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Characterization and transcriptome analysis of maize small kernel mutant smk7a in different development stages

ABSTRACT: The kernel serves as a storage organ for various nutrients and determines the yield and quality of maize. Understanding the mechanisms regulating kernel development is important for maize production. In this study, a small kernel mutant smk7a of maize was characterized. Cytological observation suggested that the development of the endosperm and embryo was arrested in smk7a in the early development stage. Biochemical tests revealed that the starch, zein protein, and indole-3-acetic acid (IAA) contents were significantly lower in smk7a compared with wild-type (WT). Consistent with the defective development phenotype, transcriptome analysis of the kernels 12 and 20 days after pollination (DAP) revealed that the starch, zein, and auxin biosynthesis related genes were dramatically downregulated in smk7a. Genetic mapping indicated that the mutant was controlled by a recessive gene located on chromosome 2. Our results suggest that disrupted nutrition accumulation and auxin synthesis cause the defective endosperm and embryo development of smk7a.

ORGANISM(S): Zea mays

PROVIDER: GSE221594 | GEO | 2023/01/25

REPOSITORIES: GEO

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Project description:Maize kernel is an important source of food, feed and industrial raw materials. The illustration of the molecular mechanisms of maize kernel development will be helpful for the manipulation of maize improvements. Although a great many researches based on molecular biology and gecetics have greatly increased our understanding on the kernel development, many of the mechanisms controlling this important process remain elusive. In current study, a microarray with approximately 58,000 probes was used to study the dynamic gene expression during kernel development from the fertilization to physiological maturity. Samples from two consecutive time-points were paired and labeled using different fluorescent dyes (Cy3 and Cy5) and hybridized in the same array. Hybridization of slides was performed according to the manufacturer’s instructions (http://www.maizearray.org/). The hybridized slides were scanned by a Genepix 4000B (Axon, USA). A loop design was applied for running the microarray. Two replicates of each pair of samples were carried out to test both the reproducibility and quality of the chip hybridizations. By comparing six consecutive time-points, namely 1, 5, 10, 15, 25 and 35 days after pollination (DAP), 3,445 differentially expressed genes were identified. These genes were then grouped into 10 clusters showing specific expression patterns using a K-means clustering algorithm. An investigation of function and expression patterns of genes expanded our understanding of the regulation mechanism underlying the important developmental processes, cell division and kernel filling. The differential expression of genes involved in plant hormone signaling pathways suggested that phytohormone might play a critical role in the kernel developmental process. Moreover, regulation of some transcription factors and protein kinases might be involved in the whole developmental process. To obtain the global gene expression profile during maize kernel development, a microarray with approximately 58,000 probes was used. The maize inbred line X178 was planted on the field. Each plant was self-pollinated by hand. The ears were harvested from healthy plants at 1, 5, 10, 15, 25 and 35 days after pollination (DAP), respectively. In order to increase the consistency & uniformity of the isolated kernels, the upper half and about one sixth of ears from the bottom were cut and discarded, the kernels were isolated from the rest part of the ears. Samples at each time-point were collected from at least thirty ears and pooled to represent the line characteristics of X178. Two sub-samples for replication in the microarray analysis were randomly drawn. Samples from two consecutive time-points were paired and labeled using different fluorescent dyes (Cy3 and Cy5) and hybridized in the same array. A loop design was applied for running the microarray. Two replicates of each pair of samples were carried out to test both the reproducibility and quality of the chip hybridizations.

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Characterization and transcriptome analysis of maize small kernel mutant smk7a in different development stages

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