Applications of pedigree-based genome mapping in wheat and barley breeding programs

The aim of the pedigree-based genome mapping project is to investigate and develop systems for implementing marker assisted selection to improve the efficiency of selection and increase the rate of genetic gain in breeding programs. Pedigree-based whole genome marker application provides a vehicle for incorporating marker technologies into applied breeding programs by bridging the gap between marker–trait association and marker implementation. We report on the development of protocols for implementation of pedigree-based whole genome marker analysis in breeding programs within the Australian northern winter cereals region. Examples of applications from the Queensland DPI&F wheat and barley breeding programs are provided, commenting on the use of microsatellites and other types of molecular markers for routine genomic analysis, the integration of genotypic, phenotypic and pedigree information for targeted wheat and barley lines, the genomic impacts of strong selection pressure in case study pedigrees, and directions for future pedigree-based marker development and analysis.     

Molecular mapping of powdery mildew resistance genes in wheat: A review

Powdery mildew, caused by Blumeria graminis f. sp. tritici (syn. Erysiphe graminis f. sp. tritici), is one of the most important diseases of common wheat (Triticum aestivum L.) worldwide. Molecular mapping and cloning of genes for resistance to powdery mildew in hexaploid wheat will facilitate the study of molecular mechanisms underlying resistance to powdery mildew diseases and help understand the structure and function of powdery mildew resistance genes, and permit marker-assisted selection in breeding programs. So far, 48 genes/alleles for resistance to powdery mildew at 32 loci have been identified and located on 16 different chromosomes, of which 21 resistance genes/alleles have been tagged by restriction fragment length polymorphisms (RFLPs), random-amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), sequence characterized amplified regions (SCARs), sequence-tagged sites (STS) or simple sequence repeats (SSRs). Several quantitative trait loci (QTLs) for adult plant resistance (APR) to powdery mildew have been associated with molecular markers. The detailed information on chromosomal location and molecular mapping of these genes has been reviewed. Isolation of powdery mildew resistance genes and development of valid molecular markers for pyramiding resistance genes in breeding programs is also discussed.     

A skeletal linkage map of Hordeum bulbosum L. and comparative mapping with barley (H. vulgare L.)

A restriction fragment length polymorphism (RFLP) based linkage map of a cross between two diploid Hordeum bulbosum (2n = 2x = 14) clones, PB1 and PB11, was constructed from 46 recombinant progeny clones. Since both parents are heterozygous, separate and combined parental maps were constructed. All of the RFLP markers screened had previously been mapped in barley (H. vulgare L.) so that comparative maps could be produced. The PB1 linkage map consists of 20 RFLP marker loci assigned to four linkage groups covering 94.3 cM. The PB11 linkage map consists of 27 RFLP marker loci assigned to six linkage groups covering 149.1 cM. Thirteen markers polymorphic in both parents were used as ‘anchors’ to create a combined linkage map consisting of 38 loci assigned to six linkage groups and covering a genetic distance of 198 cM. Marker order was highly conserved in a comparison with the linkage map of H. vulgare (Laurie etal., 1995). However, in contrast, the genetic distances for the same markers were very different being 649 cM and 198 cM respectively, a genetic distance ratio of 1: 3.3. Thus although the map was short, it can be presumed to cover half the genome of H. bulbosum. This study provides further confirmation of the close relationship between the two species and gives a basis for the development of marker mediated introgression through interspecific hybridisation between the two species. This revised version was published online in July 2006 with corrections to the Cover Date.     

Spectrum of resistance conferred by ML-O powdery mildew resistance genes in barley

Summary Ten barley mutants and five Ethiopian barley lines representing 11 independently arisen powdery mildew resistance genes in the ml-o locus were tested at the seedling stage to cultures of the powdery mildew fungus from Europe, Israel, USA. Canada, and Japan. They were resistant with infection type 0/(4) in all tests. They were also resistant to field populations of the pathogen when scored in disease nurseries at more than 78 locations in 29 countries in Europe, the Near East, North and South America. New Zealand, and Japan. This indicates that the 11 genes confer the same, world-wide spectrum of powdery mildew resistance. They have no effect on several other barley diseases such as stripe rust and leaf rust.Part of the research reported here was carried out under IAEA Research Agreement No 1043 and Research Contract No 139-74-1 BIO DK with the European Atomic Energy Community.     

