Choice of selection strategy in breeding barley for stress environments

To determine the optimum selection environment for barley (Hordeum vulgare L.) targeted at low-input, stress environment, barley lines were selected for high yield under stress (YS), high yield under non-stress (YNS), or average yield in stress and non-stress conditions (YA) during three breeding cycles (cohorts) of three years each. The lines were then tested in a total of 21 year-location combinations with average grain yields ranging from 0.35 to 4.86 t ha^-1. Yield under stress of the YS lines was between 27% and 54% higher than that of the YNS lines, with the top YS lines yielding under stress between 16% and 30% more than the top YNS lines. Realized heritability was between 0.35 and 0.67 when selection was conducted under stress and was significant in all three cohorts. By contrast, selection under non-stress gave a significant response in only one cohort, and its efficiency in improving yield under stress was significantly lower than selection under stress. The best YNS line ranked only 19th for yield under stress. The highest-yielding lines under stress were not only selected under stress, but were also landraces collected in very dry areas (< 250 mm total annual rainfall). This confirms earlier findings and supports the idea that the most effective way to improve productivity of crops grown in less-favored areas is to use locally adapted germplasm and select in the target environment(s). This revised version was published online in July 2006 with corrections to the Cover Date.     

Validating molecular markers for barley leaf rust resistance genes Rph5 and Rph7

Leaf rust, caused by Puccinia hordei , is a serious threat to barley ( Hordeum vulgare L.) production. Genes Rph5 and Rph7 confer resistance to many of the most prevalent races of P. hordei in the United States and Europe, respectively. The reliability and diagnostic capabilities of several molecular markers for these two genes were evaluated and validated for use in gene postulation, marker-assisted selection (MAS) and eventual pyramiding of genes Rph5 and Rph7 with other effective resistance genes. Fifty-eight winter barley experimental lines developed at Virginia Polytechnic Institute and State University, as well as seven barley cultivars were phenotyped for reaction to three diverse isolates of P. hordei and genotyped with molecular makers closely linked to genes Rph5 and Rph7 . Sequence tagged site markers TC2863-12.4 and ABG70 as well as simple sequence repeat marker AY642926-CA11 were reliable and diagnostic in gene postulation and have potential for use in MAS and pyramiding of genes Rph5 and Rph7 . Comparison of phenotypic and genotypic data revealed that one barley line VA04H-95 has genes Rph5 and Rph7 and at least one unknown gene.     

Predicting breeding values of spring barley accessions by using the singular value decomposition of genetic similarities

As pedigree information among parental lines is often incomplete, selection response can be enhanced if a matrix containing genetic similarities is used in the mixed model equations (MME) to predict breeding values. However, a low number of molecular markers may cause this matrix to be singular. This study was conducted to determine if breeding values are still accurate when a singular value decomposition of genetic similarities was performed setting negative singular values to zero. Two‐year data for four traits of 152 spring barley accessions, which were analyzed by 23 SSR markers, were used in the prediction of breeding values. In general, similar values of Akaike Information Criteria and of overall standard error of difference and a Spearman rank correlation coefficient between breeding values ranging from 0.92 to 0.99 were obtained independent of whether the prediction was based on a singular value decomposition of genetic similarities or not. In conclusion, the singular value decomposition of genetic similarities appears to be a suitable method in the case of singular matrices.     

Repetitive cycling and simple recurrent selection in traditional barley breeding programs

Summary A critical examination of three representative barley development programs from three barley producing areas of the world reveals that the evolution of each can be explained by the concepts of simple or phenotypic recurrent selection. Typically, each has utilized only 13 to 16 separate genetic sources in their program. Most of the sources were introduced over 50 years ago and have been progressively recombined through a simple recurrent selection process. The time period required for selection, testing, and reincorporation of improved genetic recombinants into the breeding program, or the completion of a cycle of recurrent selection, ranged from 6.5 to 10.5 years. If the major operative force in barley breeding is recurrent selection, then additional attention should be given to increasing the genetic base and reducing the time required to complete cycles of selection.     

Mapping of a gene for leaf scald resistance in barley line 'B87/14' and validation of microsatellite and RFLP markers for marker-assisted selection

Seedlings of the barley line ‘B87/14’ were resistant to 22 out of 23 Australian isolates of Rhynchosporium secalis, the causal agent of leaf scald.‘B87/14’‐based populations were developed to determine the location of the resistance locus. Scald resistance segregated as a single dominant trait in BC₁F₂ and BC₁F₃ populations. Bulked segregant analysis identified amplified fragment length polymorphisms (AFLPs) with close linkage to the resistance locus. Fully mapped populations not segregating for scald resistance located these AFLP markers on chromosome 3H, possibly within the complex Rrs1 scald locus. Microsatellite and restriction fragment length polymorphism markers adjacent to the AFLP markers were identified and validated for their linkage to scald resistance in a second segregating population, with the closest marker 2.2 cM from the resistance locus. These markers can be used for selection of the Rrs.B87 scald‐resistance locus, and other genes at the chromosome 3H Rrs1 locus.     

