The expansion of gene families encoding regulatory proteins is typically associated with the increase in complexity characteristic of multi-cellular organisms. The MYB and basic helix-loop-helix (bHLH) families provide excellent examples of how gene duplication and divergence within particular groups of transcription factors are associated with, if not driven by, the morphological and metabolic diversity that characterize the higher plants. These gene families expanded dramatically in higher plants; for example, there are approximately 339 and 162 MYB and bHLH genes, respectively, in Arabidopsis, and approximately 230 and 111, respectively, in rice. In contrast, the Chlamydomonas genome has only 38 MYB genes and eight bHLH genes. In this review, we compare the MYB and bHLH gene families from structural, evolutionary and functional perspectives. The knowledge acquired on the role of many of these factors in Arabidopsis provides an excellent reference to explore sequence-function relationships in crops and other plants. The physical interaction and regulatory synergy between particular sub-classes of MYB and bHLH factors is perhaps one of the best examples of combinatorial plant gene regulation. However, members of the MYB and bHLH families also interact with a number of other regulatory proteins, forming complexes that either activate or repress the expression of sets of target genes that are increasingly being identified through a diversity of high-throughput genomic approaches. The next few years are likely to witness an increasing understanding of the extent to which conserved transcription factors participate at similar positions in gene regulatory networks across plant species.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1365-313X.2010.04459.x

Evolutionary and comparative analysis of MYB and bHLH plant transcription factors

Phosphorus (P) is one of the essential nutrients for plants, and is indispensable for plant growth and development. P deficiency severely limits crop yield, and regular fertilizer applications are required to obtain high yields and to prevent soil degradation. To access P from the soil, plants have evolved high- and low-affinity Pi transporters and the ability to induce root architectural changes to forage P. Also, adjustments of numerous cellular processes are triggered by the P starvation response, a tightly regulated process in plants. With the increasing demand for food as a result of a growing population, the demand for P fertilizer is steadily increasing. Given the high costs of fertilizers and in light of the fact that phosphate rock, the source of P fertilizer, is a finite natural resource, there is a need to enhance P fertilizer use efficiency in agricultural systems and to develop plants with enhanced Pi uptake and internal P-use efficiency (PUE). In this review we will provide an overview of continuing relevant research and highlight different approaches towards developing crops with enhanced PUE. In this context, we will summarize our current understanding of root responses to low phosphorus conditions and will emphasize the importance of combining PUE with tolerance of other stresses, such as aluminum toxicity. Of the many genes associated with Pi deficiency, this review will focus on those that hold promise or are already at an advanced stage of testing (OsPSTOL1, AVP1, PHO1 and OsPHT1;6). Finally, an update is provided on the progress made exploring alternative technologies, such as phosphite fertilizer.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/tpj.13423

Improving phosphorus use efficiency: a complex trait with emerging opportunities.

Complex Regulation of Plant Phosphate Transporters and the Gap between Molecular Mechanisms and Practical Application: What Is Missing?

Long awns are important for seed dispersal in wild rice (Oryza rufipogon), but are absent in cultivated rice (Oryza sativa). The genetic mechanism involved in loss-of-awn in cultivated rice remains unknown. We report here the molecular cloning of a major quantitative trait locus, An-1, which regulates long awn formation in O. rufipogon. An-1 encodes a basic helix-loop-helix protein, which regulates cell division. The nearly-isogenic line (NIL-An-1) carrying a wild allele An-1 in the genetic background of the awnless indica Guangluai4 produces long awns and longer grains, but significantly fewer grains per panicle compared with Guangluai4. Transgenic studies confirmed that An-1 positively regulates awn elongation, but negatively regulates grain number per panicle. Genetic variations in the An-1 locus were found to be associated with awn loss in cultivated rice. Population genetic analysis of wild and cultivated rice showed a significant reduction in nucleotide diversity of the An-1 locus in rice cultivars, suggesting that the An-1 locus was a major target for artificial selection. Thus, we propose that awn loss was favored and strongly selected by humans, as genetic variations at the An-1 locus that cause awn loss would increase grain numbers and subsequently improve grain yield in cultivated rice.

