Genetic Diversity of Seed Dormancy and Molecular Evolution of Weedy Red Rice

Rice is the grain with the third-highest global production. In the US, Arkansas is the largest rice producing state; however, an estimated 62% of the rice fields in the state are infested with red rice, and can cause up to 80% yield reduction in rice. Among its weedy traits, seed dormancy plays an important role in its persistence, and helps red rice escape weed management techniques thereby increasing the red rice soil seedbank. Red rice also has the potential to hybridize among themselves and with cultivated rice, thus resulting in diverse phenotypes and genotypes. In this study we measured variation in seed dormancy at different after-ripening times, and incubation temperatures; determined the genetic diversity of dormant and non-dormant red rice populations; measured diversity in phenological and morphological traits among and within red rice populations collected across Arkansas; and, determined the genotype-phenotype relationship and population structure of old and recent red rice collections using sequence tagged site (STS) markers. The germination response of red rice to three temperatures (1°C, 15°C, and 35°C) and four after-ripening periods (0, 30, 60, and 90 d), was evaluated. Germination varied among and within red rice populations in response to different temperatures and after-ripening period. Highest variation in germination was observed at 15°C incubation (44-97%). Among the after-ripening periods, the optimum time to release primary dormancy was 90 d. Blackhull red rice ecotypes was more dormant and also showed higher intrapopulation variation in dormancy compared to strawhull ecotypes. To determine the genetic diversity of dormant and non-dormant red rice populations, 25 simple sequence repeat (SSR) markers associated with seed dormancy loci were used. A considerable amount of genetic variation among red rice accessions was found (Nei\u27s gene diversity (h) = 0.355), and blackhull populations (h = 0.398) were more diverse than strawhull populations (h = 0.245). Higher genetic diversity was observed within and among dormant populations than non-dormant red rice populations. Phenological and morphological characteristics were found to significantly vary among 113 strawhull, 71 blackhull, and 24 brownhull red rice accessions. Greater variation was observed among blackhull red rice, the tallest, late flowering, and highly tillering among the ecotypes. Strawhull red rice generally tillered less, but produced higher grain yield. Sequence analysis of 27 old (2002-2003 collection) and 52 recent (2008-2009 collection) red rice accessions, using 48 STS markers revealed a total of 447 SNPs. Recent blackhull red rice accessions had higher nucleotide diversity (Pi = 2.43 per Kb) than the old blackhull accessions (Pi = 1.21 per Kb). Old strawhull had lower sequence polymorphisms than old blackhull red rice. Genetic and phenotypic diversity among and within red rice ecotypes suggests the adoption of diverse weed management techniques in order to successfully control this troublesome weed.

Weedy Rice: Competitive Ability, Evolution, and Diversity

Weedy rice is conspecific, the most troublesome weed of cultivated rice identified as a threat to global rice production. The weed has inherited high reproductive ability and high dormancy by outcrossing with modern rice cultivars and wild cultivars, respectively. Traits such as rapid growth, high tillering, enhanced ability to uptake fertilizers, asynchronous maturation, seed shattering, and long dormancy periods make weedy rice more competitive than cultivated rice. Weedy rice infesting rice fields are morphologically diverse with different hull color, awn length, plant height, and variable tiller number. Morphological diversity in weedy rice can be attributed to its high genetic diversity. Introgression of alleles from cultivated rice into weedy has resulted in high genetic and morphological diversity in weedy rice. Although variations among weedy rice populations make them difficult to control, on the brighter side, competitive nature of weedy rice could be considered as raw genetic materials for rice breeding program to develop vigorous rice plants able to tolerate high biotic and abiotic stresses

Biochemical and Molecular Knowledge about Developing Herbicide-Resistant Weeds

Herbicide resistance is the genetic capacity of a weed population to survive an herbicide treatment that, under normal use conditions, would effectively control the resistant weed population. Weeds have been evolving in conventional crop cultivars worldwide from selection pressure placed on them from repeated use of herbicides. In this chapter, we intend to explain the biochemical and molecular basis of herbicide resistance in weeds. On the other hand, herbicide resistance can be a useful tool so that weed scientists can use as important approach to control and manage weeds. There are several strategies for the production of HR crops by genetic engineering and the methods used in this process will be discussed in this chapter

Consequences and Mitigation Strategies of Biotic and Abiotic Stress in Rice (<em>Oryza sativa</em> L.)

