Detection and Genetic Mapping of Quantitative Trait Loci Influencing Stem Growth Efficiency in Radiata Pine

Needle-to-stem unit rate (NESTUR) is a stem growth index of conifer seedling trees that measures the efficiency of stemwood production per unit of needle growth. Five experiments were carried out in this thesis using progenies of two unrelated full-sib radiata pine crosses. The initial experiment (experiment 1) applied the bulked segregant analysis technique to determine whether RAPD analysis could be successfully extended to the development of molecular markers for NESTUR in radiata pine. The NESTUR values of 174 progenies of the full-sib family 12038 x 10946 were determined. Based on the genotypic analysis of the individuals, two quantitative trait loci (QTL) controlling NESTUR were identified at ANOVA P-levels of 0.01-0.001. An absence of RAPD fragment markers generated by primers OPE-06 and OPA-10 was associated with low NESTUR values, while primer UBC-333 generated a 550 bp band that was associated with high NESTUR values. Linkage to components of NESTUR (increments in stem diameter and stem volume) was demonstrated for one of the QTL, while the other was unique to NESTUR, and not shared with the components. There was a significant interaction between the two QTLs. Presence of OPA-101200 locus appeared to inhibit expression of the QTL linked to UBC-333 [subscript 550]. ¶ ..

Mapping spot blotch resistance genes in four barley populations

Bipolaris sorokiniana (teleomorph: Cochliobolus sativus) is the fungal pathogen responsible for spot blotch in barley (Hordeum vulgare L.) and occurs worldwide in warmer, humid growing conditions. Current Australian barley varieties are largely susceptible to this disease and attempts are being made to introduce sources of resistance from North America. In this study we have compared chromosomal locations of spot blotch resistance reactions in four North American two-rowed barley lines; the North Dakota lines ND11231-12 and ND11231-11 and the Canadian lines TR251 and WPG8412-9-2-1. Diversity Arrays Technology (DArT)-based PCR, expressed sequence tag (EST) and SSR markers have been mapped across four populations derived from crosses between susceptible parental lines and these four resistant parents to determine the location of resistance loci. Quantitative trait loci (QTL) conferring resistance to spot blotch in adult plants (APR) were detected on chromosomes 3HS and 7HS. In contrast, seedling resistance (SLR) was controlled solely by a locus on chromosome 7HS. The phenotypic variance explained by the APR QTL on 3HS was between 16 and 25% and the phenotypic variance explained by the 7HS APR QTL was between 8 and 42% across the four populations. The SLR QTL on 7HS explained between 52 to 64% of the phenotypic variance. An examination of the pedigrees of these resistance sources supports the common identity of resistance in these lines and indicates that only a limited number of major resistance loci are available in current two-rowed germplasm

Detection and verification of malting quality QTLs using wild barley introgression lines

A malting quality quantitative trait locus (QTL) study was conducted using a set of 39 wild barley introgression lines (hereafter abbreviated with S42ILs). Each S42IL harbors a single marker-defined chromosomal segment from the wild barley accession ‘ISR 42-8’ (Hordeum vulgare ssp. spontaneum) within the genetic background of the elite spring barley cultivar ‘Scarlett’ (Hordeum vulgare ssp. vulgare). The aim of the study was (1) to verify genetic effects previously identified in the advanced backcross population S42, (2) to detect new QTLs, and (3) to identify S42ILs exhibiting multiple QTL effects. For this, grain samples from field tests in three different environments were subjected to micro malting. Subsequently, a line × phenotype association study was performed with the S42ILs in order to localize putative QTL effects. A QTL was accepted if the trait value of a particular S42IL was significantly (P < 0.05) different from the recurrent parent as a control, either across all tested environments or in a particular environment. For eight malting quality traits, altogether 40 QTLs were localized, among which 35 QTLs (87.5%) were stable across all environments. Six QTLs (15.0%) revealed a trait improving wild barley effect. Out of 36 QTLs detected in a previous advanced backcross QTL study with the parent BC2DH population S42, 18 QTLs (50.0%) could be verified with the S42IL set. For the quality parameters α-amylase activity and Hartong 45°C, all QTLs assessed in population S42 were verified by S42ILs. In addition, eight new QTL effects and 17 QTLs affecting two newly investigated traits were localized. Two QTL clusters harboring simultaneous effects on eight and six traits, respectively, were mapped to chromosomes 1H and 4H. In future, fine-mapping of these QTL regions will be conducted in order to shed further light on the genetic basis of the most interesting QTLs

