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”; to date, a number of studies have shown that the higher yield potential of the 1RS/1BL lines is caused by the higher kernel number per spike, which can be attributed to the higher spikelet number per spike (Schlegel and Meinel, 1994; Villareal et al., 1998; Zhao et al., 2012). Consistent with these data, our results showed that the 1RS/1BL translocation increased the FSN ( fertile spikelet number per spike) and TSN ( total spikelet number per spike) in nearly all environments (Appendix D). We also found that the 1RS/1BL translocation had a considerable positive effect on the SSN (sterile spikelet number per spike) and SL (spike length), which is consistent with the results of previous studies (Cui et al., 2012; Gao et al., 2015 ). QTLs were not detected for SC (spikelet compactness ) in any of the nine individual environments, suggesting that the 1RS/1BL translocation has no significant influence on spikelet compactness, which is inconsistent with the results of Tahmasebi et al. (2015). Moreover, other studies have also shown a loose connection between the 1RS/1BL translocation and spike morphological traits (Villareal et al., 1995; Griffiths et al., 2015). Collectively, these data demonstrate that the impact of the 1RS/1BL translocation on performance is highly linked to the plant’s genetic background and environmental conditions, which limit the use of 1RS/1BL translocation lines as a source of genetic variation. Thus, two 1RS specific markers (XpSaD15 and XpSc20H; Liu et al.,Compared with 1B lines, the 1RS/1BL lines had higher SL (7.2%), FSN (4.2%), SSN (24.8%), and TSN (5.9%). Consequently, four major and environmentally stable QTLs were detected at the XpSaD15 locus, and they had LOD values from 3.33 to 21.17 and explained from 6.74 to 36.69% of the variations for the combined analysis. (Figures 3; Figure S4; Appendix D). The 1RS/1BL translocation from “Y8679” was associated with increased SL, FSN, SSN, and TSN. (515)

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 (mutant allele, dominant), respectively; Eml-R1b is linked to the Xgwm1103 and Xgwm732 markers

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, Yang et. al. 2018, Kantarek et al. 2018); the gibberellin (GA)-sensitive dwarfing gene Ddw1 reduces plant height in rye; genetic analysis  in a population of recombinant inbred lines confirmed a monogenetic  dominant inheritance of Ddw1; significant phenotypic differences in plant height between homo- and heterozygotic genotypes indicate an incomplete  dominance of Ddw1; de novo transcriptome sequencing of Ddw1 mutant as  well as tall genotypes resulted in 113,547 contigs with an average  length of 318 bp covering 36.18 Mbp rye DNA, a hierarchical cluster  analysis based on individual groups of rye homologs of functionally  characterized rice genes controlling morphological or physiological  traits including plant height, flowering time and source activity  identified the gene expression profile of stems at the begin of heading  to most comprehensively mirror effects of Ddw1; genome-wide expression  profiling identified 186 transcripts differentially expressed between  semi-dwarf and tall genotypes in stems. In total, 29 novel markers have  been established and mapped to a 27.2 cM segment in the distal part of  the long arm of chromosome 5R;  Ddw1 could be mapped within a 0.4 cM  interval co-segregating with a marker representing the C20-GA2-oxidase  gene ScGA2ox12, that is up-regulated in stems of Ddw1 genotypes; the  increased expression of ScGA2ox12 observed in semi-dwarf rye as well as  structural alterations in transcript sequences associated with the  ScGA2ox12 gene implicate, that Ddw1 is a dominant gain-of-function  mutant; integration of the target interval in the wheat reference genome sequence indicated perfect micro-colinearity between the Ddw1 locus and a 831 kb segment on chromosome 5A, which resides inside of a 11.21 Mb  interval carrying the GA-sensitive dwarfing gene Rht12 in wheat (Braun et al. 2019)

