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During the processes of rice domestication and improvement, a trade-off effect between grain number and grain weight was a major obstacle for increasing yield. Here, we identify a critical gene COG1, encoding the transcription factor OsMADS17, with a 65-bp deletion in the 5′ untranslated region (5′ UTR) presented in cultivated rice increasing grain number and grain weight simultaneously through decreasing mRNA translation efficiency. OsMADS17 controls grain yield by regulating multiple genes and that the interaction with one of them, OsAP2-39, has been characterized. Besides, the expression of OsMADS17 is regulated by OsMADS1 directly. It indicates that OsMADS1-OsMADS17-OsAP2-39 participates in the regulatory network controlling grain yield, and downregulation of OsMADS17 or OsAP2-39 expression can further improve grain yield by simultaneously increasing grain number and grain weight. Our findings provide insights into understanding the molecular basis co-regulating rice yield-related traits, and offer a strategy for breeding higher-yielding rice varieties. The trade-off between grain number and grain weight is a major obstacle for increasing rice yield. Here, the authors show that variation in 5' UTR of OsMADS17 can simultaneously increase grain number and grain weight through decreasing mRNA translation efficiency. [ABSTRACT FROM AUTHOR]

Asian cultivated rice (Oryza sativa L.) has two subspecies, indica and japonica, which display clear differences in yield-related traits and environmental adaptation. Here, we developed a set of chromosome segment substitution lines (CSSLs) from an advanced backcross between japonica variety C418, as the recipient, and indica variety IR24, as the donor. Through evaluating the genotypes and phenotypes of 181 CSSLs, a total of 85 quantitative trait loci (QTLs) for 14 yield-related traits were detected, with individual QTLs explaining from 6.2 to 42.9% of the phenotypic variation. Moreover, twenty-six of these QTLs could be detected in the two trial sites (Beijing and Hainan). Among these loci, the QTLs for flag leaf width and effective tiller number, qFLW4.2 and qETN4.2, were delimited to an approximately 256-kb interval on chromosome 4. Through a comparison of nucleotide sequences and expression levels in "C418" and the CSSL CR31 containing qFLW4.2 and qETN4.2, we found that the NAL1 (LOC_Os04g52479) gene was the candidate gene for qFLW4.2 and qETN4.2. Our results show that CSSLs are powerful tools for identifying and fine-mapping QTLs, while the novel QTLs identified in this study will also provide new genetic resources for rice improvement. [ABSTRACT FROM AUTHOR]

Callus browning, a common trait derived from the indica rice cultivar (Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 (BOC1) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession (Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1, which consequently improves the genetic transformation efficiency. The presence of a Tourist-like miniature inverted-repeat transposable element (Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation. Callus browning heavily affects indica rice transformation regeneration. Here, the authors show transposon insertion in the promoter of BOC1 gene, encoding a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE protein, can upregulate its expression and decrease callus browning in cultivated rice by releasing oxidative stress. [ABSTRACT FROM AUTHOR]

Navigation requires not only the execution of locomotor programs but also high arousal and real-time retrieval of spatial memory that is often associated with hippocampal theta oscillations. However, the neural circuits for coordinately controlling these important processes remain to be fully dissected. Here we show that the activity of the neuromedin B (NMB) neurons in the nucleus incertus (NI) is tightly correlated with mouse locomotor speed, arousal level, and hippocampal theta power. These processes are reversibly suppressed by optogenetic inhibition and rapidly promoted by optogenetic stimulation of NI NMB neurons. These neurons form reciprocal connections with several subcortical areas associated with arousal, theta oscillation, and premotor processing. Their projections to multiple downstream stations regulate locomotion and hippocampal theta, with the projection to the medial septum being particularly important for promoting arousal. Therefore, NI NMB neurons functionally impact the neural circuit for navigation control according to particular brains states. In addition to activation of locomotor circuits, navigation also requires regulation of arousal and spatial memory processes. Here the authors identify neuromedin B neurons in the nucleus incertus and their subcortical projections in controlling these various processes during navigation. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) is a toxic heavy metal that is harmful to human health. Oryza nivara, a wild rice species, serves as a germplasm pool for various favorable genes that can be used in cultivated rice. To detect quantitative trait loci (QTLs) and germplasm related to Cd tolerance in O. nivara, we analyzed one set of introgression lines with a high-density genetic map. Seven QTLs related to Cd tolerance were identified on chromosomes 2, 4, 6, and 8, and an allele of one locus (Bin774) from O. nivara affected two phenotypic traits and was able to increase Cd tolerance in rice. In a further analysis of GeneChip data released by the National Center for Biotechnology Information, we explored five candidate genes induced by Cd stress in the QTL region: two oxidoreductase genes (aldo-keto reductase genes LOC_Os04g27060 and LOC_Os04g26920); one terpene synthase gene (LOC_Os04g27190); one cysteine-rich receptor-like protein kinase gene (LOC_Os04g25060); and one serine carboxypeptidase homolog gene OsSCP23 (LOC_Os04g25560). One Cd-tolerant introgression line (Ra44) was also obtained, with a significantly higher survival rate under Cd stress (93.8%) compared to recipient parent 93-11 (2.3%). Identification of candidate genes and the Cd-tolerant introgression line Ra44 should facilitate further investigation of the mechanism of rice tolerance to Cd contamination. [ABSTRACT FROM AUTHOR]

