Recombinant Chromosome Substitution Lines Research Articles

Identification of barley genetic regions influencing plant\u2013microbe interactions and carbon cycling in soil

PurposeRhizodeposition shapes soil microbial communities that perform important processes such as soil C mineralization, but we have limited understanding of the plant genetic regions influencing soil microbes. Here, barley chromosome regions affecting soil microbial biomass-C (MBC), dissolved organic-C (DOC) and root biomass were characterised.MethodsA quantitative trait loci analysis approach was applied to identify barley chromosome regions affecting soil MBC, soil DOC and root biomass. This was done using barley Recombinant Chromosome Substitution Lines (RCSLs) developed with a wild accession (Caesarea 26-24) as a donor parent and an elite cultivar (Harrington) as recipient parent.ResultsSignificant differences in root-derived MBC and DOC and root biomass among these RCSLs were observed. Analysis of variance using single nucleotide polymorphisms genotype classes revealed 16 chromosome regions influencing root-derived MBC and DOC. Of these chromosome regions, five on chromosomes 2H, 3H and 7H were highly significant and two on chromosome 3H influenced both root-derived MBC and DOC. Potential candidate genes influencing root-derived MBC and DOC concentrations in soil were identified.ConclusionThe present findings provide new insights into the barley genetic influence on soil microbial communities. Further work to verify these barley chromosome regions and candidate genes could promote marker assisted selection and breeding of barley varieties that are able to more effectively shape soil microbes and soil processes via rhizodeposition, supporting sustainable crop production systems.

Genetic dissection of quantitative and qualitative traits using a minimum set of barley Recombinant Chromosome Substitution Lines

BackgroundExploring the natural occurring genetic variation of the wild barley genepool has become a major target of barley crop breeding programmes aiming to increase crop productivity and sustainability in global climate change scenarios. However this diversity remains unexploited and effective approaches are required to investigate the benefits that unadapted genomes could bring to crop improved resilience. In the present study, a set of Recombinant Chromosome Substitution Lines (RCSLs) derived from an elite barley cultivar ‘Harrington’ as the recurrent parent, and a wild barley accession from the Fertile Crescent ‘Caesarea 26–24’, as the donor parent (Matus et al. Genome 46:1010–23, 2003) have been utilised in field and controlled conditions to examine the contribution of wild barley genome as a source of novel allelic variation for the cultivated barley genepool.MethodsTwenty-eight RCSLs which were selected to represent the entire genome of the wild barley accession, were genotyped using the 9 K iSelect SNP markers (Comadran et al. Nat Genet 44:1388–92, 2012) and phenotyped for a range of morphological, developmental and agronomic traits in 2 years using a rain-out shelter with four replicates and three water treatments. Data were analysed for marker traits associations using a mixed model approach.ResultsWe identified lines that differ significantly from the elite parent for both qualitative and quantitative traits across growing seasons and water regimes. The detailed genotypic characterisation of the lines for over 1800 polymorphic SNP markers and the design of a mixed model analysis identified chromosomal regions associated with yield related traits where the wild barley allele had a positive response increasing grain weight and size. In addition, variation for qualitative characters, such as the presence of cuticle waxes on the developing spikes, was associated with the wild barley introgressions. Despite the coarse location of the QTLs, interesting candidate genes for the major marker-trait associations were identified using the recently released barley genome assembly.ConclusionThis study has highlighted the role of exotic germplasm to contribute novel allelic variation by using an optimised experimental approach focused on an exotic genetic library. The results obtained constitute a step forward to the development of more tolerant and resilient varieties.

