The GAMYB gene in rye: sequence, polymorphisms, map location, allele-specific markers, and relationship with α-amylase activity.

Background: Transcription factor (TF) GAMYB, belonging to MYB family (named after the gene of the avian myeloblastosis virus) is a master gibberellin (GA)-induced regulatory protein that is crucial for development and germination of cereal grain and involved in anther formation. It activates many genes including high-molecular-weight glutenin and α-amylase gene families. This study presents the first attempt to characterize the rye gene encoding GAMYB in relation to its sequence, polymorphisms, and phenotypic effects.

A complex network of QTL for thousand-kernel weight in the rye genome.

Here, QTL mapping for thousand-kernel weight carried out within a 541 × Ot1-3 population of recombinant inbred lines using high-density DArT-based map and three methods (single-marker analysis with F parametric test, marker analysis with the Kruskal-Wallis K* nonparametric test, and the recently developed analysis named genes interaction assorting by divergent selection with χ test) revealed 28 QTL distributed over all seven rye chromosomes. The first two methods showed a high level of consistency in QTL detection. Each of 13 QTL revealed in the course of gene interaction assorting by divergent selection analysis coincided with those detected by the two other methods, confirming the reliability of the new approach to QTL mapping.

Identification of a novel, dominant dwarfing gene (Ddw4) and its effect on morphological traits of rye.

Shortening rye stems to improve lodging resistance is among the major tasks awaiting breeders of this cereal. The most straightforward way to achieve this goal is the implementation of a dominant dwarfing gene into high yielding cultivars. The choice of dominant dwarfing genes in rye is limited to Ddw1 and Ddw3 loci, which are well characterized with respect to map position and tightly linked molecular markers on the long arms of chromosomes 5RL and 1RL, respectively.

QTL mapping for benzoxazinoid content, preharvest sprouting, α-amylase activity, and leaf rust resistance in rye (Secale cereale L.).

Mapping population of recombinant inbred lines (RILs) representing 541 × Ot1-3 cross exhibited wide variations of benzoxazinoid (BX) content in leaves and roots, brown rust resistance, α-amylase activity in the grain, and resistance to preharvest sprouting. QTL mapping of major BX species using a DArT-based map revealed a complex genetic architecture underlying the production of these main secondary metabolites engaged in stress and allelopathy responses. The synthesis of BX in leaves and roots was found to be regulated by different QTL.

Identification of Single Nucleotide Polymorphisms Associated with Brown Rust Resistance, α-Amylase Activity and Pre-harvest Sprouting in Rye ( L.).

Rye is a crop with relatively high resistance to biotic and abiotic stresses. However, the resistance to brown rust ( f. sp.

Comparative analysis of genetic architectures for nine developmental traits of rye.

Genetic architectures of plant height, stem thickness, spike length, awn length, heading date, thousand-kernel weight, kernel length, leaf area and chlorophyll content were aligned on the DArT-based high-density map of the 541 × Ot1-3 RILs population of rye using the genes interaction assorting by divergent selection (GIABDS) method. Complex sets of QTL for particular traits contained 1-5 loci of the epistatic D class and 10-28 loci of the hypostatic, mostly R and E classes controlling traits variation through D-E or D-R types of two-loci interactions. QTL were distributed on each of the seven rye chromosomes in unique positions or as a coinciding loci for 2-8 traits.

Genetic analysis carried out in population tails reveals diverse two-loci interactions as a basic factor of quantitative traits variation in rye.

Bidirectional selective genotyping carried out independently for five quantitative traits within a biparental population of recombinant inbred lines of rye has revealed dramatic changes in alleles distribution in the population tails. A given allele, predominant in the lower tail, is often neutral for reversely directed selection or associates with the upper tail following divergent selection for a related trait. Such radical changes in the alleles distribution cannot be explained by differences in genotypic values within a single locus.

Proteomic analysis of developing rye grain with contrasting resistance to preharvest sprouting.

Significant differences in the two-dimensional electrophoresis patterns of proteins from developing rye grain were found to be associated with resistance and susceptibility to preharvest sprouting (PHS). Mass spectrometry of individual spots showing different abundance in PHS-resistant and PHS-susceptible lines identified proteins involved in: reaction to biotic and abiotic stresses, including oxidative stress, energy metabolism and regulation of gene expression. Highly differentiated abundance of proteins found in developing grain suggest that the diversification of processes leading to developing PHS resistance or PHS susceptibility starts from an early stage of grain development.

Proteomic analysis of preharvest sprouting in rye using two-dimensional electrophoresis and mass spectrometry.

Qualitative and quantitative differences were found between two-dimensional electrophoretic spectra of 546 proteins from two bulked samples of mature rye grain representing: (1) 20 recombinant inbred lines extremely resistant to preharvest sprouting and (2) 20 recombinant inbred lines extremely susceptible to preharvest sprouting. Mass spectrometry of resolved proteins showed that four spots specific for PHS susceptibility represented high molecular weight glutenin subunit, glutathione transferase, 16.9 kDa heat-shock protein, and monomeric alpha-amylase inhibitor.

Genomic architecture of alpha-amylase activity in mature rye grain relative to that of preharvest sprouting.