Conservation of powdery mildew resistance genes in three composite cross populations of barley

Summary Barley powdery mildew was used as a model to evaluate the potential of barley composite cross populations for conservation of disease resistance. The objective was to determine if increases in resistance to powdery mildew could be detected over periods of time in composite cross populations developed in California, where the disease might have had a selective influence on the populations, and the same populations grown in Montana, where no selective influence of powdery mildew was expected. Four isolates of Erysiphe graminis f. sp. hordei were used to monitor the frequencies of plants with specific mildew resistances through early, intermediate and late generations of three composite cross populations (CCII, CCV, CCXII) grown at Davis, California, and Bozeman and Moccasin, Montana. Changes in frequencies of plants resistant to the four isolates were observed between generations in all populations from the three locations. Trends in the frequencies of resistance are discussed in relation to selection pressure applied by E. graminis. It is suggested that associations with gene complexes other than resistance to E. graminis might help to explain the increased resistance observed in these studies.This research was funded in part by U.S. Agency for International Development Contract No. AID/DSAN-C-0024. The authors are grateful to Dr A. L. Kahler for seed of the composite cross populations and to Dr J. G. Moseman for the powdery mildew cultures.Cooperative investigations of the Agricultural Research Service, U.S. Department of Agriculture; the Department of Plant Pathology, Montana State University; and The Montana Agricultural Experiment Station. Journal Series Paper No. 1381 of the Montana Agricultural Experiment Station.     

Tracing sources of dwarfing genes in barley breeding in China

To study the origin ofdwarfing genes used in barley breeding inChina, pedigree data of more than 350 dwarfand semi-dwarf cultivars and entriesdeveloped since 1950 were collected. Theresults showed that 68.4% of them werederivatives of just six accessions:`Chibadamai' (CBDM), `Xiaoshanlixiahuang'(XSLXH), `Cangzhouluodamai' (CZLDM),`Aiganqi' (AGQ), `Zhepi 1' and `Yanfu Aizao3' (YFAZ 3). Therefore, these sixaccessions are considered the main donorsof dwarfing genes to barley cultivars bredin China. `CBDM', `XSLXH' and `CZLDM' arelandraces and were used between 1950 and1980. `AGQ', `Zhepi 1' and `YFAZ 3' arereleased cultivars used since 1980. `CBDM',`XSLXH', `CZLDM' and `AGQ' carry the samedwarfing gene uzu on chromosome arm3HL. `Zhepi 1' and `YFAZ 3' likely aremutations at the sdw 1 locus.     

Aluminum tolerance in barley: Methods for screening and genetic analysis

Aluminum (Al) tolerance in roots of two cultivars of barley was studied using hematoxylin staining and root re-growth procedures. This study was performed in two F₂ segregating populations originated from crosses between the tolerant FM-404 and sensitive Harrington cultivars. The F₂ progeny analysed with hematoxylin staining revealed a segregation ratio of 3 tolerant: 1 sensitive, showing that the Al tolerance is controlled by a single gene with complete dominance for tolerance. The root re-growth measures do not confirm the 3:1 ratio. This last result can be explained due to the occurrence of genes that affect root growth rate or to the difficulties found in the evaluation of root re-growth. Barley has a complex root system, which makes it difficult to measure root re-growth after an extended period in nutrient solution. Due to the simplicity, reliability and better precision, the hematoxylin staining is the best procedure to determine the Al tolerance and its inheritance in barley. This revised version was published online in August 2006 with corrections to the Cover Date.     

Identification of genes for resistance to Puccinia striiformis f. sp. hordei in 18 barley genotypes

Barley genotypes Hor 1428, Hor 2926, Hor 3209, BBA 2890, Abyssinian 14, Grannelose Zweizeilige, and Stauffers Obersulzer are resistant to all races of Puccinia striiformis f. sp. hordei so far detected in the U.S.A. Heils Franken, Cambrinus, Astrix, Emir, Hiproly, Varunda, Trumpf,Mazurka, Bigo, BBA 2890, and I 5 are resistant to some races and susceptible to others. Previous studies showed that Hor 1428, Hor 2926, Hor 3209, Abyssinian 14, Stauffers Obersulzer, I 5, Heils Franken, Emir, Astrix, Hiproly, Varunda, and Trumpf each have two genes, and BBA 2890, Grannelose Zweizeilige, Cambrinus, Mazurka, Bigo, and BBA 809 each have a single genefor resistance. To determine the genes in specific genotypes and their relationships, all possible crosses were made among the 18 genotypes. Seedlings of parents and F₂ progeny were tested under controlledconditions for resistance to selected races that were avirulent on both parents. Based on segregation within the individual crosses to selected races, at least 26 of 30 genes detected in the 18 genotypes were different. Allelic and linkage relationships of some of the genes were determined. The genetic information should be useful for understanding the host-pathogen interactions and for control of stripe rust using resistance.     

