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Evolution of Carthamus species revealed through sequence analyses of the fad2 gene family

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Abstract

The diversity of 11 fatty acid desaturase (fad2) genes has not been investigated between cultivated and wild species in the Carthamus genus. In this study, 17 C. tinctorius accessions and 28 accessions from other Carthamus species were subjected to sequence analyses of this fad2 gene family. Results showed that among these genes, fad2-1 had a major role in the conversion of oleic acid to linoleic acid. Grouping of all studied wild polyploid species and the wild diploid C. leucocaulos suggested that C. lanatus transferred its fad2-1 gene to C. turkestanicus and C. lanatus. A phylogenetic tree based on fad2-1 gene sequences also showed that C. palaestinus and C. oxyacanthus grouped with C. tinctorius individuals, suggesting that C. tinctorius is closely related to both wild species. A one base pair deletion at position 604 in the fad2-1 gene coding region correlated with high levels of oleic acid content in five mutant phenotypes of the evaluated C. tinctorius accessions. Grouping of fad2-1 and fad2-8 (Ctfad2-10) indicated that both of these genes are involved in oleate desaturases activity. The fad2-3 (Ctfad2-3) and Ctfad2-4 had the highest sequence similarity among the other fad2 genes, indicating the conservative nature of these two genes among all the studied species. Our results suggest that C. lanatus is the likely progenitor of C. turkestanicus and C. creticus (Synonym C. baeticus). Also, C. palaestinus is genetically closer to C. tinctorius but the involvement of C. oxyacanthus cannot be excluded and, this requires further investigation.

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References

  • Agrawal R, Tsujimoto H, Tandon R, Rao SR, Raina SN (2013) Species-genomic relationships among the tribasic diploid and polyploid Carthamus taxa based on physical mapping of active and inactive 18S–5.8 S–26S and 5S ribosomal RNA gene families, and the two tandemly repeated DNA sequences. Gene 521:136–144

    Article  CAS  PubMed  Google Scholar 

  • Ambreen H, Kumar S, Variath MT, Joshi G, Bali S, Agarwal M, Kumar A, Jagannath A, Goel S (2015) Development of genomic microsatellite markers in Carthamus tinctorius L. (safflower) using next generation sequencing and assessment of their cross-species transferability and utility for diversity analysis. PLoS ONE 10:e0135443

    Article  PubMed  PubMed Central  Google Scholar 

  • Ashri A, Knowles PF (1960) Cytogenetics of safflower (Carthamus L.) species and their hybrids. Agron J 52:11–17

    Article  Google Scholar 

  • Ashri A, Zimmer D, Urie A, Knowles PF (1975) Evaluation of the germ plasm collection of safflower Carthamus tinctorius L. VI. Length of planting to flowering period and plant height in Israel, Utah and Washington. Theor Appl Genet 46:359–364

    Article  CAS  PubMed  Google Scholar 

  • Cao S, Zhou X-R, Wood CC, Green AG, Singh SP, Liu L, Liu Q (2013) A large and functionally diverse family of Fad2 genes in safflower (Carthamus tinctorius L.). BMC Plant Biol 13:1

    Article  Google Scholar 

  • Castresana J (2000) Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 17:540–552. https://doi.org/10.1093/oxfordjournals.molbev.a026334

    Article  CAS  PubMed  Google Scholar 

  • Chapman MA, Burke JM (2007) DNA sequence diversity and the origin of cultivated safflower (Carthamus tinctorius L.; Asteraceae). BMC Plant Biol 7:60

    Article  PubMed  PubMed Central  Google Scholar 

  • Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucl Acids Res 32:1792–1797. https://doi.org/10.1093/nar/gkh340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Estilai A, Knowles PF (1976) Cytogenetic studies of Carthamus divaricatus with eleven pairs of chromosomes and its relationship to other Carthamus species (Compositae). Am J Bot 63:771–782. https://doi.org/10.2307/2442035

    Article  Google Scholar 

  • Estilai A, Knowles PF (1978) Relationship of Carthamus leucocaulos to other Carthemus species (Compositae). Can J Genet Cytol 20:221–233

    Article  Google Scholar 

  • Garnatje T, Garcia S, Vilatersana R, VallÈS J (2006) Genome size variation in the genus Carthamus (Asteraceae, Cardueae): systematic implications and additive changes during allopolyploidization. Ann Bot 97:461–467

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Grant V (1971) Plant speciation. Columbia University Press, New York

