Distribution characteristics of selenium, cadmium and arsenic in rice grains and their genetic dissection by genome-wide association study.

High selenium (Se) and low cadmium (Cd) and arsenic (As) contents in rice grains were good for human health. The genetic basis and relationship of Se, Cd and As concentrations in rice grains are still largely unknown. In the present study, large variations were observed in Se, Cd and As concentrations in brown and milled rice in normal and Se treatment conditions in 307 rice accessions from 3K Rice Genomes Project. Se fertilizer treatment greatly increased Se concentrations but had no obvious changes in concentrations of Cd and As both in brown and milled rice. Total of 237 QTL were identified for Se, Cd and As concentrations in brown and milled rice in normal and Se treatment conditions as well as ratio of concentrations under Se treatment to normal conditions. Only 19 QTL (13.4%) were mapped for concentrations of Se and Cd, Se and As, and Se, Cd and As in the same or adjacent regions, indicating that most Se concentration QTL are independent of Cd and As concentration QTL. Forty-three favorable alleles were identified for 40 candidate genes by gene-based association study and haplotype analysis in 14 important QTL regions. Se-enriched rice variety will be developed by pyramiding favorable alleles at different Se QTL and excluding undesirable alleles at Cd and As QTL, or combining favorable alleles at Se QTL with the alleles at Se-sensitive QTL by marker-assisted selection.

Mechanistic insights into the efficient activation of peracetic acid by pyrite for the tetracycline abatement.

Recently, iron-based heterogenous catalysts have received much attention in the activation of peracetic acid (PAA) for generating reactive radicals to degrade organic pollutants, yet the PAA activation efficiency is compromised by the slow transformation from Fe(III) to Fe(II). Herein, considering the electron-donating ability of reducing sulfur species, a novel advanced oxidation process by combining pyrite and PAA (simplified as pyrite/PAA) for the abatement of tetracycline (TC) is proposed in this study. In the pyrite/PAA process, TC can be completely removed within 30 min under neutral conditions by the synergy of homogeneous and heterogenous Fe(II) species. CH3C(O)OO• is the main radical generated from the pyrite/PAA process responsible for TC abatement. The excellent activation properties of pyrite can be attributed to the superior electron-donating ability of reducing sulfur species to facilitate the reduction of Fe(III). Meanwhile, the complexation of leached Fe2+ with TC favors PAA activation and concomitant TC abatement. In addition, the degradation pathways of TC and the toxicity of the degradation intermediates are analyzed. The pyrite/PAA process shows an excellent TC abatement efficacy in the pH range of 4.0∼10.0. The coexistence of Cl-, HCO3-, and HPO42- exhibits negligible effect on TC abatement, while the HA slightly inhibits the abatement rate of TC. This study highlights the efficient activation of PAA by pyrite and the important role of sulfur in promoting the conversion of Fe(III) to Fe(II) in the pyrite/PAA process.

Application of a novel heterogeneous sulfite activation with copper(i) sulfide (Cu2S) for efficient iohexol abatement.

Transition metal ion-activated sulfite autoxidation processes for the production of sulfate radicals (SO4˙-) have been widely investigated to achieve efficient abatement of recalcitrant organic pollutants. However, these homogeneous processes suffered from narrow effective pH range and metal release, thus restricting their practical application. In order to address this problem, we report a simple and efficient approach to iohexol abatement by a combined Cu2S and sulfite process (simplified as Cu2S/sulfite process) based on the superior activation performance of copper and the excellent electron donating capacity of the low-valent sulfur species. Compared with typical copper oxides, Cu2S can significantly accelerate the sulfite autoxidation to generate radicals, leading to 100% iohexol abatement in the Cu2S/sulfite process. The influence of solution pH and dissolved oxygen on iohexol abatement is also investigated. Qualitative and quantitative analysis of reactive radicals is performed by electron paramagnetic resonance (EPR) and radical quenching experiments. Generation of SO4˙- from sulfite activation with Cu2S mainly contributes to the iohexol abatement. X-ray photoelectron spectroscopy (XPS) suggests that copper is the main activation site and the reductive sulfur species can achieve the continuous regeneration of copper. Application potential of the Cu2S/sulfite process is also assessed. This study provides a new method for the treatment of water and wastewater containing organic micropollutants.

