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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...

Concentrations of persistent halogenated hydrocarbons (PHHs) were determined in 13 consumer fish species (a total of 390 individuals) collected from a major fish-farming region of China. The potential health risks of PHHs associated with consumption of fish from China was also systematically assessed regionally and globally. In all fish samples, DDTs, HCHs, PCBs, and PBDEs were the predominant PHH residues, with the median levels (ranges) being 6.0 (0.14-698.9), 0.50 (0.13-24.06), 0.10 (< 0.02-7.65), and 0.15 (< 0.0012-3.85) ng/g wet weight, respectively. The upper-bound (90th percentile) values of estimated daily intakes of DDT, HCHs, PCBs, and PBDEs via fish consumption were 45.5, 1.35, 0.46, and 0.30 ng/kg bw/d (urban), and 15.9, 0.47, 0.16, and 0.10 ng/kg bw/d (rural). Globally, the upper-bound outflows via fishery exportation of DDT, HCHs, PCBs, and PBDEs were 185, 5.51, 1.86, and 1.22 kg, respectively, in 2005. Japan was the largest recipient of PHHs, followed by Korea and the United States. Fish consumption assessments indicated that consumption of freshwater farmed and wild marine fish generally does not subject consumers to significant health risk as far as PHHs are concerned, while limited consumption of seawater farmed fish is advised.

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Chlorophyll content is one of the most important physiological traits as it is closely related to leaf photosynthesis and crop yield potential. So far, few genes have been reported to be involved in natural variation of chlorophyll content in rice (Oryza sativa) and the extent of variations explored is very limited. We conducted a genome-wide association study (GWAS) using a diverse worldwide collection of 529 O. sativa accessions. A total of 46 significant association loci were identified. Three F2 mapping populations with parents selected from the association panel were tested for validation of GWAS signals. We clearly demonstrated that Grain number, plant height, and heading date7 (Ghd7) was a major locus for natural variation of chlorophyll content at the heading stage by combining evidence from near-isogenic lines and transgenic plants. The enhanced expression of Ghd7 decreased the chlorophyll content, mainly through down-regulating the expression of genes involved in the biosynthesis of chlorophyll and chloroplast. In addition, Narrow leaf1 (NAL1) corresponded to one significant association region repeatedly detected over two years. We revealed a high degree of polymorphism in the 5' UTR and four non-synonymous SNPs in the coding region of NAL1, and observed diverse effects of the major haplotypes. The loci or candidate genes identified would help to fine-tune and optimize the antenna size of canopies in rice breeding.

Background:The biochemical mechanism of nicotine biodegradation is important. Results: An NADH-dependent and FAD-containing hydroxylase (HspB) for nicotine degradation was purified and mechanistically characterized. Conclusion: The hydroxylase is crucial for nicotine degradation by Pseudomonas putida. Significance: The novel HspB provides a sound basis for future studies aimed at a better understanding of the molecular principles of nicotine degradation.