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  • 1
    Publication Date: 2013-01-09
    Description: Accelerating crop improvement in sorghum, a staple food for people in semiarid regions across the developing world, is key to ensuring global food security in the context of climate change. To facilitate gene discovery and molecular breeding in sorghum, we have characterized ∼265,000 single nucleotide polymorphisms (SNPs) in 971 worldwide...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 2
    Publication Date: 2009-02-04
    Description: Sorghum, an African grass related to sugar cane and maize, is grown for food, feed, fibre and fuel. We present an initial analysis of the approximately 730-megabase Sorghum bicolor (L.) Moench genome, placing approximately 98% of genes in their chromosomal context using whole-genome shotgun sequence validated by genetic, physical and syntenic information. Genetic recombination is largely confined to about one-third of the sorghum genome with gene order and density similar to those of rice. Retrotransposon accumulation in recombinationally recalcitrant heterochromatin explains the approximately 75% larger genome size of sorghum compared with rice. Although gene and repetitive DNA distributions have been preserved since palaeopolyploidization approximately 70 million years ago, most duplicated gene sets lost one member before the sorghum-rice divergence. Concerted evolution makes one duplicated chromosomal segment appear to be only a few million years old. About 24% of genes are grass-specific and 7% are sorghum-specific. Recent gene and microRNA duplications may contribute to sorghum's drought tolerance.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Paterson, Andrew H -- Bowers, John E -- Bruggmann, Remy -- Dubchak, Inna -- Grimwood, Jane -- Gundlach, Heidrun -- Haberer, Georg -- Hellsten, Uffe -- Mitros, Therese -- Poliakov, Alexander -- Schmutz, Jeremy -- Spannagl, Manuel -- Tang, Haibao -- Wang, Xiyin -- Wicker, Thomas -- Bharti, Arvind K -- Chapman, Jarrod -- Feltus, F Alex -- Gowik, Udo -- Grigoriev, Igor V -- Lyons, Eric -- Maher, Christopher A -- Martis, Mihaela -- Narechania, Apurva -- Otillar, Robert P -- Penning, Bryan W -- Salamov, Asaf A -- Wang, Yu -- Zhang, Lifang -- Carpita, Nicholas C -- Freeling, Michael -- Gingle, Alan R -- Hash, C Thomas -- Keller, Beat -- Klein, Patricia -- Kresovich, Stephen -- McCann, Maureen C -- Ming, Ray -- Peterson, Daniel G -- Mehboob-ur-Rahman -- Ware, Doreen -- Westhoff, Peter -- Mayer, Klaus F X -- Messing, Joachim -- Rokhsar, Daniel S -- England -- Nature. 2009 Jan 29;457(7229):551-6. doi: 10.1038/nature07723.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Plant Genome Mapping Laboratory, University of Georgia, Athens, Georgia 30602, USA. paterson@uga.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19189423" target="_blank"〉PubMed〈/a〉
    Keywords: Arabidopsis/genetics ; Chromosomes, Plant/genetics ; *Evolution, Molecular ; Gene Duplication ; Genes, Plant ; Genome, Plant/*genetics ; Oryza/genetics ; Poaceae/*genetics ; Populus/genetics ; Recombination, Genetic/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Sequence Deletion/genetics ; Sorghum/*genetics ; Zea mays/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Publication Date: 2009-08-08
    Description: Maize genetic diversity has been used to understand the molecular basis of phenotypic variation and to improve agricultural efficiency and sustainability. We crossed 25 diverse inbred maize lines to the B73 reference line, capturing a total of 136,000 recombination events. Variation for recombination frequencies was observed among families, influenced by local (cis) genetic variation. We identified evidence for numerous minor single-locus effects but little two-locus linkage disequilibrium or segregation distortion, which indicated a limited role for genes with large effects and epistatic interactions on fitness. We observed excess residual heterozygosity in pericentromeric regions, which suggested that selection in inbred lines has been less efficient in these regions because of reduced recombination frequency. This implies that pericentromeric regions may contribute disproportionally to heterosis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉McMullen, Michael D -- Kresovich, Stephen -- Villeda, Hector Sanchez -- Bradbury, Peter -- Li, Huihui -- Sun, Qi -- Flint-Garcia, Sherry -- Thornsberry, Jeffry -- Acharya, Charlotte -- Bottoms, Christopher -- Brown, Patrick -- Browne, Chris -- Eller, Magen -- Guill, Kate -- Harjes, Carlos -- Kroon, Dallas -- Lepak, Nick -- Mitchell, Sharon E -- Peterson, Brooke -- Pressoir, Gael -- Romero, Susan -- Oropeza Rosas, Marco -- Salvo, Stella -- Yates, Heather -- Hanson, Mark -- Jones, Elizabeth -- Smith, Stephen -- Glaubitz, Jeffrey C -- Goodman, Major -- Ware, Doreen -- Holland, James B -- Buckler, Edward S -- New York, N.Y. -- Science. 2009 Aug 7;325(5941):737-40. doi: 10.1126/science.1174320.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉United States Department of Agriculture-Agriculture Research Service (USDA-ARS), USA. mcmullenm@missouri.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19661427" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Centromere/genetics ; *Chromosome Mapping ; Chromosomes, Plant/*genetics ; Crosses, Genetic ; Epistasis, Genetic ; Flowers/genetics/growth & development ; *Genetic Variation ; Genome, Plant ; Heterozygote ; Hybrid Vigor ; Inbreeding ; Linkage Disequilibrium ; Phenotype ; Polymorphism, Single Nucleotide ; Quantitative Trait Loci ; *Quantitative Trait, Heritable ; Recombination, Genetic ; Selection, Genetic ; Zea mays/classification/*genetics/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 4
