Mapping regulatory genes as candidates for cold and drought stress tolerance in barley

Abstract

Cereal crop yield is greatly affected in many growing areas by abiotic stresses, mainly low temperature and drought. In order to find candidates for the tolerance genes for these stresses, 13 genes encoding for transcription factors and upstream regulators were screened by amplification and SSCP on six parental genotypes of three barley mapping populations ('Nure' x 'Tremois', 'Proctor' x 'Nudinka', and 'Steptoe' x 'Morex'), and mapped as newly developed STS, SNP, and SSCP markers. A new consensus function map was then drawn using the three maps above, including 16 regulatory candidate genes (CGs). The positions of barley cold and drought tolerance quantitative trait loci (QTLs) presently described in the literature were added to the consensus map to find positional candidates from among the mapped genes. A cluster of six HvCBF genes co-mapped with the Fr-H2 cold tolerance QTL, while no QTLs for the same trait were positioned on chromosome 7H, where two putative barley regulators of CBF expression, ICE1 and FRY1, found by homology search, were mapped in this work. These observations suggest that CBF gene(s) themselves, rather than their two regulators, are at present the best candidates for cold tolerance. Four out of 12 drought tolerance QTLs of the consensus map are associated with regulatory CGs, on chromosomes 2H, 5H, and 7H, and two QTLs with effector genes, on chromosomes 5H and 6H. The results obtained could be used to guide MAS applications, allowing introduction into an ideal genotype of favourable alleles of tolerance QTLs.

Transcriptome Analysis of Cold Acclimation in Barley Albina and Xantha Mutants

“…A search for this cis-element (http://intra.psb.ugent.be:8080/PlantCARE/) in promoters of barley cold-regulated genes found several The Cbf sequences used in the analysis were BCbf1 (AF298230, probe set: contig15617_at), HvCbf1 (AF418204, probe set: contig13523_at), and the Cbf-like sequence BG367653 (probe set: contig2479_at). Beside Cbfs, HvICE1 (probe set: contig 21686_at), a barley sequence highly homologous to the Arabidopsis ICE1 (Tondelli et al, 2006) and the barley gene Hv-WRKY38 (probe set: contig4386_at; Marè et al, 2004), a cold-regulated transcription factor belonging to the ICE1 regulon were also investigated. Normalization was carried out with b-actin.…”

“…BCbf1, HvCbf1, and the Cbf-like sequence corresponding to the accession number BG367653 were cold induced to a similar extent in mutants and wild-type plants after 4 and 8 h of cold treatment, and expression was greatly reduced after 24 h of cold treatment. Beside Cbfs, a barley sequence (HvICE1; Tondelli et al, 2006) highly homologous to the Arabidopsis ICE1 (a constitutively expressed activator of Cbf induction; Chinnusamy et al, 2003) and the cold-regulated barley gene Hv-WRKY38 (a cold-induced transcription factor belonging to the ICE1 regulon; Marè et al, 2004) were also investigated and their expression profile was identical in mutants and wild-type plants (Fig. 4B).…”

“…Three Cbf-like transcripts were amplified using the following primers: BCbf1 (AF298230, probe set contig15617_at), 5#-TACATCTCGTCCGGCGACCTGTTGGAGC-3# and 5#-AACTTAGCACAATTGAATCGGATGAGATC-3# (annealing 60°C); HvCbf1 (AF418204, probe set contig13523_at), 5#-GGATGCTCATTGCCCCT-CCT-3# and 5#-AGCCCCAACACTCCTTCGGA-3# (annealing 55°C); BG367653 (probe set: contig2479_at), 5#-AGCTGGACGTCCTGAGCGA-CATG-3# and 5#-GCTCTGTTTCCCCAATTTGCAC-3# (annealing 58°C). Two additional sequences coding Hv-WRKY38 (Marè et al, 2004), 5#-CCGTC-AAAGCCTCGCAGACAAAGC-3# and 5#-TATGGAACGGAACATTTGAA-TGA-3# (annealing 58°C) and HvICE1, a barley homolog of the Arabidopsis ICE1 gene (Tondelli et al, 2006), 5#-CTGAGCAATGCAAGGATGG-3# and 5#-GACACAGGGTAGTGACATCAGG-3# (annealing 55°C) were also investigated. The transcripts were amplified from 400 ng of cDNA as template and 2 units of Taq DNA polymerase (Invitrogen) using 28 cycles (94°C for 1 min, annealing for 30 s, 72°C for 30 s) followed by a final extension step at 72°C for 7 min.…”

Changes in allele frequencies in landraces, old and modern barley cultivars of marker loci close to QTL for grain yield under high and low input conditions

“…Most contemporary studies carried out on barley adaptation to low yielding Mediterranean environments centred on identifying QTL related to stress tolerance in doubled haploid or recombinant inbred lines populations produced from single crosses (Teulat et al 2002(Teulat et al , 2003Baum et al 2003;Forster et al 2004, Francia et al 2004Tondelli et al 2006) or, more recently, on a wide collection of germplasm by association mapping (Comadran et al 2008a). The current study was set out to investigate changes in allele frequencies of marker loci close to quantitative trait loci (QTL) for yield in landraces, old, and new cultivars.…”

Key molecular and metabolic processes used for genetic engineering to improve freezing tolerance in cereals.

“…In Arabidopsis, six CBFs have been identified, while in the economically important cereals, the number of CBFs are much higher: 20 in barley (Hordeum vulgare L.) (Skinner et al, 2005), 13 in einkorn (Triticum monococcum) (Miller et al, 2006) and 37 in common wheat (Triticum aestivum L.) (Badawi et al, 2007). CBF genes are positioned in clusters on the homeologous group 5 chromosomes of the Triticeae and coincide with the FR-2 quantitative trait locus (QTL) for freezing tolerance (Vágújfalvi et al, 2003(Vágújfalvi et al, , 2005Miller et al, 2006;Tondelli et al, 2006;Båga et al, 2007;Francia et al, 2007). CBFs in Triticeae are regulated in a complex way, influenced by genotype, induction-temperature and lightregulated factors (Campoli et al, 2009).…”