Verifying the genetic relationships between three leaf rust resistance genes in barley

Summary The genetic relationships between three known genes for resistance to Puccinia hordei in barley, Pa 3, Pa5 and Pa 7, were re-examined because of conflicting reports in the literature. PA 3 was found to be independent of Pa 5 and Pa 7, but the latter two are linked with an estimated recombination value of 7.6±1.4%. Trisomic analysis confirmed Pa 7 to be on chromosome 3, but Pa 3 could not be associated with chromosomes 3 to 7 and, therefore, is inferred to be either on chromosome 1 or 2     

Molecular mapping of the brace root traits in sorghum (Sorghum bicolor L. Moench)

The presence and morphology of plant brace roots are important root architecture traits. Brace roots contribute significantly to effective anchorage and water and nutrient uptake during late growth and development, and more importantly, have a substantial influence on grain yield under soil flooding or water limited conditions. However, little is known about the genetic mechanisms that underlie brace root traits. In this study, quantitative trait loci (QTLs) for presence of brace roots from the sorghum landrace “Sansui” were mapped and associated molecular markers were identified. A linkage map was constructed with 109 assigned simple sequence repeat markers using a F₂ mapping population derived from the cross Sansui/Jiliang 2. Two QTLs associated with presence of brace roots were localized on chromosomes 6 and 7. The major QTL on chromosome 7 between markers Dsenhsbm7 and Xcup 70 explained about 52.5% of the phenotypic variation, and the minor QTL on chromosome 6 was flanked by Xtxp127 and Xtxp6 and accounted for 7.0% of phenotypic variation. These results will provide information for the improvement of sorghum root architecture associated with brace roots.     

Molecular assessment of genetic diversity in winter barley and its use in breeding

Summary During the last decades extensive progress has been achieved in winter barley breeding with respect to both, yield and resistance to fungal and viral diseases. This progress is mainly due to the efficient use of the genetic diversity present within high yielding adapted cultivars and – with respect to resistance – to the extensive evaluation of genetic resources followed by genetic analyses and introgression of respective genes by sexual recombination. Detailed knowledge on genetic diversity present on the molecular level regarding specific traits as well as on the whole genome level may enhance barley breeding today by facilitating efficient selection of parental lines and marker assisted selection procedures. In the present paper the state of the art with respect to virus diseases, i.e. Barley mild mosaic virus, Barley yellow mosaic virus, and Barley yellow dwarf virus is briefly reviewed and first results on a project aiming on a genome wide estimation of genetic diversity which in combination with data on yield and additional agronomic traits may facilitate the detection of marker trait associations and a more efficient selection of parental genotypes are presented. By field tests of 49 two-rowed and 64 six-rowed winter barley cultivars the genetic gain in yield for the period 1970–2003 was estimated at 54.6 kg ha⁻¹ year⁻¹ (r² = 0.567) for the six-rowed cultivars and at 37.5 kg ha⁻¹ year⁻¹ (r² = 0.621) for the two-rowed cultivars. Analysis of 30 SSRs revealed a non-homogenous allele distribution between two and six-rowed cultivars and changes of allele frequencies in relation to the time of release. By PCoA a separation between two and six-rowed cultivars was observed but no clear cut differentiation in relation to the time of release. In the two-rowed cultivars an increase in genetic diversity (DI) from older to newly released cultivars was detected.     

