Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration
Abstract
:1. Introduction
2. Results and Discussion
2.1. Phenotypic Variation
2.2. Association Mapping of Fiber Traits
2.3. Fiber-Related Candidate Genes
2.4. Candidate Genes Related to the Synthesis and Modification of Cell Wall Components
2.5. Candidate Genes Controlling Cell Fate Determination, Growth and Elongation
2.6. Candidate Genes Associated with Vesicular Transport, Intracellular Trafficking of the Cell Wall Components and Solute Transport across Membranes
2.7. Candidate Genes Involved in Hormonal Regulation
2.8. Candidate Genes Associated with Resistance to Plant Diseases
2.9. Network Analysis
3. Materials and Methods
3.1. Plant Material and Phenotyping
3.2. DNA Sequencing and Variant Calling
3.3. Genetic Data Analysis
3.4. GWAS
3.5. Candidate Genes
3.6. Differential Gene Expression in Fiber Cells
3.7. Co-Expression Network Construction
4. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Appendix A
Plant height | (PH) |
Technical stem length | (TL) |
Technical part weight | (TW) |
Stem diameter | (SD) |
Number of internodes | (NI) |
Distance between internodes | (DI) |
Fiber content | (FC) |
Fiber weight | (FW) |
Elementary fiber length | (ELF) |
Stem slenderness index | (SSI) |
Stem tapering index | (STI) |
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QTN | Gene | Functional Annotation | Arabidopsis Gene Name | Reference | Predicted Function |
---|---|---|---|---|---|
Chr1:27748943 | Lus10010138 | S-adenosyl-L-methionine-dependent methyltransferases superfamily protein | AT4G01240 | [34] | methylation and demethylation of cell wall proteins |
Chr2:261056 | Lus10005814 | RING/U-box superfamily protein | AT1G49230 | [35] | signaling proteins for receptor kinases, regulation of hormone signaling and abiotic/biotic stress response |
Lus10005815 | RING/U-box superfamily protein | AT1G49230 | |||
Lus10005818 | RING/U-box superfamily protein | AT1G49230 | |||
Chr2:2513654 | Lus10016317 | cell wall/vacuolar inhibitor of fructosidase 1 | AT1G47960, ATC/VIF1, C/VIF1 | [36,37] | regulation of ABA response and salt tolerance |
Chr2:4360628 | Lus10020193 | auxin efflux carrier family protein | AT5G16530, PIN5 | [38,39] | regulates intracellular auxin homeostasis and metabolism |
Chr2:4683418 | Lus10013618 | RING/U-box superfamily protein | AT5G17600 | [35] | signaling proteins for receptor kinases, regulation of hormone signaling and abiotic/biotic stress response |
Lus10013631 | peroxidase superfamily protein, class III | AT5G1782, AtperoxP57 | [40,41] | cell wall localized proteins tightly associated to its loosening and stiffening | |
Chr2:4872459 | Lus10013655 | HSP20-like chaperones superfamily protein | AT1G54400 | [42] | enhances membrane stability and detoxifies ROS by regulating the antioxidant enzymes system |
Chr2:6885020 | Lus10038682 | major facilitator superfamily protein | AT2G39210 | [43] | facilitates movement of small solutes across cell membranes |
Chr2:25126362 | Lus10006462 | cellulase (glycosyl hydrolase family 5) protein | AT1G13130 | [44] | hydrolyses the glycosidic bond |
Chr3:4704531 | Lus10019171 | microtubule-associated proteins 70-2 | AT1G24764, ATMAP70-2 | [45] | outlining tracks of cellulose production during SCW formation and delivery of cell wall components |
Chr3:5077352 | Lus10007972 | UDP-glucosyl transferase 89B1 | AT1G73880, UGT89B1 | [46] | |
Chr3:5883916 | Lus10040598 | high-affinity K+ transporter 1 | AT4G10310, ATHKT1 | [47] | reducing Na+ toxicity through K+ uptake |
Chr3:17134662 | Lus10033485 | plant glycogenin-like starch initiation protein 1 | AT3G18660, GUX1, PGSIP1 | [48] | glucuronyl transferase responsible for the addition of GlcA residues onto xylan and for secondary wall deposition |
