Analysis of differentially expressed genes in transcriptomes of two pear genotypes under drought stress

WANG Hua; WANG Wangwei; LIU Chunyi; WANG Qiaoqiao; ZHU Liwu; XU Xiaoniu

doi:10.7671/j.issn.1001-411X.2018.04.010

Journal of South China Agricultural University > 2018 > 39(4): 61-67. > DOI: 10.7671/j.issn.1001-411X.2018.04.010

WANG Hua, WANG Wangwei, LIU Chunyi, WANG Qiaoqiao, ZHU Liwu, XU Xiaoniu. Analysis of differentially expressed genes in transcriptomes of two pear genotypes under drought stress[J]. Journal of South China Agricultural University, 2018, 39(4): 61-67. DOI: 10.7671/j.issn.1001-411X.2018.04.010

Citation:

PDF (721 KB)

Analysis of differentially expressed genes in transcriptomes of two pear genotypes under drought stress

1.
Key Laboratory of Pomology, Anhui Agricultural University, Hefei 230036, China
2.
School of Forestry and Landscape Architecture, Anhui Agricultural University, Hefei 230036, China

More Information

Received Date: December 24, 2017
Available Online: May 17, 2023

Graphical Abstract

Abstract

Abstract

Object
To discover key genes related to drought resistance of pear plants based on transcriptome data, and provide a theoretical foundation for the breeding of drought resistant pear varieties.

Method
High through-put transcriptome sequencing by illumina Hi Seq TM 2000 was performed using leaves of ‘Huangguan’ pear (Pyrus bretschneideri ‘Xuehuali’×P. pyrifolia ‘Shinsseiki’) and ‘Hwangkumbae’ pear (P. pyrifolia ‘Niitaka’×P. pyrifolia ‘Nijisseiki’) under normal irrigation and drought stress treatments. Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) databases were used to analyze the differentially expressed genes (DEGs) in two pear genotypes.

Result
There were 4 377 and 3 841 DEGs comparing two pear genotypes under control irrigation and drought stress, respectively. Among these DEGs, 1 340 DEGs were only found under drought stress. There were 1 387, 922 and 1 235 DEGs in three ontologies including biological process, molecular function and cellular component, respectively. There were 349, 139 and 151 DEGs enriched in terms related to drought response of plant including metabolic process, stress response and biomembrane, respectively. The 1 340 DEGs only found under drought stress were matched to 102 KEGG pathways, and three of the pathways were related to phytohormone biosynthesis. Furthermore, among the 1 340 DEGs, 37 genes were annotated as transcription factors which belonged to 17 transcription factor families, and the ethylene responsive factor (ERF) family had 11 DEGs.

Conclusion
In this study, some genes related to endogenous hormone metabolism and transcription factors are found to express differentially in two pear genotypes under drought stress. These genes are probably closely related to the genotypic differences in drought resistance. Our results provide a basis for future study of the molecular mechanism of drought resistance of pear plant.
- pear,
- drought,
- transcriptome,
- differentially expressed gene,
- metabolic pathway,
- transcription factor

FullText(HTML)

References (30)

