|
Notes and explanations (reference is given in brackets)
1 parts of the gene are sequenced by (190, 191)
2 both sequences were derived from the Sec2 locus of rye chromosome 2R
3 RFLP was localized on two different chromosomes
4 linked to the RFLP marker Xpsr596 (253)
5 linked to the RFLP marker Xpsr1077 (253)
6 linked to the RFLP marker Xwg59 (253)
7 linked to the RFLP marker Xpsr929 (253)
8 linked to the RFLP marker Xiag23 (253)
9 recombination frequency modified by sex (264)
10 also found on chromosome 4R of Secale montanum
11 there were two genes originally described, Pm8 and Pm17, but Hsam & Zeller (256) determined them as allelic, so by the authors they were renamed
as one gene, Pm1
12 renamed in 2006 by the authors from Ssp1,Ssp2 to Ssp3, and Ssp3 to Ssp5 after (42), (299), (412)
13 based on linkages the gene was relocated in 2006 by the author from 2RL to 3RS
14 symbol “Spf” (spikelet fertility) was renamed in 2007 by the author as “QTL13-1RS”
15 symbol “sy” (asynapsis) or desynapsis) was renamed by the author as “asc” or “dsc”
16 QTL was renamed in 2009 by the author based on (346, 404, 407, 430)
17 P(Edu) was renamed as En(edu) according to the uniform nomenclature used in this compilation
18 about 4,200 rRNA genes are present in rye; within the cereals there are basically two loci for 5S DNA; one locus identified by repet. units 320-468 bp on chromosome 1, the other locus with repet. sequences 469-500 bp on chromosome 5
19 it is located 111 bp downstream for the stop codon of the psbI gene on the opposite strand
20 the gene seems to be homoeologous to a cluster of genes coding for frost tolerance/vernalization sensitivity in wheat (Fr1, Vrn1) and barley (Sh2) (227)
21 the gene Dw on chromosome 5RL was renamed as dw8 by
the authors; the designation Dw by Devos et al. (206) is probably incorrect, since it seems to be a recessive gene for the short straw character
22 the map distance covers 142 kb-region of a rice BAC clone, gi:18997259 (329)
23 the underlined bold-marked ATG is an open codon
24 relocalized by the author in 2006
25 renamed by the author in 2006; Tw1 and Tw2 showing complementary gene interaction (363, 425)
26 relocated from 4RL to 7RS according; an inducible gene; linked to the aluminum malate transporter gene (365)
27 the nucleotide sequence “pScJNK1” was localized in the 2RL1.2 by (366) in Secale vavilovii and confirmed by (367) at the same position in Secale montanum
28 probably not correct localized since the linked gene Alt3 was relocated from 4RL to 7RS by (365)
29 the major recessive gene controlling the male sterility is allelic with the male sterility genes of the C- and R-types; the Pampa-type is completely different and controlled by the dominant gene(s) and mitochondrial DNA showing different restriction fragment patters; the major gene ms1(Rfg1)
is located on chromosome 4RL; the sites of the minor genes ms2 and ms3 were found on 3R and 6R, resp.; the hybrids produced by crossing male steriles of G-type with inbreds show normal pollination and, therefore, are tolerant to ergot infection, similar as normal rye populations
30 the order of loci is from (proximal) Xwg199–Ha1–beta-Amy1 (distal) according a translocation mapping study (385)
31 this1397-bp DNA fragment corresponds to the rpoC2 chloroplast RNA polymerase gene; two rye species, Secale montanum and S. cereale,
did not practically differ in the structure of this DNA fragment (the nucleotide sequences were 99% identical); the extent of the homology of various stretches of the rpoC2 rye gene with the corresponding sequences in maize and rice was 81–95%, whereas the deduced amino acid sequences of rpoC2 in rye, wheat, maize, and rice were considerably identical (96–97% of homology); the fragment of the rpoC2 gene differed from the corresponding sequences in three other grass species primarily by a short (49 bp) insert into the region of numerous short repeats corresponding to nucleotides 15750/15751, 28728/28729, and 27472/27473 in wheat, maize, and rice, respectively
