Curation of wheat maps to improve map accuracy and QTL detection

Three Australian doubled haploid populations were used to illustrate the importance of map curation in order to improve the quality of linkage maps and quantative trait locus (QTL) detection. The maps were refined and improved by re-examining the order of markers, inspection of the genetic maps in relation to a consensus map, editing the marker data for double crossovers, and determining estimated recombination fractions for all pairs of markers. The re-ordering of markers and replacing genotypes at double crossovers with missing values resulted in an overall decrease in the length of the maps. Fewer apparent genotyping errors, associated with the presence of double recombinants, were identified with restriction fragment length polymorphisms (RFLPs) than with other types of markers used in this study. The complications that translocations may cause in the ordering of markers and subsequent QTL analysis were investigated. QTL analysis using both the original and revised maps indicated that QTL peaks were more sharply located or had improved log-likelihood (LOD) scores in the revised maps. An accurate indication of the QTL peak and a significant LOD score are both essential for the identification of markers suitable for marker-assisted selection. Recommendations are provided for the improvement of the quality of linkage maps.

A workshop report on wheat genome sequencing: International Genome Research on Wheat Consortium

Sponsored by the National Science Foundation and the U.S. Department of Agriculture, a wheat genome sequencing workshop was held November 10-11, 2003, in Washington, DC. It brought together 63 scientists of diverse research interests and institutions, including 45 from the United States and 18 from a dozen foreign countries (see list of participants at http://www.ksu.edu/igrow). The objectives of the workshop were to discuss the status of wheat genomics, obtain feedback from ongoing genome sequencing projects, and develop strategies for sequencing the wheat genome. The purpose of this report is to convey the information discussed at the workshop and provide the basis for an ongoing dialogue, bringing forth comments and suggestions from the genetics community.

Comparative organization of wheat homoeologous group 3S and 7L using wheat-rice synteny and identification of potential markers for genes controlling xanthophyll content in wheat

EST and genomic DNA sequencing efforts for rice and wheat have provided the basis for interpreting genome organization and evolution. In this study we have used EST and genomic sequencing information and a bioinformatic approach in a two-step strategy to align portions of the wheat and rice genomes. In the first step, wheat ESTs were used to identify rice orthologs and it was shown that wheat 3S and rice 1 contain syntenic units with intrachromosomal rearrangements. Further analysis using anchored rice contiguous sequences and TBLASTX alignments in a second alignment step showed interruptions by orthologous genes that map elsewhere in the wheat genome. This indicates that gene content and order is not as conserved as large chromosomal blocks as previously predicted. Similarly, chromosome 7L contains syntenic units with rice 6 and 8 but is interrupted by combinations of intrachromosomal and interchromosomal rearrangements involving syntenic units and single gene orthologs from other rice chromosome groups. We have used the rice sequence annotations to identify genes that can be used to develop markers linked to biosynthetic pathways on 3BS controlling xanthophyll production in wheat and thus involved in determining flour colour.

Genes controlling seed dormancy and pre-harvest sprouting in a rice-wheat-barley comparison

Pre-harvest sprouting results in significant economic loss for the grain industry around the world. Lack of adequate seed dormancy is the major reason for pre-harvest sprouting in the field under wet weather conditions. Although this trait is governed by multiple genes it is also highly heritable. A major QTL controlling both pre-harvest sprouting and seed dormancy has been identified on the long arm of barley chromosome 5H, and it explains over 70% of the phenotypic variation. Comparative genomics approaches among barley, wheat and rice were used to identify candidate gene(s) controlling seed dormancy and hence one aspect of pre-harvest sprouting. The barley seed dormancy/pre-harvest sprouting QTL was located in a region that showed good synteny with the terminal end of the long arm of rice chromosome 3. The rice DNA sequences were annotated and a gene encoding GA20-oxidase was identified as a candidate gene controlling the seed dormancy/pre-harvest sprouting QTL on 5HL. This chromosomal region also shared synteny with the telomere region of wheat chromosome 4AL, but was located outside of the QTL reported for seed dormancy in wheat. The wheat chromosome 4AL QTL region for seed dormancy was syntenic to both rice chromosome 3 and 11. In both cases, corresponding QTLs for seed dormancy have been mapped in rice.

