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Phalaris aquatica L. (phalaris) is a cool-season perennial grass originating from the Mediterranean Basin, north-west Africa and Middle Eastern regions that is used for livestock agriculture mainly in temperate areas with dry summers. It has been the subject of breeding programs in Australia, South America, New Zealand and the USA. Increased knowledge of relationships between wild and cultivated germplasm through use of molecular markers has the potential to facilitate future breeding gains. For this purpose, we conducted an analysis of P. aquatica by using 3905 polymorphic DArTseq SNP markers. Genetic diversity as measured by expected heterozygosity was similar for wild (HE = 0.14; n = 57) and cultivated (HE = 0.13; n = 37) accessions. Diversity in wild germplasm was generally continuous in nature, largely related to geographical location, with a division at the broadest scale into eastern and western clades, with more admixture in the western than the eastern clade. Structure analysis of wild germplasm indicated six subpopulations consistent with country of origin, with some admixture among subpopulations likely resulting from natural and human influences. There were nine subpopulations among wild and cultivated accessions combined. This population structure should be considered if genomic selection is applied in P. aquatica. Analysis of molecular variance indicated that 71% of the genetic variation occurred within subpopulations and 29% among subpopulations. Genetic distances were low among cultivated germplasm from most countries except the USA, which was more distinct. Evaluation of material from the US pool by breeding programs in other countries, and additional material from the less utilised eastern clade, may be worthwhile.

This study applied newly developed Diversity Arrays Technology (DArT) and soybean and mungbean DArT libraries for quantitative trait locus (QTL) linkage analysis in recombinant inbred lines (RILs) from three soybean crosses that had previously been assessed for physiological response to severe drought stress. The phenotypic assessments had identified statistically significant genetic variation among and within the RIL populations and their parents for three drought-related responses: epidermal conductance (ge) and relative water content (RWC) during stress, and plant recovery after stress. The new linkage maps containing only DArT markers for the three populations individually contained 196–409 markers and 15–22 linkage groups (LGs), with an aggregate length ranging from 409.4 to 516.7 cM. An integrated map constructed by using the marker data from all three RIL populations comprised 759 DArT markers, 27 LGs and an expanded length of 762.2 cM. Two populations with the landrace accession G2120 as a parent, CPI 26671 × G2120 (CG) and Valder × G2120 (VG), respectively contained 106 and 34 QTLs. In each of these populations, 10 LGs harboured QTLs associated with RWC, ge and recovery ability, of which six similar LGs were associated with drought tolerance. A BLAST (Basic Local Alignment Search Tool) search for sequences of 19 selected DArT markers linked to QTLs conditioning the drought-response traits indicated that 18 DArT markers were unique and aligned to 12 soybean chromosomes. Comparison of these sequenced DArT markers with other markers associated with drought-related QTLs in previously reported studies using other marker types confirmed that five of them overlapped, whereas the remaining 13 were new. Except for chromosome 15, the chromosomes with which the DArT QTLs in the CG and VG populations were associated were those that had been shown to harbour drought-related QTLs in previous studies. A BLASTx protein database search identified soPt-856602 as being associated with the gene for a probable glycosyltransferase At5g03795-like isoform X1 on chromosome 6. Although the several QTLs identified in the study were all of relatively minor effect, it was concluded that, because the DArT technology involves large numbers of markers and enables many lines to be genotyped simultaneously, it should help the process of manipulating multiple QTLs and so enhance their likely cumulative effect.

Physiological drought stress responses were assessed in recombinant inbred lines (RILs) from three soybean (Glycine max (L.) Merr.) crosses, in preparation for quantitative trait locus (QTL) analyses using Diversity Arrays Technology (DArT) markers. The three RIL populations were derived from pairwise crosses between three genotypes, cv. Valder, CPI 26671 and G2120, which in previous studies had differed in drought-stress response. Of particular interest was the landrace variety G2120, which in the previous reports had recovered better after severe drought. To assess drought-stress response, the plants were grown in deep cylindrical pots in the glasshouse and exposed to severe water deficit followed by re-watering. Two plants to be genotyped were grown in each pot, together with one plant of G2120, which served as a reference plant against which the responses of the two other plants were assessed. Traits recorded included measures of relative water content (RWC), epidermal conductance (ge) and recovery in growth following re-watering. The responses in the reference and parental plants and the RIL populations were broadly consistent with previous studies. As plant-available water in the soil declined, both RWC and ge declined, although the relation between RWC and ge was exponential, rather than linear as in previous studies. Analysis of variance revealed large environmental effects on most of the traits, which resulted in high coefficients of variation and low estimates of broad-sense heritability. However, there were significant differences at both the population and genotype levels for all key traits, confirming the presence of genetic variation for drought-stress response. Some opportunities for enhancing the observed genetic differences and reducing the environmental noise in future studies are canvassed. Application of the observed phenotypic data reported in this paper in subsequent QTL analyses based on DArT markers is reported in the companion paper.

