Genetic diversity can be measured by several criteria, including phenotype, pedigree, allelic diversity at marker loci, and allelic diversity at loci controlling phenotypes of interest. Abundance, high level of polymorphism, and ease of genotyping make simple sequence repeats (SSRs) an excellent molecular marker system for genetics diversity analyses. In this study, we used a set of mapped SSRs to survey three representative groups of barley germplasm: a sample of crop progenitor (Hordeum vulgare subsp. spontaneum) accessions, a group of mapping population parents, and a group of varieties and elite breeding lines. The objectives were to determine (i) how informative SSRs are in these three sets of barley germplasm resources and (ii) the utility of SSRs in classifying barley germplasm. A total of 687 alleles were identified at 42 SSR loci in 147 genotypes. The number of alleles per locus ranged from 4 to 31, with an average of 16.3. Crop progenitors averaged 10.3 alleles per SSR locus, mapping population parents 8.3 alleles per SSR locus, and elite breeding lines 5.8 alleles per SSR locus. There were many exclusive (unique) alleles. The polymorphism information content values for the SSRs ranged from 0.08 to 0.94. The cluster analysis indicates a high level of diversity within the crop progenitors accessions and within the mapping population parents. It also shows a lower level of diversity within the elite breeding germplasm. Our results demonstrate that this set of SSRs was highly informative and was useful in generating a meaningful classification of the germplasm that we sampled. Our long-term goal is to determine the utility of molecular marker diversity as a tool for gene discovery and efficient use of germplasm.

In crop breeding, the interest of predicting the performance of candidate cultivars in the field has increased due to recent advances in molecular breeding technologies. However, the complexity of the wheat genome presents some challenges for applying new technologies in molecular marker identification with next-generation sequencing. We applied genotyping-by-sequencing, a recently developed method to identify single-nucleotide polymorphisms, in the genomes of 384 wheat (Triticum aestivum) genotypes that were field tested under three different water regimes in Mediterranean climatic conditions: rain-fed only, mild water stress, and fully irrigated. We identified 102,324 single-nucleotide polymorphisms in these genotypes, and the phenotypic data were used to train and test genomic selection models intended to predict yield, thousand-kernel weight, number of kernels per spike, and heading date. Phenotypic data showed marked spatial variation. Therefore, different models were tested to correct the trends observed in the field. A mixed-model using moving-means as a covariate was found to best fit the data. When we applied the genomic selection models, the accuracy of predicted traits increased with spatial adjustment. Multiple genomic selection models were tested, and a Gaussian kernel model was determined to give the highest accuracy. The best predictions between environments were obtained when data from different years were used to train the model. Our results confirm that genotyping-by-sequencing is an effective tool to obtain genome-wide information for crops with complex genomes, that these data are efficient for predicting traits, and that correction of spatial variation is a crucial ingredient to increase prediction accuracy in genomic selection models.

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.

1997). As a consequence, genetic diversity in cultivated crops has been drastically reduced compared with their Foliar diseases of barley (Hordeum vulgare L.) such as spot blotch wild ancestors. The widespread cultivation of varieties [caused by Cochliobolus sativus (Ito & Kuribayashi) Drechs. ex Dawith a narrow genetic base can increase vulnerability stur], net type net blotch (NTNB; caused by Pyrenophora teres f. of crop plants to biotic and abiotic stresses whose unexteres Drechs), Septoria speckled leaf blotch (SSLB; caused by Septoria passerinii Sacc.), leaf scald [caused by Rhynchosporium secalis pected occurrence is ever increasing because of global (Oudem.) J. J. Davis], and powdery mildew (caused by Blumeria changes in environments and agricultural systems. In graminis f. sp. hordei Em. Marchal) can result in significant yield barley, only 40 to 56% of the alleles found in wild barley reductions in many production areas. The wild progenitor of cultivated are present in elite breeding lines and cultivated barleys barley, Hordeum vulgare subsp. spontaneum is well known as a rich (Ellis et al., 2000; Matus and Hayes, 2002). Therefore, source of disease resistance. To determine the location of H. vulgare developing strategies to incorporate novel allelic variasubsp. spontaneum-derived alleles for disease resistance, we contion into cultivated barley is an important activity.ducted quantitative trait locus (QTL) analysis of a recombinant inbred Many diseases can severely affect the productivity line (RIL) population derived from a cross between the resistant H. and quality of barley in different growing regions of the vulgare subsp. spontaneum accession OUH602 and the two-rowed world. In the USA, leaf scald, caused by the fungus R. malting cultivar Harrington. A total of 151 simple sequence repeats (SSR) markers were mapped into 11 linkage groups, covering 948 secalis, is a serious disease in the Pacific Northwest, cM. Major QTLs for resistance to each disease were identified: one California and the Mid-Atlantic region where yield for spot blotch resistance on chromosome 1(7H); three for NTNB losses can reach 35 to 40% (Mathre, 1997). In the Midresistance on chromosomes 3(3H), 4(4H), and 5(1H); two for SSLB west, net type net blotch (NTNB, caused by P. teres), resistance on chromosomes 2(2H) and 6(6H); one for leaf scald resisspot blotch (caused by C. sativus), and Septoria speckled tance on chromosome 5(1H); and two for powdery mildew resistance leaf blotch (SSLB, caused primarily by S. passerinii) are on chromosomes 4(4H) and 5(1H). Resistance alleles for each QTL important foliar diseases of barley resulting in yield were contributed by OUH602, except those for NTNB and powdery reductions from 5 to 35% each year (Steffenson et al., mildew resistance on chromosome 5(1H) and chromosome 4(4H), 1996; Toubia-Rahme and Steffenson, 2004). Leaf scald respectively. The two QTLs identified for SSLB resistance are novel.and spot blotch are also considered major barley dis-All other QTLs mapped to regions where known ...

Different physiological traits have been proposed as key traits associated with yield potential as well as performance under water stress. The aim of this paper is to examine the genotypic variability of leaf chlorophyll, stem water-soluble carbohydrate content and carbon isotope discrimination (Δ13C), and their relationship with grain yield (GY) and other agronomical traits, under contrasting water conditions in a Mediterranean environment. The study was performed on a large collection of 384 wheat genotypes grown under water stress (WS, rainfed), mild water stress (MWS, deficit irrigation), and full irrigation (FI). The average GY of two growing seasons was 2.4, 4.8, and 8.9 Mg ha−1 under WS, MWS, and FI, respectively. Chlorophyll content at anthesis was positively correlated with GY (except under FI in 2011) and the agronomical components kernels per spike (KS) and thousand kernel weight (TKW). The WSC content at anthesis (WSCCa) was negatively correlated with spikes per square meter (SM2), but positively correlated with KS and TKW under WS and FI conditions. As a consequence, the relationships between WSCCa with GY were low or not significant. Therefore, selecting for high stem WSC would not necessary lead to genotypes of GY potential. The relationship between Δ13C and GY was positive under FI and MWS but negative under severe WS (in 2011), indicating higher water use under yield potential and MWS conditions.