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Reduced-representation sequencing (RRS) provides cost-effective and time-saving genotyping platforms. Despite the outstanding advantage of RRS in throughput, the obtained genotype data usually contain a large number of errors. Several error correction methods employing the hidden Markov model (HMM) have been developed to overcome these issues. These methods assume that markers have a uniform error rate with no bias in the allele read ratio. However, bias does occur because of uneven amplification of genomic fragments and read mismapping. In this paper, we introduce an error correction tool, GBScleanR, which enables robust and precise error correction for noisy RRS-based genotype data by incorporating marker-specific error rates into the HMM. The results indicate that GBScleanR improves the accuracy by more than 25 percentage points at maximum compared to the existing tools in simulation data sets and achieves the most reliable genotype estimation in real data even with error-prone markers.

Efficient oxygen transport via enhanced root aerenchyma and a barrier to impede radial oxygen loss (ROL) from roots to rhizosphere is essential for plants inhabiting wetland conditions. When grown in stagnant conditions, a rice mutant drp7 (dripping wet leaf 7), lacking a functional Leaf Gas Film-1 (LGF1) gene, forms poor aerenchyma spaces and a weak barrier to ROL in roots; whereas its wild-type (cv. Kinmaze) develop high root aerenchyma spaces and a tight barrier to ROL in roots. LGF1-overexpression lines in the drp7 mutant background were developed. The formation of a tight barrier to ROL was recovered in the overexpression lines when grown in stagnant conditions. In contrast, the aerenchyma formation was only partly recovered. Transgenic rice introducing the LGF1 promoter::GUS gene was used to visualize tissue-specificity of gene expression in roots. The GUS expression profiles indicated higher activity of the LGF1 gene in the hypodermis/exodermis cell layers near the root tips in stagnant but not in control conditions. Moreover, ROL from roots and extensive chemical characterization of roots were conducted. The formation of specific wax compounds in enzymatically separated root hypodermal/exodermal cell layers was higher in the wild-type genotype in comparison to the mutant line. The LGF1-overexpression lines showed significant increase in the amount of root waxes, in comparison to the mutant line. The identification of the LGF1 gene as a gene that is responsible for the development of tight barriers to ROL represents a major advance in the development of waterlogging tolerant plants.

Flooding is an abiotic stress which has adverse impacts on plants because it impairs breath. The diffusion rates of dissolved gases are about 104-fold slower than gases in the air, so that submerged organ can become low in O2 restricting respiration. In addition, restricted access to CO2 can also limit photosynthesis of submerged leaves. As climate change is predicted to result in more increased rain and floods in the world, it is essential to understand the adaptation mechanism of the plant to the flooded environment for further sustainable crop production. Rice, which is the major staple crop grown in waterlogged soil, adapted to flooding environment. Therefore, to understand the flood tolerance of crop, we dissected the physiological and anatomical features of rice as a role model on continuously growing in the paddy field. Physiological analysis of O2 dynamics using O2 optode in rice imposed to various flood regimes revealed that the emergence of leaves from underwater prevented the nighttime severe hypoxia during submergence. In addition, nighttime gene expressions dynamics related to anaerobic metabolism were highly induced in the completely submerged plant than the partially submerged plant, which maintained the contact with the air. Moreover, anatomical analysis of rice morphology by the confocal laser microscope showed that rice forms connected hollow tissues/organs over whole plant body including leaf blade, leaf sheath, stem, and root, for translocation of gas taken from leaves above underwater to the submerged organ. These series of results indicated the gas translocation via the snorkeling function of hollow tissues/organs connected over whole plant body maintains the physiological activity of submerged rice, therefore rice is able to continuously grow in a flooded environment.

Floods impede gas (O2and CO2) exchange between plants and the environment. A mechanism to enhance plant gas exchange under water comprises gas films on hydrophobic leaves, but the genetic regulation of this mechanism is unknown. We used a rice mutant (dripping wet leaf 7, drp7) which does not retain gas films on leaves, and its wild-type (Kinmaze), in gene discovery for this trait. Gene complementation was tested in transgenic lines. Functional properties of leaves as related to gas film retention and underwater photosynthesis were evaluated. Leaf Gas Film 1 (LGF1) was identified as the gene determining leaf gas films. LGF1 regulates C30 primary alcohol synthesis, which is necessary for abundant epicuticular wax platelets, leaf hydrophobicity and gas films on submerged leaves. This trait enhanced underwater photosynthesis 8.2-fold and contributes to submergence tolerance. Gene function was verified by a complementation test of LGF1 expressed in the drp7 mutant background, which restored C30 primary alcohol synthesis, wax platelet abundance, leaf hydrophobicity, gas film retention, and underwater photosynthesis. The discovery of LGF1 provides an opportunity to better understand variation amongst rice genotypes for gas film retention ability and to target various alleles in breeding for improved submergence tolerance for yield stability in flood-prone areas.

Apart from playing a key role in important biochemical reactions, molecular oxygen (O2) and its by-products also have crucial signaling roles in shaping plant developmental programs and environmental responses. Even under normal conditions, sharp O2 gradients can occur within the plant when cellular O2 demand exceeds supply, especially in dense organs such as tubers, seeds and fruits. Spatial and temporal variations in O2 concentrations are important cues for plants to modulate development (van Dongen & Licausi, 2015; Considine et al., 2016). Environmental conditions can also expand the low O2 regions within the plant. For example, excessive rainfall can lead to partial or complete plant submergence resulting in O2 deficiency in the root or the entire plant (Voesenek & Bailey-Serres, 2015). Climate change associated increases in precipitation events have made flooding a major abiotic stress threatening crop production and food sustainability. This increased flooding and associated crop losses highlight the urgency of understanding plant flooding responses and tolerance mechanisms.

Apart from playing a key role in important biochemical reactions, molecular oxygen (O2) and its by-products also have crucial signaling roles in shaping plant developmental programs and environmental responses. Even under normal conditions, sharp O2 gradients can occur within the plant when cellular O2 demand exceeds supply, especially in dense organs such as tubers, seeds and fruits. Spatial and temporal variations in O2 concentrations are important cues for plants to modulate development (van Dongen & Licausi, 2015; Considine et al., 2016). Environmental conditions can also expand the low O2 regions within the plant. For example, excessive rainfall can lead to partial or complete plant submergence resulting in O2 deficiency in the root or the entire plant (Voesenek & Bailey-Serres, 2015). Climate change associated increases in precipitation events have made flooding a major abiotic stress threatening crop production and food sustainability. This increased flooding and associated crop losses highlight the urgency of understanding plant flooding responses and tolerance mechanisms.