Evaluation of quantitative resistance to yellow rust (Puccinia striiformis f. sp. hordei) in the ICARDA/CIMMYT barley breeding programme

The resistance to yellow rust (Puccinia striiformis f. sp. hordei) of 500 advanced barley lines from the ICARDA/CIMMYT breeding programme in Mexico was evaluated on seedlings in the greenhouse and on adult plants in the field. A high frequency of advanced lines (85.8%) showed a susceptible reaction (infection type ≥ 7) on seedlings after inoculation with isolate Mex-1, representing a Mexican variant of race 24. This indicates the absence of effective hypersensitive resistance. In addition, the same advanced lines showed a large variation in disease severity in the field, ranging from 0 to 95%. More than 76% of the advanced lines with a susceptible reaction in the seedling stage demonstrated low disease severity (10% or less in the adult plant). Consequently, these advanced lines possess high levels of quantitative resistance. Two aspects in the ICARDA/CIMMYT barley breeding programme may explain the large number of advanced lines with high levels of quantitative resistance. First, a recurrent selection approach is applied when advanced (F₅) lines reaching homozygosity are intercrossed. Second, low levels of disease are accepted in the selection process instead of selecting the ultimate green plant. Both aspects combined allow the accumulation of quantitative resistance. Certain cultivars released from South-American national programmes in the late 1970s and early 1980s in Peru (UNA-80), Bolivia (IBTA 80) and Ecuador (Teran) are still resistant, demonstrating the durable nature of quantitative resistance to yellow rust.     

Effects of selection and opportunities for recombination in doubled-haploid populations of barley (Hordeum vulgare L.)

Doubled-haploid breeding systems are typically based on sampling gametes from F₁ plants. However, in the case of repulsion linkages, additional recombination could be advantageous. Pre-selection of gamete donors might also shift progeny performance in a desired direction. The objectives of this study were to quantify the effects of an additional round of recombination and assess the effectiveness of pre-anthesis selection in the production of barley doubled haploids. Assessments were conducted on: 1. 100 F₁-derived lines representing a subset of lines used in previous genome-mapping studies; 2. 100 random F₂-derived lines; and 3. 50 F₂-derived lines from gamete donors selected for early heading. An additional round of recombination had only a modest effect on generating more favourable genotypes. Pre-anthesis selection was ineffective in generating an earlier heading population. According to published quantitative-trait locus (QTL) analyses based on the F₁ -derived population, there are few repulsion linkages between QTL determining the traits measured in this experiment. Any advantages to be gained from postponing the generation of derivation of doubled haploids must be weighed against the delay and additional cost.     

Development of EST‐SSR markers for diversity and breeding studies in opium poppy

All publicly available opium poppy expressed sequence tag (EST) sequences, totalling 20 885, were assembled into unigenes and examined for simple sequence repeats (SSRs). Nearly 19% of the 14 957 unigenes contained SSRs with 4% harbouring more than one SSR. Average density of the SSRs was 1 SSR per 3.6 kb of non‐redundant EST sequence. Trinucleotide SSRs were most frequently identified (39%), and many of the most prevalent motifs were AT‐rich. Flanking primers were designed for 86% of the SSRs and 67 primer pairs were tested on 37 opium poppy accessions and seven related species. All markers were transferable to the related species. Polymorphism information content (PIC) values for the markers were intermediate for comparisons within opium poppy (average of 0.27) and slightly higher for comparisons across species (average of 0.29). The markers were found to be useful for diversity analysis as they successfully distinguished among Turkish opium poppy accessions and land races.     

Postulation of leaf-rust resistance genes in Czech and Slovak barley cultivars and breeding lines

Leaf‐rust resistance (Rph) genes in 61 Czech and Slovak barley cultivars and 32 breeding lines from registration trials of the Czech Republic were postulated based on their reaction to 12 isolates of Puccinia hordei with different combinations of virulence genes. Five known Rph genes (Rph2, Rph3, Rph4, Rph7, and Rph12) and one unknown Rph gene were postulated to be present in this germplasm. To corroborate this result, the pedigree of the barley accessions was analysed. Gene Rph2, as well as Rph4, originated from old European cultivars. The donor of Rph3, which has been mainly used by Czech and Slovak breeders, is ‘Ribari’ (‘Baladi 16’). Rph12 originates from barley cultivars developed in the former East Germany. Rph7 in the registered cultivar ‘Heris’ originates from ‘Forrajera’. A combination of two genes was found in 10 cultivars. Nine heterogeneous cultivars were identified; they were composed of one component with an identified Rph gene and a second component without any resistance gene. No gene for leaf rust resistance was found in 17 of the accessions tested. This study demonstrates the utility of using selected pathotypes of P. hordei for postulating Rph genes in barley.     

