The rhg1-b allele of soybean is widely used for resistance against soybean cyst nematode (SCN), the most economically damaging pathogen of soybeans in the United States. Gene silencing showed that genes in a 31-kilobase segment at rhg1-b, encoding an amino acid transporter, an α-SNAP protein, and a WI12 (wound-inducible domain) protein, each contribute to resistance. There is one copy of the 31-kilobase segment per haploid genome in susceptible varieties, but 10 tandem copies are present in an rhg1-b haplotype. Overexpression of the individual genes in roots was ineffective, but overexpression of the genes together conferred enhanced SCN resistance. Hence, SCN resistance mediated by the soybean quantitative trait locus Rhg1 is conferred by copy number variation that increases the expression of a set of dissimilar genes in a repeated multigene segment.

The soybean cyst nematode (SCN) resistance locus Rhg1 is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2-kb unit contains four genes. One allele of Rhg1, Rhg1-b, is responsible for protecting most US soybean production from SCN. Whole-genome sequencing was performed, and PCR assays were developed to investigate allelic variation in sequence and copy number of the Rhg1 locus across a population of soybean germplasm accessions. Four distinct sequences of the 31.2-kb repeat unit were identified, and some Rhg1 alleles carry up to three different types of repeat unit. The total number of copies of the repeat varies from 1 to 10 per haploid genome. Both copy number and sequence of the repeat correlate with the resistance phenotype, and the Rhg1 locus shows strong signatures of selection. Significant linkage disequilibrium in the genome outside the boundaries of the repeat allowed the Rhg1 genotype to be inferred using high-density single nucleotide polymorphism genotyping of 15 996 accessions. Over 860 germplasm accessions were found likely to possess Rhg1 alleles. The regions surrounding the repeat show indications of non-neutral evolution and high genetic variability in populations from different geographic locations, but without evidence of fixation of the resistant genotype. A compelling explanation of these results is that balancing selection is in operation at Rhg1.

Oxygen deficiency is one of the major stresses to plants under waterlogging. A low‐oxygen‐signaling pathway is the most important mechanism for adaptation and survival under anaerobic conditions. To find genes related to the oxygen concentration in root environment in common wheat roots, we investigated the transcriptional expression in vitro for low‐oxygen treatment. Dramatic increases in the transcripts of a TaMyb1 (Triticum aestivum Myb transcription factor 1) gene occurred under hypoxia. Presence of TaMyb1 on the 3BL was confirmed by using Chinese Spring aneuploid accessions including nullisomic–tetrasomic and ditelosomic lines. The transcriptional expression of TaMyb1 was continued until approximate anoxia, being enhanced by light under hypoxia, but little expression during anoxia could be shown by Northern hybridization. The TaMyb1 expression was high in the epidermis, endodermis and the cortex adjacent to the endodermis under hypoxia but undetectable in the vascular tissues or cortex, which contained aerenchyma. TaMyb1 transcription levels in roots gradually increased as the result of treatment with NaCl. Slight increases in expression were noted during the early stages of exogenous treatment of with both abscisic acid and polyethylene glycol. Little and constant expressions were detected as the result of citric acid treatment. Our data suggested that the expression of TaMyb1 in roots could be strongly related to the oxygen concentration in root environment and the wheat plant responses to abiotic stresses.

Pectin, one of the main components of plant cell wall, is deesterified by the pectin methylesterase (PME). PME activity is regulated by inhibitor proteins known as the pectin methylesterase inhibitor (PMEI), which plays a key role in wounding, osmotic stress, senescence and seed development. However, the role of PMEI in many plant species still remains to be elucidated, especially in wheat. To facilitate the expression analysis of the TaPMEI gene, RT-PCR was performed using leaf, stem and root tissues that were treated with exogeneous application of phytohormones and abiotic stresses. High transcription was detected in salicylic acid (SA) and hydrogen peroxide treatments. To elucidate the subcellular localization of the TaPMEI protein, the TaPMEI:GFP fusion construct was transformed into onion epidermal cells by particle bombardment. The fluorescence signal was exclusively detected in the cell wall. Using an enzyme assay, we confirmed that PME was completely inhibited by TaPMEI. These results indicated that TaPMEI was involved in inhibition of pectin methylesterification and may play a role in the plant defense mechanism via cell wall fortification.

Previously, the genes encoding non-specific lipid transfer proteins (nsLTPs) of the Poaceae family appear to evidence different genomic distribution and somewhat different shares of EST clones, which is suggestive of independent duplication(s) followed by functional diversity. To further evaluate the evolutionary fate of the Poaceae nsLTP genes, we have identified Ka/Ks values, conserved, mutated or lost cis-regulatory elements, responses to several elicitors, genome-wide expression profiles, and nsLTP gene-coexpression networks of both (or either) wheat and rice. The Ka/Ks values within each group and between groups appeared to be similar, but not identical, in both species. The conserved cis-regulatory elements, e.g. the RY repeat (CATGCA) element related to ABA regulation in group A, might be reflected in some degree of long-term conservation in transcriptional regulation post-dating speciation. In group A, wheat nsLTP genes, with the exception of TaLTP4, evidenced responses similar to those of plant elicitors; however, the rice nsLTP genes evidenced differences in expression profiles, even though the genes of both species have undergone purifying selection, thereby suggesting their independent functional diversity. The expression profiles of rice nsLTP genes with a microarray dataset of 155 gene expression omnibus sample (GSM) plates suggest that subfunctionalization is not the sole mechanism inherent to the evolutionary history of nsLTP genes but may, rather, function in concert with other mechanism(s). As inferred by the nsLTP gene-coexpression networks, the functional diversity of nsLTP genes appears not to be randomized, but rather to be specialized in the direction of specific biological processes over evolutionary time.