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

Abstract

BackgroundRye (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. 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.Methodology/Principal FindingsRecombinant 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.Conclusions/SignificanceThrough 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.

Chromosomal localization of selected SCARs converted from new RAPD, ISSR and R-ISSR markers linked to rye (Secale cereale L.) tolerance to nutrient deprivation stress identified using bulk segregant analysis

“…This localization was established based on linkage to chromosomally-specific markers Xpm137, Xpm144 and Xpsr-370 in population [153/79-1 x Ot1-3]RIL and to marker Xpsr-370 in population [Ot0-6 x Ot1-3]RIL (Figure 4). Localization of these markers was identified and multiply verified on other genetic maps (Milczarski et al 2007;Masojć et al 2009, Myśków, 2010 and on a consensus map of rye (Milczarski et al 2011).…”

In silico integration of quantitative trait loci for seed yield and yield-related traits in Brassica napus

“…For example, Mace et al (2009) (Mace et al 2009) used simple projection to integrate genetic maps in barley by using one map as a "base" or reference map. The program "JoinMap" (Van Ooijen 2006) has also been used for map integration in rye (Milczarski et al 2011) and barley (Muñoz-Amatriaín et al 2011), and the program "Merge-Map" , based on directed acyclic graphs (DAGs), has been used in map integration in cowpeas (Muchero et al 2009) and Brassica ).…”

Agronomic Properties Assessed for Population of Recombinant Inbred Lines of Rye (Seceale cereale L.) with Known Responses to Nutrient Deficiency Stress at the Seedling Stage

“…They were presented only for in vitro cultures in a very good review by Hazarika (2006). Additionally, an interesting verification of the obtained results can be carried out after identification of QTLs of the described agronomic traits and comparing them with the results of research presented by Milczarski (2010) and Milczarski et al (2011). What is more, identification of QTLs of biometric traits of seedlings analyzed under both low and high level of nitrogen and potassium can be attempted, and the results can be compared to the QTLs described for root architecture of plants growing under conditions of different abiotic stresses by Tuberosa et al (2002), Mano et al (2006), Zhu et al (2005), Liu et al (2008), including the conditions of nitrogen deficiencies (Tuberosa and Salvi, 2007).…”

“…The similar mechanisms of plant response to stress of drought and nutrient deficiencies (Ashraf and Harris, 2005) may confirm also research results by Rzepka-Plevneš et al (1997a), describing inbred line Ot1-3 as susceptible to nutrient stress, and may only suggest the possibility of inheriting the genes that determine lack of tolerance to drought from its descendant cultivar Kungs II (Persson, 1976). On the other hand, inbred line Ot1-3 has low activity of α-amylase and has been used as a maternal form -donor of resistance genes in research on sprouting in rye (Masojć et al, 2009, Milczarski et al, 2011.…”