A QTL on the short arm of wheat (Triticum aestivum L.) chromosome 3B affects the stability of grain weight in plants exposed to a brief heat shock early in grain filling

Background: Molecular markers and knowledge of traits associated with heat tolerance are likely to provide breeders with a more efficient means of selecting wheat varieties able to maintain grain size after heat waves during early grain filling. Results: A population of 144 doubled haploids derived from a cross between the Australian wheat varieties Drysdale and Waagan was mapped using the wheat Illumina iSelect 9,000 feature single nucleotide polymorphism marker array and used to detect quantitative trait loci for heat tolerance of final single grain weight and related traits. Plants were subjected to a 3 d heat treatment (37 °C/27 °C day/night) in a growth chamber at 10 d after anthesis and trait responses calculated by comparison to untreated control plants. A locus for single grain weight stability was detected on the short arm of chromosome 3B in both winter- and autumn-sown experiments, determining up to 2.5 mg difference in heat-induced single grain weight loss. In one of the experiments, a locus with a weaker effect on grain weight stability was detected on chromosome 6B. Among the traits measured, the rate of flag leaf chlorophyll loss over the course of the heat treatment and reduction in shoot weight due to heat were indicators of loci with significant grain weight tolerance effects, with alleles for grain weight stability also conferring stability of chlorophyll ('stay-green') and shoot weight. Chlorophyll loss during the treatment, requiring only two non-destructive readings to be taken, directly before and after a heat event, may prove convenient for identifying heat tolerant germplasm. These results were consistent with grain filling being limited by assimilate supply from the heat-damaged photosynthetic apparatus, or alternatively, accelerated maturation in the grains that was correlated with leaf senescence responses merely due to common genetic control of senescence responses in the two organs. There was no evidence for a role of mobilized stem reserves (water soluble carbohydrates) in determining grain weight responses. Conclusions: Molecular markers for the 3B or 6B loci, or the facile measurement of chlorophyll loss over the heat treatment, could be used to assist identification of heat tolerant genotypes for breeding.Hamid Shirdelmoghanloo, Julian D. Taylor, Iman Lohraseb, Huwaida Rabie, Chris Brien, Andy Timmins, Peter Martin, Diane E. Mather, Livinus Emebiri and Nicholas C. Collin

Next generation characterisation of cereal genomes for marker discovery

Cereal crops form the bulk of the world's food sources and thus their importance cannot be understated. Crop breeding programs increasingly rely on high-resolution molecular genetic markers to accelerate the breeding process. The development of these markers is hampered by the complexity of some of the major cereal crop genomes, as well as the time and cost required. In this review, we address current and future methods available for the characterisation of cereal genomes, with an emphasis on faster and more cost effective approaches for genome sequencing and the development of markers for trait association and marker assisted selection (MAS) in crop breeding programs

Functional characterization of barley betaglucanless mutants demonstrates a unique role for CslF6 in (1,3;1,4)-β-D-glucan biosynthesis

