BackgroundIn plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana. In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages.ResultsWe used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed.ConclusionsThis study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development.

The maize (Zea mays ssp. mays) wild ancestor, teosinte, has three times the seed protein content of most modern inbreds and hybrids, but the mechanisms responsible for this trait are unknown. We created a contiguous haplotype DNA sequence of a teosinte, Zea mays ssp. Parviglumis, with Trio-Binning, and map-based cloned a major high-protein QTL, teosinte high protein 9 (Thp9) on chromosome 9. Thp9 encodes an asparagine synthetase 4 that is highly expressed in teosinte, but not in the B73 inbred, where a deletion in the 10 th intron of Thp9-B73 causes incorrect splicing of Thp9-B73 transcripts. Transgenic expression of Thp9-teosinte in B73 significantly increased seed protein content. Introgression of Thp9-teosinte into modern maize inbreds and hybrids greatly enhanced free amino acid accumulation, especially asparagine, throughout the plant, increasing seed protein content without affecting yield. Thp9-teosinte appears to increase nitrogen utilization efficiency, important for promoting a high yield under low nitrogen conditions.

SummaryHeterosis, or hybrid vigour, is a predominant phenomenon in plant genetics, serving as the basis of crop hybrid breeding, but the causative loci and genes underlying heterosis remain unclear in many crops. Here, we present a large‐scale genetic analysis using 5360 offsprings from three elite maize hybrids, which identifies 628 loci underlying 19 yield‐related traits with relatively high mapping resolutions. Heterotic pattern investigations of the 628 loci show that numerous loci, mostly with complete–incomplete dominance (the major one) or overdominance effects (the secondary one) for heterozygous genotypes and nearly equal proportion of advantageous alleles from both parental lines, are the major causes of strong heterosis in these hybrids. Follow‐up studies for 17 heterotic loci in an independent experiment using 2225 F2 individuals suggest most heterotic effects are roughly stable between environments with a small variation. Candidate gene analysis for one major heterotic locus (ub3) in maize implies that there may exist some common genes contributing to crop heterosis. These results provide a community resource for genetics studies in maize and new implications for heterosis in plants.

The present study profiled and analyzed gene expression of the maize ear at four key developmental stages. Based on genome-wide profile analysis, we detected differential mRNA of maize genes. Some of the differentially expressed genes (DEGs) were predicted to be potential candidates of maize ear development. Several well-known genes were found with reported mutant analyses, such as, compact plant2 (ct2), zea AGAMOUS homolog1 (zag1), bearded ear (bde), and silky1 (si1). MicroRNAs such as microRNA156 were predicted to target genes involved in maize ear development. Antisense transcripts were widespread throughout all the four stages, and are suspected to play important roles in maize ear development. Thus, identification and characterization of important genes and regulators at all the four developmental stages will contribute to an improved understanding of the molecular mechanisms responsible for maize ear development.

Muscle development in domesticated animals is important for meat production. Furthermore, intramuscular fat content is an important trait of meat intended for consumption. Here, we examined differences in the expression of factors related to myogenesis, adipogenesis and skeletal muscle growth during fetal muscle development of lean (Yorkshire) and obese (Chenghua) pig breeds. At prenatal days 50 (d50) and 90 (d90), muscles and sera were collected from pig fetuses. Histology revealed larger diameters and numbers of myofibers in Chenghua pig fetuses than those in Yorkshire pig fetuses at d50 and d90. Yorkshire fetuses had higher serum concentrations of myostatin (d90), a negative regulator for muscle development, and higher mRNA expression of the growth hormone receptor Ghr (d90), myogenic MyoG (d90) and adipogenic LPL (d50). By contrast, Chenghua fetuses exhibited higher serum concentration of growth hormone (d90), and higher mRNA expression of myogenic MyoD (d90) as well as adipogenic PPARG and FABP4 (d50). Our results revealed distinct expression patterns in the two pig breeds at each developmental stage before birth. Compared with Chenghua pigs, development and maturation of fetal skeletal muscles may occur earlier in Yorkshire pigs, but the negative regulatory effects of myostatin may suppress muscle development at the later stage.