    Google Scholar 

  • Guan L-L, Wang Y-B, Shen H, Hou K, Xu Y-W, Wu W (2012a) Molecular cloning and expression analysis of genes encoding two microsomal oleate desaturases (FAD2) from safflower (Carthamus tinctorius L.). Plant Mol Biol Rep 30:139–148

    Article  CAS  Google Scholar 

  • Guan L-L, Xu Y-W, Wang Y-B, Chen L, Shao J-f, Wu W (2012b) Isolation and characterization of a temperature-regulated microsomal oleate desaturase gene (CtFAD2-1) from safflower (Carthamus tinctorius L.). Plant Mol Biol Rep 30:391–402

    Article  CAS  Google Scholar 

  • Hanelt P (1963) Monographische Ubersicht der Gattung Carthamus L. (Compositae). Z Feddes Repert 67:41–180

    Google Scholar 

  • Heaton T, Klisiewicz J (1981) A disease-resistant safflower alloploid from Carthamus tinctorius L. × C. lanatus L. Can J Plant Sci 61:219–224

    Article  Google Scholar 

  • Hou CT, Shaw J-F (2009) Biocatalysis and agricultural biotechnology. CRC Press, Boca Raton

    Book  Google Scholar 

  • Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • ISO (2014) ISO 12966-1:2014. Gas chromatography of fatty acid methyl esters—part 1: guidelines on modern gas chromatography of fatty acid methyl esters. Developed by ISO/TC 34/SC 11: animal and vegetable fats and oils. International Organization for Standardization, Geneva

    Google Scholar 

  • ISO (2017) ISO 12966-2:2017. Gas chromatography of fatty acid methyl esters—part 2: preparation of methyl esters of fatty acids) with some modifications. Developed by ISO/TC 34/SC 11: animal and vegetable fats and oils. International Organization for Standardization, Geneva

    Google Scholar 

  • Khidir MO, Knowles PF (1970a) Cytogenetic studies of Carthamus species (Compositae) with 32 pairs of chromosomes. I. Intrasectional hybridization. Am J Bot 57:123–129

    Article  Google Scholar 

  • Khidir MO, Knowles PF (1970b) Cytogenetic studies of Carthamus species (Compositae) with 32 pairs of chromosomes. II. Intrasectional hybridization. Can J Genet Cytol 12:90–99. https://doi.org/10.1139/g70-015

    Article  Google Scholar 

  • Knowles PF (1969) Centers of plant diversity and conservation of crop germ plasm: safflower. Econ Bot 23:324–329. https://doi.org/10.1007/BF02860678

    Article  Google Scholar 

  • Knowles PF, Hill A (1964) Inheritance of fatty acid content in the seed oil of a safflower introduction from Iran. Crop Sci 4:406–409

    Article  CAS  Google Scholar 

  • Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu Q, Cao S, Zhou X-R, Wood C, Green A, Singh S (2013) Nonsense-mediated mRNA degradation of CtFAD2-1 and development of a perfect molecular marker for olol mutation in high oleic safflower (Carthamus tinctorius L.). Theor Appl Genet 126:2219–2231. https://doi.org/10.1007/s00122-013-2129-2

    Article  CAS  PubMed  Google Scholar 

  • Liu L, Guan LL, Wu WWL, Wang L (2016) A review of fatty acids and genetic characterization of safflower (Carthamus tinctorius L.) seed oil. World J Tradit Chin Med 2:48–52

    Article  Google Scholar 

  • López González G (1989) Acerca de la clasificación natural del género Carthamus L., sl. Anales del Jardin Botanico de Madrid, Rueda, pp 11–34

    Google Scholar 

  • Majidi MM, Zadhoush S (2014) Molecular and morphological variation in a world-wide collection of safflower. Crop Sci 54:2109–2119. https://doi.org/10.2135/cropsci2013.12.0850

    Article  Google Scholar 

  • McPherson MA, Good AG, Topinka AKC, Hall LM (2004) Theoretical hybridization potential of transgenic safflower (Carthamus tinctorius L.) with weedy relatives in the New World. Can J Plant Sci 84:923–934

    Article  Google Scholar 

  • Meka PK, Tripathi V, Singh R (2007) Synthesis of biodiesel fuel from safflower oil using various reaction parameters. J Oleo Sci 56:9–12. https://doi.org/10.5650/jos.56.9