Seed priming with selenium: Effects on germination, seedling growth, biochemical attributes, and grain yield in rice growing under flooding conditions.

Prevalent irregular rainfall, flooding for weed control, and unleveled fields in the middle and lower reaches of the Yangtze River all contribute to flooding stress on germination and growth of direct-seeded rice (Oryza sativa L.). Herein, some experiments were conducted so as to assess the effects of seed priming with selenium (Se) on the germination and growth of rice under hypoxia. The experiment was arranged in a completely randomized factorial design with two factors and five replicates. Factors included Se concentration (0, 30, and 60 µmol/L) and duration of flooding stress (0, 2, 4, and 8 days). The experimental results showed that Se accelerated seed germination and increased emergence index and final emergence percentage. Additionally, Se increased shoot and root lengths and dry weights, but high Se concentration (60 µmol/L) reduced 18-day-old seedling dry weight under long-term flooding (8 days). Furthermore, Se reduced malondialdehyde content and increased starch hydrolysis efficiency in seeds, superoxide dismutase, peroxidase, catalase, and glutathione peroxidase activities and seedling soluble protein and total chlorophyll contents. Se improved seedling total Se and organic Se contents while increasing total dry weight and yield. Notably, the highest yield was obtained after a 4-day flooding period. Although Se priming favored rice seedling emergence and growth under flooding conditions, Se concentrations equal or above 60 µmol/L increased the risk of seedling death during long-term flooding (≥8 days).

Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study.

BACKGROUND: Soil salinity is one of the main environmental conditions that affects rice production. Identifying the genetic loci that affect rice salt tolerance (ST)-related traits at the seedling stage, especially under saline field conditions, is crucial for ST rice breeding by pyramiding ST genes that act at different developmental stages. RESULTS: Large phenotypic variations were observed in 708 rice accessions, and yield and its related traits were considerably limited when exposed to salt stress. In a genome-wide association study (GWAS), 2255 marker-trait association signals were detected for all measured traits, and the significant SNPs were distributed in 903 genes. Of these, 43 genes processed same functional annotation, and the gene ontology terms "biological processes" and "molecular function" with the known genes responsive to salt stress in rice. Further haplotype analysis detected 15 promising candidates significantly associated with the target traits, including five known genes and 10 novel genes. We identified seven accessions carrying favorable haplotypes of four genes significantly associated with grain yield that performed well under saline stress conditions. CONCLUSIONS: Using high density SNPs within genes to conduct GWAS is an effective way to identify candidate genes for salt tolerance in rice. Five known genes (OsMYB6, OsGAMYB, OsHKT1;4, OsCTR3, and OsSUT1) and two newly identified genes (LOC_Os02g49700, LOC_Os03g28300) significantly associated with grain yield and its related traits under saline stress conditions were identified. These promising candidates provide valuable resources for validating potential ST-related genes and will facilitate rice breeding for salt tolerance through marker-assisted selection.

Examining two sets of introgression lines reveals background-independent and stably expressed QTL that improve grain appearance quality in rice (Oryza sativa L.).

