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Abstract Background Resistance to soil waterlogging stress is an important plant breeding objective in high rainfall or poorly drained areas across many countries in the world. The present study was conducted to identify quantitative trait loci (QTLs) associated with waterlogging tolerance (e.g. leaf chlorosis, plant survival and biomass reduction) in barley and compare the QTLs identified across two seasons and in two different populations using a composite map constructed with SSRs, RFLP and Diversity Array Technology (DArT) markers. Results Twenty QTLs for waterlogging tolerance related traits were found in the two barley double haploid (DH) populations. Several of these QTLs were validated through replication of experiments across seasons or by co-location across populations. Some of these QTLs affected multiple waterlogging tolerance related traits, for example, QTL Qwt4-1 contributed not only to reducing barley leaf chlorosis, but also increasing plant biomass under waterlogging stress, whereas other QTLs controlled both leaf chlorosis and plant survival. Conclusion Improving waterlogging tolerance in barley is still at an early stage compared with other traits. QTLs identified in this study have made it possible to use marker assisted selection (MAS) in combination with traditional field selection to significantly enhance barley breeding for waterlogging tolerance. There may be some degree of homoeologous relationship between QTLs controlling barley waterlogging tolerance and that in other crops as discussed in this study.

Abstract Background Bulked segregant analysis (BSA) identifies molecular markers associated with a phenotype by screening two DNA pools of phenotypically distinct plants for markers with skewed allele frequencies. In contrast to gel-based markers, hybridization-based markers such as SFP, DArT or SNP generate quantitative allele-frequency estimates. Only DArT, however, combines this advantage with low development and assay costs and the ability to be deployed for any plant species irrespective of its ploidy level. Here we investigate the suitability of DArT for BSA applications using a barley array as an example. Results In a first test experiment, we compared two bulks of 40 Steptoe/Morex DH plants with contrasting pubescent leaves (mPub) alleles on chromosome 3H. At optimized levels of experimental replication and marker-selection threshold, the BSA scan identified 433 polymorphic markers. The relative hybridization contrast between bulks accurately reflected the between-bulk difference in the frequency of the mPub allele (r = 0.96). The 'platform noise' of DArT assays, estimated by comparing two identical aliquots of a DNA mixture, was significantly lower than the 'pooling noise' reflecting the binomial sampling variance of the bulking process. The allele-frequency difference on chromosome 3H increased in the vicinity of mPub and peaked at the marker with the smallest distance from mPub (4.6 cM). In a validation experiment with only 20 plants per bulk we identified an aluminum (Al) tolerance locus in a Dayton/Zhepi2 DH population on chromosome 4H with < 0.8 cM precision, the same Al-tolerance locus that had been mapped before in other barley populations. Conclusion DArT-BSA identifies genetic loci that influence phenotypic characters in barley with at least 5 cM accuracy and should prove useful as a generic tool for high-throughput, quantitative BSA in plants irrespective of their ploidy level.

Abstract Background Molecular marker technologies are undergoing a transition from largely serial assays measuring DNA fragment sizes to hybridization-based technologies with high multiplexing levels. Diversity Arrays Technology (DArT) is a hybridization-based technology that is increasingly being adopted by barley researchers. There is a need to integrate the information generated by DArT with previous data produced with gel-based marker technologies. The goal of this study was to build a high-density consensus linkage map from the combined datasets of ten populations, most of which were simultaneously typed with DArT and Simple Sequence Repeat (SSR), Restriction Enzyme Fragment Polymorphism (RFLP) and/or Sequence Tagged Site (STS) markers. Results The consensus map, built using a combination of JoinMap 3.0 software and several purpose-built perl scripts, comprised 2,935 loci (2,085 DArT, 850 other loci) and spanned 1,161 cM. It contained a total of 1,629 'bins' (unique loci), with an average inter-bin distance of 0.7 ± 1.0 cM (median = 0.3 cM). More than 98% of the map could be covered with a single DArT assay. The arrangement of loci was very similar to, and almost as optimal as, the arrangement of loci in component maps built for individual populations. The locus order of a synthetic map derived from merging the component maps without considering the segregation data was only slightly inferior. The distribution of loci along chromosomes indicated centromeric suppression of recombination in all chromosomes except 5H. DArT markers appeared to have a moderate tendency toward hypomethylated, gene-rich regions in distal chromosome areas. On the average, 14 ± 9 DArT loci were identified within 5 cM on either side of SSR, RFLP or STS loci previously identified as linked to agricultural traits. Conclusion Our barley consensus map provides a framework for transferring genetic information between different marker systems and for deploying DArT markers in molecular breeding schemes. The study also highlights the need for improved software for building consensus maps from high-density segregation data of multiple populations.