Seed dormancy is an important trait during the domestication of major crops. Dormant seeds are unable to germinate under conditions normally suitable for non-dormant seeds. Quantitative trait loci (QTLs) and genes affecting seed dormancy in sorghum remain largely unknown. To identify the genomic regions controlling seed dormancy in sorghum, we produced two F segregating populations from two crosses between a deep dormant weedy line B140 (as the female parent) and two weak dormant grain lines CK60B and MS138B (as the male parents). A genetic linkage map of the B140/CK60B population was constructed with 216 simple sequence repeat (SSR) markers spanning 1710.3 cM. One QTL on chromosome 4 and two QTLs on chromosome 7 were identified in the B140/CK60B population. They accounted for 17.9 to 24.9% of the phenotypic variance using a simple interval mapping method. The QTL on chromosome 4 was verified in another F mapping population (MS138B/B140). To understand the mechanism of dormancy, we conducted an expression analysis of four sorghum genes encoding homologs of dormancy genes of other plant species: Vp1 (maize), DOG1 (Arabidopsis), qSD12 and Sdr4 (rice). We demonstrated that there were clear differences in the expression level of all these four genes between the two parental lines with different seed dormancy level, and their expression were also tissue-specific with the expression levels of qSD12 low throughout all growth stages and tissues in B140. Our findings will help to define the genetic mechanism of seed dormancy in sorghum, and the identified QTLs may be useful biomarker for selection in sorghum improvement programs. [ABSTRACT FROM AUTHOR]

Plant height and tiller number are indispensible for the establishment of grain production in rice ( Oryza sativa L.). A new rice mutant high- tillering dwarf 3 ( htd3) exhibiting more tiller number and shorter culm length than the wild-type Guichao 2 (GC2, an indica cultivar) was used to investigate the global gene expression patterns at days after germination 25 (DAG25) and DAG60. In this study, we identified 305 and 987 genes with at least twofold change in gene expression level at DAG25 and DAG60 respectively using the rice microarray chip. Gene ontology enrichment analysis of these twofold change regulated genes revealed that large numbers of genes were involved in binding activity, catalytic activity and metabolic process. The chip results also showed that some of the regulated genes involved in diverse molecular pathways, including gibberellin pathway, brassinosteroid pathway and auxin signal, had significant differences in gene expression abundance at DAG60. This genome-wide gene expression analysis could provide a new opportunity to uncover the regulation mechanisms of the development of culm and tiller, two important components of yields in rice. [ABSTRACT FROM AUTHOR]

The developmental regulation of grasses lemma and palea and their relationship to the floral organs in dicots had been variously explicated and extensively debated. Here, we characterized a triangular hull mutant th1- 1 from EMS-mutagenized Oryza sativa ssp. indica cv. 93-11. The th1- 1 mutant exhibited obviously triangular hull with tortuous and slender lemma/palea. Using a map-based cloning strategy, the TH1 gene was narrowed down to a 60-kb region on the long arm of chromosome 2. Sequence verification revealed that the th1- 1 mutant harbored 1-bp deletion in exon 2 of LOC_Os02g56610 which resulted in a frame-shift mutation. The RNA-interference transgenic plants of LOC_Os02g56610 displayed a similar phenotype to the th1 mutant. Consequently, LOC_Os02g56610 was identified as the TH1 gene which encoded 248 amino acids and contained a DUF640 domain. RT-PCR analysis and GUS staining showed that the transcripts of TH1 mainly accumulated in young inflorescence, lemma and palea of spikelet. These results suggested that TH1 was an important gene controlling the lemma and palea development in rice. [ABSTRACT FROM AUTHOR]

The transition from the prostrate growth of ancestral wild rice (O. rufipogon Griff.) to the erect growth of Oryza sativa cultivars was one of the most critical events in rice domestication. This evolutionary step importantly improved plant architecture and increased grain yield. Here we find that prostrate growth of wild rice from Yuanjiang County in China is controlled by a semi-dominant gene, PROG1 (PROSTRATE GROWTH 1), on chromosome 7 that encodes a single Cys2-His2 zinc-finger protein. prog1 variants identified in O. sativa disrupt the prog1 function and inactivate prog1 expression, leading to erect growth, greater grain number and higher grain yield in cultivated rice. Sequence comparison shows that 182 varieties of cultivated rice, including 87 indica and 95 japonica cultivars from 17 countries, carry identical mutations in the prog1 coding region that may have become fixed during rice domestication. [ABSTRACT FROM AUTHOR]

Discusses the identification and mapping of quantitative trait loci (QTL) controlling cold-tolerance of Chinese common wild rice, Oryza rufipogan at booting to flowering stages. Recipient and donor rice; Chromosomes containing QTL for cod-tolerance; Sterility QTL that could reduce the seed set rate of the backcross progenics.

The molecular mechanisms of symbiosis in cultivated peanut with a 'crack entry' infection process are largely understudied. In this study, we investigated the root transcriptional profiles of two pairs of non-nodulating (nod−) and nodulating (nod+) sister inbred peanut lines, E4/E5 and E7/E6, and their nod+ parents, F487A and PI262090 during rhizobial infection and nodule initiation by using RNA-seq technology. A total of 143, 101, 123, 215, 182, and 289 differentially expressed genes (DEGs) were identified in nod− E4, E7 and nod+ E5, E6, F487A, and PI262090 after inoculation with Bradyrhizobium sp. Different deficiencies at upstream of symbiotic signaling pathway were revealed in the two nod− genotypes. DEGs specific in nod+ genotypes included orthologs to some known symbiotic signaling pathway genes, such as NFR5, NSP2, NIN, ERN1, and many other novel and/or functionally unknown genes. Gene ontology (GO) enrichment analysis of nod+ specific DEGs revealed 54 significantly enriched GO terms, including oxidation-reduction process, metabolic process, and catalytic activity. Genes related with plant defense systems, hormone biosynthesis and response were particularly enriched. To our knowledge, this is the first report revealing symbiosis-related genes in a genome-wide manner in peanut representative of the 'crack entry' species. [ABSTRACT FROM AUTHOR]