QTL Mapping Using RIL Population.

Genetic maps are an excellent tool for the analysis of important traits, the development of which is the result of the combined expression of several genes, enabling the genomic localization of the factors determining them. Such features, characterized by a normal distribution of values, are referred to as quantitative or polygenic. The analysis of their genetic background using a chromosome map is called the mapping of quantitative traits loci (QTL).

Genetic Map Construction Using F and RIL/DH Mapping Population.

Genetic mapping is the determination of the position and relative genetic distance between genes or molecular markers in the chromosomes of a particular species. The construction of genetic maps uses data from the genotyping of the mapping population. Among the different mapping populations used, two are relatively common: the F and recombinant inbred lines (RILs) obtained as a result of the controlled crossing of genetically diverse parental forms (e.

Variation between glaucous and non-glaucous near-isogenic lines of rye (Secale cereale L.) under drought stress.

Glaucous (811, L35, and RXL10) and non-glaucous (811bw, L35bw, and RXL10bw) near-isogenic lines (NILs) of rye (Secale cereale L.) forming three pairs of inbred lines were the subject of the research. The research aimed to study the relationship between wax cover attributes and the physio-biochemical drought reactions and yield of rye NILs and to uncover the differences in drought resistance levels of these lines.

In search of the relationship between the rye polyamine oxidase (PAO) gene and resistance to powdery mildew (PM).

Powdery mildew (PM), a common cereal disease in cultivated areas, including Europe and other temperate regions, is caused by the fungus Blumeria graminis. While PM is one of the most important wheat leaf diseases globally, rye is highly tolerant to PM. It has been reported that in barley infected with PM, polyamine oxidase (PAO) activity related to the production of hydrogen peroxide (HO) has increased, which may promote defense against biotrophic or hemibiotrophic pathogens.

Functional Genomics for Plant Breeding.

To face the rapidly growing world human population, an increase in agricultural productivity and production is necessary to overcome the enhanced food demand [...

Correlation between leaf epicuticular wax composition and structure, physio-biochemical traits and drought resistance in glaucous and non-glaucous near-isogenic lines of rye.

The objective of this research was to investigate the differences between glaucous and non-glaucous near-isogenic lines (NILs) of winter rye (Secale cereale L.) in terms of epicuticular wax layer properties (weight, composition, and crystal morphology), selected physiological and biochemical responses, yield components, above-ground biomass, and plant height under soil drought stress. An important aspect of this analysis was to examine the correlation between the above characteristics.

Chromosome-scale genome assembly provides insights into rye biology, evolution and agronomic potential.

Rye (Secale cereale L.) is an exceptionally climate-resilient cereal crop, used extensively to produce improved wheat varieties via introgressive hybridization and possessing the entire repertoire of genes necessary to enable hybrid breeding. Rye is allogamous and only recently domesticated, thus giving cultivated ryes access to a diverse and exploitable wild gene pool.

How Machine Learning Methods Helped Find Putative Rye Wax Genes Among GBS Data.

The standard approach to genetic mapping was supplemented by machine learning (ML) to establish the location of the rye gene associated with epicuticular wax formation (glaucous phenotype). Over 180 plants of the biparental F population were genotyped with the DArTseq (sequencing-based diversity array technology). A maximum likelihood (MLH) algorithm (JoinMap 5.

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.

Genetic Parameters and QTLs for Total Phenolic Content and Yield of Wheat Mapping Population of CSDH Lines under Drought Stress.

A doubled haploid population of 94 lines from the Chinese Spring × SQ1 wheat cross (CSDH) was used to evaluate additive and epistatic gene action effects on total phenolic content, grain yield of the main stem, grain number per plant, thousand grain weight, and dry weight per plant at harvest based on phenotypic and genotypic observations of CSDH lines. These traits were evaluated under moderate and severe drought stress and compared with well-watered plants. Plants were grown in pots in an open-sided greenhouse.