    Article  CAS  Google Scholar 

  • Miquel M, Browse J (1992) Arabidopsis mutants deficient in polyunsaturated fatty acid synthesis. Biochemical and genetic characterization of a plant oleoyl-phosphatidylcholine desaturase. J Biol Chem 267:1502–1509

    CAS  PubMed  Google Scholar 

  • Murthy I, Anjani K (2007) Fatty acid composition in Carthamus species. In: 7th international safflower conference, WAGGA WAGGA Australia Directorate of Oilseeds Research, Rajendranagar, Hyderabad-500

  • Nazari M, Mirlohi A, Majidi MM (2017) Effects of drought stress on oil characteristics of Carthamus species. J Am Oil Chem Soc 94:247–256. https://doi.org/10.1007/s11746-016-2938-y

    Article  CAS  Google Scholar 

  • Okuley J, Lightner J, Feldmann K, Yadav N, Lark E (1994) Arabidopsis FAD2 gene encodes the enzyme that is essential for polyunsaturated lipid synthesis. Plant Cell 6:147–158

    CAS  PubMed  PubMed Central  Google Scholar 

  • Pearl SA, Bowers JE, Reyes-Chin-Wo S, Michelmore RW, Burke JM (2014) Genetic analysis of safflower domestication. BMC Plant Biol 14:43. https://doi.org/10.1186/1471-2229-14-43

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rapson S, Wu M, Okada S, Das A, Shrestha P, Zhou X-R, Wood C, Green A, Singh S, Liu Q (2015) A case study on the genetic origin of the high oleic acid trait through FAD2-1 DNA sequence variation in safflower (Carthamus tinctorius L). Front Plant Sci 6:691. https://doi.org/10.3389/fpls.2015.00691

    Article  PubMed  PubMed Central  Google Scholar 

  • Sabzalian MR, Saeidi G, Mirlohi A (2008) Oil content and fatty acid composition in seeds of three safflower species. J Am Oil Chem Soc 85:717–721. https://doi.org/10.1007/s11746-008-1254-6

    Article  CAS  Google Scholar 

  • Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454

    Article  CAS  PubMed  Google Scholar 

  • Sasanuma T, Sehgal D, Sasakuma T, Raina SN (2008) Phylogenetic analysis of Carthamus species based on the nucleotide sequence of the nuclear SACPD gene and chloroplast trn L–trn F IGS region. Genome 51:721–727

    Article  CAS  PubMed  Google Scholar 

  • Schank S, Knowles P (1964) Cytogenetics of hybrids of Carthamus species (Compositae) with ten pairs of chromosomes. Am J Bot 51:1093–1102

    Article  Google Scholar 

  • Schlueter JA, Vasylenko-Sanders IF, Deshpande S, Yi J, Siegfried M, Roe BA, Schlueter SD, Scheffler BE, Shoemaker RC (2007) The FAD2 gene family of soybean. Crop Sci 47:S-14-S-26

    Article  Google Scholar 

  • Sehgal D, Raina SN, Devarumath RM, Sasanuma T, Sasakuma T (2009) Nuclear DNA assay in solving issues related to ancestry of the domesticated diploid safflower (Carthamus tinctorius L.) and the polyploid (Carthamus) taxa, and phylogenetic and genomic relationships in the genus Carthamus L. (Asteraceae). Mol Phylogenetics Evol 53:631–644. https://doi.org/10.1016/j.ympev.2009.07.012

    Article  CAS  Google Scholar 

  • Vilatersana R, Susanna A, Garcia-Jacas N, Garnatje T (2000) Karyology, generic delineation and dysploidy in the genera Carduncellus, Carthamus and Phonus (Asteraceae). Bot J Linean Soc 134:425–438. https://doi.org/10.1006/bojl.2000.0349

    Article  Google Scholar 

  • Vilatersana R, Garnatje T, Susanna A, Garcia-Jacas N (2005) Taxonomic problems in Carthamus (Asteraceae): RAPD markers and sectional classification. Bot J Linn Soc 147:375–383. https://doi.org/10.1111/j.1095-8339.2005.00375.x

    Article  Google Scholar 

  • You FM, Li P, Kumar S, Ragupathy R, Li Z, Fu Y-B, Cloutier S (2014) Genome-wide identification and characterization of the gene families controlling fatty acid biosynthesis in flax (linum usitatissimum L.). J Proteom Bioinform 7:310–326. https://doi.org/10.4172/jpb.1000334

    Article  CAS  Google Scholar 

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Acknowledgements

The authors would like to thank Dr. Allen Good of the University of Alberta for providing us with seeds of Carthamus accessions and Haeyon Oh for the FAME analyses.