Rice (Oryza sativa) is the staple food for more than 3.5 billion people worldwide. Yield levels in Asia have tripled and are expected to increase by 70% over the next 30 years due to population growth. In the US, Arkansas accounts for more than 50% of rice production. Over the last 68 years, rice production has continued to grow in Mississippi, placing it in fourth place after Arkansas, Louisiana, and California. Due to increasing rice acreage, regionally and worldwide, the need to develop abiotic stress tolerant rice has increased. Unfortunately, current rice breeding programs lack genetic diversity, and many traits have been lost through the domestication of cultivated rice. Currently, stressors stemming from the continued effects of climate change continue to impact rice. This chapter highlights current research that strives to discover abiotic and biotic stress tolerant rice. This chapter calls for directed research in genetics and genomics to address the need to discover biotic and abiotic stress tolerant traits. While many genes have been uncovered to arm rice against these stresses, decreased genetic variability in current rice traits presents a small gene pool for discovery

A cusp-capturing PINN for elliptic interface problems

In this paper, we propose a cusp-capturing physics-informed neural network (PINN) to solve discontinuous-coefficient elliptic interface problems whose solution is continuous but has discontinuous first derivatives on the interface. To find such a solution using neural network representation, we introduce a cusp-enforced level set function as an additional feature input to the network to retain the inherent solution properties; that is, capturing the solution cusps (where the derivatives are discontinuous) sharply. In addition, the proposed neural network has the advantage of being mesh-free, so it can easily handle problems in irregular domains. We train the network using the physics-informed framework in which the loss function comprises the residual of the differential equation together with certain interface and boundary conditions. We conduct a series of numerical experiments to demonstrate the effectiveness of the cusp-capturing technique and the accuracy of the present network model. Numerical results show that even using a one-hidden-layer (shallow) network with a moderate number of neurons and sufficient training data points, the present network model can achieve prediction accuracy comparable with traditional methods. Besides, if the solution is discontinuous across the interface, we can simply incorporate an additional supervised learning task for solution jump approximation into the present network without much difficulty

An efficient neural-network and finite-difference hybrid method for elliptic interface problems with applications

A new and efficient neural-network and finite-difference hybrid method is developed for solving Poisson equation in a regular domain with jump discontinuities on embedded irregular interfaces. Since the solution has low regularity across the interface, when applying finite difference discretization to this problem, an additional treatment accounting for the jump discontinuities must be employed. Here, we aim to elevate such an extra effort to ease our implementation by machine learning methodology. The key idea is to decompose the solution into singular and regular parts. The neural network learning machinery incorporating the given jump conditions finds the singular solution, while the standard finite difference method is used to obtain the regular solution with associated boundary conditions. Regardless of the interface geometry, these two tasks only require supervised learning for function approximation and a fast direct solver for Poisson equation, making the hybrid method easy to implement and efficient. The two- and three-dimensional numerical results show that the present hybrid method preserves second-order accuracy for the solution and its derivatives, and it is comparable with the traditional immersed interface method in the literature. As an application, we solve the Stokes equations with singular forces to demonstrate the robustness of the present method

The Influence of Type 2 Diabetes and Glucose-Lowering Therapies on Cancer Risk in the Taiwanese

