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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 - AD 1  and  G. barbadense - AD 2  and its possible ancestral diploids  G. raimondii - D 5  and  G. arboreum - A 2 , 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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-017-3594-9) contains supplementary material, which is available to authorized users.

bmc genomics

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