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Authors and Affiliations

  1. Department of Agronomy and Plant Breeding, College of Agriculture, Isfahan University of Technology, Isfahan, 84156-8311, Iran

    Fariba Shafiei-Koij, Aghafakhr Mirlohi & Mohamad Mahdi Majidi

  2. Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Ave, Ottawa, ON, K1A 0C6, Canada

    Sridhar Ravichandran & Sylvie Cloutier

  3. Canadian Grain Commission, 303 Main Street, Winnipeg, MB, R3C 3G7, Canada

    Véronique J. Barthet

  4. Department of Biology, School of Mathematics and Statistics, Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada

    Nicolas Rodrigue

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  1. Fariba Shafiei-Koij
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12298_2019_739_MOESM1_ESM.tif

Fig. S1 PCR amplicons at 63 °C annealing temperature for 11 fad2 genes on agarose gel. For each fad2 gene, nine amplicons were observed so that three amplicons are related to each primer pairs. Numbers 1, 2 and 3 represented first, second and third primer pairs for each fad2 gene. The abbreviations of T, P and O represented C. tinctorius (Goldasht), C. palaestinus and C. oxyacanthus (Cosh) genotypes, respectively. A 1 kb plus DNA ladder (ThermoFisher) was used and the corresponding sizes have been labelled. (TIFF 3101 kb)

Supplementary material 2 (TIFF 3170 kb)

12298_2019_739_MOESM3_ESM.tif

Fig. S2 PCR amplicons at 63 °C annealing temperature for some fad2 genes on agarose gel. For each fad2 gene, nine amplicons were observed so that three amplicons are related to each primer pairs. Numbers 1, 2 and 3 represented first, second and third primer pairs for each fad2 gene. The abbreviations of T, P and O represented C. tinctorius (Goldasht), C. palaestinus and C. oxyacanthus (Cosh) genotypes, respectively. A 1 kb plus DNA ladder (ThermoFisher) was used and the corresponding sizes have been labelled. (TIFF 1302 kb)

12298_2019_739_MOESM4_ESM.tif

Fig. S3 Dendrogram of the fad2-1 gene accessions representing ten Carthamus species based on Illumina MiSeq concatenated sequence data of 45 accessions. The length of branches represented the relative sequence differences: the shorter branch lengths, the more similar sequences; Numbers above the branches indicate bootstrap values. Information on Carthamus species can be found in Table 1. (TIFF 2661 kb)

Fig. S4

Dendrogram of the fad2-2 gene from ten Carthamus species representing 45 accessions based on Illumina MiSeq concatenated sequence data (TIFF 1095 kb)

Fig. S5

Dendrogram of the fad2-2 gene accessions representing ten Carthamus species based on Illumina MiSeq concatenated sequence data of 45 accessions. The length of branches represented the relative sequence differences: the shorter branch lengths, the more similar sequences; Numbers above the branches indicate bootstrap values. Information on Carthamus species can be found in Table 1. (TIFF 2534 kb)

Fig. S6

Dendrogram of the fad2-3 gene from ten Carthamus species representing 45 accessions based on Illumina MiSeq concatenated sequence data (TIFF 1126 kb)

Fig. S7

Dendrogram of the fad2-3 gene accessions representing ten Carthamus species based on Illumina MiSeq concatenated sequence data of 45 accessions. The length of branches represented the relative sequence differences: the shorter branch lengths, the more similar sequences; Numbers above the branches indicate bootstrap values. Information on Carthamus species can be found in Table 1. (TIFF 2446 kb)

Fig. S8

Dendrogram of the fad2-4 gene from ten Carthamus species representing 45 accessions based on Illumina MiSeq concatenated sequence data (TIFF 1038 kb)

Fig. S9

Dendrogram of the fad2-4 gene accessions representing ten Carthamus species based on Illumina MiSeq concatenated sequence data of 45 accessions. The length of branches represented the relative sequence differences: the shorter branch lengths, the more similar sequences; Numbers above the branches indicate bootstrap values. Information on Carthamus species can be found in Table 1. (TIFF 2454 kb)

Fig. S10

Dendrogram of the fad2-5 gene from ten Carthamus species representing 45 accessions based on Illumina MiSeq concatenated sequence data (TIFF 990 kb)