Morphological and genetic characterisation of the root system architecture of selected barley recombinant chromosome substitution lines using an integrated phenotyping approach

Discoveries on the genetics of resource acquisition efficiency are limited by the ability to measure plant roots in sufficient number and with adequate genotypic variability. This paper presents a root phenotyping study that explores ways to combine live imaging and computer algorithms for model-based extraction of root growth parameters. The study is based on a subset of barley Recombinant Chromosome Substitution Lines (RCSLs) and a combinatorial approach was designed for fast identification of the regions of the genome that contribute the most to variations in root system architecture (RSA). Results showed there was a strong genotypic variation in root growth parameters within the set of genotypes studied. The chromosomal regions associated with primary root growth differed from the regions of the genome associated with changes in lateral root growth. The concepts presented here are discussed in the context of identifying root QTL and its potential to assist breeding for novel crops with improved root systems.

Combined effects of rhizodeposit C and crop residues on SOM priming, residue mineralization and N supply in soil

Fluxes of rhizodeposit carbon (C) to soil stimulate microbial activity affecting soil organic matter (SOM) decomposition and, in turn, nutrient fluxes in soil. In agricultural soils, residues from previous crops also have major impacts on SOM and nutrient cycling, and their turnover by microbes is likely to be indirectly impacted by rhizodeposition. However, the combined effects of rhizodeposit C and inputs of C from dead plant materials in soil on native SOM decomposition are unclear. In this study, we assessed (i) the individual and combined effects of barley rhizodeposition and ryegrass root residue inputs (as a model for residue input from previous crop) on SOM mineralization, (ii) the intraspecies variation within barley in impacting residue mineralization, and (iii) whether genotypes that stimulate high mineralization rates of plant residues in soil also directly benefit through increased nutrient uptake from these residues. We continuously applied 13C depleted CO2 to selected barley recombinant chromosome substitution lines (RCSLs) to trace the flow of barley root-derived C in surface soil CO2 efflux, soil microbial biomass and soil particle-size fractions. In addition, 13C and 15N enriched ryegrass root residues were mixed into soil to trace the mineralization of residue-derived C and the residue-derived nitrogen (N) uptake by plants. Our results show (i) genotype-specific variation in impacting total soil CO2 efflux and its component sources: SOM-derived C, barley root-derived C and/or ryegrass residue-derived C, (ii) residue effects on total C and SOM-derived C respired as CO2, (iii) genotype-residue combined effects on SOM primed C, that were very similar to the sum of primed C caused by planting or residue addition alone (except for the last sampling date), and (iv) that plant uptake of residue released N between genotypes was linked to genotype impacts on residue mineralization. These results suggest that impacts of plant rhizodeposition and residue inputs had additive effects on SOM priming. Furthermore, these results demonstrate, for the first time, genotype differences in impacting the mineralization of recent plant-derived organic materials in soil, and reveal that this process directly contributes to plant nutrition.

<b>Identification of QTL underlying agronomic, morphological and physiological traits in barley under rainfed conditions using SNP markers

Barley ( Hordeum vulgare L.) is considered a good genetic model for evaluating mechanisms of drought tolerance, and it is the most important threat to crop production worldwide. This study aimed to identify single-nucleotide polymorphisms (SNPs) associated with agronomic, morphological and physiological traits in a population of 137 recombinant chromosome substitution lines (RCSL) of barley, which were evaluated under rainfed conditions, in Cauquenes, southern Chile (35°58’ S, 72°17’ W). The annual precipitation was 299 mm during the growing season. Fifty-two significant QTLs were detected for the studied traits, which explained between 5% and 13.8% of the phenotypic variation. A genomic region on chromosome 1H (that comprises SNPs 2711-234 and 1923-265) accounted for 13.4% and 13.8%, respectively, of the grain yield variation. In addition, SNPs 8388-578 and 7639-122 on the chromosome 5H had a moderate effect, explaining 12.8% of the plant height variation. Moreover, some SNPs were associated with more than one trait, and clusters of QTLs for yield and related traits were also found. Finally, the QTLs identified in the present study are of particular interest for barley-breeding purposes under rainfed conditions.

SNP-Based QTL Mapping of 15 Complex Traits in Barley under Rain-Fed and Well-Watered Conditions by a Mixed Modeling Approach.

