Mei-Zhen Zhu

A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase

Grain weight is one of the most important components of grain yield and is controlled by quantitative trait loci (QTLs) derived from natural variations in crops. However, the molecular roles of QTLs in the regulation of grain weight have not been fully elucidated. Here, we report the cloning and characterization of GW2, a new QTL that controls rice grain width and weight. Our data show that GW2 encodes a previously unknown RING-type protein with E3 ubiquitin ligase activity, which is known to function in the degradation by the ubiquitin-proteasome pathway. Loss of GW2 function increased cell numbers, resulting in a larger (wider) spikelet hull, and it accelerated the grain milk filling rate, resulting in enhanced grain width, weight and yield. Our results suggest that GW2 negatively regulates cell division by targeting its substrate(s) to proteasomes for regulated proteolysis. The functional characterization of GW2 provides insight into the mechanism of seed development and is a potential tool for improving grain yield in crops.

A rice quantitative trait locus for salt tolerance encodes a sodium transporter

Many important agronomic traits in crop plants, including stress tolerance, are complex traits controlled by quantitative trait loci (QTLs). Isolation of these QTLs holds great promise to improve world agriculture but is a challenging task. We previously mapped a rice QTL, SKC1, that maintained K+ homeostasis in the salt-tolerant variety under salt stress, consistent with the earlier finding that K+ homeostasis is important in salt tolerance. To understand the molecular basis of this QTL, we isolated the SKC1 gene by map-based cloning and found that it encoded a member of HKT-type transporters. SKC1 is preferentially expressed in the parenchyma cells surrounding the xylem vessels. Voltage-clamp analysis showed that SKC1 protein functions as a Na+-selective transporter. Physiological analysis suggested that SKC1 is involved in regulating K+/Na+ homeostasis under salt stress, providing a potential tool for improving salt tolerance in crops.

QTLs for Na+ and K+ uptake of the shoots and roots controlling rice salt tolerance

An F2 and an equivalent F3 population derived from a cross between a high salt-tolerance indica variety, Nona Bokra, and a susceptible elite japonica variety, Koshihikari, were produced. We performed QTL mapping for physiological traits related to rice salt-tolerance. Three QTLs for survival days of seedlings (SDSs) under salt stress were detected on chromosomes 1, 6 and 7, respectively, and explained 13.9% to 18.0% of the total phenotypic variance. Based on the correlations between SDSs and other physiological traits, it was considered that damage of leaves was attributed to accumulation of Na+ in the shoot by transport of Na+ from the root to the shoot in external high concentration. We found eight QTLs including three for three traits of the shoots, and five for four traits of the roots at five chromosomal regions, controlled complex physiological traits related to rice salt-tolerance under salt stress. Of these QTLs, the two major QTLs with the very large effect, qSNC-7 for shoot Na+ concentration and qSKC-1 for shoot K+ concentration, explained 48.5% and 40.1% of the total phenotypic variance, respectively. The QTLs detected between the shoots and the roots almost did not share the same map locations, suggesting that the genes controlling the transport of Na+ and K+ between the shoots and the roots may be different.

A previously unknown zinc finger protein, DST, regulates drought and salt tolerance in rice via stomatal aperture control

Abiotic stresses, such as drought and salinity, lead to crop growth damage and a decrease in crop yields. Stomata control CO(2) uptake and optimize water use efficiency, thereby playing crucial roles in abiotic stress tolerance. Hydrogen peroxide (H(2)O(2)) is an important signal molecule that induces stomatal closure. However, the molecular pathway that regulates the H(2)O(2) level in guard cells remains largely unknown. Here, we clone and characterize DST (drought and salt tolerance)-a previously unknown zinc finger transcription factor that negatively regulates stomatal closure by direct modulation of genes related to H(2)O(2) homeostasis-and identify a novel pathway for the signal transduction of DST-mediated H(2)O(2)-induced stomatal closure. Loss of DST function increases stomatal closure and reduces stomatal density, consequently resulting in enhanced drought and salt tolerance in rice. These findings provide an interesting insight into the mechanism of stomata-regulated abiotic stress tolerance, and an important genetic engineering approach for improving abiotic stress tolerance in crops.

Genetic control of rice plant architecture under domestication

The closely related wild rice species Oryza rufipogon is considered the progenitor of cultivated rice (Oryza sativa). The transition from the characteristic plant architecture of wild rice to that of cultivated rice was one of the most important events in rice domestication; however, the molecular basis of this key domestication transition has not been elucidated. Here we show that the PROG1 gene controls aspects of wild-rice plant architecture, including tiller angle and number of tillers. The gene encodes a newly identified zinc-finger nuclear transcription factor with transcriptional activity and is mapped on chromosome 7. PROG1 is predominantly expressed in the axillary meristems, the site of tiller bud formation. Rice transformation experiments demonstrate that artificial selection of an amino acid substitution in the PROG1 protein during domestication led to the transition from the plant architecture of wild rice to that of domesticated rice.

Overexpression of the trehalose-6-phosphate phosphatase gene OsTPP1 confers stress tolerance in rice and results in the activation of stress responsive genes.

Trehalose plays a protective role in yeast and microorganisms under abiotic stresses. However, little is known about its role in higher plants when subjected to environmental challenges. A systematic search of rice databases discovered a large TPS/TPP gene family in the rice genome, which is similar to that found in Arabidopsis thaliana, especially in the gene family structure. Expression analysis demonstrated that OsTPP1 was initially and transiently up-regulated after salt, osmotic and abscisic acid (ABA) treatments but slowly up-regulated under cold stress. OsTPP1 overexpression in rice enhanced tolerance to salt and cold stress. Analysis of the overexpression lines revealed that OsTPP1 triggered abiotic stress response genes, which suggests a possible transcriptional regulation pathway in stress induced reprogramming initiated by OsTPP1. The current study revealed the mechanism of an OsTPP gene involved in stress tolerance in rice and also suggested the use of OsTPP1 in abiotic stress engineering of crops.

