A differential gene expression analysis of miRNA in Dactylis glomerata in response to flooding stress

doi:10.11686/cyxb2021130

Abstract

Abstract:

Waterlogging stress is the main environmental factor that restricts the improvement of yield and quality of orchard grass （Dactylis glomerata） in Southwest China， and it has become a category of abiotic stress that can’t be ignored， from a research perspective. This research aimed to identify functional genes related to waterlogging tolerance of orchard grass， and explore its regulation mechanisms， as a means of improving the waterlogging tolerance of this grass. In this research， the waterlogging tolerant variety “Dian bei” was studied. After being subjected to flooding stress for 0， 8 and 24 h， RNA was extracted from orchard grass leaves and sequencing was carried out using an Illumina Hiseq sequencing platform. A total of 208 differentially expressed genes were identified under flooding stress， 38 genes were up-regulated and 34 genes were down-regulated， accounting for 34.62% of the differentially expressed genes （DEGs）. The genes identified as differentially in “Dian bei” orchard grass under flooding stress mainly belong to five miRNA gene families： miR166， miR167， miR159， miR396 and miR156. Based on the predicted function of target genes of differentially expressed miRNA and functional analysis using GO（gene ontology） and KEGG （kyoto encyclopedia of genes and genomes） of target genes， it was determined that the identified DEGs were mainly involved in plant stress response processes， such as cellular processes， metabolic processes， the IL-17 signaling pathway， Th17 cell differentiation， and others. These results provide initial direction for further study of the molecular regulation and response mechanisms of orchard grass under flooding stress.

Key words: Dactylis glomerata, flooding stress, waterlogging tolerance, miRNA, differential expression

Xing-yun YANG, Dan-dan QIAO, Ya-jie ZHANG, Shao-qing WANG, Jun-cai REN, Ming-yang LI, Ming-hao QU, Pan-pan SHANG, Cheng YANG, Lin-kai HUANG, Bing ZENG. A differential gene expression analysis of miRNA in Dactylis glomerata in response to flooding stress[J]. Acta Prataculturae Sinica, 2022, 31(6): 150-162.

Figures/Tables 9

References 63

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样本 Sample	质控前reads数 Total reads	质控后reads数 Clean reads	定位到基因组上的sRNA总数 Total mapped sRNA	Q₂₀ （%）	Q₃₀ （%）	GC （% ）
DB-0 h-1	13115501	6911279	690667	99.6	98.8	52.9
DB-0 h-2	12506705	7412332	847591	99.8	99.3	52.1
DB-0 h-3	13129146	6898821	711644	99.8	99.4	51.8
DB-8 h-1	10196159	5869117	1032354	99.5	98.7	51.5
DB-8 h-2	12254067	7088163	1113861	99.2	98.1	51.2
DB-8 h-3	11877997	7548708	1138457	99.6	99.0	51.6
DB-24 h-1	11852644	8729342	1401312	99.8	99.3	52.0
DB-24 h-2	12412282	8960959	1337594	99.8	99.6	51.6
DB-24 h-3	12481155	9370332	1435461	99.8	99.3	52.1

样本 Sample	质控前reads数 Total reads	质控后reads数 Clean reads	定位到基因组上的sRNA总数 Total mapped sRNA	Q₂₀ （%）	Q₃₀ （%）	GC （% ）
DB-0 h-1	13115501	6911279	690667	99.6	98.8	52.9
DB-0 h-2	12506705	7412332	847591	99.8	99.3	52.1
DB-0 h-3	13129146	6898821	711644	99.8	99.4	51.8
DB-8 h-1	10196159	5869117	1032354	99.5	98.7	51.5
DB-8 h-2	12254067	7088163	1113861	99.2	98.1	51.2
DB-8 h-3	11877997	7548708	1138457	99.6	99.0	51.6
DB-24 h-1	11852644	8729342	1401312	99.8	99.3	52.0
DB-24 h-2	12412282	8960959	1337594	99.8	99.6	51.6
DB-24 h-3	12481155	9370332	1435461	99.8	99.3	52.1

样本Sample	数据库miRBase	外显子Exon	内含子Intron	基因间Intergenic	重复序列Repeat
DB-0 h	11.00	30.81	13.00	95.46	99.6
DB-8 h	15.80	17.02	11.86	93.30	99.8
DB-24 h	14.00	22.14	8.73	90.51	99.5

样本Sample	数据库miRBase	外显子Exon	内含子Intron	基因间Intergenic	重复序列Repeat
DB-0 h	11.00	30.81	13.00	95.46	99.6
DB-8 h	15.80	17.02	11.86	93.30	99.8
DB-24 h	14.00	22.14	8.73	90.51	99.5

DB 0 h vs 8 h	DB 0 h vs 24 h	DB 8 h vs 24 h
miR166 （28）	miR166 （20）	miR166 （30）
miR167 （9）	miR159 （13）	miR159 （13）
miR159 （9）	miR167 （9）	miR167 （11）
miR156 （8）	miR396 （7）	miR156 （7）
miR396 （5）	miR156 （6）	miR396 （5）