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We report characteristics of soybean genetic diversity and structure from the resequencing of 481 diverse soybean accessions, comprising 52 wild (Glycine soja) selections and 429 cultivated (Glycine max) varieties (landraces and elites). This data was used to identify 7.8 million SNPs, to predict SNP effects relative to genic regions, and to identify the genetic structure, relationships, and linkage disequilibrium. We found evidence of distinct, mostly independent selection of lineages by particular geographic location. Among cultivated varieties, we identified numerous highly conserved regions, suggesting selection during domestication. Comparisons of these accessions against the whole U.S. germplasm genotyped with the SoySNP50K iSelect BeadChip revealed that over 95% of the re-sequenced accessions have a high similarity to their SoySNP50K counterparts. Probable errors in seed source or genotype tracking were also identified in approximately 5% of the accessions.
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Genoma de Planta , Glycine max/genética , Polimorfismo de Nucleótido Simple , Productos Agrícolas/genética , Fabaceae/genética , Genotipo , Geografía , Desequilibrio de Ligamiento , Selección GenéticaRESUMEN
INTRODUCTIONLike RNA, proteins can be localized in situ on tissue sections. In situ localization or immunohistochemistry provides information on the cellular and subcellular distribution of proteins in different tissues. This protocol describes an alternative to the use of ABC (a preformed Avidin:Biotinylated enzyme Complex used in conjunction with a biotinylated secondary antibody) for non-fluorescent detection in immunohistochemistry. Here, an alkaline-phosphatase-coupled secondary antibody is used with colorimetric substrates for antigen detection.
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INTRODUCTIONAntisense RNA is typically labeled using digoxygenin (DIG), which is subsequently detected with an anti-DIG antibody coupled to alkaline phosphatase. This protocol describes the synthesis and hydrolysis of a DIG-labeled probe to be used for in situ hybridization.
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INTRODUCTIONBoth radioactive and nonradioactive probes can be used to detect RNA in situ. Radioactive in situ hybridizations are believed by many to be more sensitive, but the localization of signal is considerably less precise than for nonradioactive in situs, and each experiment takes much longer. Thus, nonradioactive in situ hybridization is generally preferred. Antisense RNA is typically labeled using digoxygenin (DIG), which is subsequently detected with an anti-DIG antibody coupled to alkaline phosphatase. This protocol describes in situ hybridization of a DIG-labeled probe to paraffin-embedded sections of plant tissue. Double labeling using both DIG- and fluorescein isothiocyanate (FITC)-conjugated ribonucleotides is also described.
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A collection of Arabidopsis lines with T-DNA insertions in known sites was generated to increase the efficiency of functional genomics. A high-throughput modified thermal asymmetric interlaced (TAIL)-PCR protocol was developed and used to amplify DNA fragments flanking the T-DNA left borders from approximately 100000 transformed lines. A total of 85108 TAIL-PCR products from 52964 T-DNA lines were sequenced and compared with the Arabidopsis genome to determine the positions of T-DNAs in each line. Predicted T-DNA insertion sites, when mapped, showed a bias against predicted coding sequences. Predicted insertion mutations in genes of interest can be identified using Arabidopsis Gene Index name searches or by BLAST (Basic Local Alignment Search Tool) search. Insertions can be confirmed by simple PCR assays on individual lines. Predicted insertions were confirmed in 257 of 340 lines tested (76%). This resource has been named SAIL (Syngenta Arabidopsis Insertion Library) and is available to the scientific community at www.tmri.org.
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Arabidopsis/genética , ADN Bacteriano/genética , Agrobacterium tumefaciens/genética , Sitios de Unión/genética , Cromosomas de las Plantas/genética , ADN Bacteriano/química , ADN de Plantas/química , ADN de Plantas/genética , Bases de Datos Genéticas , Genoma de Planta , Internet , Mutagénesis Insercional , Plantas Modificadas Genéticamente , Reacción en Cadena de la Polimerasa/métodos , Semillas/genética , Análisis de Secuencia de ADNRESUMEN
The genome of the japonica subspecies of rice, an important cereal and model monocot, was sequenced and assembled by whole-genome shotgun sequencing. The assembled sequence covers 93% of the 420-megabase genome. Gene predictions on the assembled sequence suggest that the genome contains 32,000 to 50,000 genes. Homologs of 98% of the known maize, wheat, and barley proteins are found in rice. Synteny and gene homology between rice and the other cereal genomes are extensive, whereas synteny with Arabidopsis is limited. Assignment of candidate rice orthologs to Arabidopsis genes is possible in many cases. The rice genome sequence provides a foundation for the improvement of cereals, our most important crops.