An-1 Encodes a Basic Helix-Loop-Helix Protein That Regulates Awn Development, Grain Size, and Grain Number in Rice

Challenges of modifying root traits in crops for agriculture.

The invention discloses a protein of rice root hair growth control gene OsRHL1 coding, which has an amino acid sequence expressed by SEQ ID NO: 2. The invention further simultaneously discloses genes coding the protein, which has a nucleotide sequence expressed by SEQ ID NO: 1. The invention further simultaneously discloses a method for modifying rice root hair, including transforming rice cells by using the gene and cultivating the rice cells after transformation into plants.

Rice fibril controlling gene OsRHL1 and uses thereof

For coded distributed computing (CDC), polynomial code is one prevalent encoding method for CDC (called Poly-CDC). It suffers from poor numerical stability due to the Vandermonde matrix serving as the coefficient matrix which needs to be inverted, and whose condition number increases exponentially with the size of the matrix or equivalently with the number of parallel worker nodes. To improve the numerical stability, especially for large networks, we propose a Newton-like polynomial code (NLPC)-based CDC (NLPC-CDC), with a design dedicated for both matrix–vector and matrix–matrix multiplications. The associated proof of the constructed code possesses a (n,k)-symmetrical combination property (CP), where symmetrical means the worker nodes have identical computation volume, CP means the k-symmetrical original computing tasks are encoded into n(n≥k)-symmetrically coded computing tasks, and the arbitrary k resulting from the n-coded computing tasks can recover the intended computing results. Extensive numerical studies verify the significant numerical stability improvement of our proposed NLPC-CDC over Poly-CDC.

/pdf/newton-like-polynomial-coded-distributed-computing-for-pwk77gdr.pdf

Newton-like Polynomial-Coded Distributed Computing for Numerical Stability

Millions of matrix dimensions in matrix multiplication will have high requirements on node computing power and storage space. Coded Distributed Computing (CDC) can solve this problem by dividing large-dimensional matrices into small matrices and then assigning them to machines in the computing cluster to perform matrix multiplication in parallel. In order to adapt to the reality that computer clusters are usually composed of heterogeneous workers with different computing capabilities, and overcome the performance limitations of CDC based on the isomorphism of computing power, Coded Elastic Computing (CEC) is proposed. However, the existing CEC discards the received information and directly starts a new round of computation after an elastic event occurs, resulting waste of computing time and resources. In this paper, we propose to employ the received information to redesign the allocation scheme. We first determine the offline machine number and the data segment it should have returned as the missing part of decoding that needs to be recomputed. We then count the total number of lost data for each segment of data and calculate the amount of tasks that each machine should undertake. Finally, the amount of tasks actually undertaken by each machine is calculated by solving the system of linear equations. Through experiments, we show the effectiveness of our proposed allocation scheme, in terms of saving resources and time, and accelerating the calculation speed, when compared with the original scheme.

Computing Resource Allocation for Heterogeneous Coded Distributed Computing

Root hairs are highly polarized long tubular outgrowths from the surface of epidermal trichoblast cells. Root hair development is a simple process that has facilitated for the study of cell fate determination and tissue differentiation in higher plants. Root hair patterning types in dicot and monocot plants are different. Rice is a monocot model plant with type II root hair pattern. The method to examine root hair fine structure and cell shape in rice may help elucidate the mechanism of cell initiation and differentiation in monocot plants. Compared with the critical-point-drying SEM, the Cryo-SEM method has great advantage, as the Cryo-SEM can well maintain the delicate structure of root hairs in their natural situation. Here we provide the methodology developed to investigate several rice mutants with impaired root hair cells using Cryo-SEM.

Analysis of rice root hair morphology using cryo-scanning electron microscopy.

/pdf/a-transcription-factor-with-a-bhlh-domain-regulates-root-431wzha486.pdf

A transcription factor with a bHLH domain regulates root hair development in rice.

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