Esra Nurten Yer

Drought-Responsive Hsp70 Gene Analysis in Populus at Genome-Wide Level

The heat shock protein 70 (Hsp70) family members are known as molecular chaperones. They play a crucial role in protecting plant cells and tissues from thermal or abiotic stress through protein folding and in assembly, stabilization, activation, and degradation processes. Although many studies have been performed to identify molecular functions of individual family members, there is a limited study on genome-wide identification and characterizations of Hsps in the Populus model tree genus. We have identified 34 poplar Hsp70 genes, which were phylogenetically clustered into three major groups. Gene structure and motif composition are relatively conserved in each group. Mainly tandem and infrequently segmental duplications have a significant role in poplar Hsp70 gene expansion. The in silico microRNA (miRNA) and target transcript analyses identified that a total of 19 PtHsp70 genes were targeted by 27 plant miRNAs. PtHSP70-14 and PtHSP70-33 are the most targeted by miR390 and miR414 family members, respectively. For determination of drought response to Hsp70 genes, publicly available RNA-seq data were analyzed. Poplar Hsp70s are differentially expressed upon exposure to different drought stress conditions. Expression analysis of PtHsp70 genes was also examined under drought stress in drought-sensitive and drought-resistant Populus clones with quantitative real-time PCR (qRT-PCR). PtHsp70-16 and PtHsp70-26 genes might provide adaptation to drought stress for both clones. Because of high expression responses to drought in only resistant Populus clone, PtHsp70-25 and PtHsp70-33 genes might be used for determination of drought-tolerant clones for molecular breeding studies. This research provides a fundamental clue for contribution of PtHsp70s to drought tolerance in poplar.

Identification and expression profiling of all Hsp family member genes under salinity stress in different poplar clones

Heat shock proteins (Hsps) play a key role for regulation of the changes during different stress conditions including salinity, drought, heavy metal and extreme temperature. Molecular based studies on the response mechanisms of forest trees to abiotic stresses started in 2006 when Populus trichocarpa genome sequence was completed as a model tree species. In recent years, bioinformatic analyzes have been carried out to determine functional gene regions of tree species. In this study, sHsp, Hsp40, Hsp60, Hsp90 and Hsp100 gene family members were identified in poplar genome. Some bioinformatics analyses were conducted, such as: identification of DNA/protein sequences, chromosomal localization, gene structure, calculation of genomic duplications, determination of phylogenetic groups, examination of protected motif regions, identification of gene ontology categories, modeling of protein 3D structure, determination of miRNA targeting genes, examination of sHsp, Hsp40, Hsp60, Hsp90 and Hsp100 gene family members in transcriptome data during salinity stress. As a result of bioinformatic analyzes made on P. trichocarpa genome; 60, 145, 49, 34, 12 and 90 genes belonging to members of sHsp, Hsp40, Hsp60, Hsp70, Hsp90 and Hsp100 protein families were firstly defined within the scope of this study. A total of 390 genes belonging to all Hsps gene families were characterized using different bioinformatics tools. In addition, salinity stress was applied to Populus tremula L. (Samsun) naturally grown in Turkey, Hybrid poplar species I-214 (Populus euramericana Dode. Guinier) and Black Poplar species (Populus nigra L.), Geyve and N.03.368.A clones. The expression levels of the selected Hsps genes were determined by the qRT-PCR method. After salt stress application in various poplar clones, expression levels of genes including PtsHsp-11, PtsHsp-21, PtsHsp-36, PtHsp40-113, PtHsp40-117, PtHsp60-31, PtHsp60-33, PtHsp60-38, PtHsp60-49, PtHsp70-09, PtHsp70-12, 33, PtHsp90-09, PtHsp90-12, PtHsp100-21, and PtHsp100-75 were increased. The role of the Hsps genes during salt stress has been revealed. Together with detailed bioinformatics analyses, gene expression analysis greatly contributes to understand functions of these gene family members. This research serves as a blueprint for future studies and offers a significant clue for the further study of the functions of this important gene family. Moreover, determined genes in this study can also be used for cloning studies in agricultural practices.

Growth Stages of Bare Rooted Seedlings of Taurus Cedar and Anatolian Black Pine in Eskisehir Forest Nursery Conditions

Bu calismada, Eskisehir Orman fidanligi kosullarinda yetistirilen farkli orijinlere ait 1+0 ve 2+0 yasli ciplak koklu fidanlarda rutin yetistirme islemleri sonucu; “Kuru madde degisim” yontemiyle “fidan gelisim donemleri” belirlenmistir. Fidanlar, ozel herhangi bir isleme tabi tutulmadan normal yetisme/yetistirme kosullari altinda; ilk gelisme, hizli gelisme, duraklama, odunlasma ve gercek durgunluk donemlerinin yilin hangi donemiyle ortustugu incelenmistir. Fidanlik kosullarina ve ture ozgu gelisim evrelerinin tespitiyle; uygun gubreleme ve sulama rejimleri, kok kesimi, seyreltme, ot alma zamani ve sokum gibi kulturel islemler icin en uygun zamanin belirlenmesi amaclanmistir. Calisma sonucuna gore; 2+0 yasli Toros Sediri fidanlari icin fidan gelisim donemleri; Mart basi - Nisan ortasi durgimluktan cikis donemi, Mayis ayi basi — Temmuz ayi basi gelisme ve hizli gelisme donemi, Temmuz ayi sonu - Agustos ayi ortasi yavaslama donemi, Eylul ayi ortasindan itibaren odunlasma donemine girdigi tespit edilmistir. 2+0 yasli, Anadolu karacami fidanlari icin fidan gelisim donemleri; Mart basi Nisan ortasi durgunluktan cikis donemi, Mayis basi - Temmuz sonu gelisme ve hizli gelisme donemi, Agustos ayinin ortasindan itibaren ve Kasim ayi basina kadar yavaslama ve odunlasma donemini gecirmislerdir. 1+0 yasli Anadolu karacami fidanlari ise; Mayis ayi ortasi - Haziran ayi ortasi fidecik donemi, Temmuz ayi basi — Agustos ayi ortasi gelisme ve hizli gelisme donemi, Eylul ayi ortasi ve Ekim ayi sonu yavaslama ve odunlasma donemi olarak fidan gelisim donemleri belirlenmistir