Bi-directional selective genotyping (BSG) carried out on two opposite groups of F(9)(541 × Ot1-3) recombinant inbred lines (RILs) with extremely low and extremely high alpha-amylase activities in mature (dry) grain of rye, followed by molecular mapping, revealed a complex system of selection-responsive loci. Three classes of loci controlling alpha-amylase activity were discerned, including four major AAD loci on chromosomes 3R (three loci) and 6RL (one locus) responding to both directions of the disruptive selection, 20 AAR loci on chromosomes 2RL (three loci), 3R (three loci), 4RS (two loci), 5RL (three loci), 6R (two loci) and 7R (seven loci) responding to selection for low alpha-amylase activity and 17 AAE loci on chromosomes 1RL (seven loci), 2RS (two loci), 3R (two loci), 5R (two loci) and 6RL (four loci) affected by selection for high alpha-amylase activity. The majority of the discerned AA loci also showed responsiveness to selection for preharvest sprouting (PHS).

A consensus map of chromosome 6R in rye (Secale cereale L.).

Four F(2) mapping populations derived from crosses between rye inbred lines DS2 x RXL10, 541 x Ot1-3, S120 x S76 and 544 x Ot0-20 were used to develop a consensus map of chromosome 6R. Thirteen marker loci that were polymorphic in more than one mapping population constituted the basis for the alignment of the four maps using the JoinMap v. 3.

QTLs for resistance to preharvest sprouting in rye (Secale cereale L.).

Grain quality of rye is often negatively affected by sprouting - a complex trait with a poorly understood genetic background and strong interaction with weather conditions. The aim of this report was to detect the main quantitative trait loci (QTLs) underlying preharvest sprouting resistance in rye, measured as a percentage of sprouted kernels after spraying spikes with water for 7 days. Simple and composite interval mapping, carried out in 3 environments on 94 F3 and F4 families of the cross between sprouting-susceptible (541) and sprouting-resistant (Ot1-3) inbred lines, revealed 5 QTLs located on chromosome arms 1RL, 2RL, 5RL, 6RL and 7RL.

New genetic map of rye composed of PCR-based molecular markers and its alignment with the reference map of the DS2 x RXL10 intercross.

A new genetic map of rye, developed by using the 541 x Ot1-3 F2 intercross, consists of 148 marker loci, including 99 RAPDs, 18 SSRs, 14 STSs, 9 SCARs and 7 ISSRs, and spans the distance of 1401.4 cM. To the 7 rye chromosomes, 8 linkage groups were assigned and compared with the reference map of the DS2 x RXL10 F2 intercross by using 24 common markers.

Rye SCAR markers for male fertility restoration in the P cytoplasm are also applicable to marker-assisted selection in the C cytoplasm.

The study aimed at testing the usefulness of recently developed SCAR markers on rye (Secale cereale L.) chromosome 4R in hybrid breeding based on the C source of male sterility-inducing cytoplasm. Of 10 markers studied, 4 revealed polymorphisms between 2 inbred lines (544cms-C and Ot0-20) crossed to develop F2 and BC1 mapping populations.

Mapping QTLs for alpha-amylase activity in rye grain.

Genetic control of alpha-amylase activity in rye grain was investigated by QTL mapping based on DS2 x RXL10 intercross consisting of 99 F5-6 families propagated at one location during four vegetation seasons. A wide range of variation in alpha-amylase activity and transgression effects were found among families and parental lines. This variation was shown to be determined in 40.

Saturating rye genetic map with amplified fragment length polymorphism (AFLP) and random amplified polymorphic DNA (RAPD) markers.

A linkage map of rye, previously developed using DS2 x RXL10 F2 mapping population, was enriched with 179 AFLP and 19 RAPD marker loci. The current map covers 1386 cM and contains 480 markers including 200 RFLPs, 179 AFLPs, 88 RAPDs, 12 protein loci and one dwarfing gene. AFLPs generated by EcoRI/MseI primer combinations were distributed over the entire genome as distinct loci or clusters of 2-14 tightly linked DNA fragments.

The application of molecular markers in the process of selection.

Molecular markers are modern diagnostic tools, which may help breeders to solve practical problems. They facilitate cultivar identification, the determination of genetic similarities among breeding stocks and enable the calculation of polymorphism level, heterozygosity or self-pollination rate. But the main expectation with respect to molecular markers is their potential use in marker-assisted selection (MAS).

The mapping of QTLS for chlorophyll content and responsiveness to gibberellic (GA3) and abscisic (ABA) acids in rye.

Genetic maps containing molecular markers are useful tools for the identification of genes underlying quantitative traits (QTLs). Three traits important for plant physiology, i.e.

Linkage groups and the indirect chromosome location of cms-P-linked AFLPs.

Twenty-five AFLPs, previously linked to fertility restoration genes for the male-sterilizing PAMPA cytoplasm (cms-P) in a restricted rye population, were studied in an enlarged population of 120 plants. A strong association with the trait was verified for 19 of the markers. The recombination of these markers was tested and two linkage groups were identified: one consisting of six and the other of eight AFLPs.