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. For QTL analyses, two high-density consensus maps of two populations (RIL-S and RIL-M) of recombinant inbred lines (RIL) were applied. Plant height (Ph), length of spikes (Sl) and the number of spikelets per spike (Sps) were studied in both populations. Additionally, the number of kernels per spike under isolation (Kps), the weight of kernels per spike (Kw) and thousand kernel weight (Tkw) were assessed in the RIL-M population. Except for Tkw, the majority of the traits were correlated to each other. The non-parametric Kruskal–Wallis (K-W) test and composite interval mapping (CIM) revealed 18/48 and 24/18 regions of rye chromosomes engaged in the determination of Ph, Sl and Sps in the RIL-S and RIL-M populations, respectively. An additional 18/15 QTLs controlling Kps, Kw and Tkw were detected on a map of the RIL-M population. A numerous group of QTLs detected via CIM remained in agreement with the genomic regions found when the K-W test was applied. Frequently, the intervals indicated by CIM were narrower. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s13353-013-0186-5) contains supplementary material, which is available to authorized users

Minimizing ergot infection in hybrid rye by a SMART breeding approach

In Hybridsorten bei Winterroggen führt das Restorergen Rfp1 zu einer vollständigen Restauration der männlichen Fertilität und trägt dazu bei, die Kontamination des Erntegutes mit Mutterkorn zu minimieren. Wir beschreiben Ergebnisse zur Validierung neuer Rfp1-Selektionsmarker an Elitezuchtmaterial des Roggens. Für alle per molekularer Markeranalyse genotypisierten Individuen wurde eine perfekte Übereinstimmung zwischen der postulierten genetischen Konstitution am Restorerlocus Rfp1 und dem Pollenschüttungsvermögen in den Testkreuzungsnachkommenschaften beobachtet. Rekombination zwischen den untersuchten Rfp1-Markern zeigt, dass die neuen Selektionsmarker dazu geeignet sind, rekombinativ verkleinerte, Rfp1-tragende Genomsegmente zu identifizieren. Es konnte gezeigt werden, dass die mit Rfp1 assoziierten, eng gekoppelten Markerallele diagnostisch für Rfp1 sind. Die vorgestellten Ergebnisse belegen, dass die neuen Selektionsmarker eine effiziente Genotypisierung aktueller Elitezuchtlinien im Hinblick auf das Rfp1-Restorergen ermöglichen. Für die mit Rfp1 assoziierten Selektionsmarker konnte in der vorliegenden Studie auch Kopplung mit dem Restorergen Rfc1 nachgewiesen werden. Diese Kopplungsbeziehungen lassen die validierten Marker daher für eine indirekte Selektion von Maintainer-Genotypen des C-Plasmas geeignet erscheinen. Die beobachtete Kopplung von STS-Markern zu Rfp1 bzw. Rfc1 bestätigt frühere Vermutungen, dass in dieser Region auf Chromosom 4RL entweder mehrere Restorergene lokalisiert sind oder es sich bei den betreffenden Restorergenen um Allele desselben Genortes handelt.The restorer gene Rfp1 results in an almost complete restoration of male fertility in hybrid rye varieties and, thus, contributes to minimize harvest contamination with ergot. Here, we report on the validation of recently established Rfp1 markers located on chromosome 4RL in elite breeding lines of rye. The Rfp1 genotypes, as deduced by molecular-marker analysis, perfectly corresponded with the degree of male fertility assessed in test crosses of individual genotpes with male sterile testers. Recombination could be observed between Rfp1 markers indicating their potential to reduce the donor chromosome segment carrying Rfp1. These marker alleles proved to be diagnostic for Rfp1 in current breeding lines. Taken together, results presented qualify the novel markers as efficent molecular tools to assess the restorer gene Rfp1 in elite breeding lines of rye. In addition, we have observed linkage of the Rfp1 markers to the restorer gene Rfc1. Thus, the validated markers should be applicable for marker-assisted selection strategies of maintainer genotypes of the male sterility inducing C cytoplasm, which occur at low frequency in European rye populations as well. The observed linkage of the STS markers to both Rfp1 and Rfc1 supports the assumption that the restorer genes identified on chromosome 4RL are either alleles of a single restorer gene or represent different linked genes located in this sub-genomic region

