Genome-wide SNP discovery, linkage mapping, and analysis of QTL for morpho-physiological traits in rice during vegetative stage under drought stress.

Drought tolerance in rice is controlled by several genes and is inherited quantitatively. Low genetic map density and the use of phenotypic traits that do not reflect the corresponding tolerance level have been obstacles in genetic analyses performed to identify genes that control drought-tolerant traits in rice. The current study aimed to construct a genetic map from high-density single-nucleotide polymorphism (SNP) markers generated from genome sequences of recombinant inbred lines (RILs), derived from IR64 × Hawara Bunar. Moreover, it sought to analyze the quantitative trait loci (QTL) and identify the drought tolerance candidate genes. A linkage map along 1980 cM on the 12 rice chromosomes was constructed employing 55,205 SNP markers resulting from the RIL genome sequences. A total of 175 morpho-physiological traits pertaining to drought stress were determined. A total of 41 QTLs were detected in 13 regions on rice chromosomes 1, 3, 6, 8, 9, and 12. Moreover, three hotspot QTL regions were found on chromosomes 6 and 8, along with two major QTL on chromosome 9. Differential gene expression for the loci within the QTL physical map intervals revealed many potential candidate genes. The markers tightly linked to the QTL and their candidate genes can potentially be used for pyramiding in marker-assisted breeding in order to achieve genetic improvement concerning the tolerance of rice to drought stress. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12298-021-01095-y.

Evaluation of PCR-HRM, RFLP, and direct sequencing as simple and cost-effective methods to detect common EGFR mutations in plasma cell-free DNA of non-small cell lung cancer patients.

BACKGROUND: Lung cancer patients with mutations in epidermal growth factor receptor (EGFR) gene are treated with tyrosine kinase inhibitor (TKI). AIMS: We aimed to evaluate polymerase chain reaction (PCR)-high-resolution melting (HRM), restriction fragment length polymorphism (RFLP), and direct sequencing (DS) to detect EGFR mutations in cell-free DNA (cfDNA) before and after TKI treatment in real-world settings of a developing country. METHODS: Paired cytology and plasma samples were collected from 116 treatment-naïve lung cancer patients. DNA from both plasma and cytology specimens was isolated and analyzed using PCR-HRM (to detect exon 19 insertion/deletion), RFLP (to genotypes L858R and L861Q), and DS (to detect uncommon mutations G719A, G719C, or G719S [G719Xaa] in exon 18 and T790M and insertion mutations in exon 20). RESULTS: EGFR genotypes were obtained in all 116 (100%) cfDNA and 110/116 (94.82%) of cytological specimens of treatment-naïve patient (baseline samples). EGFR-activating mutations were detected in 46/110 (40.6%) plasma samples, and 69/110 (63.2%) mutations were found in routine cytology samples. Using cytological EGFR genotypes as reference, we found that sensitivity and specificity of baseline plasma EGFR testing varied from 9.1% to 39.39% and 83.12% to 96.55%, respectively. In particular, the sensitivity and specificity of this assay in detecting baseline T790M mutations in exon 20 were 30% and 89.58%, respectively. Three months after TKI treatment, plasma T790M and insertion exon 20 mutations appeared in 5.4% and 2.7% patients, respectively. CONCLUSIONS: Despite low sensitivity, combined DS, RFLP, and PCR-HRM was able to detect EGFR mutations in plasma cfDNA with high specificity. Moreover, TKI resistance exon 20 insertions mutation was detected as early as 3 months post TKI treatment.

Differential physiological responses and tolerance to potentially toxic elements in biodiesel tree Jatropha curcas.

Environmental pollution by potentially toxic elements (PTEs) has become a serious problem with increasing industrialization and the disturbance of natural biogeochemical cycles. Jatropha is an oilseed-bearing shrub with high potential for biodiesel production in arid regions. In this study, we examined the physiological responses of this plant to five representative PTEs (Cd, Cr, Cu, Ni, and Zn) in a hydroponic culture. Application of higher concentrations of Cd and Zn led to severe leaf chlorosis, and Cd, Cu, and Ni treatments resulted in significant growth retardation. Higher enrichment of the applied PTEs in the shoots was observed for Zn- and Cd-treated plants, with the latter reaching 24-fold enrichment in plants exposed to 10 µM Cd, suggesting that Jatropha can cope with relatively higher internal concentrations of toxic Cd. Although Cd stress led to the disturbance of essential mineral homeostasis and photosynthesis, this induced an increase in thiol compounds in the roots, suggesting defensive responses of Jatropha to PTEs. This study showed that Jatropha exhibits distinct sensitivities and physiological responses to different PTEs. This study also provides basic knowledge for diagnosing the physiological status of Jatropha trees for potential dual use in afforestation and as a sustainable energy supply.

Overexpression of Hevea brasiliensis ethylene response factor HbERF-IXc5 enhances growth and tolerance to abiotic stress and affects laticifer differentiation.

Ethylene response factor 1 (ERF1) is an essential integrator of the jasmonate and ethylene signalling pathways coordinating a large number of genes involved in plant defences. Its orthologue in Hevea brasiliensis, HbERF-IXc5, has been assumed to play a major role in laticifer metabolism and tolerance to harvesting stress for better latex production. This study sets out to establish and characterize rubber transgenic lines overexpressing HbERF-IXc5. Overexpression of HbERF-IXc5 dramatically enhanced plant growth and enabled plants to maintain some ecophysiological parameters in response to abiotic stress such as water deficit, cold and salt treatments. This study revealed that HbERF-IXc5 has rubber-specific functions compared to Arabidopsis ERF1 as transgenic plants overexpressing HbERF-IXc5 accumulated more starch and differentiated more latex cells at the histological level. The role of HbERF-IXc5 in driving the expression of some target genes involved in laticifer differentiation is discussed.