Synthetic hexaploid wheats (SHWs) and their synthetic derivative lines (SDLs) are being used as a means of introducing novel genetic variation into bread wheat (BW). Phenotypic information for days to flowering, height, grain weight and grain yield was collected from multiple environments for three SDL families, each with ~50 lines, and their elite BW parents. In general, the SDLs were earlier flowering and taller with larger grain size, but similar grain yield to the BWs. The three SDL families and their SHW and BW parents were genotyped using mapped DArT (diversity arrays technology) markers. Within each SDL family, SHW-specific DArT markers were used to identify SHW-derived chromosomal regions that appeared to be preferentially retained in the SDL families, as determined by retention at frequencies >0.25, the expected frequency for Mendelian segregation. Regions on chromosomes 2BS and 7BL appeared to be preferentially retained in all three SDL families, while regions on chromosomes 1AL, 1BS, 3BS, 5AS, 5BL, and 7AS were preferentially retained in two of the three SDL families. Other regions were preferentially retained in single families only, including some regions located on the D genome. Single-marker regression analysis was performed using the preferentially retained markers and identified markers and regions that were significantly associated with one or more of the four traits measured. Comparative mapping also indicates that these preferentially retained markers and chromosome regions may co-locate with previously identified QTLs for anthesis, height, grain weight and/or grain yield. Therefore, SHWs may contain novel alleles at these loci in these regions for these traits, which may provide a selective advantage to the SDLs. This approach could provide a useful method for identifying chromosomal regions of interest with potentially novel alleles for introgression for further BW improvement.

European winter canola (Brassica napus L.) cultivars harbour genes for durable resistance to the fungus Leptosphaeria maculans, which causes blackleg disease under Australian environmental conditions. Previous studies have shown that resistance in winter-type cultivars Maxol and Columbus is controlled by two genes, Rlm1 and Rlm3, which have been mapped using randomly amplified polymorphic DNA markers onto chromosome A7. We mapped a doubled-haploid population that consisted of 101 lines from a cross between Maxol*1 and Westar-10 using diversity arrays technology and simple sequence repeat (SSR)-based markers. Two SSR marker loci, Xol12-e03 and Xra2-a05b, flanked the Rlm1 locus at an interval of 6.7 cM, which corresponds to ~3.2 Mb of the Brassica rapa genomic sequence; this region contains several genes encoding putative kinase and leucine-rich repeat-type disease-resistance proteins. SSR markers were further tested for their linkage with the Rlm1 locus in an independent population derived from Columbus*3/Westar-10. Our results showed that SSR markers linked to Rlm1 can be useful for monitoring Rlm1 gene introgression in breeding populations derived from Maxol and Columbus.

This study has employed multicolour fluorescence in situ hybridisation (MCFISH) and Diversity Arrays Technology (DArT) markers to determine the segregation of parental A, B and D genome material into the progeny of a cross between a hexaploid bread wheat (Triticum aestivum L. var. 2-49) and a tetraploid durum wheat [T. turgidum L. spp. durum (Desf.) var. Bellaroi]. In the F2 progeny from a 2-49/Bellaroi cross, 82 out of 83 F2 plants investigated with DArT analysis carried some D genome material, principally as entire chromosomes, while 40 plants included at least one complete copy of all seven D genome chromosomes. Twelve plants containing partial D chromosomes were identified. MCFISH analysis of 26 additional F2 plants of the same cross showed that all 26 plants contained varying amounts of D genome material of which three carried single A-D translocations. In addition two telocentric D genome chromosomes were detected. The D genome content of each line and the breakpoint positions of the three A-D translocations were confirmed with DArT marker analysis. Overall results indicate a random recombination of A and B genome loci from the hexaploid female parent and the tetraploid male parent in this F2 population and a significant retention of the maternal D genome material. This study illustrates that the combined application of the MCFISH and DArT techniques provides a powerful approach for the analysis of crosses between cereal genotypes of different ploidy.

Diversity Arrays Technology (DArT™) was evaluated as a tool for determining molecular diversity of wheat landraces held within the Australian Winter Cereals Collection (AWCC). Initially, a set of 44 wheat landraces was evaluated with 256 DArT markers. The dataset was compared with the results obtained using 16 amplified fragment length polymorphism (AFLP) primer combinations and 63 simple sequence repeat (SSR) markers, mapped on the 21 chromosomes, from a previous study. The DArT markers exhibited a strong positive correlation with AFLP and SSR, with each marker type distinguishing similar relationships among the 44 landrace accessions. The DArT markers exhibited a higher polymorphic information content than AFLP, and were comparable with that obtained with SSR. Three hundred and fifty-five DArT markers were then used to evaluate genetic diversity among 705 wheat landrace accessions from within the AWCC, chosen to represent 5 world regions. DArT analysis was capable of distinguishing accessions from different geographic regions, and suggested that accessions originating from Nepal represent a unique gene pool within the collection. A statistical resampling of DArT loci indicated that 10–20 loci were enough to distinguish the maximum molecular diversity present within the collection. This research demonstrates the efficacy of the DArT platform as a tool for efficient examination of wheat diversity. As an ex situ germplasm repository, the AWCC contains wheat accessions of high genetic diversity, from genetically differentiated collection sites, even though diversity was under-represented in some countries represented in the repository.