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Data from: Whole genome sequencing of elite rice cultivars as a comprehensive information resource for marker assisted selection
- 负责人：
- 关键词：
- Rice Genomic variation High throughput sequencing Copy Number Variation Marker assisted selection
- DOI：
- doi:10.5061/dryad.8hg32
- 摘要：
- or genomic selection. In this work we present sequencing and bioinformatics analyses of 104 rice varieties belonging to the major subspecies of Oryza
Data from: Patterns and evolution of nucleotide landscapes in seed plants
- 负责人：
- Glémin, Sylvain
- DOI：
- doi:10.5061/dryad.p12305b2
- 摘要：
- s well known in plants. Most studies have focused on the GC-poor and homogeneous Arabidopsis genome and the much more GC-rich and heterogeneous rice (Oryza sativa) genome
Data from: Analysis of evolutionary relationships provides new clues to the origins of weedy rice
- 负责人：
- DOI：
- doi:10.5061/dryad.sqv9s4n0h
- 摘要：
Weedy rice (Oryza sativa f. spontanea) is considered to be a pest in modern rice production
Data from: More than one way to evolve a weed: Parallel evolution of U.S. weedy rice through independent genetic mechanisms
- 负责人：
- 关键词：
- Agricultural weeds domestication genotyping by sequencing (GBS) QTL mapping parallel evolution weedy rice
- DOI：
- doi:10.5061/dryad.566h9
- 摘要：
- . Within domesticated rice (Oryza sativa), there has also been independent evolution of weedy strains from different cultivated varieties. This makes it poss
Data from: Identification, characterization, and transcription analysis of xylogen-like arabinogalactan proteins in rice (Oryza sativa L.)
- 负责人：
- 关键词：
- phylogenetic tree
- DOI：
- doi:10.5061/dryad.44tj3
- 摘要：
- Background: Xylogen, a chimeric arabinogalactan protein containing a non-specific lipid transfer protein domain, can promote xylem cell differentiation. No comprehensive study has been carried out on the XYLP gene family in rice. As a first step in research on this gene family and as a useful strategy in general, a genome-wide analysis of the OsXYLP gene family is thus needed. Results: In this study, we identified 21 XYLP genes from the rice genome and comprehensively analyzed their protein structures, phylogenetic relationships, chromosomal locations, and gene duplication status. Our results indicate that gene duplication has played major roles in the expansion of the OsXYLP gene family. We used expressed sequence tag, microarray, massively parallel signature sequencing, and quantitative real-time PCR data to analyze OsXYLP gene expression during various developmental stages and under abiotic stress conditions. We found that many OsXYLP genes are abundantly expressed in vascular tissues and seeds, with some genes regulated under hormonal or abiotic stresses. In addition, we identified knockout mutants of OsXYLP7 and OsXYLP16 and discovered that the mutant xylp7 has a defect in stem height. Conclusions: We analyzed expression profiles of 21 XYLP genes and characterized the structures and evolutionary relationships of their proteins. Our results demonstrate that the rice XYLP gene family may play roles in plant vascular system development and hormone signaling. Among the 21 detected OsXYLPs, 19 are newly identified genes encoding arabinogalactan proteins. Our results provide comprehensive insights that will assist future research on the biological functions of the rice XYLP gene family.
Data from: Cell wall composition and bioenergy potential of rice straw tissues are influenced by environment, tissue type, and genotype
- 负责人：
- DOI：
- doi:10.5061/dryad.7ss03
- 摘要：
- Breeding has transformed wild plant species into modern crops, increasing the allocation of their photosynthetic assimilate into grain, fiber, and other products for human use. Despite progress in increasing the harvest index, much of the biomass of crop plants is not utilized. Potential uses for the large amounts of agricultural residues that accumulate are animal fodder or bioenergy, though these may not be economically viable without additional efforts such as targeted breeding or improved processing. We characterized leaf and stem tissue from a diverse set of rice genotypes (varieties) grown in two environments (greenhouse and field) and report bioenergy-related traits across these variables. Among the 16 traits measured, cellulose, hemicelluloses, lignin, ash, total glucose, and glucose yield changed across environments, irrespective of the genotypes. Stem and leaf tissue composition differed for most traits, consistent with their unique functional contributions and suggesting that they are under separate genetic control. Plant variety had the least influence on the measured traits. High glucose yield was associated with high total glucose and hemicelluloses, but low lignin and ash content. Bioenergy yield of greenhouse-grown biomass was higher than field-grown biomass, suggesting that greenhouse studies overestimate bioenergy potential. Nevertheless, glucose yield in the greenhouse predicts glucose yield in the field (??=?0.85, p?
Data from: Waterbird response to variable-timing of drawdown in rice fields after winter-flooding
- 负责人：
- DOI：
- doi:10.5061/dryad.6q5k86q
- 摘要：
- agricultural land, primarily rice (Oryza sativa). Each year non-breeding waterbird habitat decreases in the late winter as flooded agricultural fields are drained aft
Data from: Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition
- 负责人：
- 关键词：
- genomic selection genomics-assisted breeding rice genome-wide association study genotyping-by-sequencing
- DOI：
- doi:10.5061/dryad.7369p
- 摘要：
- Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.
Data from: Inferring roles in defense from metabolic allocation of rice diterpenoids
- 负责人：
- Peters, Reuben J.
- DOI：
- doi:10.5061/dryad.339k00b
- 摘要：
- h natural products from the important crop plant rice (Oryza sativa) are diterpenoids whose biosynthesis proceeds via either ent- or syncopalyl diphosphate (CPP
Data from: Identification and analysis of novel salt responsive candidate gene based SSRs (cgSSRs) from rice (Oryza sativa L.)
- 负责人：
- 关键词：
- Microsatellite genic-SSR cgSSR salt tolerance salt responsive gene rice molecular diversity candidate gene rice genotype
- DOI：
- doi:10.5061/dryad.dj51c
- 摘要：
- Background: Majority of the Asian people depend on rice for nutritional energy. Rice cultivation and yield are severely affected by soil salinity stress worldwide. Marker assisted breeding is a rapid and efficient way to develop improved variety for salinity stress tolerance. Genomic microsatellite markers are an elite group of markers, but there is possible uncertainty of linkage with the important genes. In contrast, there are better possibilities of linkage detection with important genes if SSRs are developed from candidate genes. To the best of our knowledge, there is no such report on SSR markers development from candidate gene sequences in rice. So the present study was aimed to identify and analyse SSRs from salt responsive candidate genes of rice. Results: In the present study, based on the comprehensive literature survey, we selected 220 different salt responsive genes of rice. Out of them, 106 genes were found to contain 180 microsatellite loci with, tri-nucleotide motifs (56%) being most abundant, followed by di-(41%) and tetra nucleotide (2.8%) motifs. Maximum loci were found in the coding sequences (37.2%), followed by in 5′UTR (26%), intron (21.6%) and 3′UTR (15%). For validation, 19 primer sets were evaluated to detect polymorphism in diversity analysis among the two panels consisting of 17 salt tolerant and 17 susceptible rice genotypes. Except one, all primer sets exhibited polymorphic nature with an average of 21.8 alleles/primer and with a mean PIC value of 0.28. Calculated genetic similarity among genotypes was ranged from 19%-89%. The generated dendrogram showed 3 clusters of which one contained entire 17 susceptible genotypes and another two clusters contained all tolerant genotypes. Conclusion: The present study represents the potential of salt responsive candidate gene based SSR (cgSSR) markers to be utilized as novel and remarkable candidate for diversity analysis among rice genotypes differing in salinity response.
