Phytic acid (myo-inositol-1, 2, 3, 4, 5, 6-hexakisphosphate or Ins P6) typically represents approximately 75% to 80% of maize (Zea mays) seed total P. Here we describe the origin, inheritance, and ...seed phenotype of two non-lethal maize low phytic acid mutants, lpa1-1 and lpa2-1. The loci map to two sites on chromosome 1S. Seed phytic acid P is reduced in these mutants by 50% to 66% but seed total P is unaltered. The decrease in phytic acid P in mature lpa1-1 seeds is accompanied by a corresponding increase in inorganic phosphate (Pi). In mature lpa2-1 seed it is accompanied by increases in Pi and at least three other myo-inositol (Ins) phosphates (and/or their respective enantiomers): D-Ins(1,2,4,5,6) P5; D-Ins (1,4,5,6) P4; and D-Ins(1,2,6) P3. In both cases the sum of seed Pi and Ins phosphates (including phytic acid) is constant and similar to that observed in normal seeds. In both mutants P chemistry appears to be perturbed throughout seed development. Homozygosity for either mutant results in a seed dry weight loss, ranging from 4% to 23%. These results indicate that phytic acid metabolism during seed development is not solely responsible for P homeostasis and indicate that the phytic acid concentration typical of a normal maize seed is not essential to seed function.
The program InDeVal was originally developed to help researchers find known regions of insertion/deletion activity (with the exception of isolated single-base indels) in newly determined Poaceae ...trnL-F sequences and compare them with 533 previously determined sequences. It is supplied with input files designed for this purpose. More broadly, the program is applicable for finding specific target regions (referred to as "variable regions") in DNA sequence. A variable region is any specific sequence fragment of interest, such as an indel region, a codon or codons, or sequence coding for a particular RNA secondary structure.
InDeVal input is DNA sequence and a template file (sequence flanking each variable region). Additional files contain the variable regions and user-defined messages about the sequence found within them (e.g., taxa sharing each of the different indel patterns).Variable regions are found by determining the position of flanking sequence (referred to as "conserved regions") using the LPAM (Length-Preserving Alignment Method) algorithm. This algorithm was designed for InDeVal and is described here for the first time. InDeVal output is an interactive display of the analyzed sequence, broken into user-defined units. Once the user is satisfied with the organization of the display, the information can be exported to an annotated text file.
InDeVal can find multiple variable regions simultaneously (28 indel regions in the Poaceae trnL-F files) and display user-selected messages specific to the sequence variants found. InDeVal output is designed to facilitate comparison between the analyzed sequence and previously evaluated sequence. The program's sensitivity to different levels of nucleotide and/or length variation in conserved regions can be adjusted. InDeVal is currently available for Windows in Additional file 1 or from http://www.sci.muni.cz/botany/elzdroje/indeval/.
Phylogenetic studies of organelle DNA sequences at low taxonomic levels present a researcher with specific experimental design challenges. Such studies require sampling of large numbers of ...individuals, many of which share identical haplotypes. The process is often limited by time and money required for DNA sequencing. A variety of mutation detection methods has been developed to circumvent this limitation. This paper briefly reviews the available methods and presents some of their advantages and disadvantages. The applicability of these methods to nuclear DNA studies is discussed.
Statistical methods are proposed for analyzing the experimental design, preliminary results, and final results of phylogenetic studies of organelle DNA sequence at low taxonomic levels. Such studies ...require sampling numerous individuals, many of which share identical haplotypes. The proportions of the haplotypes sampled can help answer the following questions: (1) Is one haplotype so dominant that the particular DNA region is without meaningful variation within the scope of the study? (2) Were all prevalent haplotypes found? (3) What are the proportions of each haplotype within the studied group? (4) What percentage of the studied group can be confidently asserted to belong to the haplotypes that were found? Examples are given in which the statistics techniques are applied to data drawn from the botanical literature. Tables are included as a quick reference for the researcher who wishes to circumvent calculation. A Microsoft® Excel 2000 spreadsheet (titled "HaploPro.xls") for performing some of the more complicated calculations is offered online. Finally, the limitations of these methods and their applicability to nuclear DNA and other characters studies are discussed.
Studies of organelle DNA sequence at low taxonomic levels present a researcher with specific experimental design challenges. Such studies require sampling numerous individuals, many of which share ...identical haplotypes. The process is often limited by the time and money required for DNA sequencing. A number of screening techniques have been devised to combat this limitation, but many have not found wide-spread use in botany. An ideal screening technique would be fast, easy, safe, inexpensive, detect 100% of mutations, be suitable for DNA fragments of about 1 kb, and not require complex equipment. This paper compares the heteroduplex analysis (HA) and chemical cleavage of mismatch (CCM) methods for detecting known point mutations and a deletion in a 1 kb region of non-coding cpDNA from the Poa pratensis agg. A new CCM visualization method, staining with SYBR® Green II, was tested.
Chromosome numbers for Eleocharis palustris subsp. palustris (based on 70 samples from Austria, Bulgaria, Croatia, the Czech Republic, Germany, Greece, Hungary, Lithuania, Romania, Russia, Slovakia, ...Slovenia, and Sweden) and Eleocharis palustris subsp. vulgaris (based on 74 samples from Austria, the Czech Republic, Denmark, Germany, Ireland, Latvia, Luxembourg, the Netherlands, Portugal, and Sweden) are given. Also the chromosome number estimates based on relative DNA contents of plants from 8 localities E. palustris subsp. palustris from Croatia, the Czech Republic, Germany, Italy, Israel, and Slovenia, and from 18 localities of E. palustris subsp. vulgaris from the Czech Republic, Germany and Sweden are included. In E. palustris subsp. palustris, 2n=16 prevailed, the mixoploid 2n=15, 16 was rare and a lone hypoploid 2n=15 was detected. In E. palustris subsp. vulgaris 2n=38 was most frequently detected, the hyperploid 2n=39 and mixoploid 2n=38, 39 were common, and the hypoploid 2n=36 and mixoploids in which 2n ranges from 36 to 42 were rarer. Distribution maps based on plants investigated either by chromosome counting or by flow cytometry, augmented by similar data from published sources are given for both subspecies in Europe.
Phytic acid (
myo
-inositol-1, 2, 3, 4, 5, 6-hexa
kis
phosphate or Ins P
6
) typically represents approximately 75% to 80% of maize (
Zea mays
) seed total P. Here we describe the origin, ...inheritance, and seed phenotype of two non-lethal maize
low phytic acid
mutants,
lpa1-1
and
lpa2-1
. The loci map to two sites on chromosome 1S. Seed phytic acid P is reduced in these mutants by 50% to 66% but seed total P is unaltered. The decrease in phytic acid P in mature
lpa1-1
seeds is accompanied by a corresponding increase in inorganic phosphate (P
i
). In mature
lpa2-1
seed it is accompanied by increases in P
i
and at least three other
myo
-inositol (Ins) phosphates (and/or their respective enantiomers):
d
-Ins(1,2,4,5,6) P
5
;
d
-Ins (1,4,5,6) P
4
; and
d
-Ins(1,2,6) P
3
. In both cases the sum of seed P
i
and Ins phosphates (including phytic acid) is constant and similar to that observed in normal seeds. In both mutants P chemistry appears to be perturbed throughout seed development. Homozygosity for either mutant results in a seed dry weight loss, ranging from 4% to 23%. These results indicate that phytic acid metabolism during seed development is not solely responsible for P homeostasis and indicate that the phytic acid concentration typical of a normal maize seed is not essential to seed function.
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