Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions

Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies(GWAS). Several rice populations have been re-sequenced in the past decade;however, many major Chinese rice cultivars were not included in these studies. Here, we report large-scale genomic and phenotypic datasets for a collection mainly comprised of 1,275 rice accessions of widely planted cultivars and parental hybrid rice lines from China. The population was divided into three indica/Xian and three japonica/Geng phylogenetic subgroups that correlate strongly with their geographic or breeding origins. We acquired a total of 146 phenotypic datasets for 29 agronomic traits under multi-environments for different subpopulations. With GWAS, we identified a total of 143 significant association loci, including three newly identified candidate genes or alleles that control heading date or amylose content. Our genotypic analysis of agronomically important genes in the population revealed that many favorable alleles are underused in elite accessions, suggesting they may be used to provide improvements in future breeding efforts. Our study provides useful resources for rice genetics research and breeding.

Long Non-coding RNAs and Their Biological Roles in Plants

With the development of genomics and bioinformatics, especially the extensive applications of high-throughput sequencing technology, more transcriptional units with little or no protein-coding potential have been discovered. Such RNA molecules are called non- protein-coding RNAs （npcRNAs or ncRNAs）. Among them, long npcRNAs or ncRNAs 0npcRNAs or lncRNAs） represent diverse classes of transcripts longer than 200 nucleotides. In recent years, the lncRNAs have been considered as important regulators in many essential biological processes. In plants, although a large number of lncRNA transcripts have been predicted and identified in few species, our current knowledge of their biological functions is still limited. Here, we have summarized recent studies on their identification, characteristics, classification, bioinformatics, resources, and current exploration of their biological functions in olants.

Identification of salt-tolerance QTL in rice(Oryza sativa L.)

Quantitative trait loci (QTLs) controlling salt-tolerance at the seedling stage in rice (Oryza sativa L.) were identified by interval mapping (SIM) and composite interval mapping (CIM) using a doubled haploid population ZJDH and its high resolution genetic linkage map. The population was derived from an inter-subspecific cross between an indica variety Zhaiyeqing8 (ZYQ8) and a japonica variety Jingxi17 (JX17). Analysis of survival days of seedlings treated with 0.7% NaCl revealed that a major salt-tolerance quantitative trait locus (QTL), Std, was present between markers RG612 and C131 on chromosome 1 when using both MAPMAKER/QTL 1.1 and PLABQTL 1.0 (SIM).Its allele which contributes to salt-tolerance was from ZYQ8. In addition, seven more QTLs which give additive effect on salt-tolerance are identified when using PLABQTL(CIM), and most of them were from JX17.

Identification and characterization of rice blast resistance gene Pid4 by a combination of transcriptomic profiling and genome analysis

Map-based cloning of plant disease resistance (R) genes is time-consuming. Here, we reported the isolation of blast R gene Pid4 using comparative transcriptomic profiling and genome-wide sequence analysis. Pid4 encodes a coiled-coil nucleotide-binding site leucine-rich repeat(CC-NBS-LRR) protein and is constitutively expressed at diverse developmental stages in the rice variety Digu. The Pid4 protein is localized in both the nucleus and cytoplasm. Introduction of Pid4 into susceptible rice cultivars confers race-specific resistance to leaf and neck blast. Amino acid sequence comparison and blast resistance spectrum tests showed that Pid4 is a novel R gene, different from the previously reported R genes located in the same gene cluster. A Pid4 Indel marker was developed to facilitate the identification of Pid4 in different rice varieties. We demonstrated that a plant R gene can be quickly isolated using transcriptomic profiling coupled with genome-wide sequence analysis.

Starch RVA profile parameters of rice are mainly controlled by Wx gene

Quantitative trait locus (QTLs) mapping for rapid visco analyser (RVA) profile parameters has been carried out by using a double haploid (DH) population derived from a cross between indica variety Zhai-Ye-Qing 8 and j’aponica variety Jing-Xi 17 and its genetic linkage map. The results indicate that the segregation of the RVA profiles is continually distributed a-mong the DH lines, and some DH lines show transgressive segregation for all the parameters.