Fig. S11

Dendrogram of the fad2-5 gene accessions representing ten Carthamus species based on Illumina MiSeq concatenated sequence data of 45 accessions. The length of branches represented the relative sequence differences: the shorter branch lengths, the more similar sequences; Numbers above the branches indicate bootstrap values. Information on Carthamus species can be found in Table 1. (TIFF 2592 kb)

Fig. S12

Dendrogram of the fad2-6 gene from ten Carthamus species representing 45 accessions based on Illumina MiSeq concatenated sequence data (TIFF 976 kb)

Fig. S13

Dendrogram of the fad2-6 gene accessions representing ten Carthamus species based on Illumina MiSeq concatenated sequence data of 45 accessions. The length of branches represented the relative sequence differences: the shorter branch lengths, the more similar sequences; Numbers above the branches indicate bootstrap values. Information on Carthamus species can be found in Table 1. (TIFF 2693 kb)

Fig. S14

Dendrogram of the fad2-7 gene from ten Carthamus species representing 45 accessions based on Illumina MiSeq concatenated sequence data (TIFF 923 kb)

Fig. S15

Dendrogram of the fad2-7 gene accessions representing ten Carthamus species based on Illumina MiSeq concatenated sequence data of 45 accessions. The length of branches represented the relative sequence differences: the shorter branch lengths, the more similar sequences; Numbers above the branches indicate bootstrap values. Information on Carthamus species can be found in Table 1. (TIFF 2739 kb)

Fig. S16

Dendrogram of the fad2-8 gene from ten Carthamus species representing 45 accessions based on Illumina MiSeq concatenated sequence data (TIFF 1022 kb)

Fig. S17

Dendrogram of the fad2-8 gene accessions representing ten Carthamus species based on Illumina MiSeq concatenated sequence data of 45 accessions. The length of branches represented the relative sequence differences: the shorter branch lengths, the more similar sequences; Numbers above the branches indicate bootstrap values. Information on Carthamus species can be found in Table 1. (TIFF 2783 kb)

Fig. S18

Dendrogram of the Ctfad2-4 gene from ten Carthamus species representing 45 accessions based on Illumina MiSeq concatenated sequence data (TIFF 1059 kb)

Fig. S19

Dendrogram of the Ctfad2-4 gene accessions representing ten Carthamus species based on Illumina MiSeq concatenated sequence data of 45 accessions. The length of branches represented the relative sequence differences: the shorter branch lengths, the more similar sequences; Numbers above the branches indicate bootstrap values. Information on Carthamus species can be found in Table 1. (TIFF 2760 kb)

Fig. S20

Dendrogram of the Ctfad2-8 gene from ten Carthamus species representing 45 accessions based on Illumina MiSeq concatenated sequence data (TIFF 1033 kb)

Fig. S21

Dendrogram of the Ctfad2-8 gene accessions representing ten Carthamus species based on Illumina MiSeq concatenated sequence data of 45 accessions. The length of branches represented the relative sequence differences: the shorter branch lengths, the more similar sequences; Numbers above the branches indicate bootstrap values. Information on Carthamus species can be found in Table 1. (TIFF 2686 kb)

Fig. S22

Dendrogram of the Ctfad2-9 gene from ten Carthamus species representing 45 accessions based on Illumina MiSeq concatenated sequence data (TIFF 1039 kb)

Fig. S23

Dendrogram of the Ctfad2-9 gene accessions representing ten Carthamus species based on Illumina MiSeq concatenated sequence data of 45 accessions. The length of branches represented the relative sequence differences: the shorter branch lengths, the more similar sequences; Numbers above the branches indicate bootstrap values. Information on Carthamus species can be found in Table 1. (TIFF 2747 kb)

Fig. S24

Dendrogram of ten Carthamus species derived from the 11 fad2 genes based on Illumina MiSeq concatenated dataset of the 45 accessions. (TIFF 779 kb)

Fig. S25

Deduced amino acid sequence of the fad2-1 gene in 35 accessions of Carthamus. (PDF 1653 kb)

Supplementary material 27 (DOCX 54 kb)

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Shafiei-Koij, F., Ravichandran, S., Barthet, V.J. et al. Evolution of Carthamus species revealed through sequence analyses of the fad2 gene family. Physiol Mol Biol Plants 26, 419–432 (2020). https://doi.org/10.1007/s12298-019-00739-4

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