Association of Candidate Genes With Submergence Response in Perennial Ryegrass

A comparison of shared patterns of differential gene expression and gene ontologies in response to water-stress in roots and leaves of four diverse genotypes of Lolium and Festuca spp. temperate pasture grasses

Ryegrasses (Lolium spp.) and fescues (Festuca spp.) are closely related and widely cultivated perennial forage grasses. As such, resilience in the face of abiotic stresses is an important component of their traits. We have compared patterns of differentially expressed genes (DEGs) in roots and leaves of two perennial ryegrass genotypes and a single genotype of each of a festulolium (predominantly Italian ryegrass) and meadow fescue with the onset of water stress, focussing on overall patterns of DEGs and gene ontology terms (GOs) shared by all four genotypes. Plants were established in a growing medium of vermiculite watered with nutrient solution. Leaf and root material were sampled at 35% (saturation) and, as the medium dried, at 15%, 5% and 1% estimated water contents (EWCs) and RNA extracted. Differential gene expression was evaluated comparing the EWC sampling points from RNAseq data using a combination of analysis methods. For all genotypes, the greatest numbers of DEGs were identified in the 35/1 and 5/1 comparisons in both leaves and roots. In total, 566 leaf and 643 root DEGs were common to all 4 genotypes, though a third of these leaf DEGs were not regulated in the same up/down direction in all 4 genotypes. For roots, the equivalent figure was 1% of the DEGs. GO terms shared by all four genotypes were often enriched by both up- and down-regulated DEGs in the leaf, whereas generally, only by either up- or down-regulated DEGs in the root. Overall, up-regulated leaf DEGs tended to be more genotype-specific than down-regulated leaf DEGs or root DEGs and were also associated with fewer GOs. On average, only 5–15% of the DEGs enriching common GO terms were shared by all 4 genotypes, suggesting considerable variation in DEGs between related genotypes in enacting similar biological processes.

Natural variation and genomic prediction of growth, physiological traits, and nitrogen-use efficiency in perennial ryegrass under low-nitrogen stress

Genomic prediction of nitrogen-use efficiency (NUE) has not previously been studied in perennial grass species exposed to low-N stress. Here, we conducted a genomic prediction of physiological traits and NUE in 184 global accessions of perennial ryegrass (Lolium perenne) in response to a normal (7.5 mM) and low (0.75 mM) supply of N. After 21 d of treatment under greenhouse conditions, significant variations in plant height increment (ΔHT), leaf fresh weight (LFW), leaf dry weight (LDW), chlorophyll index (Chl), chlorophyll fluorescence, leaf N and carbon (C) contents, C/N ratio, and NUE were observed in accessions , but to a greater extent under low-N stress. Six genomic prediction models were applied to the data, namely the Bayesian method Bayes C, Bayesian LASSO, Bayesian Ridge Regression, Ridge Regression-Best Linear Unbiased Prediction, Reproducing Kernel Hilbert Spaces, and randomForest. These models produced similar prediction accuracy of traits within the normal or low-N treatments, but the accuracy differed between the two treatments. ΔHT, LFW, LDW, and C were predicted slightly better under normal N with a mean Pearson r-value of 0.26, compared with r=0.22 under low N, while the prediction accuracies for Chl, N, C/N, and NUE were significantly improved under low-N stress with a mean r=0.45, compared with r=0.26 under normal N. The population panel contained three population structures, which generally had no effect on prediction accuracy. The moderate prediction accuracies obtained for N, C, and NUE under low-N stress are promising, and suggest a feasible means by which germplasm might be initially assessed for further detailed studies in breeding programs.

Association of candidate genes with drought tolerance traits in zoysiagrass germplasm

Drought stress negatively influences the growth and physiology of perennial grasses. The objective of this study was to identify associations of candidate genes with drought tolerance traits in 96 zoysiagrass (Zoysia Willd.) accessions. Germplasm varied largely in leaf wilting, canopy and air temperature difference (CAD), leaf water content (LWC), chlorophyll fluorescence (Fv/Fm), leaf dry weight (LDW), stolon dry weight (SDW), rhizome dry weight (RZW), and root dry weight (RDW) under drought stress across the two experiments in 2014 and 2015 in a greenhouse. The population exhibited three subgroups based on molecular marker analysis and had minimum relative kinship. Associations between single nucleotide polymorphisms (SNPs) in BADH encoding betaine aldehyde dehydrogenase, DREB1 encoding DREB-like protein 1, Ndhf encoding NADH dehydrogenase subunit F, CAT encoding catalase, and VP1 encoding H⁺-pyrophosphatase were analyzed with trait under drought stress (D) and relative values compared to the control (R). Twenty-seven mark and trait associations were detected in year 2014, 2015, and a two-year combination across four genes, including 13 associations in 7 SNP loci in BADH, 9 associations in 5 SNP loci in DREB1, 3 associations in one SNP locus in Ndhf, and 2 associations in one SNP locus in CAT. Of them, one SNP in BADH was associated with D-RDW or D-SDW, three SNPs in DREB1 were associated with D-RZW, D-RDW, R-LWC, and D-CAD, and one SNP in CAT was associated with D-SDW. Nucleotide changes in these SNP loci caused non-synonymous amino acid substitutions. The results indicated that allelic diversity in genes involved in antioxidant metabolism, osmotic homeostasis, and dehydration responsive transcription factor could contribute to growth and physiological variations in zoysiagrass under drought stress.

Improving Flooding Tolerance of Crop Plants

A major problem of climate change is the increasing duration and frequency of heavy rainfall events. This leads to soil flooding that negatively affects plant growth, eventually leading to death of plants if the flooding persists for several days. Most crop plants are very sensitive to flooding, and dramatic yield losses occur due to flooding each year. This review summarizes recent progress and approaches to enhance crop resistance to flooding. Most experiments have been done on maize, barley, and soybean. Work on other crops such as wheat and rape has only started. The most promising traits that might enhance crop flooding tolerance are anatomical adaptations such as aerenchyma formation, the formation of a barrier against radial oxygen loss, and the growth of adventitious roots. Metabolic adaptations might be able to improve waterlogging tolerance as well, but more studies are needed in this direction. Reasonable approaches for future studies are quantitative trait locus (QTL) analyses or genome-wide association (GWA) studies in combination with specific tolerance traits that can be easily assessed. The usage of flooding-tolerant relatives or ancestral cultivars of the crop of interest in these experiments might enhance the chances of finding useful tolerance traits to be used in breeding.