Identification of differentially expressed genes at two key endosperm development stages using two maize inbreds with large and small grain and integration with detected QTL for grain weight

Liu, Y. Y.; Li, J. Z.; Li, Y. L.; Wei, Mei; Cui, Qingxin; Wang, Q. L.

doi:10.1007/s00122-010-1321-x

Cited by 9 publications

(6 citation statements)

References 62 publications

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“…This could also contribute to the identification of genes or proteins that play important roles in the biological and chemical processes involved in the developmental process [ 19 ]. By constructing and analyzing cDNA libraries, endosperm development was thoroughly characterized and some tissue-specific genes were obtained [ 1 , 2 , 5 , 7 , 8 , 30 ]. At least 5,000 different genes could be expressed during endosperm development.…”

Section: Introductionmentioning

confidence: 99%

Dynamic Proteomic Characteristics and Network Integration Revealing Key Proteins for Two Kernel Tissue Developments in Popcorn

et al. 2015

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The formation and development of maize kernel is a complex dynamic physiological and biochemical process that involves the temporal and spatial expression of many proteins and the regulation of metabolic pathways. In this study, the protein profiles of the endosperm and pericarp at three important developmental stages were analyzed by isobaric tags for relative and absolute quantification (iTRAQ) labeling coupled with LC-MS/MS in popcorn inbred N04. Comparative quantitative proteomic analyses among developmental stages and between tissues were performed, and the protein networks were integrated. A total of 6,876 proteins were identified, of which 1,396 were nonredundant. Specific proteins and different expression patterns were observed across developmental stages and tissues. The functional annotation of the identified proteins revealed the importance of metabolic and cellular processes, and binding and catalytic activities for the development of the tissues. The whole, endosperm-specific and pericarp-specific protein networks integrated 125, 9 and 77 proteins, respectively, which were involved in 54 KEGG pathways and reflected their complex metabolic interactions. Confirmation for the iTRAQ endosperm proteins by two-dimensional gel electrophoresis showed that 44.44% proteins were commonly found. However, the concordance between mRNA level and the protein abundance varied across different proteins, stages, tissues and inbred lines, according to the gene cloning and expression analyses of four relevant proteins with important functions and different expression levels. But the result by western blot showed their same expression tendency for the four proteins as by iTRAQ. These results could provide new insights into the developmental mechanisms of endosperm and pericarp, and grain formation in maize.

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Section: Introductionmentioning

confidence: 99%

Dynamic Proteomic Characteristics and Network Integration Revealing Key Proteins for Two Kernel Tissue Developments in Popcorn

et al. 2015

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“…Identi cation zmzfp2 mutant form small kernels In our previous study, we isolated a candidate gene, RING Zinc Finger Protein (ZmZFP2, Zm00001d033780), from two crucial developmental stages of endosperm in a dent maize inbred Dan232 with large-sized kernels, and a popcorn inbred N04 with small-sized kernels Liu, et al 2010). ZmZFP2 comprises six exons and a C4HC3-type RING zinc nger domain (Fig.…”

Section: Resultsmentioning

confidence: 99%

“…In our previous studies, a candidate EST (PE12C5) was isolated from four suppression subtractive hybridization (SSH) libraries constructed from the key developmental stages of endosperm in two maize inbred lines, a regular dent inbred Dan232 (large-sized kernel) and a popcorn inbred N04 (small-sized kernel) Liu, et al 2010). In this study, we identi ed ZmZFP2 as a regulatory factor for kernel development.…”

Section: Introductionmentioning

confidence: 99%

ZmZFP2 encoding a C4HC3-type RING zinc finger protein regulates kernel size and weight in maize

