Even as the study of plant genomics rapidly develops through the use of high-throughput sequencing techniques, traditional plant phenotyping lags far behind. Here we develop a high-throughput rice phenotyping facility (HRPF) to monitor 13 traditional agronomic traits and 2 newly defined traits during the rice growth period. Using genome-wide association studies (GWAS) of the 15 traits, we identify 141 associated loci, 25 of which contain known genes such as the Green Revolution semi-dwarf gene, SD1. Based on a performance evaluation of the HRPF and GWAS results, we demonstrate that high-throughput phenotyping has the potential to replace traditional phenotyping techniques and can provide valuable gene identification information. The combination of the multifunctional phenotyping tools HRPF and GWAS provides deep insights into the genetic architecture of important traits.

SummaryEnhancer trapping has provided a powerful strategy for identifying novel genes and regulatory elements. In this study, we adopted an enhancer trap system, consisting of the GAL4/VP16±UAS elements with GUS as the reporter, to generate a trapping population of rice. Currently, 31 443 independent transformants were obtained from two cultivars using Agrobacterium-mediated T-DNA insertion. PCR tests and DNA blot hybridization showed that about 94% of the transformants contained T-DNA insertions. The transformants carried, on average, two copies of the T-DNA, and 42% of the transformants had single-copy insertions. Histochemical assays of approximately 1000 T 0 plants revealed various patterns of the reporter gene expression, including expression in only one tissue, and simultaneously in two or more tissues. The expression pattern of the reporter gene in T 1 families corresponded well with the T 0 plants and segregated in a 3 : 1 Mendelian ratio in majority of the T 1 families tested. The frequency of reporter gene expression in the enhancer trap lines was much higher than that in gene trap lines reported previously. Analysis of¯anking sequences of T-DNA insertion sites from about 200 transformants showed that almost all the sequences had homology with the sequences in the rice genome databases. Morphologically conspicuous mutations were observed in about 7.5% of the 2679 T 1 families that were ®eld-tested, and segregation in more than one-third of the families ®t the 3 : 1 ratio. It was concluded that GAL4/VP16±UAS elements provided a useful system for enhancer trap in rice.

Transition from the vegetative phase to reproductive phase is a crucial process in the life cycle of higher plants. Although the molecular mechanisms of flowering regulation have been extensively characterized in a number of plant species, little is known regarding how the transition process initiates. Here, we show that the Rice Indeterminate 1 (RID1) gene acts as the master switch for the transition from the vegetative to reproductive phase. RID1 encodes a Cys-2/His-2-type zinc finger transcription factor that does not have an ortholog in Arabidopsis spp. A RID1 knockout (rid1), mutated by T-DNA insertion, never headed after growing for >500 days under a range of growth conditions and is thus referred to as a never-flowering phenotype. This mutation-suppressed expression of the genes is known to be involved in flowering regulation, especially in the Ehd1/Hd3a pathway and a series of RFT homologs. RID1 seems to be independent of the circadian clock. A model was proposed to place RID1 in the molecular pathways of flowering regulation in rice, for which there are two indispensable elements. In the first, RID1 is controlling the phase transition and initiation of floral induction. In the other, the

With increasing demand for novel traits in crop breeding, the plant research community faces the challenge of quantitatively analyzing the structure and function of large numbers of plants. A clear goal of high-throughput phenotyping is to bridge the gap between genomics and phenomics. In this study, we quantified 106 traits from a maize (Zea mays) recombinant inbred line population (n = 167) across 16 developmental stages using the automatic phenotyping platform. Quantitative trait locus (QTL) mapping with a high-density genetic linkage map, including 2,496 recombinant bins, was used to uncover the genetic basis of these complex agronomic traits, and 988 QTLs have been identified for all investigated traits, including three QTL hotspots. Biomass accumulation and final yield were predicted using a combination of dissected traits in the early growth stage. These results reveal the dynamic genetic architecture of maize plant growth and enhance ideotype-based maize breeding and prediction.

This paper presents SgxPectre Attacks that exploit the recently disclosed CPU bugs to subvert the confidentiality and integrity of SGX enclaves. Particularly, we show that when branch prediction of the enclave code can be influenced by programs outside the enclave, the control flow of the enclave program can be temporarily altered to execute instructions that lead to observable cache-state changes. An adversary observing such changes can learn secrets inside the enclave memory or its internal registers, thus completely defeating the confidentiality guarantee offered by SGX. To demonstrate the practicality of our SgxPectre Attacks, we have systematically explored the possible attack vectors of branch target injection, approaches to win the race condition during enclave's speculative execution, and techniques to automatically search for code patterns required for launching the attacks. Our study suggests that any enclave program could be vulnerable to SgxPectre Attacks since the desired code patterns are available in most SGX runtimes (e.g., Intel SGX SDK, Rust-SGX, and Graphene-SGX). Most importantly, we have applied SgxPectre Attacks to steal seal keys and attestation keys from Intel signed quoting enclaves. The seal key can be used to decrypt sealed storage outside the enclaves and forge valid sealed data; the attestation key can be used to forge attestation signatures. For these reasons, SgxPectre Attacks practically defeat SGX's security protection. This paper also systematically evaluates Intel's existing countermeasures against SgxPectre Attacks and discusses the security implications.