High-density quantitative trait locus mapping revealed genetic architecture of leaf angle and tassel size in maize

The maize leaf angle and tassel size have close relationships with grain yield. These traits had undergone a strong selection and great morphological changes during domestication and improvement. To understand the genetic architecture of these morphological traits, an F2:3 population was developed using the cross of Lv28 by H082183, the latter having more erect leaves and small tassels. Using a modified hidden Markov model (HMM), the genetic map covering 1495.79 cM was obtained from 1965 bin markers. QTL mapping identified six leaf angle QTL, seven tassel branch number QTL, and ten tassel dry weight QTL, including three large-effect QTL (R2 > 10%) qLA1_2, qLA2, and qTBN8. The inflorescence development gene tasselseed2 (ts2) and zea floricaula leafy2 (zfl2) were co-located in the interval of qTW1 and qTW2_1. Seven genes in qLA1_2 showed evidence of selection during maize improvement, including two protein kinase genes (GRMZM2G138475 and GRMZM2G114093) and two trehalose-phosphatase genes (GRMZM2G347280 and GRMZM2G008226). Interestingly, the significant SNPs associated with tassel branch number and the selection region in qTBN8 were consistent at 5′ non-coding region of GRMZM5G873917. And the nucleotide diversity analysis revealed that the 5′ regulatory region of GRMZM5G873917 was under strong selection. These results provide insights into genetic architectures of maize morphological traits and alleles which have potentials in maize breeding.