Positional Cloning And Dissection Of A Major Plant Height QTL-qph1and The Ys Mutant Gene And Its Modifier In Maize

Plant height is an important determinant of maize grain yield. For the past few decades, the increased maize production was mainly contributed by compact planting. However, an increase in plant height is often resulted from the high planting density, which will reduce logging resistance and cause yield loss. Thus, selecting hybrids with moderate reduced plant and high yield potential has become a new objective in maize improvement. Knocking out essential plant height genes often result in severe phenotype and great yield loss, so quantitative loci underlying plant height serve as good candidates for this breeding goal. Although a great many plant height QTLs have been identified, few were cloned and employed in maize improvement. On the other hand, modifier genes that can modify the segregation, expression and phenotype of the target genes were found to have extensive existence in maize genome. Although the gene-background interaction caused by modifiers is a common observation, the molecular mechanism underlies it remains largely unknown. The phenotype of virescent mutant B73ys (yellow seedling) recovers within2weeks, but the same ys locus under PH09B background has more severe phenotypes such as late recovery, retarded growth in greenhouse and fails to servive in the field. Through map-based cloning, association analysis, expression assay and gene transformation, we cloned the major plant height QTL-qphl and validated its functional site; also, the ys gene and its modifier were both cloned and validated, the molecular mechanism of their interaction has been proposed. Results for these studies include:1. Two lines from Zong3/87-1RIL population were employed for developing the near-isogenic line RIL88(QPH1) and fine mapping population BC6F2of QTL-qphl.50recombinants of11crossover types were identified through the screening of8030individuals in BC6F2, defining qph1to a1590bp interval on BAC AC210610on maize chromosome1.2. The confidence interval of qphl located on the5th exon of maize Br2gene (Brachytic2/ZmPGP1), which functions as an efflux carrier in polar auxin transport. Five SNPs were identified in the target region; only SNP5259(T) resulted in an amino acid substitution from Arginine to Leucine and was proposed to be the functional site of qphl. Revealed by association analysis, the four synonymous SNPs did not associate with plant height and SNP5259was a rare SNP that harbored by only five temperate inbreds. Expression levels of qphl between RIL88(qph1)RIL88(QPH1) had no significant difference; and showed by protein structure prediction, the amino acid substitution was located on the9tha-helix in the trans-membrane domain of Br2with its residue facing the inner side of the channel; SNP5259(T) has converted the hydrophilic, positively charged Arg into a hydrophobic and nutra leucine, the substitution very likely had impaired polar auxin transport.3. qphl was evaluated in4F2populations and6pairs of RIL88(qph1)/RIL88(QpH1) derived F1S, it was proved to have a large and stable effect on plant height and ear height under multiple genetic backgrounds with no or a slight impact on yield. Moreover, density test performed on RIL88(qphl)×Ye107and RIL88(QpH1)×Ye107further suggested that qphl derived hybrid has a shorter plant height and less yield loss under high planting density.4. The maize yellow seedling (ys) mutant gene on Chr.9was cloned with the BC1population of B73ys and Mo17. It encodes the ClpPl subunit of the chloroplast targeting Clp protease complex and was designated as Chr.9_ClpP1. A141bp MITE insertion at the4th exon/intron junction that impired pre-mRNA splicing was validated as the causative mutation. The modifier (Chr：1_ClpP1) of ys gene on Chr.1was cloned with the F2population of B73and Mo17, which was paralogous to the ys gene.5. Expression assay detected a significant induction of ys-modifier alleles in both B73ys and Mo17ys than in their wild type counterparts, however the same induction was not observed in PH09Bys. Futhermore, allele specific expression of the two ys-modifier alleles in B73and EF09B with2F1S, B73xEF09B and B73ys×PH09Bys, again detected their different responses to the ys mutation on chr.9. Thus, functional complementation between duplicate/paralogous genes under cis-regulation has been proposed as the molecular mechanism underlying the interaction between ys and its modifier.