A High Density Consensus Map of Rye (Secale cereale L.) Based on DArT Markers

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. The genomic resources currently available for rye are underdeveloped in comparison with other crops of similar economic importance. The aim of this study was to create a highly saturated, multilocus linkage map of rye via consensus mapping, based on Diversity Arrays Technology (DArT) markers.Recombinant inbred lines (RILs) from 5 populations (564 in total) were genotyped using DArT markers and subjected to linkage analysis using Join Map 4.0 and Multipoint Consensus 2.2 software. A consensus map was constructed using a total of 9703 segregating markers. The average chromosome map length ranged from 199.9 cM (2R) to 251.4 cM (4R) and the average map density was 1.1 cM. The integrated map comprised 4048 loci with the number of markers per chromosome ranging from 454 for 7R to 805 for 4R. In comparison with previously published studies on rye, this represents an eight-fold increase in the number of loci placed on a consensus map and a more than two-fold increase in the number of genetically mapped DArT markers.Through the careful choice of marker type, mapping populations and the use of software packages implementing powerful algorithms for map order optimization, we produced a valuable resource for rye and triticale genomics and breeding, which provides an excellent starting point for more in-depth studies on rye genome organization

Occurrence and genetic identity of male sterility-inducing cytoplasm in rye (Secale spp.).

Individual plants of 50 open-pollinated cultivars originated from 23 world-wide countries, 18 inbred lines and 9 wilde species and/or subspecies of rye were tested for the presence of sterility-inducing vs. normal cytoplasm, using conventional plasmotype/genotype interaction test. One  to fourteen random plants from each population were crossed as females to inbred lines representing nonrestorer genotype in both, Pampa and Vavilovii, types of sterility-inducing cytoplasm. The F1  and Bc1 or F2 progenies were scored for male fertility/sterility expression. The results showed that male sterility-inducing cytoplasm was common in the sample of a  world-wide rye population. Out of a total 629 single plants tested, 366 plants had sterility-inducing cytoplasm and all of them were derivatives of a cultivated rye populations. Among 50 cultivars and local populations of cultivated rye either normal or sterilizing cytoplasm was found in 9 and 19 populations, respectively, while 22 populations consisted of both plant types, with normal and sterilizing cytoplasm. A random sample of 61 male sterile Bc2 - Bc3 single plant progenies (a new sources of cms) developed from 28 populations were crossed to the L1 inbred line, acting as nonrestorer in Pampa and as restorer in Vavilovii cytoplasm, in an attempt to identify the type of sterility-inducing cytoplasm detected. Fifty of the 61 F1 progenies were male fertile indicating the presence of Vavilovii cytoplasm. Eleven F1 progenies were either male sterile or segregating but  backcrossing of male sterile segregates resulted in male sterile Bc1 and Bc2 progenies, thus  indicating that they all had Pampa cytoplasm. These progenies originated from plants of 6 South-American populations

Variability in Expression of Male Fertility in Triticale (Xtriticosecale Wittmack) With Triticum Timopheevi Cytoplasm

We present a reliable, visual method for evaluation of the level of male fertility during flowering, that is indispensable for breeding of hybrid cultivars of winter triticale based on the cms-T.timopheevi system. Detailed observations of anther development were performed on 20 F2 and BC1 plants derived from crosses between male-sterile and fertility restoring lines. Variation of anther development within florets, spikelets, spikes, and among spikes of the same plant was examined..

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

Abstract 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. To the best of our knowledge, this is the first study on the localization of loci controlling RL on high density consensus genetic map of rye. Results Genotypic analysis led to the identification of 43 quantitative trait loci (QTLs) for RL, grouped into 28 intervals, which confirms the multigenic base of the trait stated for wheat and rice. Four stable QTLs were located on chromosomes 3R, 5R, and 7R. Co-localization of QTL for RL and for different morphological, biochemical and physiological traits may suggests pleiotropic effects of some QTLs. QTLs for RL were associated with QTLs for such morphological traits as: grain number and weight, spike number per plant, compactness of spike, and plant height. Two QTLs for RL were found to coincide with QTLs for drought tolerance (4R, 7R), two with QTLs for heading earliness (2R, 7R), one with α-amylase activity QTL (7R) and three for pre-harvest sprouting QTL (1R, 4R, 7R). The set of molecular markers strongly linked to RL was selected, and the putative candidate genes controlling the process of RL were identified. Twelve QTLs are considered as linked to candidate genes on the base of DArT sequences alignment, which is a new information for rye. Conclusions Our results expand the knowledge about the network of QTLs for different morphological, biochemical and physiological traits and can be a starting point to studies on particular genes controlling RL and other important agronomic traits (yield, earliness, pre-harvest sprouting, reaction to water deficit) and to appoint markers useful in marker assisted selection (MAS). A better knowledge of the rye genome and genes could both facilitate rye improvement itself and increase the efficiency of utilizing rye genes in wheat breeding