Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement.) is one of the most important cereal crops in the world. There have been landmark achievements in rice improvement over the past 50 y, especially in the indica subspecies. A major breakthrough resulted from the independent development of a series of semidwarf varieties in China and by the International Rice Research Institute (IRRI) in the 1950s and 1960s, leading to the "green revolution" in rice. Since then, semidwarfness has been a basic characteristic for almost all modern varieties. Based on semidwarf varieties, improvement for other traits, such as abiotic stress resistance, broad-spectrum resistances to biotic stresses, and better grain quality, has also been achieved. Another major breakthrough stemmed from the exploitation of hybrid vigor in China (1), resulting in the largescale adoption of hybrid rice since the 1970s. Jointly, these breakthroughs have greatly increased rice productivity in the past several decades globally.Genomic studies in recent years have identified a large number of loci that were under selection during rice domestication (2). However, there has been very limited study to identify loci or genomic regions that have been under selection due to breeding. Next-generation sequencing technologies have enabled sequencing of a large number of rice accessions at relatively low cost, providing opportunities to inspect the genomic regions selected in the history of crop improvement. Meanwhile, genome-wide association studies (GWAS) have provided an effective approach to analyze the genetic architecture of complex traits and allow identification of candidate genes for further improvement of agronomically important traits (3,4).In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions, which revealed a large number of differentially selected regions associated with breeding efforts between two major subpopulations in indica. These selected regi...

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The degradation of cyanobacterial blooms often causes hypoxia and elevated concentrations of ammonia, which can aggravate the adverse effects of blooms on aquatic organisms. However, it is not clear how one stressor would work in the presence of other coexistent stressors. We studied the toxic effects of elevated ammonia under hypoxia using a common yet important cladoceran species Daphnia similis isolated from heavily eutrophicated Lake Taihu. A 3 × 2 factorial experimental design was conducted with animals exposed to three un-ionized ammonia levels under two dissolved oxygen levels. Experiments lasted for 14 days and we recorded the life-history traits such as survival, molt, maturation, and fecundity. Results showed that hypoxia significantly decreased survival time and the number of molts of D. similis, whereas ammonia had no effect on them. Elevated ammonia significantly delayed development to maturity in tested animals and decreased their body sizes at maturity. Both ammonia and hypoxia were significantly detrimental to the number of broods, the number of offspring per female, and the number of total offspring per female, and significantly synergistic interactions were detected. Our data clearly demonstrate that elevated ammonia and hypoxia derived from cyanobacterial blooms synergistically affect the cladoceran D. similis.

The copper/zinc superoxide dismutase (Cu/Zn-SOD) is a representative antioxidant enzyme that is responsible for the conversion of superoxide to oxygen and hydrogen peroxide in aerobic organisms. Cu/Zn-SOD mRNAs have been cloned from many species and employed as useful biomarkers of oxidative stresses. In the present study, we cloned Cu/Zn-SOD cDNA from the cladoceran Daphnia magna, analyzed its catalytic properties, and investigated mRNA expression patterns after exposure to known oxidative stressors. The full-length Cu/Zn-SOD of the D. magna (Dm-Cu/Zn-SOD) sequence consisted of 703 bp nucleotides, encoding 178 amino acids, showing well-conserved domains that were required for metal binding and several common characteristics. The deduced amino acid sequence of Dm-Cu/Zn-SOD showed that it shared high identity with Daphnia pulex (88%), Alvinella pompejana (56%), and Cristaria plicata (56%). The phylogenetic analysis indicated that Dm-Cu/Zn-SOD was highly homologous to D. pulex. The variation of Dm-Cu/Zn-SOD mRNA expression was quantified by real-time PCR, and the results indicated that the expression was up-regulated after 48-h exposure to copper, un-ionized ammonia, and low dissolved oxygen. This study shows that the Dm-Cu/Zn-SOD mRNA could be successfully employed as a biomarker of oxidative stress, which is a common mode of toxicity for many other aquatic hazardous materials.

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Global warming and increased nutrient fluxes cause cyanobacterial blooms in freshwater ecosystems. These phenomena have increased the concern for human health and ecosystem services. The mass occurrences of toxic cyanobacteria strongly affect freshwater zooplankton communities, especially the unselective filter feeder Daphnia. However, the molecular mechanisms of cyanobacterial toxicity remain poorly understood. This study is the first to combine the established body growth rate (BGR), which is an indicator of life-history fitness, with differential peptide labeling (iTRAQ)-based proteomics in Daphnia magna influenced by microcystin-producing (MP) and microcystin-free (MF) Microcystis aeruginosa. A significant decrease in BGR was detected when D. magna was exposed to MP or MF M. aeruginosa. Conducting iTRAQ proteomic analyses, we successfully identified and quantified 211 proteins with significant changes in expression. A cluster of orthologous groups revealed that M. aeruginosa-affected differential proteins were strongly associated with lipid, carbohydrate, amino acid, and energy metabolism. These parameters could potentially explain the reduced fitness based on the cost of the substance metabolism.

1. Freshwater cyanobacterial blooms are a worldwide environmental issue. These blooms often comprise both non-toxic and toxic species and strains. Populations of some zooplankton, including Daphnia, have been shown to adapt locally to toxic Microcystis through maternal effects. However, Microcystis populations vary spatially and temporally in the absolute and relative abundances of non-toxic and toxic genotypes. 2. We examined variation in induction of tolerance to toxic cyanobacteria in offspring from two Daphnia magna clones (JS and AH) fed diets containing Scenedesmus by itself or in combination with either a non-toxic or a toxic clone of Microcystis aeruginosa. The diets containing Microcystis included relatively more cyanobacteria within each week of the 3 week experiment (week 1-10%, week 2-20%, week 3-40%). Daphnia neonates were collected from these three treatments at the end of the third week and fed a diet containing Scenedesmus and toxic Microcystis for 3 weeks before a suite of lifehistory, physiological and biochemical measurements were made on the surviving animals. 3. Neonates from mothers fed toxic and non-toxic Microcystis showed enhanced growth and reproduction compared to neonates produced from mothers fed only Scenedesmus. Our results showed that Daphnia neonates could be induced to tolerate toxic cyanobacteria when their mothers were fed diets containing non-toxic or toxic strains of cyanobacteria. Furthermore, elevated RNA-DNA ratios, superoxide dismutase activity and catalase activity in neonates fed diets containing non-toxic or toxic Microcystis clones suggested that the mechanisms behind these changes involved processes associated with metabolism and antioxidation. 4. Our study shows that non-toxic cyanobacteria can induce tolerance to toxic cyanobacteria and further elucidates the general importance of maternal effects on tolerance of cyanobacteria in herbivorous zooplankton.

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