References

[1]	GIORGI F, LIONELLO P. Climate change projections for the Mediterranean region[J]. Global Planet Change, 2008, 63(2/3): 90-104.
[2]	WU J, WANG L F, LI L, WANG S. De novo assembly of the common bean transcriptome using short reads for the discovery of drought-responsive genes[J]. PLoS One, 2014, 9(10): e109262.
[3]	HWANG I G, KIM H Y, WOO K S, et al. Isolation and identification of the antioxidant DDMP from heated pear (Pyrus pyrifolia Nakai)[J]. Prev Nutr Food Sci, 2013, 18(1): 76-79.
[4]	ZHANG Y C, SHEN Y J, XU X L, et al. Characteristic of the water-energy-carbon fluxes of irrigated pear orchards in the North China Plain[J]. Agr Water Manage, 2013, 128(1): 140-148.
[5]	山仑. 植物水分利用效率和半干旱地区农业用水[J]. 植物生理学通讯, 1994, 30(1): 61-66.
[6]	STRUTHERS R, IVANOVA A, TITS L, et al. Thermal infrared imaging of the temporal variability in stomatal conductance for fruit trees[J]. Intl J Appl Earth Obs Geoinf, 2015, 39: 9-17.
[7]	ZARAFSHAR M, AKBARINIA M, ASKARI H, et al. Morphological, physiological and biochemical responses to soil water deficit in seedlings of three populations of wild pear tree (Pyrus boisseriana)[J]. Biotechnol Agron Soc Environ, 2014, 18(3): 31-35.
[8]	HUSSAIN S, NIU Q F, QIAN M J, et al. Genome-wide identification, characterization, and expression analysis of the dehydrin gene family in Asian pear (Pyrus pyrifolia)[J]. Tree Genet Genomes, 2015, 11(5): 110.
[9]	LI K Q, XU X Y, HUANG X S. Identification of differentially expressed genes related to dehydration resistance in a highly drought-tolerant pear, Pyrus betulaefolia, as through RNA-Seq[J]. PLoS One, 2016, 11(2): e0149352.
[10]	LI T, LI X Y, TAN D M, et al. Distinct expression profiles of ripening related genes in the ‘Nanguo’ pear (Pyrus ussuriensis) fruits[J]. Sci Hortic, 2014, 171: 78-82.
[11]	LI R Q, YU C, LI Y R, et al. SOAP2: an improved ultrafast tool for short read alignment[J]. Bioinformatics, 2009, 25(15): 1966-1967.
[12]	董丽丽, 龚凌燕, 陈磊, 等. 石榴肉桂酰辅酶A还原酶基因的克隆与表达分析[J]. 南京农业大学学报, 2016, 39(5): 747-753.
[13]	NAKASHIMA K, YAMAGUCHI-SHINOZAKI K. ABA signaling in stress-response and seed development[J]. Plant Cell Rep, 2013, 32(7): 959-970.
[14]	MEHROTRA R, BHALOTHIA P, BANSAL P. Abscisic acid and abiotic stress tolerance - different tiers of regulation[J]. J Plant Physiol, 2014, 171(7): 486-496.
[15]	ROCK C D, ZEEVAART J A. The ABA mutant of Arabidopsis thaliana is impaired in epoxy-carotenoid biosynthesis[J]. Proc Natl Acad Sci USA, 1991, 88(17): 7496-7499.
[16]	MISAWA N, SATOMI Y, KONDO K, et al. Structure and functional analysis of a marine bacterial carotenoid biosynthesis gene cluster and astaxanthin biosynthetic pathway proposed at the gene level[J]. J Bacteriol, 1995, 177(22): 6575-6584.
[17]	AUDRAN C, GONNEAU M, NORTH H, et al. Localisation and expression of zeaxanthin epoxidase mRNA in Arabidopsis in response to drought stress and during seed development[J]. Aust J Plant Physiol, 2001, 28(11): 1161-1173.
[18]	QIN X, ZEEVAART J A. Overexpression of a 9-cis-epoxycarotenoid dioxygenase gene in Nicotiana plumbaginifolia increases abscisic acid and phaseic acid levels and enhances drought tolerance[J]. Plant Physiol, 2002, 128(2): 544-551.
[19]	GONZÁLEZ-GUZMÁN M, APOSTOLOVA N, BELLlÉS J M, et al. The short-chain alcohol dehydrogenase ABA2 catalyzes the conversion of xanthoxin to abscisic aldehyde[J]. Plant Cell, 2002, 14(8): 1833-1846.
[20]	SEO M, AOKI H, KOIWAI H, et al. Comparative studies on the Arabidopsis aldehyde oxidase(AAO) gene family revealed a major role of AAO3 in ABA biosynthesis in seeds[J]. Cell Physiol, 2004, 45(11): 1694-703.
[21]	吴蓓, 李梦瑶, 王广龙, 等. AgERF4 转录因子基因的克隆与表达分析[J]. 园艺学报, 2016, 43(11): 2193-2202.
[22]	吴凡, 张超, 郭加, 等. 牡丹切花ERF转录因子基因的分离与表达分析[J]. 园艺学报, 2016, 43(1): 109-120.
[23]	PARK H Y, SEOK H Y, WOO D H, et al. AtERF71/HRE2 transcription factor mediates osmotic stress response as well as hypoxia response in Arabidopsis[J]. Biochem Biophys Res Commun, 2011, 414(1): 135-141.
[24]	DOSSA K, WEI X, LI D, et al. Insight into the AP2/ERF transcription factor superfamily in sesame and expression profiling of DREB subfamily under drought stress[J]. BMC Plant Biol, 2016, 16(1): 171.
[25]	ZHANG X, ZHANG Z, CHEN J, et al. Expressing TERF1 in tobacco enhances drought tolerance and abscisic acid sensitivity during seedling development[J]. Planta, 2005, 222(3): 494-501.
[26]	ZHAO Y, WEI T, YIN K Q, et al. Arabidopsis RAP2.2 plays an important role in plant resistance to Botrytis cinerea and ethylene responses[J]. New Phytol, 2012, 195(2): 450-460.
[27]	ZHANG G, CHEN M, CHEN X, et al. Phylogeny, gene structures, and expression patterns of the ERF gene family in soybean (Glycine max L.)[J]. J Exp Bot, 2008, 59(15): 4095-4107.
[28]	CHAKRAVARTHY S, TUORI R P, D’ASCENZO M D, et al. The tomato transcription factor Pti4 regulates defense-related gene expression via GCC box and non-GCC box elements[J]. Plant Cell, 2003, 15(12): 3033-3050.
[29]	XUE G P, LOVERIDGE C W. HvDRF1 is involved in abscisic acid-mediated gene regulation in barley and produces two forms of AP2 transcriptional activators, interacting preferably with a CT-rich element[J]. Plant J, 2004, 37(3): 326-339.
[30]	LICAUSI F, OHME-TAKAGI M, PERATA P. APETALA2/Ethylene responsive factor (AP2/ERF) transcription factors: Mediators of stress responses and developmental programs[J]. New Phytol, 2013, 199(3): 639-649.

Cited By

Get Citation

PDF

XML

Article views (1400) PDF downloads (1912)

Turn off MathJax

Article Contents

Abstract

References

Analysis of differentially expressed genes in transcriptomes of two pear genotypes under drought stress

Abstract

References

Catalog

Export File

Citation

Format

Content