RFLP diversity within and between major groups of barley in Europe

Restriction fragment length polymorphism (RFLP) diversity has been determined and analyzed as expressed by 33 single‐ or low‐copy clone/ enzyme combinations at 32 loci distributed over all chromosomes of the barley genome within a sample of 223 European barley accessions comprised of pure line (single‐head progenies) genotypes. The accessions have been selected to include landraces and widely grown cultivars derived from crossbreeding during the 20th century in North‐, West‐ and Central European countries. Genetic diversity obtained from 83 alleles across all accessions is characterized by the diversity index H = 0.385. The diversity indices determined for landraces and cultivars were almost equal, with the difference between spring (H = 0.260) and winter (H = 0.415) barley approaching statistical significance, while comparisons of other groupings only revealed statistically insignificant trends. A more detailed analysis based on differences in allele frequency distributions at each locus (clone/enzyme combinations resp.) revealed very clear differences related to the existence, continuity and dynamics of changes in group‐specific RFLP profiles. With the majority (69%) of RFLP alleles at 23 out of 32 loci on all barley chromosomes involved, contributions from chromosomes 1H, 3H, 4H and 5H seem to be of special importance. Differences in the overall average of abundance indicate higher levels of genetic diversity within both groups of winter barley compared with both groups of spring barley, from which the most frequent alleles at 15 (2‐rowed spring barley) and 17 (6‐rowed spring barley) RFLP loci approach fixation. The results of this study are discussed in relation to the history of barley cultivation and barley breeding in Europe, and possible explanations for group‐specific differences in the RFLP profiles of landraces and cultivars as well as for the high levels of (nearly) fixed alleles of both subsets of spring barley, and with respect to progress in barley breeding that it has been possible to obtain within the rather narrow RFLP profiles.     

Genetic diversity of barley cultivars grown in Spain, estimated by RFLP, similarity and coancestry coefficients

This study was conducted with the objective of characterizing the genetic variation among a representative set of 37 barley cultivars currently grown in Spain, using restriction fragment length polymorphism (RFLP) markers. Thirty-two RFLP probes, in combination with three restriction enzymes, were used to analyse polymorphism at the molecular level. Genetic distances (GD), based on RFLP band patterns, and coancestry coefficients (f), based on pedigree records, were calculated. Of the 95 clone-enzyme combinations analysed, 71 (74.7%) were polymorphic, representing 246 RFLP patterns. A cluster analysis of GD split the sample into five distinct germplasm groups that were consistent with the history of the cultivars (winter European, spring European, CIMMYT-ICARDA materials, the single cultivar ‘Dobla’ and Spanish local materials). The Spanish group was the most distinct one and had unique alleles at markers close to major loci determining phonological adaptation. The probes which best distinguished among groups were also identified. Genetic similarity estimates were moderately consistent with f (for cultivars with complete pedigrees). The implications for integration of diversity studies into breeding programmes are discussed.     

Potential for effective marker-assisted selection of three quantitative trait loci conferring adult plant resistance to powdery mildew in elite wheat breeding populations

Three quantitative trait loci (QTL) associated with adult plant resistance (APR) to powdery mildew (Blumeria graminis) in wheat (Triticum aestivum) cultivar ‘Massey’ were mapped in a previous study. The three QTL were located on chromosomes 2A, 2B and 1B, and explained 50% of the total phenotypic variation. A 293 recombinant inbred line (RIL) breeding population (UJ) derived from the cross of ‘USG 3209’, a derivative of ‘Massey’, and ‘Jaypee’ was used to evaluate the potential effectiveness of marker‐assisted selection (MAS) for APR. Powdery mildew severities of the 293 UJ RILs were evaluated in 2002 (F_{5 : 6}) and 2003 (F_{6 : 7}) under natural disease pressure in the field. The 293 RILs were also evaluated for disease severity in a 2004 (F_{7 : 8}) greenhouse experiment using a composite of five different isolates of B. graminis. Selection of RILs possessing the QTL on chromosome 2A, and to a lesser extent, the one on chromosome 1B was effective in identifying powdery mildew resistance in both greenhouse and field experiments. Overall, selecting RILs with QTL on chromosomes 2A and 2B was most successful in identifying highly resistant RILs, which had mean mildew severities of 4.4% and 3.2% in 2002 and 2003 field experiments, respectively. Breeders implementing MAS programs for APR to powdery mildew via selection of RILs containing the two QTL on chromosomes 2A and 2B likely will obtain RILs having high levels of resistance in the field, however combining all three QTL may ensure greater durability.     