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
Ddw3	dominant	1RL	sensitive	Yang et al. 2018
Ddw4 syn Dw4	dominant	3R, centromere	sensitive	Kanzarek et al. 2018
dw1 syn d1	recessive	7R	sensitive	Sybenga & Prakken 1962
dw2 syn d2	recessive	2R	sensitive	De Vries & Sybenga 1984
dw3	recessive	3R		De Vries & Sybenga 1984
dw4	recessive	1R		Melz 1989
dw5	recessive	4R		Melz 1989
dw6	recessive	5R	insensitive	Melz 1989, Börner et al. 1992
dw7	recessive	6R		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)

⁵⁷ PCR experiments using primers designed from different rye-origin sequences showed that the absence of a chromosomal rye-origin band in wheat–rye addition lines results from sequence elimination rather than restrict changes on primer annealing sites, as noted in triticale; the level of genome restructuring events evaluated in all seven wheat–rye addition lines, i.e. rye chromosomes, compared to triticale, indicated that the unbalanced genome merger situation observed in the addition lines induced a new round of genome rearrangement, suggesting that the lesser the amount of rye chromatin introgressed into wheat the larger the outcome of genome reshuffling (475)

⁵⁸ anthocyanine biosynthesis pathway (ABP) genes encoding enzymes acting at different steps of the pathway: chalcone-flavanone isomerase (CHI), flavanone 3-hydroxylase (F3H), anthocyanidin synthase (ANS), and anthocyanidin-3-glucoside rhamnosyltransferase (3RT); the rye ABP genes locations are (Chi on chromosome 5RL, F3h on 2RL, Ans on 6RL, 3Rt on 5RL;  the regulatory Rc (red coleoptile) gene on 4RL is in agreement with the chromosomal rearrangements established between rye and wheat chromosomes; expression of the ABP structural genes showed that F3h activation by the Rc gene is critical for the red coleoptile trait formation; the rye regulatory Rc gene can activate wheat target gene F3h and vice versa wheat Rc induces expression of rye F3h; the Chi gene (the total length of the sequenced gene varied from 1039 to 1052bp among cultivars) carries only one intron instead of three in Poaceae; one intron loss occurred early in the evolution of the Triticeae tribe, while another intron loss was only detected in rye Chi gene; the Chi gene was mapped 9.3 cM distal to the RFLP marker Xscb35 and 4.4 cМ proximal to the locus 3Rt encoding another flavonoid synthesis enzyme anthocyanidin-3-glucoside rhamnosyltransferase (489)

⁵⁹ Petkus rye was bred since 1882 by F. von LOCHOW at Petkus, south of Berlin (Germany); the material derived from the landrace “Probsteier Roggen” (x Prinaer Roggen ?), marketed by Probsteier land- und forstwirtschaftlicher Verein, Schönberg, near Kiel (Germany)

⁶⁰ a rye doubled haploid (DH) mapping population (Amilo × Voima) segregating for pre-harvest sprouting was generated through anther culture of F1 plants; distorted segregation of markers (P<0.05) was detected on all chromosomes; one major quantitative trait locus (QTL) affecting alpha-amylase activity was found, which explained 16.1% of phenotypic variation;  the QTL was localized on the long arm (central ?) of chromosome 5R; microsatellites Xscm74, Xrms1115, and Xscm77 were nearest to the QTL (<2.5 cM)

⁶¹ Studying exons of the ScMATE1 gene supported the existence of a high genetic diversity in the Secale genus. The resulting phylogenetic relationships obtained reinforce the dendrograms obtained with the dominant markers and shows the inconsistency prevailing in S. vavilovii. This is in agreement with the revision of the genus Secale made by Frederiksen and Petersen (1998) who didn’ft recognize S. vavilovii as a species and just distinguished S. cereale and S. strictum.