32 assembly of two orthologous proteins associated with meiotic chromosome axes in Arabidopsis thaliana (Asy1 and Zyp1) was studied immunologically at meiotic prophase of meiosis of wild type rye (Secale cereale)
and its synaptic mutant sy10, using antibodies derived from A. thaliana; the temporal and spatial expression of the two proteins were similar in wild type rye, but with one notable difference; unlike A. thaliana,
in which foci of the transverse filament protein Zyp1 appear to linearise commensurately with synapsis, linear tracts of Asy1 and Zyp1 protein form independently at leptotene and early zygotene of rye, and co-align into triple structures resembling synaptonemal complexes (SCs) only at later stages of synapsis; the sy10 mutant also forms spatially separate linear tracts of Asy1 and Zyp1 proteins at leptotene and early zygotene, and these co-align but do not form regular triple structures at mid-prophase; electron microscopy of spread axial elements reveals extensive asynapsis with some exchanges of pairing partners; indiscriminate SCs support non-homologous chiasma formation at metaphase I, as revealed by multi-color fluorescence in situ hybridisation enabling reliable identification of all the chromosomes of the complement; scrutiny of chiasmate and non-chiasmate ("sticky") associations of chromosomes at this stage revealed some specificity in the associations of homologous and non-homologous chromosomes
33 when the menadione reductase (MNR), the nicotinamide adenine dinucleotide dehydrogenase (NDH) and diaphorase (DIA) isozymes were studied in the allohexaploid Triticum aestivum cv. “Chinese Spring" and in five diploid Triticeae species, it turned out that the Mnr1, Ndh3 and Dia1 loci were located on the chromosome arms 3AL, 3BL and 3DL of T. aestivum, respectively; these loci were also located on the 3H chromosome of Hordeum vulgare cv. “Betzes", the 3L chromosome of Aegilops longissima and the 6RL chromosome arm of Secale cereale cv. “Imperial"; the chromosomal location results together with the segregation studies support a tetrameric behaviour of the MNR1, NDH3 and DIA1 isozymes; the Ndh1 and Dia3 loci were located on homoeologous group 4 showing a monomeric behaviour; the chromosomal locations and linkage data of the Mnr, Ndh and Dia loci suggest that Mnr1 = Ndh3 = Dia1, Ndh1 = Dia3 and Ndh2 = Dia2
34 when genomic DNA clone coding for a rye secalin gene (gSec2A) was isolated from a wheat translocation line carrying the 2RS.2BL chromosome, using a previously identified partial secalin (Sec2)
cDNA clone as a probe, the predicted N-terminal amino-acid sequence of the gSec2A gene was identical to the N-terminal sequence obtained for Sec2 polypeptide bands isolated from SDS-PAGE gels; bacterially expressed gSec2A protein was identical in size to that of the smallest Sec2 polypeptide band observed on SDS PAGE gels and is recognized by a monoclonal antibody specific for Mr 75,000 2RS %-secalins; overall, the predicted protein sequence of gSec2A was most similar (50 %) to the family of %-gliadins and consists of a short N-terminal region containing one cysteine residue followed by a glutamine/proline-rich repetitive domain and a long C-terminal domain containing eight cysteine residues; the repetitive domain can be divided into two regions; one region coded for 15 units, each consisting of eight amino acids similar in sequence to that found in the P-secalins and C-hordeins; the second region coded for 17 units each consisting of a sequence of 7-10 amino acids similar to that observed in %-gliadins (390)
35 the character was first described in deatail by Leighty and Taylor (391); they noted that the traits is differentially expressed among rye
varieties, such as “Abruzzes”, “Rümker 1”, “Rümker 2”, “St. Johns”, “Rosen”, “Virginia”, “Rimpau”, or “Mexican”; glabrous necked individuals occured in a frequency between 0.6 to 8 %, respectively;observation were
