Identification of traits and genes associated with lodging resistance in maize

Lodging is a major problem limiting maize yield worldwide. However, the mechanisms of lodging resistance remain incompletely understood for maize. Here, we evaluated 443 maize accessions for lodging resistance in the field. Five lodging-resistant accessions and five lodging-sensitive accessions were selected for further research. The leaf number, plant height, stem diameter, and rind penetrometer resistance were similar between lodging-resistant and-sensitive inbred lines. The average thickness of sclerenchymatous hypodermis layer was thicker and the vascular area was larger in the lodging-resistant lines compared with lodging-sensitive lines. Although total lignin content in stem tissue did not significantly differ between lodging-resistant and-sensitive lines, phloroglucinol staining revealed that the lignin content of the cell wall in the stem cortex and in the stem vascular tissue near the cortex was higher in the lodging-resistant lines than in the lodging-sensitive lines. Analysis of strand-specific RNA-seq transcriptome showed that a total of 793 genes were up-regulated and 713 genes were down-regulated in lodging-resistant lines relative to lodging-sensitive lines. The up-regulated genes in lodging-resistant lines were enriched in cell wall biogenesis. These results indicated that modification of cell wall biosynthesis would contribute to lodging resistance of maize.

The Arabidopsis Anaphase-Promoting Complex/Cyclosome Subunit 1 is Critical for Both Female Gametogenesis and Embryogenesis

Anaphase-promoting complex/cyclosome （APC/C）, a multisubunit E3 ligase, plays a critical role in cell cycle control, but the functional characterization of each subunit has not yet been completed. To investigate the function of APC1 in Arabidopsis, we analyzed four mutant alleles of APC1, and found that mutation in APC1 resulted in significantly reduced plant fertility, accumulation of cyclin B, and disrupted auxin distribution in embryos. The three mutant alleles apcl-1, apcl-2 and apcl-3 shared variable defects in female gametogenesis including degradation, abnormal nuclear number, and disrupted polarity of nuclei in the embryo sac as well as in embryogenesis, in which embryos were arrested at multiple stages. All of these defects are similar to those previously identified in apc4. The mutant apcl-4, in which the T-DNA was inserted after the transmembrane domain at the C-terminus, showed much more severe phenotypes; that is, most of the ovules were arrested at the one-nucleate female gametophyte stage （stage FG1）. In the apcl apc4 double mutants, the fertility was further reduced by one-third in apcl-ll＋ apc4-1/＋, and in some cases no ovules even survived in siliques of apcl-4/＋ apc4-1/＋. Our data thus suggest that APC1, an essential component of APC/C, plays a synergistic role with APC4 both in female gametogenesis and in embryogenesis.

A nuclear-encoded mitochondrial gene AtCIB22 is essential for plant development in Arabidopsis

Complex I （the NADH：ubiquinone oxidoreductase） of the mitochondrial respiratory chain is a complicated, multi-subunit, membrane- bound assembly and contains more than 40 different proteins in higher plants. In this paper, we characterize the Arabidopsis homologue （designated as AtCIB22） of the B22 subunit of eukaryotic mitochondriai Complex I. AtCIB22 is a single-copy gene and is highly con- served throughout eukaryotes. AtCIB22 protein is located in mitochondria and the AtC1B22 gene is widely expressed in different tissues. Mutant Arabidopsis plants with a disrupted AtC1B22 gene display pleiotropic phenotypes including shorter roots, smaller plants and de- layed flowering. Stress analysis indicates that the AtC1B22 mutants＇ seed germination and early seedling growth are severely inhibited by sucrose deprivation stress but more tolerant to ethanol stress. Molecular analysis reveals that in moderate knockdown AtCIB22 mutants, genes including cell redox proteins and stress related proteins are significantly up-regulated, and that in severe knockdown AtCIB22 mu- tants, the alternative respiratory pathways including NDA1, NDB2, AOXla and AtPUMP1 are remarkably elevated. These data demon- strate that AtCIB22 is essential for plant development and mitochondrial electron transport chains in Arabidopsis. Our findings also en- hance our understanding about the physiological role of Complex I in plants.

Overexpression of a New Putative Membrane Protein Gene AtMRB1 Results in Organ Size Enlargement in Arabidopsis

Arabidopsis AtMRB1 is predicted to encode a novel protein of 432 amino acid residues in length, with four putative transmembrane domains. In the present study, characterization of AtMRB1 is conducted. Green fluorescent protein （GFP） fusion protein assay showed that AtMRB1 was located in the plasma membrane. Transgenic lines overexpressing AtMRB1 driven by a CaMV 35S promoter were generated. Statistic analysis showed that, during the seedling stage, the organ sizes of the transgenic lines including hypocotyl length, root length and root weight were significantly larger than those of the wild type plants under both light and dark conditions. In the adult plant stage, the AtMRB1 overexpressor plants were found to have larger organ sizes in terms of leaf length and width, and increased number of cauline leaves and branches when bolting. Further observation indicated that the larger leaf size phenotype was due to a larger number of mesophyll cells, the size of which was not altered. Quantitative real-time polymerase chain reaction analysis showed that the transcription of ANT, ROT3 and GRF5 were upregulated in the AtMRBl.overexpressor plants. These data suggest that AtMRB1 is possibly a positive regulator of organ size development in Arabidopsis, mainly through cell number control.

HTPdb and HTPtools:Exploiting maize haplotypetag polymorphisms for germplasm resource analyses and genomics-informed breeding

Along with rapid advances in high-throughput-sequencing technology,the development and application of molecular markers has been critical for the progress that has been made in crop breeding and genetic research.Desirable molecular markers should be able to rapidly genotype tens of thousands of breeding accessions with tens to hundreds of markers.In this study,we developed a multiplex molecular marker,the haplotype-tag polymorphism(HTP),that integrates Maize6H-60K array data from 3,587 maize inbred lines with 6,375 blocks from the recombination block map.After applying strict filtering criteria,we obtained 6,163 highly polymorphic HTPs,which were evenly distributed in the genome.Furthermore,we developed a genome-wide HTP analysis toolkit,HTPtools,which we used to establish an HTP database(HTPdb)covering the whole genomes of 3,587 maize inbred lines commonly used in breeding.A total of 172,921 non-redundant HTP allelic variations were obtained.Three major HTPtools modules combine seven algorithms(e.g.,chain Bayes probability and the heterotic-pattern prediction algorithm)and a new plotting engine named“BCplot”that enables rapid visualization of the background information of multiple backcross groups.HTPtools was designed for big-data analyses such as complex pedigree reconstruction and maize heterotic-pattern prediction.The HTP-based analytical strategy and the toolkit developed in this study are applicable for high-throughput genotyping and for genetic mapping,germplasm resource analyses,and genomics-informed breeding in maize.