Character changes and Transcriptomic analysis of a cassava sexual Tetraploid

Abstract

Background: Cassava (Manihot esculenta Crantz) is an important food crop known for its high starch content. Polyploid breeding is effective in its genetic improvement, and use of 2n gametes in sexual polyploid breeding is one of the potential methods for cassava breeding and improvement. In our study, the cassava sexual tetraploid (ST), which carries numerous valuable traits, was successfully generated by hybridizing 2n female gametes SC5 (♀) and 2n male gametes SC10 (♂). However, the molecular mechanisms remain unclear. To understand these underlying molecular mechanisms behind the phenotypic alterations and heterosis in ST plants, we investigated the differences in gene expression between polyploids and diploids by determining the transcriptomes of the ST plant and its parents during the tuber root enlargement period. We also compared the characters and transcriptomes of the ST plant with its parents.

Results: The ST plant was superior in plant height, stem diameter, leaf area, petiole length, plant weight, and root weight than the parent plants, except the leaf number, which was lower. The number of starch granules was higher in the roots of ST plants than those in the parent plants after five months (tuber root enlargement period), which could be due to a higher leaf net photosynthetic rate leading to early filling of starch granules. Based on transcriptome analysis, we identified 2934 and 3171 differentially expressed genes (DEGs) in the ST plant as compared to its female and male parents, respectively. Pathway enrichment analyses revealed that flavonoid biosynthesis and glycolysis/gluconeogenesis were significantly enriched in the ST plants, which might contribute to the colors of petiole (purple-red), root epidermis (dark brown), and tuber starch accumulation, respectively.

Conclusions: After sexual polyploidization, the phenotype of ST has changed significantly in comparison to their diploid parents, mainly manifest as enlarged biomass, yield, early starch filling, deep colored petiole and root epidermis. The tetraploid plants were also mature early due to early starch grain filling. Owing to enriched flavonoid biosynthesis and glycolysis/gluconeogenesis, they are possibly resistant to adversity stresses and provide better yield, respectively.

Keywords: Characters; Differentially expressed genes; Manihot esculenta Crantz; Sexual tetraploids; Transcriptome.

Fig. 1

Ploidy determination of the hybrid cassava variety. a Diploid cassava variety images captured by flow cytometry; b Hybrid cassava variety images captured by flow cytometry; c Chromosomes of diploid foliage, 2n = 2x = 36; d Chromosomes of hybrid variety F1 foliage, 2n = 2x = 72; e Chromosomes of clones F2 foliage, 2n = 2x = 72; f Chromosomes of clones F3 foliage, 2n = 2x = 72

Fig. 2

Phenotypic observation of the cassava sexual tetraploids and their diploid parents. a Sexual tetraploid and its parent diploid plants five months after planting; b Leaves of the cassava sexually tetraploid and its diploid parents; c Tuber roots of the cassava sexual tetraploid and its diploid parents (the top of the pictures are the cross-sections of the tuber roots of ST, SC10, and SC5, respectively)

Fig. 3

Transmission electron microscopy of starch granules in the tuber roots of the ST, SC10, and SC5, respectively

Fig. 4

The correlation heat maps among the three bioreplications for each variety. The abscissa and ordinate represent each sample, and each block of abscissa and ordinate represent the correlation between X and Y samples. The darkest (green) color in the graph represents the largest Pearson correlation coefficient between the X and Y samples and the lightest (white) color represents the smallest Pearson correlation coefficient between the X and Y samples

Fig. 5

a Venn diagrams for transcriptome analysis of the expressed genes detected in the three cassava varieties; b The histograms of differentially expressed gene between samples. Ascissa: pairs of samples; ordinate: number of differentially expressed genes; red represents up-regulated genes; green represents down-regulated genes

Fig. 6

a GO classification of DEGs between the ST and SC5; b GO classification of DEGs between the ST and SC10

Fig. 7

a The top 20 of the KEGG pathway enrichment of DEGs between the ST and SC5; b The top 20 of KEGG pathway enrichment of DEGs between the ST and SC10

Fig. 8

Glycolysis/gluconeogenesis pathway of the cassava roots; the positions of the up-regulated DEGs are marked in red, and the positions of the down-regulated DEGs are marked in green

Fig. 9

a Relative expression levels of DEGs determined by q-PCR; b Transcriptome data for DEGs expression