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Background: Barley semi-dwarf genes have been extensively explored and widely used in barley breeding programs. The semi-dwarf gene ari-e from Golden Promise is an important gene associated with some agronomic traits and salt tolerance. While ari-e has been mapped on barley chromosome 5H using traditional markers and next-generation sequencing technologies, it has not yet been finely located on this chromosome. Results: We integrated two methods to develop molecular markers for fine-mapping the semi-dwarf gene ari-e: (1) specific-length amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) to develop SNP markers, and (2) the whole-genome shotgun sequence to develop InDels. Both SNP and InDel markers were developed in the target region and used for fine-mapping the ari-e gene. Linkage analysis showed that ari-e cosegregated with marker InDel-17 and was delimited by two markers (InDel-16 and DGSNP21) spanning 6.8 cM in the doubled haploid (DH) Dash × VB9104 population. The genetic position of ari-e was further confirmed in the Hindmarsh × W1 DH population which was located between InDel-7 and InDel-17. As a result, the overlapping region of the two mapping populations flanked by InDel-16 and InDel-17 was defined as the candidate region spanning 0.58 Mb on the POPSEQ physical map. Conclusions: The current study demonstrated the SLAF-seq for SNP discovery and whole-genome shotgun sequencing for InDel development as an efficient approach to map complex genomic region for isolation of functional gene. The ari-e gene was fine mapped from 10 Mb to 0.58 Mb interval. [ABSTRACT FROM AUTHOR]

Rhynchosporium secalis can overcome a single resistance gene of barley in a relatively short period of time. Novel genes and quantitative trait locis (QTLs) are therefore vital to control scald in barley. A population of 220 double haploid lines was developed from a cross of Vlamingh and WABAR2147, where Vlamingh showed adult plant resistance (APR) and WABAR2147 showed seedling resistance to a group of isolates. The population was tested for APR to scald under natural infection in two consecutive seasons in addition to a seedling screen with three isolates. One single gene was mapped to chromosome 6H based on the seedling test, and two QTLs ( QSc.VlWa.4H and QSc.VlWa.6H) were mapped to chromosomes 4H and 6H based on APR. Epistatic interaction was observed between the two QTLs, and environment/QTL interaction was only observed for QSc.VlWa.6H which co-segregated with the seedling resistance gene and contributed to basal resistance against scald during whole growth stages. QSc.VlWa.4H explained 42.5 and 57.8 % of the phenotypic variation in the two independent trials when the effect of QSc.VlWa.6H was excluded from the analysis. We developed a high-density consensus genetic map with 7,876 molecular makers and anchored 43 QTLs and 7 genes for scald resistance from different mapping populations. No known QTLs or genes were reported in a similar position to QSc.VlWa.4H, and it was the first major QTL for APR of scald on chromosome 4HS in barley. Combination of the two QTLs achieved better and stable scald resistance across four different environments. [ABSTRACT FROM AUTHOR]

Photoperiod response is a key determinant for barley adaptation to diverse environments. A major quantitative trait locus (QTL) for response to long photoperiod was identified in Australia (Perth, 31°56′S) and China (Wuhan, 30°33′N) using 178 doubled haploid lines derived from a cross of an Australian barley, Baudin, and a Canadian barley, AC Metcalfe. The QTL was detected as a major QTL in the 18-h photoperiod glasshouse experiments and mapped to the Xp12m50B199- Xp13m47B399 interval on chromosome 4H with a LOD score of 57 in Australia and confirmed in China. The single QTL accounted for 77.48 and 37.81% of phenotypic variation for long photoperiod response in Australia and China, respectively. The same QTL also controlled heading date in Australia, under normal and extended photoperiod conditions, and in China, under extended photoperiod and late-sown conditions. The QTL advanced heading date by 27.8 days in Australia and 42.5 days in China under a 18-h photoperiod. In addition, QTL for heading date were identified on chromosomes 2H and 3H. The chromosome 3H QTL was associated with the denso gene and detected in all conditions, but the chromosome 2H QTL was only detected in Australia. The new photoperiod response QTL, Qhea.BM.4- 13/Qpho.BM.4- 13, on chromosome 4H and its associated markers will provide an alternative for plant breeders developing new varieties for different environments using marker-assisted selection. [ABSTRACT FROM AUTHOR]

A number of technologies are available to increase the abundance of DNA markers and contribute to developing high resolution genetic maps suitable for genetic analysis. The aim of this study was to expand the number of Diversity Array Technology (DArT) markers on the wheat array that can be mapped in the wheat genome, and to determine their chromosomal location with respect to simple sequence repeat (SSR) markers and their position on the cytogenetic map. A total of 749 and 512 individual DArT and SSR markers, respectively, were identified on at least one of four genetic maps derived from recombinant inbred line (RIL) or doubled haploid (DH) populations. A number of clustered DArT markers were observed in each genetic map, in which 20–34% of markers were redundant. Segregation distortion of DArT and SSR markers was also observed in each mapping population. Only 14% of markers on the Version 2.0 wheat array were assigned to chromosomal bins by deletion mapping using aneuploid lines. In this regard, methylation effects need to be considered when applying DArT marker in genetic mapping. However, deletion mapping of DArT markers provides a reference to align genetic and cytogenetic maps and estimate the coverage of DNA markers across the wheat genome. [ABSTRACT FROM AUTHOR]