made at Arlington Experiment Farm (Virginia, USA) in 1923; the character is inherited as “simple dominant”, 2007
36 renamed by the author in 2007 from Lr, Lra, Pr1 to Lr1;
the latter designation is not identical with the designation of (380) and (401)
37 TAXI (Triticum aestivum xylanase inhibitor) proteins are present in wheat flour and are known to inhibit glycosyl hydrolase family 11 endoxylanases, enzymes which are commonly applied in grain processing; by PCR-based molecular identification the genes encoding endoxylanase inhibitors HVXI and SCXI, the TAXI-like proteins from barley (Hordeum vulgare) and rye (Secale cereale)
can be investigated; the HVXI coding sequence encodes a mature protein of 384 amino acids preceded by a 19 amino acid long signal sequence; SCXI-II/III has an open reading frame encoding a signal peptide of 21 amino
acids and a mature protein of 375 amino acids; as for TAXI-I, no introns are detected in the untranslated regions and coding sequences identified; rice TAXI-type proteins clustered together with the cereal
endoxylanase inhibitors; dicotyledonous proteins with sequence similarity to TAXI-I, including the tomato xyloglucan-specific endoglucanase inhibiting protein, form a different clade; the TAXI-type proteins are part
of a superfamily of proteins all involved in plant responses to biotic or abiotic stress for which a function as glycosyl hydrolase inhibitors can be suggested; TAXI-I gene can be identified on wheat chromosome 3B,
SCXI-II/III gene be identified on rye chromosome 6R, 2008
38 it was found that the gene, Hm1 (in maize), is present in all grasses since shortly after their evolutionary origin and protects them against a lethal leaf blight and ear mold disease of the fungus Cochliobolus carbonum Race 1 (CCR1), 2008
39 Revolver discovered in the Triticeae plants is a novel class of transposon-like gene and a major component of the large cereal genome; an 89 bp segment of Revolver that is enriched in the genome of rye was isolated by deleting the DNA sequences common to rye and wheat; the entire structure of Revolver was determined by using rye genomic clones, which were screened by the 89 bp probe; Revolver consists of 2929-3041 bp with an inverted repeated sequence on each end and is dispersed through all seven chromosomes of the rye genome; Revolver is transcriptionallyactive, and the isolated full-length cDNA (726 bp) reveals that Revolver harbors a single gene consisting of three exons (342, 88, and 296 bp) and two introns (750 and 1237 bp), and encodes139 amino acid residues of protein, which shows similarity to some transcriptional regulators; Revolver variants ranging from 2665 to 4269 bp, in which 5' regions were destructed, indicate structural diversities around the first exon; Revolver does not share identity with any known class I or class II autonomous transposable elements of any living species; DNA blot analysis of Triticeae plants shows that Revolver has existed since the diploid progenitor of wheat, and has been amplified or lost in several species during the evolution of the Triticeae; according to the rules of symbolization the gene Revolver was renamed by the authors as REV1, 2008
40 the cytosolic isoform of plant acetyl-CoA
carboxylase is a multidomainenzyme involved in the synthesis of very-long-chain fatty acids and in secondary metabolism; chromosome mapping of wheat identified one locus containing cytosolic acetyl-CoA carboxylase
genes(Acc2) and a related partially processed pseudogene (phi-Acc-2) in the distal region of the long arm of wheat homoeologous group 3 chromosomes; another locus containing Acc2-related
sequences is present in the distal regionof the long arm of chromosome 5D of wheat; two major Acc-2clades appeared before the divergence of barley and rye from wheat, 2008
41 the barley low temperature responsive gene blt14 was