The novel quantitative trait locus GL3.1 controls rice grain size and yield by regulating Cyclin-T1;3

Increased crop yields are required to support rapid population growth worldwide. Grain weight is a key component of rice yield, but the underlying molecular mechanisms that control it remain elusive. Here, we report the cloning and characterization of a new quantitative trait locus (QTL) for the control of rice grain length, weight and yield. This locus, GL3.1, encodes a protein phosphatase kelch (PPKL) family — Ser/Thr phosphatase. GL3.1 is a member of the large grain WY3 variety, which is associated with weaker dephosphorylation activity than the small grain FAZ1 variety. GL3.1-WY3 influences protein phosphorylation in the spikelet to accelerate cell division, thereby resulting in longer grains and higher yields. Further studies have shown that GL3.1 directly dephosphorylates its substrate, Cyclin-T1;3, which has only been rarely studied in plants. The downregulation of Cyclin-T1;3 in rice resulted in a shorter grain, which indicates a novel function for Cyclin-T in cell cycle regulation. Our findings suggest a new mechanism for the regulation of grain size and yield that is driven through a novel phosphatase-mediated process that affects the phosphorylation of Cyclin-T1;3 during cell cycle progression, and thus provide new insight into the mechanisms underlying crop seed development. We bred a new variety containing the natural GL3.1 allele that demonstrated increased grain yield, which indicates that GL3.1 is a powerful tool for breeding high-yield crops.

OsHAL3 mediates a new pathway in the light-regulated growth of rice

Plants show distinct morphologies in different light conditions through a process called photomorphogenesis. A predominant feature of photomorphogenesis is the reduced growth of seedlings under light conditions compared with darkness. For this adaptive event, the most well-known molecular mechanism involves photoreceptor-mediated inhibition of cell elongation. However, it is not known whether additional pathways exist. Here, we describe a newly discovered pathway of light-modulated plant growth mediated by the halotolerance protein HAL3, a flavin mononucleotide (FMN)-binding protein involved in cell division. We found that light, especially blue light, suppresses growth of rice seedlings by reducing the activity of Oryza sativa (Os) HAL3. Both in vitro and in vivo studies showed that OsHAL3 is structurally inactivated by light through photo-oxidation and by direct interaction with photons. In addition, the transcriptional expression of OsHAL3 is synergistically regulated by different light conditions. Further investigation suggested that OsHAL3 promotes cell division by recruiting a ubiquitin system, rather than by its 4′-phosphopantothenoylcysteine (PPC) decarboxylase activity. Our results uncover a new mechanism for light-regulated plant growth, namely, light not only inhibits cell elongation but also suppresses cell division through HAL3 and E3 ubiquitin ligase. This study thus brings new insights into our understanding of plant photomorphogenesis.

Identification of quantitative trait Loci for lipid metabolism in rice seeds.

Plant seed oil is important for human dietary consumption and industrial application. The oil trait is controlled by quantitative trait loci (QTLs), but no QTLs for fatty acid composition are known in rice, the monocot model plant. QTL analysis was performed using F(2) and F(2:3) progeny from a cross of an indica variety and a japonica variety. Gas chromatography-mass spectrometry (GC-MS) analysis revealed significant differences between parental lines in fatty acid composition of brown rice oil, and 29 associated QTLs in F(2) and/or F(2:3) populations were identified throughout the rice genome, except chromosomes 9 and 10. Eight QTLs were repeatedly identified in both populations across different environments. Five loci pleiotropically controlled different traits, contributing to complex interactions of oil with fatty acids and between fatty acids. Nine rice orthologs of Arabidopsis genes encoding key enzymes in lipid metabolism co-localized with 11 mapped QTLs. A strong QTL for oleic (18:1) and linoleic (18:2) acid were associated with a rice ortholog of a gene encoding acyl-CoA:diacylglycerol acyltransferase (DGAT), and another for palmitic acid (16:0) mapped similarly to the acyl-ACP thioesterase (FatB) gene ortholog. Our approach rapidly and efficiently identified candidate genes for mapped QTLs controlling fatty acid composition and oil concentration, providing information for improving rice grain quality by marker assisted selection.

A two-locus interaction causes interspecific hybrid weakness in rice

Reproductive barriers perform a vital role during speciation. Hybrid weakness, the poorer development of hybrids compared with their parents, hinders gene exchange between different species at the postzygotic stage. Here we show that two incompatible dominant loci (Hwi1 and Hwi2) involving three genes are likely to determine the high temperature-dependent expression of hybrid weakness in interspecific hybrids of rice. Hwi1 comprises two leucine-rich repeat receptor-like kinase (LRR–RLK) genes, 25L1 and 25L2, which are specific to wild rice (Oryza rufipogon) and induce hybrid weakness. Hwi2, a rare allele that is predominantly distributed in indica rice (Oryza sativa), encodes a secreted putative subtilisin-like protease. Functional analysis indicated that pyramiding of Hwi1 and Hwi2 activates the autoimmune response in the basal nodes of hybrids, interrupting root formation and then impairing shoot growth. These findings bring new insights into our understanding of reproductive isolation and may benefit rice breeding.