Steve R. Larson

Linkage mapping of two mutations that reduce phytic acid content of barley grain

Abstract This study describes the inheritance and linkage map positions of two low phytic acid barley (Hordeum vulgare) mutations, lpa1-1 and lpa2-1, that dramatically reduce grain phytic acid content and increase inorganic seed phosphorus (P). Wide-cross, F2 mapping populations were constructed by mating six-rowed varieties, ‘Steptoe’ and/or ‘Morex’, with two-rowed ‘Harrington’lpa donor lines homozygous for either lpa1-1 or lpa2-1. The barley lpa1-1 mutation showed normal inheritance patterns, whereas a deficiency of homozygous lpa2-1/lpa2-1 F2 plants was observed. We identified a codominant, STS-PCR marker (aMSU21) that cosegregated with lpa1-1 in a population of 41 F2 plants. The aMSU21 marker was then mapped to a locus on barley chromosome 2H, using a North American Barley Genome Mapping Project (NABGMP) doubled haploid population (‘Harrington’בMorex’). We determined that lpa2-1 is located within a recombination interval of approximately 30 cM between two AFLP markers that were subsequently mapped to barley chromosome 7H by integration with the same NABGMP population. Recent comparative mapping studies indicate conserved genetic map orders of several homologous molecular marker loci in maize and the Triticeae species that also show corresponding linkage to the biochemically similar lpa2 mutations of maize and barley. This observation suggests that barley and maize lpa2 mutations may affect orthologous genes. No such evidence for correspondence of the phenotypically similar lpa1 mutations of barley and maize has been revealed.

Linkage mapping of maize and barley myo-inositol 1-phosphate synthase DNA sequences : correspondence with a low phytic acid mutation

Abstract We sequenced and genetically mapped the myo-inositol 1-phosphate synthase (MIPS) genes of maize (Zea mays L.) and barley (Hordeum vulgare L). Our objective was to determine whether the genetic map positions of these MIPS loci correspond with the location of the low phtyic acid 1 (lpa1) mutations that were previously identified in maize and barley. Seven MIPS-homologous sequences were mapped to positions on maize chromosomes 1S, 4L, 5S, 6S, 8L, 9S and 9L, and a similar number of divergent MIPS sequences were amplified from maize. To the extent that we can compare across different genetic mapping populations, the position of the MIPS gene on maize chromosome 1S is identical to the location of the maize lpa1 mutation. However, only one MIPS sequence was identified in barley and this gene was mapped to a locus on chromosome 4H that is separate from the barley lpa1 mutation on chromosome 2H. Although several RFLP markers linked to the barley MIPS gene on chromosome 4H also detect loci near barley lpa1 on chromosome 2H, our experiments failed to reveal a second MIPS gene that could be associated with the barley lpa1 mutation. Therefore, genetic mapping results from this study support the MIPS candidate-gene hypothesis for maize lpa1, but do not support the MIPS candidate-gene-hypothesis for barley lpa1. These opposing results contradict the hypothesis that maize lpa1 and barley lpa1 are mutations of orthologous genes, which is suggested by the similar biochemical phenotypes of these mutants. Yet, comparisons of RFLP mapping studies show loci that are homologous between maize chromosome 1S, barley chromosome 4H and barley chromosome 2H, including regions flanking the respective MIPS and/or lpa1 loci. This putative relationship, between the regions flanking the lpa1 mutations on maize 1S and barley 2H, also supports the assertion that these mutations are orthologous despite contradictory results between our maize and barley candidate-gene experiments.

Development of Salinity‐Tolerant Wheat Recombinant Lines from a Wheat Disomic Addition Line Carrying a Thinopyrum junceum Chromosome

Three Triticum aestivum L. × Thinopyrum junceum (L.) A. Löve partial amphidiploids (2n=8x=56; 21″ ABD + 7″ Eb/Ee) and 11 derived disomic addition lines (2n=44) were screened for salt tolerance in hydroponic solutions. One addition line (AJDAj5, 21″ ABD + 1″ Eb) had salt tolerance comparable to that in partial amphidiploids. It was crossed to a wheat line having the PhI allele from Aegilops speltoides Tausch to induce homoeologous pairing. F2 plants were subjected to salt screening and advanced to 30 F3 families, which were screened again. Four F3 lines were more tolerant than AJDAj5 when screened in a final electrical conductivity of 42 dS/m. Because one of the four lines was sterile, only three lines were further verified for their salinity tolerance and were cytologically and molecularly analyzed. These lines were translocation lines with 42 chromosomes having tiny fluorescent hybridization signals detected at interstitial positions of less condensed chromosomes using the genomic in situ hybridization technique. Amplified fragment length polymorphism analyses revealed the presence of very few (ca. 4%) putative markers specific to the Eb‐chromosome addition line. These lines also had from 2% to 14% of markers specific to the Ph inhibitor line and a few new AFLP markers that were not found in the two parental lines and the common wheat background, cv. Chinese Spring. Two recombinant lines were more salt tolerant than either parent, while the third one was as tolerant as either parent, which was more tolerant than Chinese Spring. The former two lines are valuable germplasm for breeding salt‐tolerant wheat cultivars.