The bioinformatics challenges in comparative analysis of cereal genomes-an overview

Comparative genomic analysis is the cornerstone of in silico-based approaches to understanding biological systems and processes across cereal species, such as rice, wheat and barley, in order to identify genes of agronomic interest. The size of the genomic repositories is nearly doubling every year, and this has significant implications on the way bioinformatics analyses are carried out. In this overview the concepts and technology underpinning bioinformatics as applied to comparative genomic analysis are considered in the context of other manuscripts appearing in this issue of Functional and Integrative Genomics.

The organization of genes tightly linked to the Ha locus in Aegilops tauschii, the D-genome donor to wheat

The grain hardness locus, Ha, is located at the distal end of the short arm of chromosome 5D in wheat. Three polypeptides, puroindoline-a, puroindoline-b, and grain softness protein (GSP-1), have been identified as components of friabilin, a biochemical marker for grain softness, and the genes for these polypeptides are known to be tightly linked to the Ha locus. However, this region of the chromosome 5D has not been well characterized and the physical distance between the markers is not known. Separate lambda clones containing the puroindoline-a gene and the puroindoline-b gene have been isolated from an Aegilops tauschii (the donor of the D genome to wheat) genomic lambda library and investigated. Considerable variation appears to exist in the organization of the region upstream of the gene for puroindoline-b among species closely related to wheat. Using in situ hybridization the genes for puroindoline-a, -b, and GSP-1 were demonstrated to be physically located at the tip of the short arm of chromosome 5 of A. tauschii. Four overlapping clones were isolated from a large-insert BAC library constructed from A. tauschii and of these one contained genes for all of puroindoline-a, puroindoline-b, and GSP-1. The gene for puroindoline-a is located between the other two genes at a distance no greater than approximately 30 kb from either gene. The BAC clone containing all three known genes was used to screen a cDNA library constructed from hexaploid wheat and cDNAs that could encode novel polypeptides were isolated.

The starch branching enzyme I locus from Aegilops tauschii, the donor of the D genome to wheat

Analysis of DNA from Aegilops tauschii revealed that sequences hybridisable to the starch branching enzyme I (SBE I) gene were contained within a 53-kb fragment. There were at least four genes or gene fragments but of these only one appeared to encode the SBE I observed in the endosperm. Two large-insert DNA clones that encode SBE I from A. tauschii were isolated. Hybridisation analysis confirmed the presence of multiple SBE I gene type sequences within this DNA fragment of approximately 100 kb. Fluorescent in situ hybridisation (FISH) on extended DNA fibres provided further evidence of the close proximity of three of these genes. Sequence analysis was undertaken and this demonstrated that wSBE I-D3, wSBE I-D2 and wSBE I-D4 genes were clustered within 27 kb of DNA; of these only wSBE I-D4 encodes the SBE I purified from the endosperm. Multiple but distinct cDNAs containing SBE I-related sequences have been reported and these could arise from the SBE I locus by different transcription/splicing regimes.

Early expression of grain hardness in the developing wheat endosperm

Seeds from near-isogenic hard and soft wheat lines were harvested at regular intervals from 5 days post-anthesis to maturity and examined for hardness using the single kernel characterisation system (SKCS). SKCS analysis revealed that hard and soft lines could be distinguished from 15 days post-anthesis (dpa). This trend continued until maturity where the difference between the hard and soft lines was most marked. SKCS could not be applied to the small 5- and 10-dpa wheat kernels. Fresh developing endosperm material was examined using light microscopy and no visible differences between the cultivars were detected. When air-dried material was examined using scanning electron microscopy (SEM) differences between soft and hard lines were visible from as early as 5 dpa. Accumulation of puroindoline a and puroindoline b was investigated in developing seeds using both Western blotting and ELISA. Low levels of puroindoline a could be detected in the soft cultivar from 10 dpa, reaching a maximum at 32 dpa. In the hard cultivar, puroindoline a levels were negligible throughout grain development. Puroindoline b accumulates in both the soft and hard cultivars from 15 dpa, but overall contents were higher in the soft cultivar. These findings indicate that endosperm hardness is expressed very early in developing grain when few starch granules and storage proteins were deposited in the endosperm cells. Further, the near-isogenic soft and hard Heron lines could be differentiated by SEM at a stage in development when the accumulation of puroindolines could not be detected by the methods used in this study.

Mapping and validation of the genes for resistance to Pyrenophora teres f. teres in barley (Hordeum vulgare L.)

