Selective sweeps identification in distinct groups of cultivated rye (Secale cereale L.) germplasm provides potential candidate genes for crop improvement

Background: During domestication and subsequent improvement plants were subjected to intensive positive selection for desirable traits. Identification of selection targets is important with respect to the future targeted broadening of diversity in breeding programmes. Rye (Secale cereale L.) is a cereal that is closely related to wheat, and it is an important crop in Central, Eastern and Northern Europe. The aim of the study was (i) to identify diverse groups of rye accessions based on high-density, genome-wide analysis of genetic diversity within a set of 478 rye accessions, covering a full spectrum of diversity within the genus, from wild accessions to inbred lines used in hybrid breeding, and (ii) to identify selective sweeps in the established groups of cultivated rye germplasm and putative candidate genes targeted by selection.Results: Population structure and genetic diversity analyses based on high-quality SNP (DArTseq) markers revealed the presence of three complexes in the Secale genus: S. sylvestre, S. strictum and S. cereale/vavilovii, a relatively narrow diversity of S. sylvestre, very high diversity of S. strictum, and signatures of strong positive selection in S. vavilovii. Within cultivated ryes we detected the presence of genetic clusters and the influence of improvement status on the clustering. Rye landraces represent a reservoir of variation for breeding, and especially a distinct group of landraces from Turkey should be of special interest as a source of untapped variation. Selective sweep detection in cultivated accessions identified 133 outlier positions within 13 sweep regions and 170 putative candidate genes related, among others, to response to various environmental stimuli (such as pathogens, drought, cold), plant fertility and reproduction (pollen sperm cell differentiation, pollen maturation, pollen tube growth), and plant growth and biomass production.Conclusions: Our study provides valuable information for efficient management of rye germplasm collections, which can help to ensure proper safeguarding of their genetic potential and provides numerous novel candidate genes targeted by selection in cultivated rye for further functional characterisation and allelic diversity studies

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

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. To further enhance the agronomic potential of rye, we produced a chromosome-scale annotated assembly of the 7.9-gigabase rye genome and extensively validated its quality by using a suite of molecular genetic resources. We demonstrate applications of this resource with a broad range of investigations. We present findings on cultivated rye's incomplete genetic isolation from wild relatives, mechanisms of genome structural evolution, pathogen resistance, low-temperature tolerance, fertility control systems for hybrid breeding and the yield benefits of rye-wheat introgressions.Peer reviewe

Improving Yield and Yield Stability in Winter Rye by Hybrid Breeding

Rye is the only cross-pollinating small-grain cereal. The unique reproduction biology results in an exceptional complexity concerning genetic improvement of rye by breeding. Rye is a close relative of wheat and has a strong adaptation potential that refers to its mating system, making this overlooked cereal readily adjustable to a changing environment. Rye breeding addresses the emerging challenges of food security associated with climate change. The systematic identification, management, and use of its valuable natural diversity became a feasible option in outbreeding rye only following the establishment of hybrid breeding late in the 20th century. In this article, we review the most recent technological advances to improve yield and yield stability in winter rye. Based on recently released reference genome sequences, SMART breeding approaches are described to counterbalance undesired linkage drag effects of major restorer genes on grain yield. We present the development of gibberellin-sensitive semidwarf hybrids as a novel plant breeding innovation based on an approach that is different from current methods of increasing productivity in rye and wheat. Breeding of new rye cultivars with improved performance and resilience is indispensable for a renaissance of this healthy minor cereal as a homogeneous commodity with cultural relevance in Europe that allows for comparatively smooth but substantial complementation of wheat with rye-based diets, supporting the necessary restoration of the balance between human action and nature

AB-QTL analysis for â-glucan content in oats

The advanced-backcross QTL analysis (AB-QTL analysis), as proposed by Tanksley and Nelson (1996), was chosen as an directed approach to introduce QTLs for B-glucan content and other important traits from a genebank accession into cultivar breeding programmes. In this presentation first results from an oat AB-QTL project are presented. Three BC2S1 populations consisting of 98, 73 and 67 lines, respectively, were derived from the cross 'Iltis' x IA H611-447, the latter of which served as a donor for high â-glucan content. In 2003 the first field nursery was performed with the 237 BC2S4 families at three locations with two replications per location. The most important agronomical and quality traits have been analysed. Segregation between lines was evident in yield components and yield, plant height and quality parameters like â-glucan content. Some transgressive lines for yield and yield components were found and have to be validated in the next generations. The transgressive progenies did not outperform the most recent high-yielding cultivars. To find useful markers for the QTL analysis, 144 oat SSRs were screened, of which 26 were polymorphic between the parents and 5 showed segregation in the first population. Additionally, 128 EcoRI/MseI AFLP primer combinations were detected, of which 32 primer combinations showed 176 polymorphic bands between the parents. The polymorphic AFLP markers, together with STS markers, will be used to genotype the three populations, starting with the first population. This genotyping is on the way. Tanksley SD, Nelson JC 1996: Theoretical and Applied Genetics 92:191 203vokMyynti MTT tietopalvelu

Two Rye Genes Responsible for Abnormal Development of Wheat–Rye Hybrids Are Linked in the Vicinity of an Evolutionary Translocation on Chromosome 6R

The post-zygotic reproductive isolation (RI) in plants is frequently based on the negative interaction of the parental genes involved in plant development. Of special interest is the study of such types of interactions in crop plants, because of the importance of distant hybridization in plant breeding. This study is devoted to map rye genes that are incompatible with wheat, determining the development of the shoot apical meristem in wheat–rye hybrids. Linkage analysis of microsatellite loci, as well as genes of embryo lethality (Eml-R1) and hybrid dwarfness (Hdw-R1) was carried out in hybrids of Chinese Spring wheat with recombinant inbred lines as well as interline rye hybrids. Eml-R1 and Hdw-R1 could be mapped proximal and distal of two closely linked EST-SSR markers, Xgrm902 and Xgrm959, on rye chromosome 6R. Both rye genes are located on a segment of chromosome 6R that contains a breakpoint of evolutionary translocation between the ancestral chromosomes of homeologous groups 6 and 3. The obtained results are discussed in relation to genes interacting in developmental pathways as a class of causal genes of RI