Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection

Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL) mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa—indica and tropical japonica—as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups

Meta-analysis Followed by Replication Identifies Loci in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as Associated with Systemic Lupus Erythematosus in Asians

Systemic lupus erythematosus (SLE) is a prototype autoimmune disease with a strong genetic involvement and ethnic differences. Susceptibility genes identified so far only explain a small portion of the genetic heritability of SLE, suggesting that many more loci are yet to be uncovered for this disease. In this study, we performed a meta-analysis of genome-wide association studies on SLE in Chinese Han populations and followed up the findings by replication in four additional Asian cohorts with a total of 5,365 cases and 10,054 corresponding controls. We identified genetic variants in or near CDKN1B, TET3, CD80, DRAM1, and ARID5B as associated with the disease. These findings point to potential roles of cell-cycle regulation, autophagy, and DNA demethylation in SLE pathogenesis. For the region involving TET3 and that involving CDKN1B, multiple independent SNPs were identified, highlighting a phenomenon that might partially explain the missing heritability of complex diseases

Exploring the Potential of Aerated Concrete and Clay Bricks from Construction and Demolition Waste as Adsorbents for Pb(II) Removal from Aqueous Solutions

This study aimed to evaluate the potential of utilizing aerated concrete (AC) and clay bricks (CB) sourced from construction and demotion waste (CDW) as low-cost adsorbents for the removal of Pb2+ from aqueous solutions. The effects of various parameters, including particle size, solution pH, contact time, adsorbent dosage, and initial Pb2+ concentration, were analyzed through batch experiments. The results indicated that AC performed more efficiently in removing lead ions than CB under all the tested conditions. The highest removal efficiency of Pb2+ with AC was 99.0%, which was achieved at a pH of 5.0, contact time of 1 h, an adsorbent dosage of 5 g/L, and an initial Pb2+ concentration of 100 mg/L. The maximum adsorption capacities of AC and CB were 201.6 mg/g and 56.3 mg/g, respectively. The adsorption isotherm data of the adsorbents were successfully modeled using both the Langmuir and Freundlich models. The removal of lead ions from aqueous solutions by both adsorbents is primarily achieved through adsorption and microprecipitation. Compared to CB, AC exhibited superior performance, attributed to its larger specific surface area, pore volume, and alkalinity. The cost-effectiveness and availability of AC make it a promising candidate for treating of Pb-contaminated wastewater, providing a new way for resource utilization of CDW

Levels and Patterns of Nucleotide Variation in Domestication QTL Regions on Rice Chromosome 3 Suggest Lineage-Specific Selection

Oryza sativa or Asian cultivated rice is one of the major cereal grass species domesticated for human food use during the Neolithic. Domestication of this species from the wild grass Oryza rufipogon was accompanied by changes in several traits, including seed shattering, percent seed set, tillering, grain weight, and flowering time. Quantitative trait locus (QTL) mapping has identified three genomic regions in chromosome 3 that appear to be associated with these traits. We would like to study whether these regions show signatures of selection and whether the same genetic basis underlies the domestication of different rice varieties. Fragments of 88 genes spanning these three genomic regions were sequenced from multiple accessions of two major varietal groups in O. sativa—indica and tropical japonica—as well as the ancestral wild rice species O. rufipogon. In tropical japonica, the levels of nucleotide variation in these three QTL regions are significantly lower compared to genome-wide levels, and coalescent simulations based on a complex demographic model of rice domestication indicate that these patterns are consistent with selection. In contrast, there is no significant reduction in nucleotide diversity in the homologous regions in indica rice. These results suggest that there are differences in the genetic and selective basis for domestication between these two Asian rice varietal groups.</p

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

<p>Abstract</p> <p>Background</p> <p>DNA methylation plays important biological roles in plants and animals. To examine the rice genomic methylation landscape and assess its functional significance, we generated single-base resolution DNA methylome maps for Asian cultivated rice <it>Oryza sativa</it> ssp<it>. japonica</it>, <it>indica</it> and their wild relatives, <it>Oryza rufipogon</it> and <it>Oryza nivara</it>.</p> <p>Results</p> <p>The overall methylation level of rice genomes is four times higher than that of <it>Arabidopsis</it>. Consistent with the results reported for <it>Arabidopsis</it>, methylation in promoters represses gene expression while gene-body methylation generally appears to be positively associated with gene expression<b>.</b> Interestingly, we discovered that methylation in gene transcriptional termination regions (TTRs) can significantly repress gene expression, and the effect is even stronger than that of promoter methylation. Through integrated analysis of genomic, DNA methylomic and transcriptomic differences between cultivated and wild rice, we found that primary DNA sequence divergence is the major determinant of methylational differences at the whole genome level, but DNA methylational difference alone can only account for limited gene expression variation between the cultivated and wild rice. Furthermore, we identified a number of genes with significant difference in methylation level between the wild and cultivated rice.</p> <p>Conclusions</p> <p>The single-base resolution methylomes of rice obtained in this study have not only broadened our understanding of the mechanism and function of DNA methylation in plant genomes, but also provided valuable data for future studies of rice epigenetics and the epigenetic differentiation between wild and cultivated rice.</p