Identification and deployment of disease resistance genes are key objectives of Australian barley breeding programs. Two doubled haploid (DH) populations derived from Tallon × Kaputar (TK) and VB9524 × ND11231 (VN) crosses were used to identify markers for net type net blotch (NTNB) (Pyrenophora teres f. teres). The maps included 263 and 250 markers for TK and VN populations, respectively. The TK population was screened with 5 pathotypes and the VN population with 1 pathotype of NTNB as seedlings in the glasshouse. In addition, the TK population was subjected to natural infection in the field at Hermitage Research Station, Qld. Analyses of the markers were performed using the software packages MapManager and Qgene. One region on chromosome 6H was strongly associated with resistance to NTNB in both populations (R2 = 83% for TK and 66% for VN). In the TK population, 2 more quantitative trait loci (QTLs) were identified on chromosomes 2H and 3H, with R2 values of 30% and 31%, respectively. These associations were consistent over all pathotypes studied during the seedling stage. The same QTL on chromosome 6H was also found to be highly significantly associated (R2 = 65%) with the adult plant (field) response in the TK population. There are several very closely linked markers showing strong associations in these regions. Association of the 4 markers on chromosome 6H QTL with resistance to the NTNB has been validated in 2 other DH populations derived from barley crosses Pompadour × Stirling and WPG8412 × Stirling. These markers present an opportunity for marker assisted selection of lines resistant to NTNB in barley breeding programs.

Mapping and QTL analysis of the barley population Tallon × Kaputar

A genetic map of barley with 224 AFLP and 39 simple sequence repeat (SSR) markers was constructed using a doubled haploid (DH) mapping population from a cross between the varieties Tallon and Kaputar. Linkage groups were assigned to individual barley chromosomes using the published map locations of the SSR markers as reference points. This genetic map was used to identify markers with linkage to agronomic, disease, and quality traits in barley. The population, which comprised 65 lines, was tested in a range of environments across Australia. Quantitative trait loci (QTLs) analyses were performed using software packages MapMaker, MapManager, and Qgene. Significant associations with markers were found for several traits. Grain yield showed significant association with regions on chromosomes 2H, 3H, and 5H over a range of sites throughout Australia. Regions on chromosomes 2H and 3H explained 30% and 26% of variation in lodging, respectively. Among quality traits, diastatic power was associated with regions on chromosomes 1H, 2H, and 5H (R2 = 37%). Hot water extract was associated with a region on chromosome 6H and a marker not assigned to a chromosome (R2 = 45%). There were also environment-specific QTLs for the traits analysed. The markers identified here present an opportunity for marker assisted selection of lines for these traits in barley breeding programs.Mapping and QTL analysis of Tallon × Kaputar

A major QTL controlling seed dormancy and pre-harvest sprouting/grain α-amylase in two-rowed barley (Hordeum vulgare L.)

Barley seed dormancy is controlled by multiple genes that have a strong interaction with the environment. Lack of adequate dormancy results in pre-harvest sprouting in the field under wet weather conditions. On the other hand, too much dormancy has a detrimental effect in the malting house. There is only a very 'narrow window' of dormancy for malting barley. Harrington barley, which has been a dominant malting variety in the international market and widely used in Australia barley breeding programs, is highly susceptible to pre-harvest sprouting. A doubled haploid (DH) population derived from a cross of Chebec/Harrington was used to search for molecular markers linked with seed dormancy and pre-harvest sprouting. One major quantitative trait locus (QTL) was identified to control pre-harvest sprouting measured by α-amylase activity in barley grains, and could explain >70% of the phenotypic variation. This QTL was located on chromosome 5HL and flanked by restriction fragment length polymorphism (RFLP) marker CDO506 and simple sequence repeat (SSR) marker GMS1. The SSR marker (GMS1) linked with this QTL was further validated in a Stirling/Harrington DH population. A minor QTL on chromosome 2H accounted for 8% of phenotypic variation. Two QTLs for seed dormancy were located on chromosomes 2H and 5HL. The major QTL for dormancy coincided with the QTL for pre-harvest sprouting at chromosome 5HL and explained 61% of phenotypic variation. Since the presence of the Harrington allele at this locus favoured not only pre-harvest sprouting, but also increased malting extract, diastatic power, α-amylase, and free amino acid nitrogen, development of high malting quality varieties with pre-harvest sprouting tolerance would appear to be difficult.