New molecular markers linked to qualitative and quantitative powdery mildew and scald resistance genes in barley for dry areas

A partial genetic linkage map was constructed on 71 doubled-haploid lines derived from a cross between the barley lines Tadmor and WI2291 with 181 molecular markers. The segregating population was used to detect markers linked to the gene Mlg conferring resistance to powdery mildew (Erysiphe graminis f. sp. hordei) and to genes for quantitative resistance to scald (Rhynchosporium secalis). The gene Mlg on chromosome 4H was flanked by two AFLP markers at a distance of 2.0 and 2.4 cM, respectively. QTLs for resistance to scald were detected on chromosomes 2H and 3H. This association of molecular markers with qualitative and quantitative disease resistance loci represents a valuable starting-point for marker-assisted selection. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular mapping of S-c, an F1 pollen sterility gene in cultivated rice

Hybrids between indica and japonica rice varieties usually show partial sterility, and are a major limiting factor in the utilization of heterosis at subspecific level. When studying male-gamete (pollen) abortion, a possibly important cause for sterility, six loci (S-a, S-b, S-c, S-d, S-e and S-f) for F₁ pollen sterility were identified. Here we report genetic and linkage analysis of S-c locus using molecular markers in a cross between Taichung 65, a japonica variety carrying allele S-c ^j, and its isogenic line TISL5, carrying alleleS-c ^j. Our results show that pollen sterility occurring in the hybrids is controlled by one locus. We used 208 RFLP markers, as well as 500 RAPD primers, to survey the polymorphism between Taichung 65 and TISL5. Six RFLP markers located on a small region of chromosome 3, detected different RFLP patterns. Co-segregation analysis of fertility and RFLP patterns with 123 F₂ plants confirmed that the markers RG227, RG391, R1420 were completely linked with the S-c locus. The genetic distances between the markers C730, RG166 and RG369 and the S-c locus were 0.5 cM, 3.4 cM, and 3.4 cM respectively. Distorted F₂ ratios were also observed for these 4 RFLP markers in the cross. This result suggests that the `one locus sporo-gametophytic' model could explain F₁ hybrid pollen sterility in cultivated rice. RG227, the completely linked marker, has been converted to STS marker for marker-assisted selection. This revised version was published online in August 2006 with corrections to the Cover Date.     

Molecular mapping of genes determining hairy leaf character in common wheat with respect to other species of the Triticeae

Two major genes controlling leaf pubescence were mapped on chromosomes 4BL (Hl1) and 7BS (Hl2 ^Aesp ) in wheat (Saratovskaya 29) and a wheat/Aegilops introgression line (102/00^I), respectively, together with quantitative trait loci (QTLs) determining hairiness of the leaf margin (QHl.ipk-4B, QHl.ipk-4D) and auricle (QPa.ipk-4B, QPa.ipk-4D) on the long arms of chromosomes 4B and 4D, respectively. The QTLs on chromosome 4D were contributed by a synthetic wheat and, therefore, originated from Aegilops tauschii. The homoeologous group 4 wheat/A. tauschii genes/QTLs detected in the present study were aligned with the barley pubescence genes Hln/Hsh and Hs _b and the hairy peduncle rye gene Hp1. The locus seems to be pleiotropically responsible for the pubescence of different plant organs in different species of the Triticeae. Another homoeologous series may be present on the short arms of the homoeologous group 7 chromosomes, based on the results of an allelic test cross between the Chinese local cultivar Hong-mang-mai carrying Hl2 and the wheat/Aegilops speltoides introgression line 102/00^I.     

Ethrel-a male gametocide that can replace the male sterility genes in barley

Summary The use of ethrel for hand crossing in recurrent selection programs with barley is advocated.     

SSR-based genetic diversity assessment among Tunisian winter barley and relationship with morphological traits

For studying genetic diversity caused byselection for adaptation and end-use, 17microsatellites (SSR), representative ofthe barley genome, were used in 26 barley(Hordeum vulgare L.) accessions andcultivars in Tunisia. Theaccessions/cultivars originate fromdifferent geographic regions and are ofdifferent end-use. For the 15 polymorphicSSR, the mean number of alleles per locuswas 3.6 and the average polymorphisminformation content was 0.45. Clusteranalysis based on SSR data and onmorphological data clearly differentiatethe genotypes according to their type(local landraces vs. varieties), row-numberand end-use. The correlation between bothdiversity measures was highly significant(r = 0.25, p<10^-5) and thecorrespondence between the clustering basedon SSR and morphological data wasrelatively good. Our results show the largegenetic diversity of the Tunisian barleycultivars and the association of thisdiversity with adaptation traits.     