This study identified single nucleotide polymorphism (SNP) markers associated with 15 complex traits in a breeding population of barley (Hordeum vulgare L.) consisting of 137 recombinant chromosome substitution lines (RCSL), evaluated under contrasting water availability conditions in the Mediterranean climatic region of central Chile. Given that markers showed a very strong segregation distortion, a quantitative trait locus/loci (QTL) mapping mixed model was used to account for the heterogeneity in genetic relatedness between genotypes. Fifty-seven QTL were detected under rain-fed conditions, which accounted for 5–22% of the phenotypic variation. In full irrigation conditions, 84 SNPs were significantly associated with the traits studied, explaining 5–35% of phenotypic variation. Most of the QTL were co-localized on chromosomes 2H and 3H. Environment-specific genomic regions were detected for 12 of the 15 traits scored. Although most QTL-trait associations were environment and trait specific, some important and stable associations were also detected. In full irrigation conditions, a relatively major genomic region was found underlying hectoliter weight (HW), on chromosome 1H, which explained between 27% (SNP 2711-234) and 35% (SNP 1923-265) of the phenotypic variation. Interestingly, the locus 1923-265 was also detected for grain yield at both environmental conditions, accounting for 9 and 18%, in the rain-fed and irrigation conditions, respectively. Analysis of QTL in this breeding population identified significant genomic regions that can be used for marker-assisted selection (MAS) of barley in areas where drought is a significant constraint.

Barley genotype influences stabilization of rhizodeposition-derived C and soil organic matter mineralization

Rhizodeposition is an important source of substrate for microbial communities, supporting activities including soil organic matter (SOM) and nutrient cycling. Therefore, it is a potential trait of interest for crop plants, particularly in the context of variety selection for sustainable production systems. However, we do not have a good understanding of (i) whether there is significant variation in root-C deposition between varieties of important agricultural crops and (ii) whether variation in C deposition between varieties leads to major differences in C cycling in soil. In two experiments, we assessed variations in C deposition amongst barley genotypes and their respective impacts on microbial activity and SOM dynamics. In experiment 1, we applied 13C–CO2 labelling to selected barley recombinant chromosome substitution lines (RCSLs) and traced root-derived C in surface soil CO2 efflux, soil microbial biomass-C (MBC), soil solution, and soil particle-size fractions. In experiment 2, we conducted MicroResp analysis using 15 ecologically relevant C substrates to assess the impacts of barley genotypes on microbial activity. Soil respiration measurements (partitioned into plant- and SOM-derived components) revealed genotype-specific effects on plant-derived C, SOM-derived C and total C respired as CO2. For particle-size fractionation, we found that incorporation of plant-derived C to the silt-and-clay fraction varied between genotypes, indicating differences in relative stabilization of root-derived C as a result of barley genotype. Our data did not indicate genotype effects on total MBC size or dissolved organic-C (DOC) in soil solutions, but significant differences in plant-derived MBC and DOC were observed. MicroResp analysis showed differential utilization of 7 substrates (glucose, trehalose, lignin, arabinose, alanine, aminobutyric acid and lysine) revealing variation in community level physiological profiles (CLPPs) of soil microbes as impacted by barley genotypes. Furthermore, we found significant clustering of microbial CLPPs as a function of RCSLs and parent lines (Caesarea 26-24 and Harrington) suggesting a strong plant genetic control of the barley microbiome, and that this genetic control is heritable. Our results demonstrate barley genotype-specific effects on soil processes, revealing the potential for germplasm selection and variety improvement in barley to support sustainable production systems.

