J. A. Clancy

Verification of barley seed dormancy loci via linked molecular markers

Seed dormancy is a relatively complex trait in barley (Hordeum vulgare L.). Several dormancy loci were identified previously by quantitative trait locus analysis. Three reciprocal crosses were made in the present study between parents carrying specific dormancy alleles via linked molecular markers to verify individual dormancy locus effects and potential expression. Analyses of F2 progenies revealed that the dormancy allele at the locus flanked by the markers Ale and ABC302 on the long arm of chromosome 7 had a major effect on dormancy, and was at least partly epistatic to the dormancy locus in the ABC309-MWG851 interval near the telomere of the long arm of chromosome 7. In the absence of the dormancy allele in the Ale-ABC302 interval, the allele in the ABC309-MWG851 interval exerted moderate to large effects on dormancy. Cytoplasmic effects on dormancy were also observed. The germination percentages of progeny with relatively high levels of dormancy were more variable than those of non-dormant or less-dormant progeny, apparently due to environmental effects. Removal of the dormancy allele in the Ale-ABC302 interval, or introducing the dormancy allele in the ABC309-MWG851 interval, should suffice for adjusting dormancy levels in breeding programs to suit various production situations and end uses. The verification of dormancy loci via linked molecular markers allows manipulation of these loci in applied breeding programs.

Inheritance and fine mapping of a major barley seed dormancy QTL

Abstract A major barley seed dormancy locus, SD1, was previously identified along with three others by quantitative trait locus (QTL) analysis in a Steptoe×Morex mapping population. Located in the centromere region of barley chromosome 7 (5H), SD1 shows the largest and most consistent effect on dormancy. Steptoe contributes the dormancy allele at SD1. The objective of this study was to determine the inheritance of and a more precise map location for SD1. A segregating population was designed and generated by marker assisted mating in which only SD1 segregated. The segregation ratio suggested a single Mendelian gene in which the dormancy allele is dominant to the non-dormancy allele at SD1. In addition, near isogenic lines (NIL) for the SD1 chromosome region were generated by molecular marker assisted backcrossing. Statistical analysis of germination percentages of these NIL revealed that there may be a gene cluster of at least three genes in the SD1 locus region. The dormancy locus, presumably SD1 or a part of the SD1 complex, was resolved into a ≈4.4 cM region.

Dissection of a malting quality QTL region on chromosome 1 (7H) of barley

Malting and brewing are major uses of barley (Hordeum vulgare L.) worldwide, utilizing 30–40% of the crop each year. A set of complex traits determines the quality of malted barley and its subsequent use for beer. Molecular genetics technology has increased our understanding of genetic control of the many malting and brewing quality traits, most of which are quantitatively inherited. The objective of this study was to further dissect and evaluate a known major malting quality quantitative trait locus (QTL) region of about 28 cM on chromosome 1 (7H). Molecular marker-assisted backcrossing was used to develop 39 isolines originating from a ‘Steptoe’ / ‘Morex’ cross. Morex, a 6–row malting type, was the donor parent and Steptoe, a 6–row feed type, was the recurrent parent. The isolines and parents were grown in four environments, and the grain was micro-malted and analyzed for malting quality traits. The effect of each Morex chromosome segment in the QTL target region was determined by composite interval mapping (CIM) and confirmed and refined by multiple interval mapping (MIM). One QTL was resolved for malt extract content, and two QTLs each were resolved for α-amylase activity, diastatic power, and malt β-glucan content. One additional putative malt extract QTL was detected at the plus border of the target region by CIM, but not confirmed by MIM. All QTLs were resolved to intervals of 2.0 to 6.4 cM by CIM, and to intervals of 2.0 cM or less by MIM. These results should facilitate marker-assisted selection in breeding improved malting barley cultivars.

Genetic relationships between preharvest sprouting and dormancy in barley

Preharvest sprouting (PHS) and dormancy (DOR) can be problems in barley production and end use quality, especially for barley used for seed and malting. Three crosses previously analyzed for DOR inheritance, were reanalyzed for PHS and DOR inheritance using artificial rain to calculate sprout score (SSc) and measure alpha-amylase activity (AA). Germination percentage of untreated grain for DOR was also measured. The crosses are ‘Steptoe’/’Morex’ (previously published), ‘Harrington’/TR306, and ‘Triumph’/Morex. Among the three crosses, DOR QTLs were located to six and PHS QTLs to five chromosomes, respectively. Chromosome 6H was never implicated. Previously identified DOR QTLs were confirmed in each cross, and most PHS QTLs coincided with DOR QTLs, but not all. Unique PHS QTLs were identified on chromosomes 1H (AA), 2H (SSc, AA), 3H (SSc, AA), and 7H (SSc, AA) and unique DOR QTLs on 1H, 2H, and 7H. Results indicate that PHS susceptibility and DOR are not always represented by opposite alleles at a locus. Some QTL regions for a given trait are conserved across crosses and some are not. Several QTLs are suitable for marker-assisted selection to balance PHS and DOR in breeding new cultivars.

Barley tissue as direct template for PCR: a practical breeding tool

A method for using alkali treated intact plant tissue as a DNA source for the polymerase chain reaction (PCR) was applied to barley. This method saves up to two days and more than USD 50 per 40 samples by eliminating the need for DNA extraction to produce template for PCR. The conditions were optimized for various barley tissues. Fresh leaves, freeze-dried leaves, and anthers worked well as templates while root, embryo, and endosperm tissues did not. The method was shown to work with several genotypes and different primers. The resulting PCR product could be cut with restriction enzyme to produce clear polymorphism without any interference. This method can be a practical breeding tool by providing a fast, inexpensive method for screening large populations.

Quantitative genetic analysis of acid detergent fibre content in barley grain

Abstract Acid detergent fibre (ADF) in cultivated barley ( Hordeum vulgare vulgare L.) grain, a major indicator of digestibility, negatively affects feed quality, especially of non-ruminant livestock and poultry. Genetic studies of barley grain ADF content have been very limited. The objectives of this study were to map quantitative trait loci (QTLs) affecting ADF content to a molecular marker linkage map in barley, and to determine interactions among the QTLs identified. A population of 150 doubled haploid lines (DHLs) derived from a cross of ‘Steptoe’/‘Morex’ was used for mapping. A total of five QTLs were identified; three with relatively large effects mapping adjacent to one another on chromosome 2H and one each on chromosomes 4H and 1H (5). The five QTLs explained 64.5% of total variation. Steptoe contributed high ADF alleles at all QTLs identified. In order to confirm that the three adjacent QTLs on chromosome 2H are distinct genetic units, three DHLs representing each QTL were selected for backcrossing to Morex. Analysis of F 2 ADF data from these three crosses showed that the three QTLs are distinct heritable genetic units. Additivity among the three major QTLs on chromosome 2H and the QTL on chromosome 1H (5) were observed.