BackgroundSalinization is a primary abiotic stress constraining global plant growth and production. Weedy rice, though highly homologous to cultivated rice, is more salt tolerant during seed germination and seedling growth; we hypothesize that this is owing to ionic homeostasis and changes in the expression of genes encoding ion transport regulators.ResultsThe four different genotypes of weedy (JYGY-1 and JYFN-4) and cultivated (Nipponbare and 9311) rice have different salt-tolerance during seed germination and seedling vegetative growth under salt stress. In this study, Na+ and Ca2+content increased in weedy and cultivated rice genotypes under salt stress while K+ and Mg2+decreased; however, JYGY-1 had the lowest Na+/K+ ratio of assessed genotypes. Genes in the high-affinity K+ transporter (HKT) and tonoplast sodium-hydrogen exchanger (NHX) families, and salt overly sensitive 1 (OsSOS1) have more than 98% homology in amino acid sequences between weedy and cultivated rice genotypes. Under salt stress, the HKT family members were differentially expressed in the roots and shoots of four different genotypes. However, the NHX family transcripts were markedly up-regulated in all genotypes, but there are significant differences between different genotypes. OsSOS1 was significantly up-regulated in roots, especially in JYGY-1genotype.ConclusionsThe results showed that different genotypes had different germination and nutrient survival under salt stress, which was related to the difference of ion content and the difference of a series of ion transport gene expression. At the same time this study will provide new insight into the similarities and differences in ion homeostasis and gene regulatory mechanisms between weedy and cultivated rice under salt stress, which can aid in novel rice breeding and growth strategies.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1586-9) contains supplementary material, which is available to authorized users.

Japanese foxtail is a grass weed in eastern China. This weed is controlled by fenoxaprop-P-ethyl, one of the most common acetyl-CoA carboxylase (ACCase)-inhibiting herbicides. Some Japanese foxtail populations have developed resistance to fenoxaprop-P-ethyl, owing to target-site mutations (amino acid substitutions) located within the carboxyl transferase domain of ACCase. In the present study, three mutations were detected in three fenoxaprop-P-ethyl–resistant Japanese foxtail populations: Ile-1781-Leu in JCJT-2, Ile-2041-Asn in JZJR-1, and Asp-2078-Gly in JCWJ-3. Two copies of ACCase (Acc1-1 and Acc1-2) were identified, but mutations were detected only in Acc1-1. The derived cleaved amplified polymorphic sequence (dCAPS) method detected these mutations successfully in Japanese foxtail. The mutation frequencies in JCJT-2, JZJR-1, and JCWJ-3 were approximately 98%, 92%, and 87%, respectively. Different cross-resistance patterns to ACCase inhibitors were found in the three resistant populations. JCJT-2 (Ile-1781-Leu) and JZJR-1 (Ile-2041-Asn) showed cross-resistance to haloxyfop-R-methyl, clodinafop-propargyl, and pinoxaden, but were susceptible to clethodim. JCWJ-3 (Asp-2078-Gly) showed cross-resistance to all tested ACCase-inhibiting herbicides.

Herbicide-resistant weeds pose a considerable threat to agriculture, but their resistance mechanisms are poorly understood. Differential gene expression analysis of a weed subjected to herbicide treatment is a key step toward more mechanistic studies. Such an analysis, often involving quantitative real-time PCR (qPCR), requires suitable reference genes as internal controls. In this study, we identified optimal reference genes in the noxious weed, Japanese foxtail. This weed has evolved resistance to acetyl-coenzyme A carboxylase (ACCase) inhibitors. We analyzed the stability of eight commonly used candidate reference genes (glyceraldehyde-3-phosphate dehydrogenase [GAPDH]; ubiquitin [UBQ]; capsine phosphatase [CAP]; beta-tubulin [TUB]; eukaryotic initiation factor 4a [EIF4A]; elongation factor-1 alpha [EF1]; 18S ribosomal RNA [18S]; 25S ribosomal RNA [25S]) from root, stem, and leaf tissue of plants that were either resistant or sensitive to ACCase inhibitors, with or without herbicide stress, using qPCR. The results were further ranked and analyzed using geNorm, NormFinder, and BestKeeper software. These analyses identified EF1 and UBQ in roots, EF1, TUB, CAP, and 18S in stems, and EF1, GAPDH, and 18S in leaves as suitable references for qPCR normalization. We have identified a set of reference genes that can be used to study herbicide resistance mechanisms in Japanese foxtail.

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Herbicide-resistant (R biotype) and -sensitive (S biotype) individuals were identified from the same population, and seed was increased for each biotype for three generations. We conducted laboratory experiments to determine the effects of temperature, light, salt stress, osmotic stress, pH, and burial depth on the germination and emergence of resistant and sensitive biotypes of Japanese foxtail. The results revealed that there was no difference in the final germination rate between the two biotypes under different temperature conditions, but time to obtain 50% germination or emergence (tE50) and mean germination time of the R biotype were higher than that of the S biotype at 10 C and 15/10 C 12-h day/night regime. In dark conditions, the final germination rate of the S biotype was higher and lower than that of the R biotype at 10 and 25 C, respectively. The overall germination rate of the R biotype was lower than that in the S biotype, and extended germination time was required in extreme conditions, such as 250 mM NaCl and −0.4 MPa osmotic potential. The change in environmental pH had no effect on the germination of the two biotypes. Emergence of the R biotype was lower than the S biotype when seed was buried at least 8 cm deep in an organic matter substrate. This study demonstrated the pleiotropic effects of a resistance allele on seed germination and emergence under different environmental conditions. Deep tillage could be used to reduce the growth and spread of resistant Japanese foxtail individuals.