Physiological and yield responses of recombinant chromosome substitution lines of barley to terminal drought in a Mediterranean‐type environment

Physiological traits and productivity of the recombinant chromosome substitution lines (RCSLs) of barley, developed through the cross of Hordeum vulgare ssp. vulgare cv. Harrington and the wild ancestor Hordeum vulgare ssp. spontaneum, were measured in plants growing in microplots (with and without irrigation) and in field conditions in two Mediterranean‐type environments, Cauquenes (rainfed) and Santa Rosa (irrigated). The objectives were to assess the degree of phenotypic variability in response to terminal drought stress and to test whether the introgression of the wild ancestor into cv. Harrington can increase the terminal drought tolerance of RCSLs of barley. Days from emergence to anthesis and from anthesis to maturity of the 80 RCSLs were reduced in only 2–4 days under water stress, in microplots. Specific leaf area (SLA) and stomatal conductance (gs) of 80 RCSLs and cv. Harrington decreased greatly under water stress in plants growing in microplots and field conditions (in 2004/05 growing season). No G × E interaction was detected except for SLA in the microplot experiment. The principal component analysis provided a clear distinction between RCSLs. Along the first principal component, it was possible to identify 24 RCSLs which represent the whole range of grain yield (GY), gs and SLA observed in the 80 RCSLs. The selected 24 RCSLs were evaluated in field conditions at Cauquenes and Santa Rosa, during two growing seasons (2007/08 and 2008/09). The gs and carbon isotope discrimination in grains (Δ13C) were significantly (P < 0.001) lower in the rainfed condition (Cauquenes), but the water‐soluble carbohydrates (WSC) in stems at anthesis and maturity was significantly (P < 0.001) higher than in well‐irrigated condition (Santa Rosa). Grain yield was reduced by 63% under drought conditions. Differences between RCSLs in gs, WSC and GY were significant (P < 0.001) in 2007/08. The stress tolerance index (STI) was highly (P < 0.01) correlated with GY in all environments (rainfed and irrigated conditions and the two growing seasons). The relationship between STI and Δ13C under rainfed condition allowed identifying drought tolerant and susceptible RCSLs; the former were high yielding lines under rainfed and irrigated conditions (and higher STI values), but with similar GY to cv. Harrington, but presented higher grain Δ13C values than cv. Harrington. The drought susceptible lines presented lower GY, STI and Δ13C values than cv. Harrington. These results suggest that H. spontaneum has contributed alleles that increase terminal drought tolerance to some of the RCSLs.

Seedling vigor variation among 80 recombinant chromosome substitution lines (RCSL) of barley ( Hordeum vulgare)

L. Inostroza, C. Quezada, W. Inostroza, I. Matus, M. Tapia, and A. del Pozo. 2011. Seedling vigor of 80 recombinant chromosome substitution lines (RCSL) of barley (Hordeum vulgare). Cien. Inv. Agr. 38 (1): 137-147. The seedling vigor of 80 barley recombinant chromosome substitution lines (RCSLs) was measured for selecting high seedling vigor genotypes. The RCSLs were derived from a cross between H. vulgare subsp. spontaneum and H. vulgare subsp. vulgare ‘Harrington’. The work was carried out under greenhouse conditions during the summer of 2008. The experimental design was an alpha lattice with 3 replicates. In each replicate, 40 plants were established, distributed in eight polyethylene pots containing sand as substrate, which were fertilized an irrigated. The emergence of seedlings, number of leaves and shoots, dry matter of leaves, shoots and roots and leaf area of fully expanded leaves were measured. In addition, growth indices were calculated: emergence rate, leaf appearance rate, relative leaf expansion rate, relative growth rate (RGR), net assimilation rate (NAR), leaf area ratio (LAR) and the allometric coefficient (K) between root and shoot dry matter. All calculated indices varied significantly among genotypes (P≤0.05) and some RCSLs showed better early vigor associated traits than ‘Harrington’. The dry matter accumulation 30 DAS (when the experiment ended) was significant and positively correlated with the RGR (r=0.61; P≤ 0.05) and NAR (r=0.41; P≤0.05). The K coefficient was negatively correlated with NAR (r=-0.40, P≤0.05). The genotypes with the greatest seminal vigor were the RCSLs 45, 92, 112 and ‘Harrington’, whereas the RCSLs 5, 19, 47 and 121 presented the lowest seminal vigor.

