Kernel row number (KRN) is an important component of yield during the domestication and improvement of maize and controlled by quantitative trait loci (QTL). Here, we fine-mapped a major KRN QTL, KRN4, which can enhance grain productivity by increasing KRN per ear. We found that a ~3-Kb intergenic region about 60 Kb downstream from the SBP-box gene Unbranched3 (UB3) was responsible for quantitative variation in KRN by regulating the level of UB3 expression. Within the 3-Kb region, the 1.2-Kb Presence-Absence variant was found to be strongly associated with quantitative variation in KRN in diverse maize inbred lines, and our results suggest that this 1.2-Kb transposon-containing insertion is likely responsible for increased KRN. A previously identified A/G SNP (S35, also known as Ser220Asn) in UB3 was also found to be significantly associated with KRN in our association-mapping panel. Although no visible genetic effect of S35 alone could be detected in our linkage mapping population, it was found to genetically interact with the 1.2-Kb PAV to modulate KRN. The KRN4 was under strong selection during maize domestication and the favorable allele for the 1.2-Kb PAV and S35 has been significantly enriched in modern maize improvement process. The favorable haplotype (Hap1) of 1.2-Kb-PAV-S35 was selected during temperate maize improvement, but is still rare in tropical and subtropical maize germplasm. The dissection of the KRN4 locus improves our understanding of the genetic basis of quantitative variation in complex traits in maize.

One-sentence summary: Maize GIF1 promotes meristematic function in leaves and stems but restricts indeterminacy in the inflorescence by regulating the expression of several known inflorescence architecture-related genes.The authors responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (www.plantcell.org) are: Zuxin Zhang (zuxinzhang@mail.hzau.edu.cn) and Sarah Hake (hake@berkeley.edu). ABSTRACTPlant architecture results from a balance of indeterminate and determinate cell fates. Cells with indeterminate fates are located in meristems, comprising groups of pluripotent cells that produce lateral organs. Meristematic cells are also found in intercalary stem tissue, which provides cells for internodes, and at leaf margins to contribute to leaf width. We identified a maize (Zea mays) mutant that has a defect in balancing determinacy and indeterminacy. The mutant has narrow leaves and short internodes, suggesting a reduction in indeterminate cells in the leaf and stem. In contrast, the mutants fail to control indeterminacy in shoot meristems. Inflorescence meristems are fasciated, and determinate axillary meristems become indeterminate. Positional cloning identified growth regulating factor-interacting factor1 (gif1) as the responsible gene. gif1 mRNA accumulates in distinct domains of shoot meristems, consistent with tissues affected by the mutation. We determined which GROWTH REGULATING FACTORs (GRFs) interact with GIF1 and carried out RNA-seq analysis. Many genes known to play roles in inflorescence architecture were differentially expressed in gif1. Chromatin immunoprecipitation identified some differentially expressed genes as direct targets of GIF1. The interactions with these

Increasing grain yield of maize (Zea mays L.) is required to meet the rapidly expanding demands for maize-derived food, feed, and fuel. Breeders have enhanced grain productivity of maize hybrids by pyramiding desirable characteristics for larger ears. However, loci selected for improving grain productivity remain largely unclear. Here, we show that a serine/threonine protein kinase encoding gene KERNEL NUMBER PER ROW6 (KNR6) determines pistillate floret number and ear length. Overexpression of KNR6 or introgression of alleles lacking the insertions of two transposable elements in the regulatory region of KNR6 can significantly enhance grain yield. Further in vitro evidences indicate that KNR6 can interact with an Arf GTPase-activating protein (AGAP) and its phosphorylation by KNR6 may affect ear length and kernel number. This finding provides knowledge basis to enhance maize hybrids grain yield.

UNBRANCHED3 (UB3), a member of the SQUAMOSA promoter binding protein-like (SPL) gene family, regulates kernel row number by negatively modulating the size of the inflorescence meristem in maize. However, the regulatory pathway by which UB3 mediates branching remains unknown. We introduced the UB3 into rice and maize to reveal its effects in the two crop plants, respectively. Furthermore, we performed transcriptome sequencing and protein-DNA binding assay to elucidate the regulatory pathway of UB3. We found that UB3 could bind and regulate the promoters of LONELY GUY1 (LOG1) and Type-A response regulators (ARRs), which participate in cytokinin biosynthesis and signaling. Overexpression of exogenous UB3 in rice (Oryza sativa) dramatically suppressed tillering and panicle branching as a result of a greater decrease in the amount of active cytokinin. By contrast, moderate expression of UB3 suppressed tillering slightly, but promoted panicle branching by cooperating with SPL genes, resulting in a higher grain number per panicle in rice. In maize (Zea mays) ub3 mutant with an increased kernel row number, UB3 showed a low expression but cytokinin biosynthesis-related genes were up-regulated and degradation-related genes were down-regulated. These results suggest that UB3 regulates vegetative and reproductive branching by modulating cytokinin biosynthesis and signaling in maize and rice.

The establishment of inflorescence architecture is critical for the reproduction of flowering plant species. The maize plant generates two types of inflorescences, the tassel and the ear, and their architectures have a large effect on grain yield and yield-related traits that are genetically controlled by quantitative trait loci (QTLs). Since ear and tassel architecture are deeply affected by the activity of inflorescence meristems, key QTLs and genes regulating meristematic activity have important impacts on inflorescence development and show great potential for optimizing grain yield. Isolation of yield trait-related QTLs is challenging, but these QTLs have direct application in maize breeding. Additionally, characterization and functional dissection of QTLs can provide genetic and molecular knowledge of quantitative variation in inflorescence architecture. In this review, we summarize currently identified QTLs responsible for the establishment of ear and tassel architecture and discuss the potential genetic control of four ear-related and four tassel-related traits. In recent years, several inflorescence architecture-related QTLs have been characterized at the gene level. We review the mechanisms of these characterized QTLs.