A genome-wide analysis of the lysophosphatidate acyltransferase (LPAAT) gene family in cotton: organization, expression, sequence variation, and association with seed oil content and fiber quality

Abstract

Background: Lysophosphatidic acid acyltransferase (LPAAT) encoded by a multigene family is a rate-limiting enzyme in the Kennedy pathway in higher plants. Cotton is the most important natural fiber crop and one of the most important oilseed crops. However, little is known on genes coding for LPAATs involved in oil biosynthesis with regard to its genome organization, diversity, expression, natural genetic variation, and association with fiber development and oil content in cotton.

Results: In this study, a comprehensive genome-wide analysis in four Gossypium species with genome sequences, i.e., tetraploid G. hirsutum- AD₁ and G. barbadense- AD₂ and its possible ancestral diploids G. raimondii- D₅ and G. arboreum- A₂, identified 13, 10, 8, and 9 LPAAT genes, respectively, that were divided into four subfamilies. RNA-seq analyses of the LPAAT genes in the widely grown G. hirsutum suggest their differential expression at the transcriptional level in developing cottonseeds and fibers. Although 10 LPAAT genes were co-localised with quantitative trait loci (QTL) for cottonseed oil or protein content within a 25-cM region, only one single strand conformation polymorphic (SSCP) marker developed from a synonymous single nucleotide polymorphism (SNP) of the At-Gh13LPAAT5 gene was significantly correlated with cottonseed oil and protein contents in one of the three field tests. Moreover, transformed yeasts using the At-Gh13LPAAT5 gene with the two sequences for the SNP led to similar results, i.e., a 25-31% increase in palmitic acid and oleic acid, and a 16-29% increase in total triacylglycerol (TAG).

Conclusions: The results in this study demonstrated that the natural variation in the LPAAT genes to improving cottonseed oil content and fiber quality is limited; therefore, traditional cross breeding should not expect much progress in improving cottonseed oil content or fiber quality through a marker-assisted selection for the LPAAT genes. However, enhancing the expression of one of the LPAAT genes such as At-Gh13LPAAT5 can significantly increase the production of total TAG and other fatty acids, providing an incentive for further studies into the use of LPAAT genes to increase cottonseed oil content through biotechnology.

Keywords: Gene expression patterns; Gossypium spp; Lysophosphatidic acid acyltransferase (LPAAT); Seed oil; Sequence variation.

Fig. 1

A phylogenetic tree of LPAATs in four Gossypium species. Sequences of other LPAAT genes and LPAAT-related genes were downloaded from NCBI website. ● Gossypium; ▼ three putative isoforms in Gossypium

Fig. 2

Genetic structures of LPAAT genes in four Gossypium species. Black boxes show exons and lines show introns

Fig. 3

Co-localisation analysis of LPAAT genes with seed oil and protein quantitative trait loci (QTL). Red color shows LPAAT genes and underlines indicate the LPAAT genes co-localisation with seed oil and protein QTL

Fig. 4

Transcript profiles of LPAAT genes in Gossypium hirsutum. a A heat map showing transcript levels of 13 LPAAT genes in ovules at three stages (0 DPA, 3 DPA, 10 DPA; shown above each lane) in two BILs. b Transcript levels of 13 LPAAT genes in −3 DPA and 0 DPA ovules of Xuzhou 142 and Xuzhou 142 fl. Color scale above dendrogram shows relative transcript levels. "L" and "S" indicate long fiber length line NMGA-062 and short fiber length line NMGA-105, respectively. "WT" and "fl" indicate Xuzhou 142 and its Xuzhou 142 fl mutant, respectively

Fig. 5

Expression patterns of eight LPAAT genes in Xuzhou 142 and Xuzhou 142 fl. Y-axis, relative expression levels. X-axis, days post anthesis. Fibers and ovules were not separated at −3, −1, 0, 1, 3, and 5 DPA. 10 F, 15 F, 20 F, 25 F DPA and 10O, 15O, 20O, and 25O DPA indicate fibers and ovules, respectively, at different stages. Error bars show standard deviation (S.D.) calculated from three replications

Fig. 6

Content of TAG and fatty acids in At-Gh13LPAAT5 transgenic yeast strains. a Gas chromatography/mass spectrometry chromatogram of fatty acids from transgenic yeasts. b The content of fatty acids in transgenic yeasts. c The total TAG content in three transgenic yeast strains from two backgrounds G. hirsutum and G. barbadense, respectively. d Expression patterns of At-Gh13LPAAT5 in three transgenic yeast strains. ** and * indicate correlation at the 0.01 and 0.05 significant levels, respectively