Single Nucleotide Polymorphism Mapping and Alignment of Recombinant Chromosome Substitution Lines in Barley

Single nucleotide polymorphism (SNP) genotyping is useful for assessing genetic variation in germplasm collections, genetic map development and detection of alien chromosome substitutions. In this study, a diversity analysis using 1,301 SNPs on a set of 37 barley accessions was conducted. This analysis showed a high polymorphism rate between the malting barley cultivar 'Haruna Nijo' and the food barley cultivar 'Akashinriki'. Haruna Nijo and Akashinriki are donors of the barley expressed sequence tag (EST) collections. A doubled haploid (DH) population derived from the cross between Haruna Nijo and Akashinriki was genotyped with 1,448 SNPs. Of these 1,448 SNPs, 734 were polymorphic and distributed on barley linkage groups (chromosomes) as follows: 1H (86), 2H (125), 3H (120), 4H (100), 5H (127), 6H (88) and 7H (88). By using cMAP, we integrated the SNP markers across high-density maps. The SNPs were also used to genotype 98 BC(3)F(4) recombinant chromosome substitution lines (RCSLs) developed from the same cross (Haruna Nijo/Akashinriki). These data were used to create graphical genotypes for each line and thus estimate the location, extent and total number of introgressions from Akashinriki in the Haruna Nijo background. The 35 selected RCSLs sample most of the Akashinriki food barley genome, with only a few missing segments. These resources bring new alleles into the malting barley gene pool from food barley.

Seedling vigor of 80 recombinant chromosome substitution lines (RCSL) of barley (Hordeum vulgare)

The seedling vigor of 80 barley recombinant chromosome substitution lines (RCSLs) was measured for selecting high seedling vigor genotypes. The RCSLs were derived from a cross between H. vulgare subsp. spontaneum and H. vulgare subsp. vulgare ‘Harrington’. The work was carried out under greenhouse conditions during the summer of 2008. The experimental design was an alpha lattice with 3 replicates. In each replicate, 40 plants were established, distributed in eight polyethylene pots containing sand as substrate, which were fertilized an irrigated. The emergence of seedlings, number of leaves and shoots, dry matter of leaves, shoots and roots and leaf area of fully expanded leaves were measured. In addition, growth indices were calculated: emergence rate, leaf appearance rate, relative leaf expansion rate, relative growth rate (RGR), net assimilation rate (NAR), leaf area ratio (LAR) and the allometric coefficient (K) between root and shoot dry matter. All calculated indices varied significantly among genotypes (P≤0.05) and some RCSLs showed better early vigor associated traits than ‘Harrington’. The dry matter accumulation 30 DAS (when the experiment ended) was significant and positively correlated with the RGR (r=0.61; P≤ 0.05) and NAR (r=0.41; P≤0.05). The K coefficient was negatively correlated with NAR (r=-0.40, P≤0.05). The genotypes with the greatest seminal vigor were the RCSLs 45, 92, 112 and ‘Harrington’, whereas the RCSLs 5, 19, 47 and 121 presented the lowest seminal vigor.

An application of high-throughput SNP genotyping for barley genome mapping and characterization of recombinant chromosome substitution lines

An oligo-nucleotide pooled assay (OPA) for high-throughput single nucleotide polymorphism (SNP) genotyping was used for genetic map development in order to coordinate marker information from multiple mapping resources in barley. A doubled haploid (DH) population derived from the cross between barley cultivar "Haruna Nijo" (Hordeum vulgare ssp. vulgare) and wild barley strain "H602" (H. vulgare ssp. spontaneum) was genotyped with 1,448 unigene-derived OPA-SNPs. Of these, 732 markers showed polymorphisms and 384 were cross-referenced with EST markers on our high-density transcript map. The OPA-SNP markers were well distributed on barley chromosomes as follows: 1H (93), 2H (131), 3H (123), 4H (97), 5H (108), 6H (92) and 7H (88). Using a cMAP platform, it was possible to integrate EST marker positions across high-density EST maps. The OPA-SNPs were used to genotype 99 BC(3)F(5) recombinant chromosome substitution lines (RCSLs) from the same cross (Haruna Nijo/H602). These data were used to create graphical genotypes for each line and thus estimate the location, extent, and total number of introgressions from the wild barley parent. The RCSLs sampled most of the wild barley genome, with only a few missing segments. With the resources we have developed, all QTL alleles segregating in this germplasm are now potential targets for map-based cloning.