Objective. To investigate the association between type 2 diabetes, glucose-lowering therapies (monotherapy with either metformin, sulphonylurea or insulin) and cancer risk in Taiwan. Methods. Using Taiwan's National Health Research Institutes database of 1,000,000 random subjects from 2000–2008, we found 61777 patients with type 2 diabetes (age ≥20 years) and 677378 enrollees with no record of diabetes. Results. After adjusting for age and sex, we found patients with diabetes to have significantly higher risk of all cancers (OR: 1.176; 95% CI: 1.149–1.204, P < 0.001). Diabetic patients treated with insulin or sulfonylureas had significantly higher risk of all cancers, compared to those treated with metformin (OR: 1.583; 95% CI: 1.389–1.805, P < 0.001 and OR: 1.784; 95% CI: 1.406–2.262, P < 0.001). Metformin treatment was associated with a decreased risk of colon and liver cancer compared to sulphonylureas or insulin treatment. Sulfonylureas treatment was associated with an increased risk of breast and lung cancer compared to metformin therapy. Conclusions. Taiwanese with type 2 diabetes are at a high risk of breast, prostate, colon, lung, liver and pancreatic cancer. Those treated with insulin or sulfonylureas monotherapy are more likely to develop colon and liver cancer than those treated with metformin

Joint Action of Herbicides on Weeds and Their Risk Assessment on Earthworm (<em>Eisenia fetida</em> L.)

Frequent and intensive use of similar modes of action herbicides increases selection pressure resulting in nature adapt and a number of herbicide-resistant weeds. The most effective methods to prevent and delay herbicide-resistant weeds are herbicide tank mixture and adjuvant mixed herbicides. This chapter intends to explain the advantages of herbicide tank mixture and adjuvant mixed herbicides. In addition, the models of estimated herbicide mixture interaction response have been explained. Although herbicide mixtures have benefits, they may present risks leading to soil pollution and affecting soil fauna such as earthworms. Therefore, we discussed the negative effect of mixture herbicides on Eisenia fetida. On the other hand, various models to calculate mixture herbicide toxicity on earthworms will be present in this chapter

Redroot pigweed (Amaranthus retroflexus L.) and lamb's quarters ‎‎(Chenopodium album L.) populations exhibit a high degree of ‎morphological and biochemical diversity

Amaranthus retroflexus L. and Chenopodium album L. are noxious weeds that have a cosmopolitan distribution. These species successfully invade and are adapted to a wide variety of diverse climates. In this paper we evaluated the morphology and biochemistry of 16 populations of A. retroflexus L. and 17 populations of C. album L.. Seeds from populations collected from Spain, France and Iran were grown together at the experimental field of the agriculture research of University of Mohaghegh Ardabili and a suite of morphological traits and biochemical traits were assessed. Among the populations of A. retroflexus L. and of C. album L. were observed significant differences for all the measured traits. The number of branches for A. retroflexus L. (12.22) and inflorescence length (14.34) for C. album L. were the two characteristics that exhibited the maximum coefficient of variation. Principal component analysis of these data identified four principal components for each species that explained 83.54 (A. retroflexus L.) and 88.98 (C. album L.) of the total variation. A dendrogram based on unweighted neighbor-joining method clustered all the A. retroflexus L. and C. album L. into two main clusters and four sub-clusters. Canonical correlation analysis was used to evaluate relationships between climate classification of origin and traits. Similarly, the measured characteristics did not group along Köppen climate classification. Both analyses support the conclusion that A. retroflexus L. and C. album L. exhibit high levels of diversity despite similar environmental histories. Both species also exhibit a high diversity of the measured biochemical compounds indicating they exhibit different metabolic profiles even when grown concurrently and sympatrically. Several of the biochemical constituents identified in our study could serve as effective indices for indirect selection of stresses resistance/tolerance of A. retroflexus L. and C. album L. The diversity of the morphological and biochemical traits observed among these populations illustrates how the unique selection pressures faced by each population can alter the biology of these plants. This understanding provides new insights to how these invasive plant species successfully colonize diverse ecosystems and suggests methods for their management under novel and changing environmental conditions