Dissection of the genetic architecture of peduncle vascular bundle-related traits in maize by a genome-wide association study.

The peduncle vascular system of maize is critical for the transport of photosynthetic products, nutrients, and water from the roots and leaves to the ear. Accordingly, it positively affects the grain yield. However, the genetic basis of peduncle vascular bundle (PVB)-related traits in maize remains unknown. Thus, 15 PVB-related traits of 386 maize inbred lines were investigated at three locations (Yongcheng, 17YC; Kaifeng, 20KF; and Yuanyang, 20YY). The repeatability for the 15 traits ranged from 35.53% to 92.13%. A genome-wide association study was performed and 69 non-redundant quantitative trait loci (QTL) were detected, including 9, 41, and 27 QTL identified at 17YC, 20KF, and 20YY, respectively. These QTL jointly explained 4.72% (SLL) to 37.30% (NSVB) of the phenotypic variation. Eight QTL were associated with the same trait at two locations. Furthermore, four pleiotropic QTL were identified. Moreover, one QTL (qPVB44), associated with NSVB_20KF, was co-localized with a previously reported locus related to kernel width, implying qPVB44 may affect the kernel width by modulating the number of small vascular bundles. Examinations of the 69 QTL identified 348 candidate genes that were classified in five groups. Additionally, 26 known VB-related homologous genes (e.g. VLN2, KNOX1, and UGT72B3) were detected in 20 of the 69 QTL. A comparison of the NSVB between a Zmvln2 EMS mutant and its wild type elucidated the function of the candidate gene ZmVLN2. These results are important for clarifying the genetic basis of PVB-related traits and may be useful for breeding new high-yielding maize cultivars.

Genome-Wide Identification of miRNAs and Their Targets Involved in the Developing Internodes under Maize Ears by Responding to Hormone Signaling.

Internode length is one of the decisive factors affecting plant height (PH) and ear height (EH), which are closely associated with the lodging resistance, biomass and grain yield of maize. miRNAs, currently recognized as important transcriptional/ post-transcriptional regulators, play an essential role in plant growth and development. However, their roles in developing internodes under maize ears remain unclear. To identify the roles of miRNAs and their targets in the development of internodes under maize ears, six miRNA and two degradome libraries were constructed using the 7th, 8th and 9th internodes of two inbred lines, 'Xun928' and 'Xun9058', which had significantly different internode lengths. A total of 45 and 54 miRNAs showed significant changes for each pairwise comparison among the 7th, 8th and 9th internodes of 'Xun9058' and 'Xun928', respectively. The expression of 31 miRNAs showed significant changes were common to the corresponding comparison groups of the 7th, 8th and 9th internodes of 'Xun9058' and 'Xun928'. For the corresponding internodes of 'Xun9058' and 'Xun928', compared with the expression of miRNAs in the 7th, 8th and 9th internodes of 'Xun928', the numbers of up-regulated and down-regulated miRNAs were 11 and 36 in the 7th internode, 9 and 45 in the 8th internode, and 9 and 25 in the 9th internode of 'Xun9058', respectively. Moreover, 10 miRNA families containing 45 members showed significant changes at least in two internodes of 'Xun928' by comparing with the corresponding internodes of 'Xun9058'. Based on the sequencing data, 20 miRNAs related to hormone signaling among the candidates, belonging to five conserved miRNA families, were selected for expression profiling using quantitative reverse-transcription polymerase chain reaction (qRT-PCR). The five miRNA families, zma-miR160, zma-miR167, zma-miR164, zma-miR169 and zma-miR393, targeted the genes encoding auxin response factor, N-acetylcysteine domain containing protein, nuclear transcription factor Y and auxin signaling F-BOX 2 through degradome sequencing. The miRNAs might regulate their targets to respond to hormone signaling, thereby regulating the internode elongation and development under maize ear. These results provide valuable reference for understanding the possible regulation mechanism of the ILs under the ear.