Genome-Wide Identification, Sequence Variation, and Expression of the Glycerol-3-Phosphate Acyltransferase (GPAT) Gene Family in Gossypium

Abstract

Cotton is an economically important crop grown for natural fiber and seed oil production. Cottonseed oil ranks third after soybean oil and colza oil in terms of edible oilseed tonnage worldwide. Glycerol-3-phosphate acyltransferase ( GPAT ) genes encode enzymes involved in triacylglycerol biosynthesis in plants. In the present study, 85 predicted GPAT genes were identified from the published genome data in Gossypium . Among them, 14, 16, 28, and 27 GPAT homologs were identified in G. raimondii, G. arboreum, G. hirsutum , and G. barbadense , respectively. Phylogenetic analysis revealed that a total of 108 GPAT genes from cotton, Arabidopsis and cacao could be classified into three groups. Furthermore, through comparison, the gene structure analyses indicated that GPAT genes from the same group were highly conserved between Arabidopsis and cotton. Segmental duplication could be the major driver for GPAT gene family expansion in the four cotton species above. Expression patterns of GhGPAT genes were diverse in different tissues. Most GhGPAT genes were induced or suppressed after salt or cold stress in Upland cotton. Eight GhGPAT genes were co-localized with oil and protein quantitative trait locus (QTL) regions. Thirty-two single nucleotide polymorphisms (SNPs) were detected from 12 GhGPAT genes, sixteen of which in nine GhGPAT genes were classified as synonymous, and sixteen SNPs in ten GhGPAT genes non-synonymous. Two SNP markers of the GhGPAT16 and GhGPAT26 genes were significantly correlated with cotton oil content in one of the three field tests. This study shed lights on the molecular evolutionary properties of GPAT genes in cotton, and provided reference for improvement of cotton response to abiotic stress and the genetic improvement of cotton oil content.

Genome-Wide Characterization and Analysis of CIPK Gene Family in Two Cultivated Allopolyploid Cotton Species: Sequence Variation, Association with Seed Oil Content, and the Role of GhCIPK6

“…Additionally, these SNPs were further analyzed in the five published cotton genome data (TM-1_NAU, TM-1_ZJU, 3-79, Xinhai 21 and Hai 7124), and nine SNPs of four GhCIPKs were confirmed as non-synonymous mutations. Primers of the nine SNPs were designed (Table S11) and screened in a backcross inbred line (BIL) population of 180 lines derived from a backcross between CRI 36 and Hai 7124 as described previously [48]. Five SNPs from four GhCIPKs were found to be significantly associated with oil content in the BIL population (Table S12).…”

“…The chromosomal location images of cotton CIPKs were visualized with Mapchart v2.2 [81] and Circos-0.67 (http://circos.ca/). Orthologous and homoeologs for CIPK genes were identified among the genomes of the diploid and allotetraploid cotton species based on phylogenetic trees and sequence alignments [48,82]. The gene duplication events of two allotetraploid cotton species were analyzed by using MCScanX software, and according to the length of aligned sequence, covered >80% between aligned gene sequences, similarly to the aligned regions (>80%) [48].…”

“…Orthologous and homoeologs for CIPK genes were identified among the genomes of the diploid and allotetraploid cotton species based on phylogenetic trees and sequence alignments [48,82]. The gene duplication events of two allotetraploid cotton species were analyzed by using MCScanX software, and according to the length of aligned sequence, covered >80% between aligned gene sequences, similarly to the aligned regions (>80%) [48]. DnaSP v5.0 software [83] was used to calculate the synonymous substitution (Ks) and nonsynonymous substitution (Ka).…”

“…We used an interspecific backcross inbred line (BIL) population of 180 lines derived from CRI 36 and Hai 7124 to validate SNP markers of cotton CIPKs. SNP primers for CIPK genes were designed using Primer v5.0 software (Table S11), and high-resolution melting (HRM) was used to analyze the relationship of SNPs and cottonseed oil content as described in previous articles [48]. The simple correlation analysis was performed using SPPS software (IBM, New York, NY, USA).…”

Identification and analysis of oil candidate genes revealed the molecular basis of oil accumulation in Gossypium hirsutum L. for cottonseed biofuels development

“…In the past several decades, some genes and TFs in oil crops also have been veri ed to be associated with lipid synthesis based on the Arabidopsis thaliana oil-related genes through multi-omics analyses. For instance, phosphoenolpyruvate carboxylase (PEPC) in upland cotton for the formation of pyruvate [17]; acetyl-CoA carboxylase (ACCase) in rapeseed [18], cotton [19], and potato [20] participate in de novo FA synthesis; fatty acylthioesterase B (FATB) in soybean [21] and cotton [22], and β-ketoacyl-ACP synthase I (KASI) and long chain acyl-CoA synthetase 9 (LACS9) in soybean [23], and KASII [24], Stearyl-ACPdesaturase (SAD) [25], and GhWRI1 [26] in cotton are involved in FA synthesis; glycerol-3-phosphate dehydrogenase (GPDH) in rapeseed [27], glycerol-3-phosphate acyltransferase (GPAT) [28] and GhDof1 [29] in cotton, 2-lysophosphatidic acid acyltransferase (LPAAT) in cotton [30], and OLEs in soybean [31] are reported to be related to TAG synthesis. Recently, Liu et al [32] identi ed GmPDAT, GmAGT, GmACP4, GmZF351 and GmPgs1 ve soybean seed oil related genes using an innovative three-dimension network construction approach, as well as genome-wide association studies and multi-omics analyses.…”