Wheat functional genomics and engineering crop improvement

Genetic mapping and determination of the organization of the wheat genome are changing the wheat-breeding process. New initiatives to analyze the expressed portion of the wheat genome and structural analysis of the genomes of Arabidopsis and rice are increasing our knowledge of the genes that are linked to key agronomically important traits.

Physical arrangement of retrotransposon-related repeats in centromeric regions of wheat

Cereal centromeres commonly contain many repetitive sequences that are derived from Ty3/gypsy retrotransposon. FISH analysis using a large DNA insert library of wheat identified a 67-kb clone (R11H) that showed strong hybridization signals on the centromeres. The R11H clone contains Ty3/gypsy retrotransposon-related sequences; both integrase and CCS1 family sequences were identified. Subsequently, we isolated additional 23 large-insert clones which also contained the integrase and CCS1 sequences. Based on the number of the integrase repeats in the clones determined by DNA gel blot analysis, we concluded that the retrotransposon-like sequences are tandemly repeated in wheat centromeres in ca. 55-kb interval on average. This conclusion is consistent with the results of FISH analysis on the extended DNA fibers.

Quality traits of wheat determined by small-scale dough testing methods

The dough properties of flours from the grain of 172 doubled haploid lines of a Cranbrook Halberd cross, grown at 3 locations, were determined with traditional and small-scale dough testing equipment. The experiments were aimed at determining the genetic factors that underpin the flour processing properties of wheat flour. Seven mixing parameters determined on a 2-g Mixograph™, as well as the maximum resistance (RMAX) and extensibility (EXT) measured on a Micro-Extension Tester, were identified as quality traits for genetic mapping studies, to identify the underlying quantitative trait loci (QTL). For each of the 3 locations in which the wheat lines were grown, relationships between the quality parameters and genetic markers were constructed for the populations. The associations of HMW- and LMW-glutenin allele combinations with the quality traits were investigated using ANOVA, linear parametric, and non-parametric methods. Of particular interest were qualitative and quantitative assessments of the extremes of the quality traits in each population. The relative contributions of the glutenincoding loci to quality were determined and it was found that the growing conditions to which wheat lines were subjected significantly affected the analyses. The nature and extent of these variations could not be explained by changes in protein content alone, and were related to environmentally induced alterations in the protein composition. From a comparison of the measurements made with the small-scale Mixograph™ with those from both the Extensograph™ and a Micro-Extension Tester, it was concluded that the same information about RMAX and EXT obtained from traditional extension testing could be obtained using small-scale dough tests. The data provided a direct validation for the application of small-scale testing for the screening of large populations. The comparisons of large and small scale testing procedures also provided the basis defining a new trait, ‘M-extensibility’, which is obtained from protein content and selected Mixograph data. This parameter was able to be measured more accurately and was shown to be closely related to the traditional extensibility measurement, and thus very useful for molecular/genetic analysis. The M-extensibility trait could be mapped as a major QTL to LMW-glutenin subunit loci on chromosomes 1B and 1D.

Gluten protein functionality in wheat flour processing: a review

Gluten protein functionality remains the basis of any understanding of the end-product quality of wheat flours. Information about this functionality has been obtained by both in vivo and in vitro studies. Recent advances include structure/function studies of deletion mutants and transformed genotypes, where the genes incorporated were both naturally occurring genes and genes which have been desired to provide specific structural features. The contributions of these specific changes in structure to the rheology of the resulting doughs allow insight into the underlying physical processes that determine dough and end-product properties.

Diagnostic DNA markers for cereal cyst nematode resistance in bread wheat

The development of cultivars resistant to cereal cyst nematode (CCN) is a primary objective in wheat breeding in the southern wheatbelt of Australia. Nine CCN resistance genes have been identified in wheat and its relatives, some of which confer resistance to the Australian pathotype of CCN (Ha13). Cultivars released in Australia with CCN resistance carry either the Cre1 or CreF gene, with the Cre3 gene present in advanced breeding lines. The biological assay for CCN resistance screening in wheat is time-consuming, not reliable on a single-plant basis, and prone to inconsistencies, thus reducing the efficiency of selection amongst breeding lines. Using gene sequences initially isolated from the Cre3 locus, a DNA-based marker selection system was developed and applied to unambiguously identify wheat lines carrying resistance alleles at theCre1 and/or Cre3 loci in breeding populations derived from diverse genetic backgrounds. Homologues of sequences from the Cre3 locus, located elsewhere in the wheat genome, can also be used to select wheat lines with a newly identified CCN resistance gene (Cre6) introgressed from Aegilops ventricosa. Application of these markers has become an integral part of the southern Australian breeding programs.