    Publication Date: 2009-08-08
    Description: Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing species Zea mays (maize). We dissected variation for flowering time with a set of 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly a million plants were assayed in eight environments but showed no evidence for any single large-effect quantitative trait loci (QTLs). Instead, we identified evidence for numerous small-effect QTLs shared among families; however, allelic effects differ across founder lines. We identified no individual QTLs at which allelic effects are determined by geographic origin or large effects for epistasis or environmental interactions. Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice and Arabidopsis.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Buckler, Edward S -- Holland, James B -- Bradbury, Peter J -- Acharya, Charlotte B -- Brown, Patrick J -- Browne, Chris -- Ersoz, Elhan -- Flint-Garcia, Sherry -- Garcia, Arturo -- Glaubitz, Jeffrey C -- Goodman, Major M -- Harjes, Carlos -- Guill, Kate -- Kroon, Dallas E -- Larsson, Sara -- Lepak, Nicholas K -- Li, Huihui -- Mitchell, Sharon E -- Pressoir, Gael -- Peiffer, Jason A -- Rosas, Marco Oropeza -- Rocheford, Torbert R -- Romay, M Cinta -- Romero, Susan -- Salvo, Stella -- Sanchez Villeda, Hector -- da Silva, H Sofia -- Sun, Qi -- Tian, Feng -- Upadyayula, Narasimham -- Ware, Doreen -- Yates, Heather -- Yu, Jianming -- Zhang, Zhiwu -- Kresovich, Stephen -- McMullen, Michael D -- New York, N.Y. -- Science. 2009 Aug 7;325(5941):714-8. doi: 10.1126/science.1174276.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉U.S. Department of Agriculture (USDA)-Agricultural Research Service (USDA-ARS), USA. esb33@cornell.edu〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19661422" target="_blank"〉PubMed〈/a〉
    Keywords: Alleles ; Chromosome Mapping ; Chromosomes, Plant/genetics ; Epistasis, Genetic ; Flowers/*genetics/growth & development ; Gene Frequency ; Genes, Plant ; Genetic Variation ; Geography ; Inbreeding ; Phenotype ; Polymorphism, Single Nucleotide ; *Quantitative Trait Loci ; Quantitative Trait, Heritable ; Recombination, Genetic ; Time Factors ; Zea mays/*genetics/growth & development/physiology
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Cellular and molecular life sciences 38 (1982), S. 13-18 
    ISSN: 1420-9071
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Medicine
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Science Ltd
    Weed research 45 (2005), S. 0 
    ISSN: 1365-3180
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: The parasitic angiosperms, Striga hermonthica and Striga asiatica, severely constrain cereal production in sub-Saharan Africa by causing huge losses in grain yield. Understanding the diversity of Striga populations is important because it allows identification of races or biotypes thus improving chances of breeding success. Amplified fragment length polymorphism (AFLP) analysis was used to study genetic diversity among 17 populations of S. asiatica and 24 populations of S. hermonthica from Kenya. A total of 349 DNA fragments ranging from 51 to 500 bp were obtained from four EcoRI and MseI primer combinations. Genetic distances for S. asiatica populations ranged from 0.009 to 0.116 with a mean of 0.032. S. hermonthica populations had a genetic distance that ranged from 0.007 to 0.025 with a mean of 0.015. Only two clusters were found in S. asiatica populations whereas no apparent structure was evident in S. hermonthica populations. There was no evidence of isolation by distance for the two species. Although the low genetic diversity suggests Striga is relatively uniform across the populations studied, it is possible that pathogenicity and virulence genes may be located in genomic regions that were not sampled. The data, however, does not provide evidence to support diversification of both Striga species in the region where the study was conducted.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1435-0653
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Arachis hypogaea L.), an important agronomic crop, exhibits a considerable amount of variability for morphological traits and for resistance to diseases and pests. In contrast, molecular marker assays have detected little variation at the nucleic acid level. Identification of molecular markers would be of great help to peanut breeders, geneticists, and taxonomists. The objectives of this work were to identify simple sequence repeat (SSR) markers in cultivated peanut and to test these markers for their ability to discriminate among accessions. Peanut total genomic DNA libraries were constructed and screened with 32P-labeled dinucleotide repeats, (GT)10 and (CT)10. DNA sequences were obtained from the SSR-containing clones and, when possible, primer pairs were designed on the basis of DNA sequences flanking the repeat motif. Primer pairs were tested in polymerase chain reaction (PCR) assays using a collection of 22 peanut DNAs, representing both cultivated peanut and wild species. In all, six SSR markers, five from the library screening procedure and one additional marker obtained from a search of publicly available DNA sequences, detected polymorphisms among the peanut DNAs. Discrimination power was high among the cultivated peanuts, with 17 unique genotypes represented among the 19 accessions tested. From two to 14 DNA fragments were amplified per SSR marker, and as a group, the six markers may amplify up to 10 putive SSR loci. The SSR markers identified in this study were more effective in detecting molecular variation in cultivated peanut than all other DNA-based marker evaluated to date.
