Transcriptional changes during ovule development in two genotypes of litchi (Litchi chinensis Sonn.) with contrast in seed size

Abstract

Litchi chinensis is a subtropical fruit crop, popular for its nutritional value and taste. Fruits with small seed size and thick aril are desirable in litchi. To gain molecular insight into gene expression that leads to the reduction in the size of seed in Litchi chinensis, transcriptomes of two genetically closely related genotypes, with contrasting seed size were compared in developing ovules. The cDNA library constructed from early developmental stages of ovules (0, 6, and 14 days after anthesis) of bold- and small-seeded litchi genotypes yielded 303,778,968 high quality paired-end reads. These were de-novo assembled into 1,19,939 transcripts with an average length of 865 bp. A total of 10,186 transcripts with contrast in expression were identified in developing ovules between the small- and large- seeded genotypes. A majority of these differences were present in ovules before anthesis, thus suggesting the role of maternal factors in seed development. A number of transcripts indicative of metabolic stress, expressed at higher level in the small seeded genotype. Several differentially expressed transcripts identified in such ovules showed homology with Arabidopsis genes associated with different stages of ovule development and embryogenesis.

Identification of Finely Mapped Quantitative Trait Locus and Candidate Gene Mining for the Three-Seeded Pod Trait in Soybean

“…The Glyma.03G029800.1 gene was identified as GmYABBY5, which helps maintain meristems during the early floral developmental stages (Zhao et al, 2017). The Arabidopsis homolog of this gene is AT2G45190, which mediates biological processes related to ovule, embryo, and flower development (Lenser et al, 2016;Pathak et al, 2016). In tomatoes, the YABBYlike transcription factor was also found to play a pivotal role in fruit size regulation (Cong et al, 2008).…”

“…For eight genes, five candidate genes were detected in the NThSP03-1 interval (i.e., Glyma.03G026100.1, Glyma.03G026300.1, Glyma.03G026400.1, Glyma.03G026900.1, and Glyma.03G029800.1). The homologous genes in the soybean genome were Glyma.01G140600.1 and Glyma.17G138200.1 (Zhao et al, 2017;Chen et al, 2018), whereas the homologous genes in the Arabidopsis genome were AT1G71820 and AT2G45190 (Nolan et al, 2009;Lenser et al, 2016;Pathak et al, 2016). Based on previous studies, functional characterization of these genes indicated that they are involved in pollen germination; pollen tube growth; meristem growth; ovule, embryos, flower, and fruit development; and cell division.…”

Transcriptome analysis at mid-stage seed development in litchi with contrasting seed size

“…The two genotypes with contrasting seed size are genetically fairly close (Nei genetic distance of 0.46) (Pathak et al 2014) as compared to the other popular cultivars in India and grouped in the same cluster as the previously reported litchi transcriptome genotypes. Developing fruits at 16, 20, 24 and 28 days after anthesis (DAA) were harvested, dipped in liquid N 2 , and stored in -80 o C (Pathak et al 2016). Seeds were excised from the stored fruits and total RNA was isolated, using Spectrum Plant Total RNA kit (Sigma Aldrich St. Louis, MO, USA), following manufacturer's protocol.…”

“…Relative expression of Trinity transcripts among RNAseq libraries from two litchi genotypes at four seed developmental stages was obtained as TPM (transcripts per million) and FPKM (fragments per kilobase of transcripts per million mapped reads), using RSEM version 1.2.9 at default parameters (Pathak et al 2016). Expression levels of different Trinity transcripts were compared among the samples by Edger Bioconductor, using script run_DE_analysis.pl as default parameter.…”

“…We have earlier (Pathak et al 2016) reported early-stage seed speci c transcriptional pro ling in two litchi genotypes with contrasting seed size. In this report, we take the earlier study forward.…”