The increasing contamination of agricultural soils with cadmium (Cd) poses a significant threat to human health and global food security. Plants initiate a series of mechanisms to reduce Cd toxicity. However, the response of maize to Cd toxicity remains poorly understood. In this study, we identified that ZmHMT3, which encodes a homocysteine S‐methyltransferases family protein, acted as a regulator of Cd tolerance in maize. Subcellular localization and in situ PCR exhibited that ZmHMT3 was localized in the cytoplasm and predominantly expressed in the phloem. Overexpression of ZmHMT3 enhanced Cd tolerance and reduced Cd concentration in both shoots and roots. In contrast, ZmHMT3 mutants attenuated Cd tolerance but did not change shoot Cd concentration. Heterologous overexpression of ZmHMT3 in rice enhanced Cd tolerance and reduced grain Cd concentration. Transcriptome analysis revealed that ZmHMT3 upregulated the expression of stress‐responsive genes, especially glutathione S‐transferases (GSTs) and transcription factors, including MYBs, NACs and WRKYs, and modulates the expression of different ATP‐binding cassette (ABC) transporters, thereby enhancing Cd tolerance. Collectively, these findings highlight the pivotal role of ZmHMT3 in Cd tolerance and as a candidate gene for improving Cd tolerance in elite maize varieties. Summary Statement: ZmHMT3 was first identified as a vital regulator of Cd tolerance in Zea mays, modulating the expression of transcription factors, glutathione S‐transferases and ABC transporters. The exploitation of ZmHMT3 presents a promising strategy for enhancing Cd tolerance in elite maize cultivars. [ABSTRACT FROM AUTHOR]

Waterlogging increasingly challenges crop production, affecting 10% of global arable land, necessitating the development of pragmatic strategies for mitigating the downside risk of yield penalty. Here, we conducted experiments under controlled (tank) and field conditions to evaluate the efficacy of nitrogenous fertiliser in alleviating waterlogging stress. Without intervention, we found that waterlogging reduced grain yields, spike numbers and shoot biomass, but had a de minimus impact on grain number per spike and increased grain weight. Soil fertiliser mitigated waterlogging damage, enhancing yields via increased spike numbers, with crop recovery post-waterlogging catalysed via improved tiller numbers, plant height and canopy greenness. Foliar nitrogen spray has little impact on crop recovery, possibly due to stomatal closure, while modest urea application during and after waterlogging yielded similar results to greater N application at the end of waterlogging. Waterlogging-tolerant genotypes (P-17 and P-52) showed superior growth and recovery during and after waterlogging compared to the waterlogging-sensitive genotypes (Planet and P-79). A comparison of fertiliser timing revealed that field fertilizer treatment two (F2: 90 kg·ha−1 at 28 DWL, 45 kg·ha−1 at sowing and 45 kg·ha−1 at 30 DR) yielded the highest and fertilizer treatment three (F3: 45 kg·ha−1 at sowing and 45 kg·ha−1 at 30 DR) recovered the lowest yield and spike number, while fertilizer treatment one (F1: 45 kg·ha−1 at 28 DWL, 45 kg·ha−1 at 0 DR, 45 kg·ha−1 at sowing and 45 kg·ha−1 at 30 DR) and four (F4: 90 kg·ha−1 at 0 DR, 45 kg·ha−1 at sowing and 45 kg·ha−1 at 30 DR) had the highest shoot biomass in the field. Treatment five (T5: 180 kg·ha−1 at 0 DR, 30 kg·ha−1 at sowing and 90 kg·ha−1 at 30 DR) presented the most favourable results in the tank. Our results provide rigorous evidence that long periods of waterlogging caused significant yield penalty, mainly due to decreased spike numbers. We contend that increasing fertiliser rates during waterlogging up to 90 kg·ha−1 can provoke crop growth and mitigate waterlogging-induced grain yield losses, and is more beneficial than applying nitrogen post-waterlogging. [ABSTRACT FROM AUTHOR]