Genetic analysis of seed dormancy QTL in barley

Seed dormancy in wild barley enables drought escape by preventing germination during the hot summer in arid environments. Dormancy in cultivated barley has different effects: it can delay the malting process and/or it can prevent pre-harvest sprouting. Thus, cloning dormancy genes in barley will contribute to understanding the domestication process and it will facilitate optimizing the trait for efficient agronomic and industrial uses. Rates of seed germination were used to evaluate dormancy on physiologically matured grain samples that were dried and stored frozen until use. With this phenotypic scoring procedure, many genetic factors controlling seed dormancy has been reported as quantitative trait loci (QTL). Of these QTL, one at the centrometic region of chromosome 5H (Qsd1) has been most frequently identified and shows the largest effect across mapping populations. We also identified this QTL using the EST map based on Haruna Nijo (H. vulgare ssp. vulgare) crossed with wild barley H602 (H. vulgare ssp. spontaneum). We have derived both doubled haploid and recombinant chromosome substitution lines (RCSLs) from this cross. At least four QTLs are segregating in this germplasm. RCSLs having only the Qsd1 segment of wild barley in a Haruna Nijo genetic background were identified and 910 BC3F2 plants were scored for dormancy. In these lines, segregation for dormancy fit a mono-factorial ratio. These germplasm resources are appropriate for map based cloning of Qsd1. Strategies for cloning Qsd1 with these resources are discussed.

Association mapping of plant height, yield, and yield stability in recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background

Grain yield and plant height of 80 recombinant chromosome substitution lines (RCSLs) of barley were measured in six environments with contrasting available moisture profiles. Two environments were in OR, USA (Moro and Pendleton) during one growing season (2004), and four in Chile (Cauquenes and Santa Rosa) during two growing seasons (2004/2005 and 2007/2008). From the yield data obtained in the different environments, yield adaptability (Finlay–Wilkinson slope) and stability (deviations from regression) were calculated. Two commercial cultivars (Harrington and Baronesse) were used as checks in all environments. Marker-quantitative trait associations were identified using 47 simple sequence repeats (SSRs) and the general linear model (GLM) implemented in TASSEL. The mean plant height and grain yield of the 80 RCSLs differed greatly across environments, reflecting differences in water availability. In all environments, there were significant differences (P < 0.05) in grain yield among RCSLs. There was also abundant variation in yield adaptability, indicating a differential response of the RCSLs to environmental conditions across environments. Using principal component analysis, it was possible to identify genotypes with better agronomic performance than the recurrent parent cv. Harrington. The association analysis revealed 21 chromosomal regions that were highly correlated with differences in grain yield, plant height and/or yield adaptability (Finlay–Wilkinson slope). In approximately one-fourth of the cases, the H. spontaneum donor contributed favorable alleles. The associations were referenced to the quantitative trait loci (QTL) for the same traits reported in the literature.

Multiple QTL‐effects of wheat Gpc‐B1 locus on grain protein and micronutrient concentrations