    Type of Medium: Electronic Resource
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  • 8
    ISSN: 1435-0653
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Sorghum bicolor (L.) Moench] inbreds were used to compare the discrimination abilities of 15 SSR primers with 104 RFLPs and to compare the associations among lines revealed by these molecular data and by pedigrees. RFLP data allowed all lines to be uniquely identified; two lines could not be distinguished by the SSR data. The mean polymorphism information content (PIC) values were 0.62 (RFLPs) and 0.58 (SSRs). Correlations for pairwise molecular profile distances with pedigree distances among the maintainer female (B) lines were 0.52 and 0.53 for RFLP and SSR data, respectively; data for the male parental restorer (R) lines were 0.41 and 0.47. This set of SSRs could be used to help genetic conservation management and to support IPP. Data from additional SSRs that collectively cover more of the genome will be required for applications to assist in breeding.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1435-0653
    Source: Springer Online Journal Archives 1860-2000
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Sorghum bicolor (L.) Moench] accessions identified as 'Orange' presently maintained by the U.S. National Plant Germplasm system (NPGS) were assayed with 15 simple sequence repeat (SSR) markers. Genotyping was performed with fluorescent primers with five primer sets in each of three multiplex polymerase chain reactions (PCRs) and automated allele sizing. A total of 96 individuals were analyzed, five plants from each of 19 Orange accessions and one individual from an elite inbred line, 'RTx430'. The SSR markers provided substantial genetic resolution among the Orange entries. Average heterozygosity estimates were low, and phenetic analyses (neighbor-joining dendograms) were generally consistent with known historical relationships among accessions. Most accessions were genetically distinct, but two redundant groups (involving a total of five entries) were found among the 19 Orange accessions evaluated. The molecular variance analysis (AMOVA) showed that 90% of the total genetic variation was partitioned among accessions, while one-tenth of the variation resulted from genetic differences between individual plants within accessions. The variance analysis also indicated that it should be possible to reduce the number of Orange accessions held by NPGS by almost half without seriously jeopardizing the overall amount of genetic variation contained in these holdings. This study demonstrated that a limited number of SSR markers can be used in a cost-efficient manner to rapidly assess variation in accessions of Orange sorghum.
    Type of Medium: Electronic Resource
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  • 10
    ISSN: 1432-2242
    Keywords: Key words AMOVA ; Conservation ; Curation ; Genetic markers ; Molecular genetic screening ; RAPD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract To better characterize and conserve crop genetic resources, the assessment of genetic identity, relatedness, and structure among entries and collections becomes a priority. In the present study, a random amplified polymorphic DNA (RAPD) assay was applied as a quick, cost-effective, and preliminary screen to quantify and partition the molecular variation among accessions. Fourteen phenotypically uniform accessions of Brassica oleracea var. capitata L. (cabbage) similarly designated as `Golden Acre' were tested with nine decamer oligonucleotide primers. These amplifications generated 110 fragments, of which 80 were polymorphic ranging in size from 370 to 1720 bp. The 80 polymorphic fragments were sufficient to distinguish between all 14 accessions. Data based on the partitioning of variation among accessions indicated that `Golden Acre' entries could be reduced to as few as four groups, with the potential loss of variation being only 4.6% of the absolute current genetic variation in those holdings as estimated from RAPD analysis. This proposed grouping would concurrently save approximately 70% [$750–1000 (US) per accession] for each cycle of regeneration (approximately 20–25 years at most) which alternatively could then be used for other priorities in B. oleracea conservation and use. This case represents but one example where targeted use of a molecular-marker assay linked with rigorous statistical analysis will be useful for plant genebank management, particularly for questions at the intraspecific level. Molecular markers will provide genebank curators with additional sources of information to better plan and organize collection holdings and use finite financial support in a more effective manner.
    Type of Medium: Electronic Resource
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