B.J. Read

Mapping of genomic regions associated with net form of netblotch resistance in barley

Quantitative trait loci (QTLs) associated with resistance to net blotch and their chromosomal locations were determined from analyses of doubled haploid progeny of Alexis/Sloop, Arapiles/Franklin, Sloop/Halcyon, and recombinant inbred lines of Sloop-sib/Alexis. Five QTLs on chromosomes 2H, 3H, and 4H were found to be associated with seedling resistance to the net form of net blotch. In Arapiles/Franklin and Alexis/Sloop populations, 4 significant QTLs explaining 9–17% of the variation in net blotch resistance were detected on 2H and 3H. A major locus, QRpts4L accounting for 64% of the variation in infection type, was detected on 4H in the Sloop/Halcyon population. In Sloop/Halcyon, 2 microsatellite markers, EBmac0906 and GMS089, and AFLP marker P13/M50-108, co-segregated and detected maximum variability for net blotch resistance as revealed by bootstrap analysis. EBmac0906 and Bmac0181 were validated in F2 progeny of an Ant29/Halcyon population and reliably predicted phenotypes of 93% of lines resistant and susceptible to net blotch. These markers may be used within breeding programs to select alleles favourable for net blotch resistance derived from Halcyon.

Mapping and QTL analysis of the barley population Chebec × Harrington

A doubled haploid population of 120 individuals was produced from the parents Chebec, an Australian 2-row barley of feed quality with resistance to the cereal cyst nematode, and Harrington, a 2-rowed, Canadian variety of premium malting quality. This paper describes 18 field and laboratory experiments conducted with the population and summarises the traits mapped and analysed. The genomic location of 25 traits and genes is described and marker–trait associations for 5 traits (malt extract, diastatic power, resistance to cereal cyst nematode, early flowering, resistance to pre-harvest sprouting) important to Australian efforts to improve malting barley varieties have been used in practical breeding programs. Detailed maps for these populations are shown in this paper, while a consensus map incorporating these maps and further experiments on the populations are described elsewhere in this issue.

Mapping and QTL analysis of the barley population Alexis × Sloop

Two populations between the German malting variety Alexis and the Australian malting variety Sloop were constructed, mapped, phenotyped, and subjected to quantitative trait loci analysis. One population consisted of 153 F4-derived recombinant inbred lines and the other of 111 doubled haploid lines. This paper describes 18 field and laboratory experiments conducted with the populations and summarises the traits mapped and analysed. The genetic basis of 5 traits (malt extract, resistance to leaf rust, resistance to powdery mildew, early flowering, plant stature) important to Australian efforts to improve malting barley varieties was elucidated. Detailed maps for these populations are shown in this paper, while a consensus map incorporating these maps and further experiments on the populations are described elsewhere in this issue.

Leaf scald resistance genes in Hordeum vulgare and Hordeum vulgare ssp. spontaneum: parallels between cultivated and wild barley

The prerequisite for breeding barley varieties with durable scald resistance is a diversity of genes each with molecular markers for their manipulation in crosses. Here we compare the outcomes of genetic analysis of scald resistance in 5 doubled haploid mapping populations of cultivated barley with 9 third-backcross families that derive from a set of diverse wild barley populations. In all cases, resistance was assessed as seedling infection type responses, but the Sloop/Halcyon population was also tested for adult plant resistance in field trials at two sites. In the latter case, the major quantitative trait locus for field resistance was coincident with that for seedling response on chromosome 3H. Most of the other cultivated barley sources of resistance in this study (1 cultivar and 3 breeders populations synthesised for resistance) also resolved to markers in the region of this 3H locus. In contrast, the genetic basis of resistance in wild barley populations resolved to at least 5 chromosome locations (1HS, 3H, 6HS, 7HL, and 7HS). Useful markers were of several kinds including proteins, isozymes, PCR based on RFLPs, AFLP, and SSR loci. Thus, wild barley increases the range of options for pyramid breeding and provides linked molecular markers that will be useful in manipulating those genes, or in the analysis of resistance in new sources.

Mapping and QTL analysis of the barley population Tallon x 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 genes for resistance to Puccinia hordei in barley

Six doubled haploid barley populations (Alexis × Sloop, Chebec × Harrington, Arapiles × Franklin, Patty × Tallon, Tallon × Kaputar, and Sloop × Halcyon) and a recombinant inbred population (WI2875-1 × Alexis) were assessed for response to selected pathotypes of the barley leaf rust pathogen, Puccinia hordei, at the seedling growth stage. Resistance genes were postulated for the parents of each population based on their reaction to selected pathotypes. In most cases, the resistance genes postulated in the cultivars were validated by QTL mapping analyses of the progeny populations. The resistance genes detected and mapped were Rph2, Rph3, Rph4, Rph12, and Rph19. The chromosomal locations of these 5 genes were consistent with previous reports, with Rph2 mapping near to the centromere on the short arm of chromosome 5H, Rph4 mapping to chromosome 1H, Rph12 mapping to the long arm of chromosome 5H, and Rph3 and Rph19 mapping ~30 cM apart on the long arm of chromosome 7H.

Quantitative trait loci controlling kernel discoloration in barley (Hordeum vulgare L.)

Barley kernel discoloration (KD) leads to substantial annual loss in value through downgrading and discounting of malting barley. KD is a difficult trait to introgress into elite varieties as it is controlled by multiple genes and strongly influenced by environment and maturity. As the first step towards marker assisted selection for KD tolerance, we mapped quantitative trait loci (QTLs) controlling KD measured by grain brightness [Minolta L; (Min L)], redness (Min a), and yellowness (Min b) in 7 barley populations. One to 3 QTLs were detected for grain brightness in various populations, and one QTL could account for 5–31% of the phenotypic variation. The QTL located around the centromere region of chromosome 2H was consistently detected in 6 of the 7 populations, explaining up to 28% of the phenotypic variation. In addition, QTLs for grain brightness were most frequently identified on chromosomes 3H and 7H in various populations. Australian varieties Galleon, Chebec, and Sloop contribute an allele to increase grain brightness on chromosome 7H in 3 different populations. A major gene effect was detected for grain redness. One QTL on chromosome 4H explained 54% of the phenotypic variation in the Sloop/Halcyon population, and was associated with the blue aleurone trait. A second QTL was detected on the long arm of chromosome 2H in 3 populations, accounting for 23–47% of the phenotypic variation. The major QTLs for grain yellowness were mapped on chromosomes 2H and 5H. There were strong associations between the QTLs for heading date, grain brightness, and yellowness. The molecular markers linked with the major QTLs should be useful for marker assisted selection for KD.