) and senescence index (SI), were normally distributed. Linkage analysis detected 15 significant quantitative trait loci (QTL). Association mapping identified 31 significant quantitative trait nucleotides (QTNs), which colocalized with 23 QTL regions and implicated 62 candidate genes. Enrichment and pathway analysis suggested that these genes may participate in water transport through the ABA signaling pathway, thereby influencing vacuolar membrane integrity and senescence progression. Integration of both mapping approaches revealed a co-located QTL, qLS13 , on chromosome 8. Further analysis nominated ZmSee2a and SPX4 as putative causal genes regulating leaf senescence. Candidate gene association analysis identified nine applicable molecular markers, seven and two markers were significantly associated with ZmSee2a and SPX4 . Elite haplotypes ZmSee2a Hap2 and SPX4 Hap1 conferred a timely delay in senescence by 2.6 and 2.1 days, respectively. Notably, pyramiding favorable natural variations in ZmSee2a and SPX4 produced an enhanced timely senescence and yield. Evolutionary analysis indicated that ZmSee2a is relatively conserved and has been under significant selection during decades of maize breeding in China, highlighting its potential role in simultaneous improvement of yield. Furthermore, this gene was significantly down-regulated in response to pollination prevention, suggesting a causal link between its expression and senescence. Together, our findings provide new genetic insights into leaf senescence regulation and offer a theoretical basis for optimizing maize harvest timing and improving the precision of subsequent crop sowing. • Genetic insights into preventing-pollination-induced leaf senescence in maize revealed by linkage and association analysis. • ABA signaling and water transport affect vacuolar membrane integrity and closely linked to leaf senescence. • Co-pyramiding of elite natural variants in both ZmSee2a and SPX4 enhanced timely senescence and grain yield in maize. • This study has implications for improving yield in double-cropping systems and securing industrial material supply.