A gain-of-function mutation in Msl10 triggers cell death and wound-induced hyperaccumulation of jasmonic acid in Arabidopsis

Jasmonates（JAs） are rapidly induced after wounding and act as key regulators for wound induced signaling pathway. However, what perceives the wound signal and how that triggers JA biosynthesis remains poorly understood. To identify components involved in Arabidopsis wound and JA signaling pathway, we screened for mutants with abnormal expression of a luciferase reporter, which is under the control of a wound-responsive promoter of an ethylene response factor（ERF） transcription factor gene, RAP2.6（Related to APetala 2.6）.The rea1（RAP2.6 expresser in shoot apex） mutant constitutively expressed the RAP2.6-LUC reporter gene in young leaves.Along with the typical JA phenotypes including shorter petioles,loss of apical dominance, accumulation of anthocyanin pigments and constitutive expression of JA response gene, rea1 plants also displayed cell death and accumulated high levels of JA in response to wounding. The phenotype of rea1 mutant is caused by a gain-of-function mutation in the C-terminus of a mechanosensitive ion channel MscS-like 10（MSL10）. MSL10 is localized in the plasma membrane and is expressed predominantly in root tip, shoot apex and vascular tissues. These results suggest that MSL10 is involved in the wound-triggered early signal transduction pathway and possibly in regulating the positive feedback synthesis of JA.

The Interactions among DWARF10,Auxin and Cytokinin Underlie Lateral Bud Outgrowth in Rice

Previous studies have shown that DWARFIO （D10） is a rice ortholog of MAX41RMS1/DAD1, encoding a carotenoid cleavage dioxygenase and functioning in strigolactones/strigolactone-derivatives （SL） biosynthesis. Here we use DIO. RNA interference （RNAi） transgenic plants similar to dlO mutant in phenotypes to investigate the interactions among DIO, auxin and cytokinin in regulating rice shoot branching. Auxin levels in node 1 of both decapitated DIO.RNAi and wild type plants decreased significantly, showing that decapitation does reduce endogenous auxin concentration, but decapitation has no clear effects on auxin levels in node 2 of the same plants. This implies that node 1 may be the location where a possible interaction between auxin and DIO gene would be detected. DIO expression in node 1 is inhibited by decapitation, and this inhibition can be restored by exogenous auxin application, indicating that DIO may play an important role in auxin regulation of SL. The decreased expression of most OsPINs in shoot nodes of DIO-RNAi plants may cause a reduced auxin transport capacity. Furthermore, effects of auxin treatment of decapitated plants on the expression of cytokinin biosynthetic genes suggest that DIO promotes cytokinin biosynthesis by reducing auxin levels. Besides, in DIO-RNAi plants, decreased storage cytokinin levels in the shoot node may partly account for the increased active cytokinin contents, resulting in more tillering phenotypes.

Transcriptional Characteristics of Xa21-mediated Defense Responses in Rice

Bacterial blight,caused by Xanthomonas oryzae pv.oryzae（Xoo）,is the most destructive bacterial disease of rice.The cloned rice gene Xa21 confers resistance to a broad spectrum of Xoo races.To identify genes involved in Xa21-mediated immunity,a whole-genome oligonucleotide microarray of rice was used to profile the expression of rice genes between incompatible interactions and mock treatments at 0,4,8,24,72 and 120 h post inoculation（hpi） or between incompatible and compatible interactions at 4 hpi,respectively.A total of 441 differentially expressed genes,designated as XDGs（Xa21 mediated differentially expressed genes）,were identified.Based on their functional annotations,the XDGs were assigned to 14 categories,including defense-related,signaling,transcriptional regulators.Most of the defense-related genes belonged to the pathogenesis-related gene family,which was induced dramatically at 72 and 120 hpi.Interestingly,most signaling and transcriptional regulator genes were downregulated at 4 and 8 hpi,suggesting that negative regulation of cellular signaling may play a role in the Xa21-mediated defense response.Comparison of expression profiles between Xa21- and other R gene-mediated defense systems revealed interesting common responses.Representative XDGs with supporting evidences were also discussed.

Microdissection and amplification of the chromosome arm 5S in a rice telo-tetrasomic

The rice aneuploids with telochromosomes are ideal genetic stocks for chromosome arm identification and microdissection. A rice telo-tetrasomic line with two extra short arms of chromosome 5 (5S) was used in the present study. The arms of 5S were microdissected from the prometaphase cells in mitosis and amplified with linker adaptor PCR (LA-PCR). The amplified fragments, ranging from 200-3000 bp, were confirmed to be from the rice chromosome arm 5S by the rice STS and microsatellite markers.

Extension of the rice DH population genetic map with microsatellite markers

Genetic mapping of microsatellite markers was carried out in a rice DH population derived from a cross between Zaiyeqing 8 (indica) and Jingxi 17 (japonica). A total of 89 microsatellite markers, including 84 (GA)-n, 2(TCT) n, 2(ATT)-n and 1(ATC) n motifs, were integrated relatively evenly into the established genetic map of the DH population. This will facilitate the utilization of microsatillite markers in rice gene mapping and marker aided breeding.