used as a probe, to isolate two different cognate clones (rlt1412, rlt1421) from a rye cDNA library prepared from low temperature-treated (+6C° day/+2C° night); the barley gene, blt14 (cig7)
was found to be present on barley chromosome two as a member of a small multigene family; it is not induced by a drought treatment
nor by foliar applications of abscisic acid; in the rye clones the presence of an N-terminal signal peptide is evident; N-terminal peptides with this structure are present on a number of extracellular eukaryotic proteins which are routed through the ER and Golgi apparatus; the deduced amino acid sequences of rlt1412 and rlt1421 contain
no known functional signatures or motifs and have no significant homology with genes of known function, 2008
42 the Alt4 Al-tolerance locus of rye contains a cluster of genes homologous to the single-copy Al-activated malate transporter (TaALMT1) Al-tolerance gene of wheat; tolerant (M39A-1-6) and intolerant (M77A-1)
rye haplotypes contain five and two genes, resp., of which two (ScALMT1-M39.1 and ScALMT1-M39.2) and one (ScALMT1-M77.1) are highly expressed in the root tip, typically the main site of plant Al
tolerance/susceptibility; all three transcripts are upregulated by exposure to Al;
high-resolution genetic mapping identified two resistant lines resulting from recombination within the gene cluster; these recombinants exclude all genes flanking the gene cluster as candidates for controlling Alt4 tolerance, including a homolog of the barley HvMATE Al-tolerance gene; in the recombinants, one hybrid gene containing a chimeric open reading frame and the ScALMT1-M39.1 gene each appeared to be sufficient to provide full tolerance; mRNA splice variation was observed for two of the rye ALMT1 genes and in one case, was correlated with a ~400-bp insertion in an intron. 2008
43 the locus for leaf estrase Est6 was determined
on different chromosomes by different authors, i.e. 2RS (206,412,430), 2RL (299), 5R (166,194,333), or 6R (18); most likely is 2RS (the author), 2009
44 relocalized by the author in 2009, based on latest references 5, 200, 206, 285, 412, 430
45 relocalized from 3RL (near centromere) to 3RS (near centromere) by the author in 2009, based on latest references fo 186, 206, 299, 412, 430; obviously, this probe differs from Xpsr56 mapped on
chromosome 7R by some authors
46 this marker was localized on the short arm of chromosome 3R by (431)
47 L-Fucose is a monosaccharide found as a component of glycoproteins and cell wall polysaccharides in higher plants; the Mur1 gene of Arabidopsis thaliana encodes a GDP-D-mannose 4,6-dehydratase catalyzing the first step in the de novo synthesis
of GDP-L-fucose from GDP-D-mannose (Bonin etal., 1997, Proc. Nail Acad. Sci. USA, 94, 2085-2090); plant genes encoding the subsequent steps in L-fucose synthesis (3,5-epimerization and 4-reduction) are rarely
described; based on sequence similarities to a bacterial gene involved in capsule synthesis a gene from Arabidopsis was cloned, designated Ger1, which encodes a bifunctional
3,5-epimerase-4-reductase in L-fucose synthesis; the combined action of the Mur1 and Ger1 gene products converts GDP-D-mannose to GDP-L-fucose in vitro demonstrating that this entire nucleotide-sugar interconversion pathway could be reconstituted using plant genes expressed in Escherichia coli; in vitro assays indicated that the GER1 protein does not act as a GDP-D-mannose 3,5-epimerase, an enzymatic activity involved in the de novo synthesis
of GDP-L-galactose and L-ascorbic acid; similarly, L-ascorbate levels in GER1 antisense plants are unchanged indicating that GDP-D-mannose 3,5-epimerase is encoded by a separate gene
48 the gene was named as Eml (embryo lethality),
because it could not be determined whether the allele for embryo lethality is dominant or recessive; the alleles were designated as determining differentiated (normal, wild-type) and undifferentiated (lethal, mutant) embryos Eml-R1a and Eml-R1b, respectively