Molecular mapping of QTLs for non-parasitic leaf spot resistance and comparison of half-sib DH populations in spring barley

Quantitative trait loci (QTLs) for resistance against non-parasitic leaf spots (NPLS) were first characterized in a spring barley double haploid population derived from the cross IPZ 24727/Barke (Behn et al., 2004). The aim of the present study was to identify QTLs for NPLS resistance in the half-sibling DH population IPZ 24727/Krona and to compare them with the QTLs of the population IPZ 24727/Barke. An anther culture-derived doubled haploid population of 536 DH lines was developed from the cross IPZ 24727 (resistant)/Krona (susceptible). Field trials were performed over two years in two replications, scoring NPLS and agronomic traits that might interact with NPLS. A molecular linkage map of 1035 cM was constructed based on AFLPs, SSRs and the mlo marker. QTL analyses for NPLS identified three QTLs that accounted for 30% of the phenotypic variation. For comparison of the QTLs from each DH population, a consensus map was generated comprising 277 markers with a length of 1199 cM. In both populations, the QTLs for NPLS mapped to chromosomes 1H, 4H and 7H. A common QTL with a great effect in both populations and over all environments was localized at the mlo locus on chromosome 4H, indicating that the mlo powdery mildew resistance locus has a considerable effect on NPLS susceptibility. The steps necessary to validate the QTLs and to improve the NPLS resistance by breeding were discussed.     

Selection environment and environmental sensitivity in barley

Summary Groups of 10 barley genotypes were selected for high grain yield under either high yielding (two groups) or low yielding conditions (two groups). The genotypes had a similar average grain yield across a wide range of yielding conditions, but differed in their linear response over environments (environmental sensitivity). The genotypes selected for high grain yield under low yielding conditions were less sensitive to changing environments than genotypes selected for high grain yield under high yielding conditions. The higher stability of genotypes selected under low yielding conditions was shown by both the linear regression analysis and the comparison of coefficients of variation. The use of a safety-first index showed that the probability of a crop failure of genotypes selected for high grain yield under high yielding conditions was between 1.8 and 2.7 times higher than for genotypes selected for high grain yield under low yielding conditions. The development of new cultivars for areas where a large proportion of the crop is grown by subsistence farmers should therefore be based on selection under low yielding conditions.     

Molecular adaptation of barley to cold and drought conditions

Summary Molecular adaptation to cold and drought involves a series of biochemical and molecular changes leading plants to improve their winter hardiness or drought resistance.We are interested to study the molecular basis of cold acclimation and drought response of barley to survive under stress. Several genes regulated by low temperatures and sometimes by drought have been isolated from the barley genome. In this review the most significant results of our recent work will be presented and discussed.The protein encoded by cDNA clone pt59 and induced in barley by cold was over-expressed in E. coli to produce the matching antibody, which in vivo recognizes a cold-induced protein of 14 kDa (COR14). The COR14 is stored in amounts only slightly greater in the cold resistant Onice than in the susceptible Gitane, although the former has a higher induction-temperature threshold of COR14 than the latter. This fact is an evolutionary advantage enabling the resistant varieties in the field to prepare for the cold well ahead of the susceptible ones.Two other cDNA clones, paf93 and cdr29, are regulated by low temperature and drought stress but not by exogenous ABA treatment. Indeed during the early stage of dehydration, the mRNAs are expressed before the induction of known ABA regulated genes such as dehydrins and when only a small increase occurs in ABA content. The sequence analysis revealed that paf93 encodes for a protein homologous to the cold-regulated protein COR47 of Arabidopsis, whereas cdr29 represents a plant gene homologous to yeast and mammalian sequences coding for acyl-Coenzyme A oxidase.Abbreviations ABA abscisic acid - COR cold regulated     

Genotypic variation in polyphenol content of barley grain

The polyphenol content in pearl barley, which is highly correlated to a browning reaction after heat treatment, was investigated using 1,347 cultivated barley varieties (H. vulgare) and two wild accessions (H. vulgare subsp. spontaneum) collected from different areas of the world. The polyphenol content in the cultivated barley shows a wide variation ranging from 0.19 to 0.75 mg/g with a nearly normal frequency distribution. The polyphenol content in the hulless varieties from Japan and Korea was low. On the other hand, the polyphenol content in wild barley was about two times higher than the average value recorded in cultivated barley. Based on HPLC analysis, five lowest-polyphenol content local varieties do not represent proanthocyanidin-free mutants. This revised version was published online in August 2006 with corrections to the Cover Date.