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GrainGenes Reference Report: PPS-125-1283

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Reference	PPS-125-1283
Title	Active retrotransposons are a common feature of grass genomes
Journal	Plant Physiology
Year	2001
Volume	125
Pages	1283-1292
Author	Vicient CM Jaaskelainen MJ Kalendar R Schulman AH
Abstract	Summary: An Essentially Derived Variety is a cultivar or inbred that largely retains the characteristics of an ancestral cultivar or inbred. The parental contribution to F2-derived inbreds (pF2) and BC1-derived inbreds (pBC1) can be estimated with molecular markers. A recombinant inbred (RI) with pF2 or pBC1 greater than a specified threshold is then considered essentially derived. Our objectives were (i) to derive the variance of pF2 and pBC1, and (ii) to determine the probability of obtaining an essentially derived RI for different numbers of marker loci in different species. The variances of pF2 and pBC1 are a function of the number of chromosomes, length of each chromosome, and number of marker loci on each chromosome. The standard errors (SE) of pF2 and pBC1 were smallest when the two marker loci closest to the ends of each chromosome were included. The minimum values of SE(pF2) and SE(pBC1) are useful for setting minimum values of thresholds for declaring essential derivation. Suppose selfing from the BC1 is permissible and the maximum error rate for falsely declaring an RI is essentially derived is set at 2.5%. The minimum value of the threshold for these conditions is 0.881 in maize (Zea mays L.). For a threshold of 0.90, the probabilities of an essentially derived RI from the BC1 generation were >6% in rye (Secale cereale L.), >3% in barley (Hordeum vulgare L.), <3% in tomato (Lycopersicon spp.), rice (Oryza spp.), and maize, and <1% wheat (Triticum aestivum L.). These results suggest that the thresholds used to declare essential derivation should differ among species
External Databases	Pubmed: 11244109
Keyword	[ Hide all but 1 of 47 ] antibody avena avena sativa bare-1 bare-1 retrotransposon barley capsid protein cereal genomes copia-like retrotransposon cycle element elements expressed sequence tags family fraction frequencies genome grass genomes hordeum vulgare impact integration life-cycle maize marker member monocot multiple oat oats oryza sativa plant retrotransposons polymorphism retrotransposon reverse transcription rice search sequence sequence tags structure tissue culture transcript transcription translation tribe triticeae ty1-copia group retrotransposons virus-like particles

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