Micronutrient malnutrition afflicts over three billion people worldwide and the numbers are continuously increasing. Developing genetically micronutrient‐enriched cereals, which are the predominant source of human dietary, is essential to alleviate malnutrition worldwide. Wheat chromosome 6B derived from wild emmer wheat [Triticum turgidum ssp. dicoccoides (Körn.) Thell] was previously reported to be associated with high Zn concentration in the grain. In the present study, recombinant chromosome substitution lines (RSLs), previously constructed for genetic and physical maps of Gpc‐B1 (a 250‐kb locus affecting grain protein concentration), were used to identify the effects of the Gpc‐B1 locus on grain micronutrient concentrations. RSLs carrying the Gpc‐B1 allele of T. dicoccoides accumulated on average 12% higher concentration of Zn, 18% higher concentration of Fe, 29% higher concentration of Mn and 38% higher concentration of protein in the grain as compared with RSLs carrying the allele from cultivated wheat (Triticum durum). Furthermore, the high grain Zn, Fe and Mn concentrations were consistently expressed in five different environments with an absence of genotype by environment interaction. The results obtained in the present study also confirmed the previously reported effect of the wild‐type allele of Gpc‐B1 on earlier senescence of flag leaves. We suggest that the Gpc‐B1 locus is involved in more efficient remobilization of protein, zinc, iron and manganese from leaves to the grains, in addition to its effect on earlier senescence of the green tissues.

QTL Analysis in Recombinant Chromosome Substitution Lines and Doubled Haploid Lines Derived from a Cross between Hordeum vulgare ssp. vulgare and Hordeum vulgare ssp. spontaneum

Recombinant chromosome substitution lines (RCSLs) were developed in BC3 generation to introduce segments of a wild barley strain ‘H602’ (Hordeum vulgare ssp. spontaneum) into a barley cultivar ‘Haruna Nijo’ (H. vulgare ssp. vulgare) genetic background. One hundred thirty four RCSLs were genotyped by 25 SSR and 60 EST markers, which were localized on a linkage map of doubled haploid lines (DHLs) derived from the same cross combination. Graphical genotyping revealed that the observed average substitution ratio of H602 segment (12.9%) agreed with the expected substitution ratio (12.5%), and a minimum set of 19 RCSLs represented the entire H602 genome. Phenotypes of five qualitative and nine quantitative traits were scored in both the RCSLs and DHLs. Five qualitative traits were localized as morphological markers on the linkage map of the DHLs, and these molecular markers were aligned on the respective chromosomal regions in the RCSLs. Simple and composite interval mapping procedures detected a total of 18 and 24 QTLs for nine qualitative traits on the RCSLs and DHLs, respectively. Several QTLs were localized at coincident or very close regions on both linkage maps. In spite of general inferior agronomic performances in wild barley, several H602 QTL alleles showed agronomically positive effects. These RCSLs should contribute to substitution of favorable alleles from wild barley into cultivated barley. These RCSLs are also available as sources of near isogenic lines, with which we can apply advanced genetic analysis methods such as isolation of QTLs and detection of epistatic interactions among QTLs.

Development and characterization of recombinant chromosome substitution lines (RCSLs) using Hordeum vulgare subsp. spontaneum as a source of donor alleles in a Hordeum vulgare subsp. vulgare background.

The ancestor of barley (Hordeum vulgare subsp. spontaneum) may be a source of novel alleles for crop improvement. We developed a set of recombinant chromosome substitution lines (RCSLs) using an accession of H. vulgare subsp. spontaneum (Caesarea 26-24, from Israel) as the donor and Hordeum vulgare subsp. vulgare 'Harrington' (the North American malting quality standard) as the recurrent parent via two backcrosses to the recurrent parent, followed by six generations of selfing. Here we report (i) the genomic architecture of the RCSLs, as inferred by simple sequence repeat (SSR) markers, and (ii) the effects of H. vulgare subsp. spontaneum genome segment introgressions in terms of three classes of phenotypes: inflorescence yield components, malting quality traits, and domestication traits. Significant differences among the RCSLs were detected for all phenotypes measured. The phenotypic effects of the introgressions were assessed using association analysis, and these were referenced to quantitative trait loci (QTL) reported in the literature. Hordeum vulgare subsp. spontaneum, despite its overall inferior phenotype, contributed some favorable alleles for agronomic and malting quality traits. In most cases, the introgression of the ancestral genome resulted in a loss of desirable phenotypes in the cultivated parent. Although disappointing from a plant breeding perspective, this finding may prove to be a useful tool for gene discovery.