Integrating QTL mapping with transcriptome analysis uncovers candidate genes of ear length in maize

Ear length (EL) is a critical determinant of yield in maize breeding, yet its genetic underpinnings remain poorly characterized. This study aimed to identify key quantitative trait loci (QTLs) and candidate genes controlling EL to enhance our understanding of the genetic basis of ear development. To characterize candidate genes governing EL regulation, a population consist of 318 BC4F4 lines, derived from B73 (recurrent parent) and Baimaya (BMY, donor parent) was used for EL related QTL mapping with 10 K maize SNP array in three environments. We identified 16 QTLs for EL across three environments and the best linear unbiased prediction (BLUP), among which, three QTLs were repeatedly detected, especially the major QTL qEL2.05, with an average phenotypic variation (PVE) of 9.40%, logarithm of odds (LOD) score of 7.49, and average additive effect of 0.65 cm. Further, near-isogenic lines (NILs) of qEL2.05 confirmed its effect, with qEL2.05BMY exhibiting significantly longer ears and larger inflorescence meristems than qEL2.05B73. Then, the integration of linkage mapping and transcriptome analysis of 5 mm immature ears of the NILs uncovered a candidate gene, Zm00001eb085560, which encoded an aldehyde dehydrogenase, and showed significantly up-regulated in qEL2.05BMY, and two missense variations between the NILs. Analysis of differentially expressed genes (DEGs) revealed significant enrichment in pathways related to the phosphatidylinositol signaling system, which have been reported to be related to the development of plant inflorescences. Furthermore, pyramiding the favorable alleles from the three stable QTLs enhanced EL more significantly than single alleles. Our findings uncover stable QTLs and a promising candidate gene governing ear length in maize. This research lays a solid foundation for future functional studies and molecular breeding aimed at improving maize yield.