49 a repetitive sequence of 411 bp, named pSaO5411, was identified in the Secale africanum genome (Ra) by random amplified polymorphic DNA (RAPD) analysis of wheat and wheat-S. africanum amphiploids; GenBank BLAST search revealed that the sequence of pSaO5411 was highly homologous to a part of a Ty1-copia retrotransposon; FISH analyses indicated that pSaO5411 was significantly hybridized to S. africanum chromosomes of a wheat-S. africanum amphiploid, and it was dispersed along the Secale chromosome
arms except the terminal regions; basing on the sequence of pSaO5411, a pair of sequence-characterized amplified region (SCAR) primers were designed, and the resultant SCAR marker was able to target both cultivated
rye and the wild Secale species, which also enabled to identify effectively the S. africanum chromatin introduced into the wheat genome
50 the wheat and rye spike normally bears one spikelet per rachis node, and the appearance of supernumerary spikelets is rare; the loci responsible for the “multirow spike” or MRS trait in wheat, and the “monstrosum spike” trait in rye were mapped by genotyping F(2) populations with microsatellite markers; both MRS and the “monstrosum'”trait are under the control of a recessive allele at a single locus; the Mrs1 locus is located on chromosome 2DS, co-segregating with the microsatellite locus Xwmc453; the placement of flanking microsatellite loci into chromosome deletion bin 2DS-5 (FL 0.47-1.0) delimited the physical location of Mrs1 to the distal half of chromosome arm 2DS, within the gene rich region 2S0.8; the Mo1 locus maps about 10 cM from the centromere on chromosome arm 2RS; the similar effect on phenotype of mo1 and mrs1, together with their presence in regions of conserved synteny, suggest that they may well be members of an orthologous set of Triticeae genes governing spike branching; the practical importance of the MRS spike is that it produces more spikelets per spike, and thereby enhances the sink capacity of wheat, which is believed to limit the yield potential of the crop
51 designated by the authors; a rye-wheat centric chromosome translocation 1RS.1BL has been widely used in wheat breeding programs around the world; increased yield of translocation lines was probably a consequence of increased root biomass; in an effort to map loci-controlling root characteristics, homoeologous recombinants of 1RS with 1BS were used to generate a consensus genetic map comprised of 20 phenotypic and molecular markers, with an average spacing of 2.5 cM; physically, all recombination events were located in the distal 40% of the arms; a total of 68 recombinants was used and recombination breakpoints were aligned and ordered over map intervals with all the markers, integrated together in a genetic map; this approach enabled dissection of genetic components of quantitative traits, such as root traits, present on 1S; to validate the hypothesis, phenotyping of 45-day-old wheat roots was performed in five lines including three recombinants representative of the entire short arm along with bread wheat parents “Pavon 76” and “Pavon 1RS.1BL”; individual root characteristics were ranked and the genotypic rank sums were subjected to Quade analysis to compare the overall rooting ability of the genotypes, it appears that the terminal 15% of the rye 1RS arm carries gene(s) for greater rooting ability in wheat