Orchardgrass (Dactylis glomerata L.) EST and SSR marker development, annotation, and transferability.

Orchardgrass, or cocksfoot [Dactylis glomerata (L.)], has been naturalized on nearly every continent and is a commonly used species for forage and hay production. All major cultivated varieties of orchardgrass are autotetraploid, and few tools or information are available for functional and comparative genetic analyses and improvement of the species. To improve the genetic resources for orchardgrass, we have developed an EST library and SSR markers from salt, drought, and cold stressed tissues. The ESTs were bi-directionally sequenced from clones and combined into 17,373 unigenes. Unigenes were annotated based on putative orthology to genes from rice, Triticeae grasses, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Of 1,162 SSR markers developed, approximately 80% showed amplification products across a set of orchardgrass germplasm, and 40% across related Festuca and Lolium species. When orchardgrass subspecies were genotyped using 33 SSR markers their within-accession similarity values ranged from 0.44 to 0.71, with Mediterranean accessions having a higher similarity. The total number of genotyped bands was greater for tetraploid accessions compared to diploid accessions. Clustering analysis indicated grouping of Mediterranean subspecies and central Asian subspecies, while the D. glomerata ssp. aschersoniana was closest related to three cultivated varieties.

Development and annotation of perennial Triticeae ESTs and SSR markers.

Triticeae contains hundreds of species of both annual and perennial types. Although substantial genomic tools are available for annual Triticeae cereals such as wheat and barley, the perennial Triticeae lack sufficient genomic resources for genetic mapping or diversity research. To increase the amount of sequence information available in the perennial Triticeae, three expressed sequence tag (EST) libraries were developed and annotated for Pseudoroegneria spicata, a mixture of both Elymus wawawaiensis and E. lanceolatus, and a Leymus cinereus x L. triticoides interspecific hybrid. The ESTs were combined into unigene sets of 8 780 unigenes for P. spicata, 11 281 unigenes for Leymus, and 7 212 unigenes for Elymus. Unigenes were annotated based on putative orthology to genes from rice, wheat, barley, other Poaceae, Arabidopsis, and the non-redundant database of the NCBI. Simple sequence repeat (SSR) markers were developed, tested for amplification and polymorphism, and aligned to the rice genome. Leymus EST markers homologous to rice chromosome 2 genes were syntenous on Leymus homeologous groups 6a and 6b (previously 1b), demonstrating promise for in silico comparative mapping. All ESTs and SSR markers are available on an EST information management and annotation database (http://titan.biotec.uiuc.edu/triticeae/).

Expression of sucrose: fructan 6-fructosyltransferase (6-SFT) and myo -inositol 1-phosphate synthase (MIPS) genes in barley (Hordeum vulgare) leaves

Summary Fructan is an important class of non-structural carbohydrates present in cool-season grasses. Sucrose: fructan 6-fructosyltransferase (6-SFT, EC 2.4.1.10), one of the enzymes thought to be involved in grass fructan biosynthesis, catalyzes the initiation and extension of 2,6-linked fructans. Myo -inositol is a central component in several metabolic pathways in higher plants. Myo -inositol 1-phosphate synthase (MIPS) (EC 5.5.1.4), the first enzyme in inositol de novo biosynthesis, catalyzes the formation of myo -inositol 1-phosphate (MIP) from glucose-6-phosphate. The expression of 6-SFT and MIPS genes is compared in barley ( Hordeum vulgare L.) leaves under various conditions. In cool temperature treatments, both 6-SFT and MIPS mRNAs accumulate within two days and then decline after four days. Under warm temperatures and continuous illumination, the amount of 6-SFT and MIPS mRNA gradually accumulated in detached leaves and increased significantly by 8 h. In contrast, we observed no significant changes over time in attached (control) leaves. Treating detached leaves with glucose or sucrose in the dark resulted in accumulations of both 6-SFT and MIPS mRNA. Homologous expression patterns for 6-SFT and MIPS genes suggest that they may be similarly regulated in barley leaves. Although sucrose and glucose may play important roles in the expression of 6-SFT and MIPS genes, regulation likely involves multiple factors.