KEY MESSAGE: A novel QTL cluster for appearance quality on Chr07 was identified using reciprocal introgression populations in different locations in China. Two secondary F 2 populations validated QTL with significant effect on appearance quality. Appearance quality (AQ) is the main determinants of market value of rice. Identification of QTL affecting AQ is the prerequisite for efficient improvement of AQ through marker-assisted selection (MAS). Two sets of reciprocal introgression lines derived from indica Minghui 63 and japonica 02428 were used to dissect the stability of QTL affecting five AQ traits, including grain length, grain width, length to width ratio, percentage of grains with chalkiness, and degree of endosperm chalkiness using 4568 bin genotype produced from 58,000 SNPs across five different environments. A total of 41 and 30 main-effect QTL were identified in MH63 and 02428 backgrounds, respectively. Among them, 9 background-independent QTL (BI-QTL) were found. There were also 13 and 10 stable-expressed QTL (SE-QTL) across at least two environments in MH63 and 02428 backgrounds, respectively. Two important BI- and SE-QTL regions (BISERs) including BISER-I harboring qPGWC5, qDEC5, qGW5.1, and qLWR5 on chromosome 5 and BISER-II harboring qGL7, qLWR7, qPGWC7, and qDEC7 on chromosome 7 were identified. The BISER-II was newly reported and validated by two secondary F2 populations in the reciprocal backgrounds. Among 59 epistatic QTL (E-QTL) detected in this study, there were only four SE- but no BI-E-QTL detected in different environments, indicating that genetic background has stronger effect on AQ traits than the environmental factors, especially for percentage of grains with chalkiness (PGWC) and degree of endosperm chalkiness (DEC) with lower heritability. BISER-I and BISER-II harboring many BI- and SE-QTL with favorable alleles from slender grain rice are much important for improvement of rice AQ by MAS.

Genome-Wide Association Study of Grain Appearance and Milling Quality in a Worldwide Collection of Indica Rice Germplasm.

Grain appearance quality and milling quality are the main determinants of market value of rice. Breeding for improved grain quality is a major objective of rice breeding worldwide. Identification of genes/QTL controlling quality traits is the prerequisite for increasing breeding efficiency through marker-assisted selection. Here, we reported a genome-wide association study in indica rice to identify QTL associated with 10 appearance and milling quality related traits, including grain length, grain width, grain length to width ratio, grain thickness, thousand grain weight, degree of endosperm chalkiness, percentage of grains with chalkiness, brown rice rate, milled rice rate and head milled rice rate. A diversity panel consisting of 272 indica accessions collected worldwide was evaluated in four locations including Hangzhou, Jingzhou, Sanya and Shenzhen representing indica rice production environments in China and genotyped using genotyping-by-sequencing and Diversity Arrays Technology based on next-generation sequencing technique called DArTseq™. A wide range of variation was observed for all traits in all environments. A total of 16 different association analysis models were compared to determine the best model for each trait-environment combination. Association mapping based on 18,824 high quality markers yielded 38 QTL for the 10 traits. Five of the detected QTL corresponded to known genes or fine mapped QTL. Among the 33 novel QTL identified, qDEC1.1 (qGLWR1.1), qBRR2.2 (qGL2.1), qTGW2.1 (qGL2.2), qGW11.1 (qMRR11.1) and qGL7.1 affected multiple traits with relatively large effects and/or were detected in multiple environments. The research provided an insight of the genetic architecture of rice grain quality and important information for mining genes/QTL with large effects within indica accessions for rice breeding.

Water use efficiency and physiological response of rice cultivars under alternate wetting and drying conditions.

One of the technology options that can help farmers cope with water scarcity at the field level is alternate wetting and drying (AWD). Limited information is available on the varietal responses to nitrogen, AWD, and their interactions. Field experiments were conducted at the International Rice Research Institute (IRRI) farm in 2009 dry season (DS), 2009 wet season (WS), and 2010 DS to determine genotypic responses and water use efficiency of rice under two N rates and two water management treatments. Grain yield was not significantly different between AWD and continuous flooding (CF) across the three seasons. Interactive effects among variety, water management, and N rate were not significant. The high yield was attributed to the significantly higher grain weight, which in turn was due to slower grain filling and high leaf N at the later stage of grain filling of CF. AWD treatments accelerated the grain filling rate, shortened grain filling period, and enhanced whole plant senescence. Under normal dry-season conditions, such as 2010 DS, AWD reduced water input by 24.5% than CF; however, it decreased grain yield by 6.9% due to accelerated leaf senescence. The study indicates that proper water management greatly contributes to grain yield in the late stage of grain filling, and it is critical for safe AWD technology.