Zhang,

Wang,

et al. 2023

Preprint

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The development of maize (Zea mays) kernels is a complex physiological process, regulated by many genes in a spatio-temporal manner. However, there remain many unknown regulatory genes involved in maize kernel development. Here, we have identified a gene (ZmZFP2), which encodes a C4HC3-type RING zinc finger protein, that regulates maize kernel weight and size based on the suppression subtractive hybridization from maize endosperm in our previous studies. Through transgenic technology, over-expression of ZmZFP2 resulted in increased kernel weight and size compared to the wild type, while mutation of the gene led to decreased kernel weight and size. Microscopic observation of developing kernels revealed that ZmZFP2 affects the number of endosperm cells and their filling, as well as the starch and protein contents of the kernels. ZmZFP2 shows constitutive expression in various maize tissues. Furthermore, transcriptome analysis revealed that the zmzfp2-ems mutation significantly interfered with multiple biological processes, especially hormone pathways and ubiquitin degradation. Together, ZmZFP2 affects kernel size and weight by influencing endosperm cell number and filling, providing a valuable potential gene for increasing maize yield.

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“…Data on gene expression have been used to identify candidate genes in animals [ 7 ], for review] and have also been employed in the search for genes involved in water-use efficiency in cereals [ 8 ]. The combination of QTL mapping data and gene expression analyses has led to the identification of candidate genes regulating grain fiber content in wheat [ 9 ] and grain weight in maize [ 10 ]. Despite the merits of this approach, the large size of many QTL, the number of genes within them and particularly their loose association with both locus and trait makes assigning individual genes or groups of genes to particular traits very challenging.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide meta-analysis of maize heterosis reveals the potential role of additive gene expression at pericentromeric loci

Thiemann

Seifert

et al. 2014

BMC Plant Biol

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BackgroundThe identification of QTL involved in heterosis formation is one approach to unravel the not yet fully understood genetic basis of heterosis - the improved agronomic performance of hybrid F1 plants compared to their inbred parents. The identification of candidate genes underlying a QTL is important both for developing markers and determining the molecular genetic basis of a trait, but remains difficult owing to the large number of genes often contained within individual QTL. To address this problem in heterosis analysis, we applied a meta-analysis strategy for grain yield (GY) of Zea mays L. as example, incorporating QTL-, hybrid field-, and parental gene expression data.ResultsFor the identification of genes underlying known heterotic QTL, we made use of tight associations between gene expression pattern and the trait of interest, identified by correlation analyses. Using this approach genes strongly associated with heterosis for GY were discovered to be clustered in pericentromeric regions of the complex maize genome. This suggests that expression differences of sequences in recombination-suppressed regions are important in the establishment of heterosis for GY in F1 hybrids and also in the conservation of heterosis for GY across genotypes. Importantly functional analysis of heterosis-associated genes from these genomic regions revealed over-representation of a number of functional classes, identifying key processes contributing to heterosis for GY. Based on the finding that the majority of the analyzed heterosis-associated genes were addtitively expressed, we propose a model referring to the influence of cis-regulatory variation on heterosis for GY by the compensation of fixed detrimental expression levels in parents.ConclusionsThe study highlights the utility of a meta-analysis approach that integrates phenotypic and multi-level molecular data to unravel complex traits in plants. It provides prospects for the identification of genes relevant for QTL, and also suggests a model for the potential role of additive expression in the formation and conservation of heterosis for GY via dominant, multigenic quantitative trait loci. Our findings contribute to a deeper understanding of the multifactorial phenomenon of heterosis, and thus to the breeding of new high yielding varieties.

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Identification of differentially expressed genes at two key endosperm development stages using two maize inbreds with large and small grain and integration with detected QTL for grain weight

Cited by 9 publications

References 62 publications

Dynamic Proteomic Characteristics and Network Integration Revealing Key Proteins for Two Kernel Tissue Developments in Popcorn

Dynamic Proteomic Characteristics and Network Integration Revealing Key Proteins for Two Kernel Tissue Developments in Popcorn

ZmZFP2 encoding a C4HC3-type RING zinc finger protein regulates kernel size and weight in maize

Genome-wide meta-analysis of maize heterosis reveals the potential role of additive gene expression at pericentromeric loci

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