⁶² Pm8 is a powdery mildew resistance gene on chromosome arm 1RS which, after widespread agricultural cultivation, is now widely overcome by adapted mildew races. Homology-based cloning and subsequent physical and genetic mapping demonstraed that Pm8 is the rye orthologue of the Pm3 allelic series of mildew resistance genes in wheat. The cloned gene was functionally validated as Pm8 by transient, single-cell expression analysis and stable transformation. Sequence analysis revealed a complex mosaic of ancient haplotypes among Pm3- and Pm8-like genes from different members of the Triticeae. The two genes have evolved independently after the divergence of the species 7.5 million years ago and kept their function in mildew resistance. During this long time span the co-evolving pathogens have not overcome these genes, which is in strong contrast to the breakdown of Pm8 resistance since its introduction into commercial wheat 70 years ago. Sequence comparison revealed that evolutionary pressure acted on the same subdomains and sequence features of the two orthologous genes

⁶³ an orthologue of the Arabidopsis thaliana CONSTANS (CO) gene, involved in photoperiodic flowering; Hd1 gene homologues have  been identified in rice, barley and wheat (Yamamoto et al. 1998; Yano et al. 2000; Kojima et al. 2002; Griffiths et al. 2003; Nemoto et al. 2003); although homologues of Hd1 are key regulators of photoperiodic flowering in plants of short-day (SD) zones (Cockram et al. 2007), they do not cause strong phenotypic effects in temperate cereals; however, transgenic experiments expressing the wheat gene in rice showed that it maintains its strong effect in the genetic background of SD  plants (Nemoto et al. 2003); a fragment of the ScHd1 gene derived from eight inbred lines  was sequenced and showed homology to other Hd1 genes from different  cereals; sequences were analysed with respect to the presence of a  single -nucleotide polymorphism (SNP) difference. A C-T transition at  position 312 of the consensus sequence was found, which distinguished  two lines from the remaining six; the deduced amino acid sequence  revealed a high identity (93%) to a Hd1-like protein from wheat; the  identified mutation allowed the localisation of ScHd1 on a genetic map of rye (6RS); a small, statistically significant linkage between ScHd1 and earliness per se (eps) and some morphological traits was  established; the chromosomal region, including the S76 allele for the ScHd1 gene islinked to earlier heading, elongated spikes, a greater number  of spikelets per spike and an increased weight of 1000 kernels

⁶⁴ Specific primers were used to clone the waxy gene from 20 rye cultivars; sequence analysis showed that waxy is 2852 bp, including 11 exons, and sequence similarity across the 20 cultivars is over 98%; the Waxy protein shows >95% similarity with those from wheat, rice, and barley, the closest genetic relationship being with wheat Wx-A type; waxy has multiple SNPs, most of which are located in the exons; amino acid variants are found to be mainly distributed in the catalytic domain in an imbalanced state; multi-factor correlation analysis revealed significant correlation among starch pasting parameters in rye flour; the waxy protein activity is significantly negatively correlated with the amylose content and amylopectin/amylose ratio; however, pasting parameters, waxy enzyme activity, and amylopectin/amylose content ratio are not correlated; the correlation of SNPs, the key catalytic site of waxy, with starch parameters and enzyme activity suggested that both starch pasting parameters and waxy protein activity are influenced by No. 260 amino acid (aa); further, the 141 and 152 aa loci were found in the enzyme-catalyzing domain of waxy; waxy enzyme activity is also influenced by the 363 aa locus in the pliable region

65Using a single nucleotide polymorphism (SNP) genotyping array, 984 polymorphic  markers were available to tag flower charactistics of wheat-rye addition lines; the addition of rye chromosomes 1R an 2R  reduced pollen fertility, while addition of rye chromosome 4R increased  anther size (Sa) by 16% and pollen grain number by 33%; the effect on  anther length is associated with increases in both cell size and the  number of endothecium cells and is attributed to the long arm of  chromosome 4R; in contrast, the effect on pollen grain number (Npg) is  attributed to the short arm of chromosome 4R; these results indicate  that rye chromosome 4R contains at least two genetic factors associated  with increased anther size and pollen grain number that can favourably  affect pollination traits in hybrid wheat

66 Designation Yrx by the author after description of stripe rust resistance of var. Kustro [527]

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