Development of an STS marker and SSRs suitable for marker-assisted selection for the BaMMV resistance gene rym9 in barley

Based on the RAPD marker OP‐C04H910 which is closely linked to the barley mild mosaic virus (BaMMV) resistance gene rym9 derived from the variety ‘Bulgarian 347’ the marker STS‐C04H910 cosegregating with OP‐C04H910 and generating a single additional band on plants carrying the recessive resistance encoding allele has been developed. Furthermore, the simple sequence repeats (SSRs) WMS6 and HVM67 have been integrated into the genetic map of the rym9 region on chromosome 4HL. Because of their close linkage to rym9 and distinct banding pattern STS‐C04H910 and HVM67 are well‐suited for marker‐ assisted selection, enhanced backcrossing procedures and pyramiding of resistance genes.     

Relationship between phenotypic and genetic diversity of parental genotypes and the frequency of transgression effects in barley (Hordeum vulgare L.)

The aim of the study was to evaluate the relationship between genetic and phenotypic distances of parents and the genetic potential of crosses as measured by the frequency of transgressive segregants in homozygous populations. Material for the study involved 17 barley cross‐combinations. In each cross, the parental genotypes, F₂ hybrids and doubled haploid (DH) lines were analysed. Yield and yield‐related traits were observed in the experiments. Phenotypic (univariate and multivariate) and genetic distances (GD) were investigated between pairs of parental genotypes. Genetic distance was evaluated by using random amplified polymorphic DNA markers. In F₂ generations, the genetic coefficient of variability (GCV) was evaluated. Within all the cross‐combinations studied, each DH line was compared with both parents to distinguish the positive and negative transgressive lines. In addition, the coefficient of gene distribution (r) along parental genomes was evaluated. Relationships between frequency of transgression and both phenotypic and GDs, GCV and r, were assessed by regression analysis. It was found that for all the traits studied the frequency of transgressive lines depended mainly on gene distribution (r). Genetic distance between parents appeared to be significant for the occurrence of transgression effects in plant height, ear length, grain weight per ear and grain yield per plot. Regression analysis has shown that phenotypic differences between parental genotypes were also important for the frequency of transgressive lines. A weak relationship was found between the variation of F₂ hybrids and the occurrence of transgressive lines. The results indicate that occurrence of transgressive segregants in a homozygous population should be considered as a phenomenon dependent simultaneously on several factors characterizing parental genotypes. Among them, the most important are: gene distribution, phenotypic diversity and GD.     

山东省玉米骨干自交系和杂交种的SSR指纹图谱构建

构建骨干品种（系）指纹图谱,可为新品种的审定和品种保护建立准确可靠的依据,也是适应玉米育种快速发展的需要。分别利用74对SSR引物对35份骨干自交系和19份主栽杂交种进行了SSR分析。筛选出10对和20对适于玉米自交系和杂交种分析的核心引物,分别检测出115和124个等位变异,将扩增条带数字化,构建了自交系和杂交种的指纹图谱,出现相同指纹图谱的概率分别为3.13×10-11和5.59×10-25。构建的指纹图谱用于玉米品种鉴定是可行的,对玉米新品种审定和品种权保护具有重要意义。     

The evaluation of superior Hordeum bulbosum L. genotypes for use in a doubled haploid barley breeding programme

Summary Eight Hordeum bulbosum selections were produced from a cross between Cb 2920/4 and Cb 2929/1, two genotypes widely used in doubled haploid breeding programmes. The selections were hybridized with barley to evaluate their ability to produce high proportions of well-differentiated haploid embryos compared with Cb 2929/1 as control. We report here an initial small-scale investigation followed by a larger-scale test in two different environments to assess seed setting, haploid embryo differentiation rates and VB hybrid formation. These VB embryos contain both parental sets of chromosomes and occur more frequently in the glasshouse during the winter. Two of the eight selections were identified as combining the desirable characteristics of both parents, namely high seed setting on cv. Vada which is partially incompatible with H. bulbosum, large numbers of well-differentiated haploid embryos and a low incidence of VB hybrids. The selections are available for release to interested research workers and plant breedersAbbreviations DH doubled haploid - VB a hybrid from H. vulgare x H. bulbosum which contains both parental sets of chromosomes