(1,3;1,4)-β-D-glucans (mixed-linkage glucans) are found in tissues of members of the Poaceae (grasses), and are particularly high in barley (Hordeum vulgare) grains. The present study describes the isolation of three independent (1,3;1,4)-β-D-glucanless (betaglucanless; bgl) mutants of barley which completely lack (1,3;1,4)-β-D-glucan in all the tissues tested. The bgl phenotype cosegregates with the cellulose synthase like HvCslF6 gene on chromosome arm 7HL. Each of the bgl mutants has a single nucleotide substitution in the coding region of the HvCslF6 gene resulting in a change of a highly conserved amino acid residue of the HvCslF6 protein. Microsomal membranes isolated from developing endosperm of the bgl mutants lack detectable (1,3;1,4)-β-D-glucan synthase activity indicating that the HvCslF6 protein is inactive. This was confirmed by transient expression of the HvCslF6 cDNAs in Nicotiana benthamiana leaves. The wild-type HvCslF6 gene directed the synthesis of high levels of (1,3;1,4)-β-D-glucans, whereas the mutant HvCslF6 proteins completely lack the ability to synthesize (1,3;1,4)-β-D-glucans. The fine structure of the (1,3;1,4)-β-D-glucan produced in the tobacco leaf was also very different from that found in cereals having an extremely low DP3/DP4 ratio. These results demonstrate that, among the seven CslF and one CslH genes present in the barley genome, HvCslF6 has a unique role and is the key determinant controlling the biosynthesis of (1,3;1,4)-β-D-glucans. Natural allelic variation in the HvCslF6 gene was found predominantly within introns among 29 barley accessions studied. Genetic manipulation of the HvCslF6 gene could enable control of (1,3;1,4)-β-D-glucans in accordance with the purposes of use

Advanced backcross-QTL analysis in spring barley (H. vulgare ssp. spontaneum) comparing a REML versus a Bayesian model in multi-environmental field trials

A common difficulty in mapping quantitative trait loci (QTLs) is that QTL effects may show environment specificity and thus differ across environments. Furthermore, quantitative traits are likely to be influenced by multiple QTLs or genes having different effect sizes. There is currently a need for efficient mapping strategies to account for both multiple QTLs and marker-by-environment interactions. Thus, the objective of our study was to develop a Bayesian multi-locus multi-environmental method of QTL analysis. This strategy is compared to (1) Bayesian multi-locus mapping, where each environment is analysed separately, (2) Restricted Maximum Likelihood (REML) single-locus method using a mixed hierarchical model, and (3) REML forward selection applying a mixed hierarchical model. For this study, we used data on multi-environmental field trials of 301 BC2DH lines derived from a cross between the spring barley elite cultivar Scarlett and the wild donor ISR42-8 from Israel. The lines were genotyped by 98 SSR markers and measured for the agronomic traits “ears per m²,” “days until heading,” “plant height,” “thousand grain weight,” and “grain yield”. Additionally, a simulation study was performed to verify the QTL results obtained in the spring barley population. In general, the results of Bayesian QTL mapping are in accordance with REML methods. In this study, Bayesian multi-locus multi-environmental analysis is a valuable method that is particularly suitable if lines are cultivated in multi-environmental field trials

Gene and QTL detection in a three-way barley cross under selection by a mixed model with kinship information using SNPs

Quantitative trait locus (QTL) detection is commonly performed by analysis of designed segregating populations derived from two inbred parental lines, where absence of selection, mutation and genetic drift is assumed. Even for designed populations, selection cannot always be avoided, with as consequence varying correlation between genotypes instead of uniform correlation. Akin to linkage disequilibrium mapping, ignoring this type of genetic relatedness will increase the rate of false-positives. In this paper, we advocate using mixed models including genetic relatedness, or ‘kinship’ information for QTL detection in populations where selection forces operated. We demonstrate our case with a three-way barley cross, designed to segregate for dwarfing, vernalization and spike morphology genes, in which selection occurred. The population of 161 inbred lines was screened with 1,536 single nucleotide polymorphisms (SNPs), and used for gene and QTL detection. The coefficient of coancestry matrix was estimated based on the SNPs and imposed to structure the distribution of random genotypic effects. The model incorporating kinship, coancestry, information was consistently superior to the one without kinship (according to the Akaike information criterion). We show, for three traits, that ignoring the coancestry information results in an unrealistically high number of marker–trait associations, without providing clear conclusions about QTL locations. We used a number of widely recognized dwarfing and vernalization genes known to segregate in the studied population as landmarks or references to assess the agreement of the mapping results with a priori candidate gene expectations. Additional QTLs to the major genes were detected for all traits as well