Transcriptome Analysis by RNA–Seq Reveals Genes Related to Plant Height in Two Sets of Parent-hybrid Combinations in Easter lily (Lilium longiflorum)

Abstract

In this study, two different hybrids of Easter lily (Lilium longiflorum), obtained from two cross combinations, along with their four parents were sequenced by high-throughput RNA-sequencing (RNA-Seq) to find out differentially expressed gene in parent-hybrid combinations. The leaf mRNA profiles of two hybrids and their four parents were RNA-sequenced with a view to identify the potential candidate genes related to plant height heterosis. In both cross combinations, based to morphological traits mid-parent heterosis (MPH) was higher than high-parent heterosis (HPH) for plant height, leaf length, and number of flowers whereas HPH was higher than MPH for flowering time. A total of 4,327 differentially expressed genes (DEGs) were identified through RNA-Seq between the hybrids and their parents based on fold changes (fc) ≥ 2 for up-and ≤-2 for down-regulation. Venn diagram analysis revealed that there were 703 common DEGs in two hybrid combinations, those were either up-or down-regulated. Most of the commonly expressed DEGs exhibited higher non-additive effects especially overdominance (75.9%) rather than additive (19.4%) and dominance (4.76%) effects. Among the 384 functionally annotated DEGs identified through Blast2GO tool, 12 DEGs were up-regulated and 16 of them were down-regulated in a similar fashion in both hybrids as revealed by heat map analysis. These 28 universally expressed DEGs were found to encode different types of proteins and enzymes those might regulate heterosis by modulating growth, development and stress-related functions in lily. In addition, gene ontology (GO) analysis of 260 annotated DEGs revealed that biological process might play dominant role in heterotic expression. In this first report of transcriptome sequencing in Easter lily, the notable universally up-regulated DEGs annotated ABC transporter A family member-like, B3 domain-containing, disease resistance RPP13/1, auxin-responsive SAUR68-like, and vicilin-like antimicrobial peptides 2-2 proteins those were perhaps associated with plant height heterosis. The genes expressed universally due to their overdominace function perhaps influenced MPH for greater plant height-largely by modulating biological processes involved therein. The genes identified in this study might be exploited in heterosis breeding for plant height of L. longiflorum. Heterosis refers to the higher performance in any trait (s) of interest of F 1 hybrid as compared to homozygous parental lines. Charles Darwin 1 described this phenomenon for the first time ever and later Shull 2 and East 3 independently confirmed this phenomenon. Improvements in many traits of different crop and livestock species have

Quantitative comparison of the storage protein distribution in glandless and glanded cottonseeds

“…Quantitatively, vicilin‐like antimicrobial peptides 2‐2 accounted for 0.1% of Gd seed protein but were relatively higher (0.8%) from Gl seed protein. It is possible that the relatively higher abundance of vicilin‐like antimicrobial peptides 2‐2 in the Gl sample is also a compensatory mechanism to increase the defense capabilities of Gl cotton, as vicilin‐like antimicrobial peptides 2‐2 function in defense related responses against a wide range of pathogens (Howlader et al., 2020).…”

Volatile Organic Compounds of Streptomyces sp. TOR3209 Stimulated Tobacco Growth by Up-Regulating the Expression of Genes Related to Plant Growth and Development

“…The sequencing library was then sequenced commercially on a Novaseq platform (Illumina) by Shanghai Personal Biotechnology Cp. Ltd. Filtration of high-quality reads by eliminating low-quality reads (Q <20), removal of adapter, assembling of the transcriptome, and quantification of transcript abundances were performed as described by Howlader et al ( 2020 ).…”

“…The gene expression levels between the samples subjected to VOC treatment and the control were estimated by using fragments per kilobase of transcript per million fragments mapped (FPKM) values, as described by Howlader et al ( 2020 ). In the transcription group, we generally took into account FPKM > 1 when the gene was expressed.…”

“…The cluster analysis of FPKM-normalized expression values was carried out, as mentioned by Howlader et al ( 2020 ), to differentiate the up- and down-regulated transcripts between the VOC treatment and the control samples, by using the cluster software version 3.0 and the Java TreeView to visualize the dendrogram. For GSEA, the KEGG pathway collection (Homo sapiens (human) Release 53.0) (Kanehisa and Goto, 2000 ) was used to define the gene sets using the GSEABase package in Bioconductor/R version 2.9.2 (Gentleman, 2004 ).…”

Combining transcriptome analysis and GWAS for identification and validation of marker genes in thePhysalis peruviana-Fusarium oxysporumpathosystem

“…In this study, we used the results from two different NGS approaches, RNA-Seq and GWAS, to identify and select candidate genes associated with the P. peruviana-Foph pathosystem. RNA-Sequencing has been widely used for analyzing gene expression patterns in different tissues and developmental stages under various conditions (Tsukagoshi et al, 2015;Brito et al, 2017;Howlader et al, 2020). Here, we analyzed the data of previously reported transcriptome libraries (Vera Alvarez et al, 2017) from cape gooseberry's root and stem tissues derived from the interaction with Foph.…”