Trends in genetic and genome analyses in wheat: a review

The size and structure of the wheat genome makes it one of the most complex crop species for genetic analysis. The development of molecular techniques for genetic analysis, in particular the use of molecular markers to monitor DNA sequence variation between varieties, landraces, and wild relatives of wheat and related grass species, has led to a dramatic expansion in our understanding of wheat genetics and the structure and behaviour of the wheat genome. This review provides an overview of these developments, examines some of the special issues that have arisen in applying molecular techniques to genetic studies in wheat, and looks at the applications of these technologies to wheat breeding and to improving our understanding of the genetic basis of traits such as disease resistance and processing quality. The review also attempts to foreshadow some of the key molecular issues and developments that may occur in wheat genetics and breeding over the next few years.

The statistical analysis of quality traits in plant improvement programs with application to the mapping of milling yield in wheat

It is well known that the response to selection for grain yield is improved with the use of appropriate experimental designs and statistical analyses. The issues are more complex for quality traits since the data are obtained from a 2-phase process in which samples are collected from the field then processed in the laboratory. This paper presents a method of analysis for quality trait data that allows for variation arising from both the field and laboratory phases. Initially, an analysis suitable for standard varietal selection is presented. This is extended to include molecular genetic marker information for the purpose of detecting quantitative trait loci. The technique is illustrated using two doubled haploid wheat (Triticum aestivum L.) populations in which the trait of interest is milling yield.

Albumin polymorphism and mapping of a dimeric a-amylase inhibitor in wheat

Any new protein or DNA marker is potentially useful to add detail to already constructed genetic chromosome maps and may be valuable in breeding programs wherever polymorphism exists. Non-gluten proteins represent 15–20% of total wheat grain proteins. Isoelectric focusing of wheat (Triticum aestivum L. em Thell.) proteins on ultrathin gels showed high resolution and was found to be a useful tool in the differentiation of wheat varieties. Seventeen hexaploid wheat varieties were screened to investigate polymorphism of albumin proteins using isoelectric focusing. Polymorphism was observed for albumin polypeptides of pI 5.20, 5.85, 6.25, and 7.1, and 8.0. The polymorphic protein of pI 7.1 was mapped by analysing doubled haploid populations from the intervarietal crosses, Cranbrook x Halberd and Synthetic x Opata 85. This protein locus was designated as Iha-B1.2, and is located on the short arm of chromosome 3B.

Construction of three linkage maps in bread wheat, Triticum aestivum

Genetic maps were compiled from the analysis of 160–180 doubled haploid lines derived from 3 crosses: Cranbrook Halberd, CD87 Katepwa, and Sunco Tasman. The parental wheat lines covered a wide range of the germplasm used in Australian wheat breeding. The linkage maps were constructed with RFLP, AFLP, microsatellite markers, known genes, and proteins. The numbers of markers placed on each map were 902 for Cranbrook Halberd, 505 for CD87 Katepwa, and 355 for Sunco Tasman. Most of the expected linkage groups could be determined, but 10–20% of markers could not be assigned to a specific linkage group. Homologous chromosomes could be aligned between the populations described here and linkage groups reported in the literature, based around the RFLP, protein, and microsatellite markers. For most chromosomes, colinearity of markers was found for the maps reported here and those recorded on published physical maps of wheat. AFLP markers proved to be effective in filling gaps in the maps. In addition, it was found that many AFLP markers defined specific genetic loci in wheat across all 3 populations. The quality of the maps and the density of markers differs for each population. Some chromosomes, particularly D genome chromosomes, are poorly covered. There was also evidence of segregation distortion in some regions, and the distribution of recombination events was uneven, with substantial numbers of doubled haploid lines in each population displaying one or more parental chromosomes. These features will affect the reliability of the maps in localising loci controlling some traits, particularly complex quantitative traits and traits of low heritability. The parents used to develop the mapping populations were selected based on their quality characteristics and the maps provide a basis for the analysis of the genetic control of components of processing quality. However, the parents also differ in resistance to several important diseases, in a range of physiological traits, and in tolerance to some abiotic stresses.