Putative candidate genes responsible for leaf rolling in rye (Secale cereale L.).

Background: Rolling of leaves (RL) is a phenomenon commonly found in grasses. Morphology of the leaf is an important agronomic trait in field crops especially in rice; therefore, majority of the rice breeders are interested in RL. There are only few studies with respect to RL of wheat and barley; however, the information regarding the genetic base of RL with respect to the shape of leaf in rye is lacking.

Effective BAC clone anchoring with genotyping-by-sequencing and Diversity Arrays Technology in a large genome cereal rye.

Identification of bacterial artificial chromosome (BAC) clones containing specific sequences is a prerequisite for many applications, such as physical map anchoring or gene cloning. Existing BAC library screening strategies are either low-throughput or require a considerable initial input of resources for platform establishment. We describe a high-throughput, reliable, and cost-effective BAC library screening approach deploying genotyping platforms which are independent from the availability of sequence information: a genotyping-by-sequencing (GBS) method DArTSeq and the microarray-based Diversity Arrays Technology (DArT).

Bidirectional selective genotyping approach for the identification of quantitative trait loci controlling earliness per se in winter rye (Secale cereale L.).

The genes controlling earliness of plants include genes responsible for vernalisation (Vrn) and photoperiod (Ppd), and those that are not entirely associated with a response to temperature or light. The last group of loci is known as earliness per se (Eps). Eps genes have been most commonly reported in the scientific literature as quantitative trait loci (QTL).

Genetic mapping of the ScHd1 gene in rye and an assessment of its relationship with earliness per se and plant morphology.

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 application of high-density genetic maps of rye for the detection of QTLs controlling morphological traits.

The development of genetic maps is, nowadays, one of the most intensive research activities of plant geneticists. One of the major goals of genome mapping is the localisation of quantitative trait loci (QTLs). This study was aimed at the identification of QTLs controlling morphological traits of rye and comparison of their localisation on genetic maps constructed with the use of genetically different germplasms.

The importance of chromosomes from the sixth homeologic group in the restoration of male fertility in winter triticale with Triticum timopheevii cytoplasm.

The sterilising cytoplasm from Triticum timopheevii is presently considered to be the most promising as regards to the seed production of triticale hybrid cultivars. This study was aimed at the utilisation of Diversity Arrays Technology (DArT) for the preliminary identification of genomic regions with loci controlling male sterility/fertility in the field-grown F2 generation of the interline hybrid between male sterile line CMS-Salvo 15/1 and restorer line Stan I. The fertility of plants was examined by visual scoring as well as by the assessment of seed setting within bagged spikes.

Detection of the quantitative trait loci for α-amylase activity on a high-density genetic map of rye and comparison of their localization to loci controlling preharvest sprouting and earliness.

The objectives of the research were to determine the position of quantitative trait loci (QTL) for α-amylase activity on the genetic map of a rye recombinant inbred line population-S120 × S76-and to compare them to known QTL for preharvest sprouting and heading earliness. Fourteen QTL for α-amylase activity on all seven chromosomes were identified. The detected QTL were responsible for 6.

A high density consensus map of rye (Secale cereale L.) based on DArT markers.

Background: Rye (Secale cereale L.) is an economically important crop, exhibiting unique features such as outstanding resistance to biotic and abiotic stresses and high nutrient use efficiency. This species presents a challenge to geneticists and breeders due to its large genome containing a high proportion of repetitive sequences, self incompatibility, severe inbreeding depression and tissue culture recalcitrance.

DArT markers tightly linked with the Rfc1 gene controlling restoration of male fertility in the CMS-C system in cultivated rye (Secale cereale L.).

The Rfc1 gene controls restoration of male fertility in rye (Secale cereale L.) with sterility-inducing cytoplasm CMS-C. Two populations of recombinant inbred lines (RIL) were used in this study to identify DArT markers located on the 4RL chromosome, in the close vicinity of the Rfc1 gene.

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.

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.

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.