52 ESTs-derived markers are useful for comparative genomic analysis and can also serve as phenotype-linked functional markers; the development of EST-derived 2RL-specific markers and the evaluation of the possibility of functional assessment of markers tagging 2RL is reported, which carries Hessian fly resistance genes (loci); to identify transcripts specific to 2RL, unigene sequences in combination with wheat progenitor genomes were used; total 275 contigs mapped to the long arms of homoeologous group 2 chromosomes were downloaded; to obtain a cluster corresponding to each of the wheat 275 contigs, unigene sequences of wheat, rice, barley, and rye were pooled for cross-species clusters. Out of 275 clusters examined, it was possible to design 112 cross-species primer pairs for genome-specific amplifications; out of 112 cross-species primer pairs, 45 primer pairs (40%) produced amplicons from at least one species (three wheat progenitors or rye); among the 45 contigs, 73% were associated with one of known functions and 82% of the contigs associated with known functions were also associated with one of the GO categories; on the basis of the oligonucleotide sequence alignment of each of 45 genome-specific amplifications, 21 amplifications (47%) were suitable for designing RR genome-specific primers, which are specific to translocated rye chromatin 2RL; six primer pairs (13%) successfully produced amplicons in the 2BS.2RL translocation lines and not in the non-2RLs; functional assessment of one of the 2RL-specific markers, NSFT03P2_Contig4445, was performed on Hessian fly infested NILs. Under Hessian fly infestation, significantly high expression of a gene tagged by a 2RL-specific marker (NSFT03P2_Contig4445) was observed 1 day after infestation; EST-derived 2RL-specific marker development provides a basis for the development of ESTs-derived markers for detecting wheat-rye translocations; in addition, these markers could be employed in elucidating functional analysis of genes on 2RL
53 rye is a diploid crop species with many outstanding qualities, and is important as a source of new traits for wheat and triticale improvement; it is highly tolerant of aluminum (Al) toxicity, and possesses a complex structure at the Alt4 Al tolerance locus not found at the corresponding locus in wheat; a BAC library of rye cv. Blanco is descripted, representing a valuable resource for rye molecular genetic studies, and assess the library's suitability for investigating Al tolerance genes; the library provides 6 x genome coverage of the 8.1 Gb rye genome, has an average insert size of 131 kb, and contains only ~2% of empty or organelle-derived clones; genetic analysis attributed the Al tolerance of “Blanco” to the Alt4 locus on the short arm of chromosome 7R, and revealed the presence of multiple allelic variants (haplotypes) of the Alt4 locus in the BAC library; BAC clones containing ALMT1 gene clusters from several Alt4 haplotypes were identified, and will provide useful starting points for exploring the basis for the structural variability and functional specialization of ALMT1 genes at this locus
54 5s ribosomal DNA includes about 5,000 copies and covers ~0.4 % of 1RS DNA; by a size of the rye genome of ~7900 Mbp and 7 chromosomes, 1RS carries 5.6% of the genome ~442 Mbp
55 dwarfing genes in rye (after T. Tenhola-Roininen 2009)
|
Dwarfing gene
|
Inheritance
|
Chromosome
|
GA sensitivity
|
Reference
|
|
Ddw1 syn Dw1 syn Hl
|
dominant
|
5RL
|
sensitive
|
Kobyliansky 1972, 150, Korzun et al. 1996
|
|
Ddw2 syn Dw2
|
dominant
|
7R
|
sensitive
|
Melz 1989
|
|
dw1 syn d1
|
recessive
|
7R
|
sensitive
|
Sybenga & Prakken 1962
|
|
dw2 syn d2
|
recessive
|
2R
|
insensitive
|
De Vries & Sybenga 1984
|
|
dw3
|
recessive
|
3R
|
insensitive
|
De Vries & Sybenga 1984
|
|
dw4
|
recessive
|
1R
|
insensitive
|
Melz 1989
|
|
dw5
|
recessive
|
4R
|
insensitive
|
Melz 1989
|
|
dw6
|
recessive
|
5R
|
insensitive
|
Melz 1989, Börner et al. 1992
|
|
dw7
|
recessive
|
6R
|
insensitive
|
Melz 1989
|
|
dw8
|
recessive
|
5RL
|
|
206
|
|
ct1
|
recessive
|
7R
|
insensitive
|
De Vries & Sybenga 1984, Börner 1991, Börner et al. 1992, Plaschke et al. 1993, 1995
|
|
ct2
|
recessive
|
5RL
|
insensitive
|
De Vries & Sybenga 1984, Börner 1991, Börner et al. 1992, Plaschke et al. 1993, 1995
|
|
ct3
|
recessive
|
7R
|
insensitive
|
Malyshev et al.2001
|
|
np
|
recessive
|
4RL
|
sensitive
|
Malyshev et al.2001
|
56 The self fertility locus “Sf2” was also mapped on chromsome 5R and “Sf3” on chromosome 4R by Melz et
al. 1988 (466)
|
|