Selection response for molecular markers associated with anthocyanin coloration and low-temperature growth traits in crested wheatgrasses

Hycrest is an outcrossing tetraploid cultivar of crested wheatgrass developed from a hybrid between an induced tetraploid form of Fairway (Agropyron cristatum) and natural tetraploid Standard (A. desertorum). The CD-II cultivar was selected from cv. Hycrest on the basis of vigorous vegetative growth and green leaf coloration during early spring. This study examines the selection response of molecular markers associated with anthocyanin coloration (AC), growth habit (GH) and other traits in Hycrest, CD-II, and two second-generation polycross (PX2) populations derived from three purple-leaf selections and three green-leaf selections of Hycrest. AC was positively correlated with prostrate GH and inversely correlated with plant height and leaf width in the experimental PX2 populations. Of the 578 AFLP markers surveyed, 13 showed pleiotropic effects on GH and AC in the PX2 populations. In all cases, marker alleles associated with prostrate GH also enhanced AC. Four of these 13 markers also showed large selecti...

Genome evolution of intermediate wheatgrass as revealed by EST-SSR markers developed from its three progenitor diploid species

Intermediate wheatgrass (Thinopyrum intermedium (Host) Barkworth & D.R. Dewey), a segmental autoallohexaploid (2n = 6x = 42), is not only an important forage crop but also a valuable gene reservoir for wheat (Triticum aestivum L.) improvement. Throughout the scientific literature, there continues to be disagreement as to the origin of the different genomes in intermediate wheatgrass. Genotypic data obtained from newly developed EST-SSR primers derived from the putative progenitor diploid species Pseudoroegneria spicata (Pursh) Á. Löve (St genome), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (J = J(b) = E(b)), and Thinopyrum elongatum (Host) D. Dewey (E = J(e) = E(e)) indicate that the V genome of Dasypyrum (Coss. & Durieu) T. Durand is not one of the three genomes in intermediate wheatgrass. Based on all available information in the literature and findings in this study, the genomic designation of intermediate wheatgrass should be changed to J(vs)J(r)St, where J(vs) and J(r) represent ancestral genomes of present-day J(b) of Th. bessarabicum and J(e) of Th. elongatum, with J(vs) being more ancient. Furthermore, the information suggests that the St genome in intermediate wheatgrass is most similar to the present-day St found in diploid species of Pseudoroegneria from Eurasia.

Conversion of an RAPD marker to an STS marker for barley variety identification

Barley (Hordeum vulgare L.) variety identification is important to the malting and brewing industries. Because many new malting cultivars (varieties) are closely related, new and more effective identification techniques are needed. We report on a series of techniques used to convert an RAPD marker to a more stable STS marker that can identify barley Stander from Robust, an important distinction for the American malting and brewing industries. The techniques included DNA extraction, RAPD amplification, random cloning of all amplified fragments, selection of clones by insert size, DNA sequencing of select inserts, design of a barley-based primer pair, and detection of a single nucleotide polymorphism using restriction endonucleaseAlu I. The barley-based primer pair was used to further sequence the RAPD fragment. Five single nucleotide polymorphisms between Robust and Stander exist, one of which was detected by electrophoresing DNA fragments differentially restricted byAlu I. The conversion technique was different from ones previously reported in that it did not require manual extraction of DNA fragments from a gel. This could be applied to other situations in which RAPD marker conversion would be desirable.

Detection of linkage disequilibrium QTLs controlling low-temperature growth and metabolite accumulations in an admixed breeding population of Leymus wildryes

Low-temperature soluble carbohydrate accumulations are commonly associated with anthocyanin coloration, attenuated growth, and cold adaptation of cool-season grasses. A total of 647 AFLP markers were tested for associations with anthocyanin coloration, tiller formation, leaf formation, cumulative leaf length, percent soluble carbohydrate, and dry matter regrowth among replicated clones of an admixed Leymus wildrye breeding population evaluated in low-temperature growth chambers. The admixed breeding population was derived from a heterogeneous population of L. cinereus × L. triticoides F1 hybrids, with two additional generations of open pollination. Two AFLP linkage maps, constructed from two full-sib mapping populations derived from the same F1 hybrid population, were integrated to produce a framework consensus map used to examine the distribution of marker-trait associations in the admixed F1OP2 population. Thirty-seven linkage blocks, spanning 258 cM (13.6%) of the 1895 cM consensus map, contained 119 (50%) of the 237 markers showing at least one possible trait association (P < 0.05). Moreover, 28 (68%) of the 41 most significant marker-trait associations (P < 0.005) were located in 15 QTL linkage blocks spanning 112.9 cM (6%) of the linkage map. The coincidence of these 28 significant marker-trait associations, and many less significant associations, in 15 relatively small linkage blocks (0.6 cM to 21.3 cM) provides evidence of admixture linkage disequilibrium QTLs (ALD QTLs) in this heterogeneous breeding population. At least four of the remaining 13 putative marker-trait associations (P < 0.005) were located in genetic map regions lacking other informative markers. The complexity of marker-trait associations results from heterogeneity within and substantial divergence among the parental accessions.