Chr3:17878746 | Lus10007051 | peroxidase superfamily protein, class III | AT2G4148, AtperoxP25 | [40,41] | cell wall localized proteins tightly associated to its loosening and stiffening |
Chr3:25379963 | Lus10037568 | homeobox-leucine zipper family protein/lipid-binding START domain-containing protein | AT1G52150, ATHB15, CNA, ICU4 | [49] | confers positional information which is required to establish the number and pattern of vascular bundles in the stem, and is involved in repression of secondary cell wall development in Arabidopsis |
Chr3:26449997 | Lus10002912 | integrase-type DNA-binding superfamily protein | AT5G25390, SHN2 | [50] | TF, regulates floral organs’ epidermal cell elongation by affecting pectin metabolism |
Chr4:184242 | Lus10030156 | glucose-1-phosphate adenylyltransferase family protein | AT2G39770, CYT1, EMB101, GMP1, SOZ1, VTC1 | [51] | provides GDP-mannose, which is used for cell wall carbohydrate biosynthesis, including lignin and protein glycosylation |
Chr4:466800 | Lus10030216 | cytochrome P450, family 78, subfamily A, polypeptide 6 | CYP78A6, EOD3 | [52,53,54] | Cell expansion, enhancer of DA-1 3 and seed and fruit development |
Chr4:647773 | Lus10030255 | DYNAMIN-like 1B | AT3G61760, ADL1B | [55] | membrane trafficking, essential for plant cytokinesis and polarized cell growth |
Chr4:1229010 | Lus10030366 | alpha/beta-hydrolases superfamily protein | AT3G62860 | [56] | breaking of carbon–carbon bonds |
Chr4:2763834 | Lus10029506 | cation/hydrogen exchanger 28 | AT3G52080, chx28 | [57] | cation/hydrogen exchange |
Chr4:7789243 | Lus10039564 | F-box/RNI-like superfamily protein | AT5G67140 | [58] | SCF ubiquitin ligase complex |
Chr4:14879575 Chr4:14879658 | Lus10041581 | lysine histidine transporter 1 | AT5G40780, LHT1 | [30] | solute transporter |
Chr4:15210519 | Lus10041644 | fucosyltransferase 1 | AT2G03220, ATFT1, ATFUT1, FT1, MUR2 | [59] | xyloglucan synthesis |
Lus10041651 | cinnamoyl CoA reductase 1 | AT1G15950, ATCCR1, IRX4 | [60] | lignin biosynthesis | |
Chr7:14140267 | Lus10025431 | RAC-like 2 | AT5G45970, ATRAC2, ATROP7 | [61] | secondary cell wall of xylem vessels |
Chr8:1099671 | Lus10013589 | syntaxin of plants 121 | AT3G11820, ATSYP121, ATSYR1, PEN1 | [62] | secretory traffic to the plasma membrane |
Chr9:693002 Chr9:695025 | Lus10010153 | NOD26-like intrinsic protein 5;1 | AT4G1038, NIP5;1, NLM6, NLM8 | [63] | aquaporin |
Lus10010190 | serine carboxypeptidase-like 34 | AT5G23210, SCPL34 | [64] | present in cell wall of elongating cells | |
Chr9:1929944 | Lus10008974 | beta-galactosidase 12 | AT4G26140, BGAL12 | [65] | plant cell wall remodeling |
Chr9:5255847 | Lus10004364 | alpha/beta-hydrolases superfamily protein | AT4G16820, PLA-I{beta]2 | [56] | breaking of carbon–carbon bonds |
Lus10004377 | homeobox protein 2 | AT4G1678, ATHB2, HAT4, HB-2 | [66] | cell expansion and cell proliferation in the response to auxin | |
Chr9:8233979 | Lus10007455 | disease resistance protein (TIR-NBS-LRR class) family | AT3G4448, cog1, RPP1 | [67] | plant immunity |
Chr9:11359847 | Lus10019631 | alpha/beta-hydrolases superfamily protein | AT1G72620 | [56] | breaking of carbon–carbon bonds |
Chr9:17239226 | Lus10042571 | aluminum-activated malate transporter family protein | AT5G46600 | [68] | transporter |
Chr9:17408991 | Lus10042531 | NAC domain-containing protein 47 | AT3G0407, NAC047, SHYG | [69] | NAC TF, localized longitudinal cell expansion |
Lus10042537 | malectin/receptor-like protein kinase family protein | AT3G04690, ANX1 | [70] | perception and relay processes at cell membranes | |
Chr9:18936691 | Lus10024808 | WUSCHEL-related homeobox 4 | AT1G46480, WOX4 | [71] | regulates the dynamic balance of division and differentiation of plant stem cells |
Lus10024818 | cytochrome P450, family 81, subfamily D, polypeptide 5 | AT4G3732, CYP81D5 | [72] | defense response | |
Chr9:19858075 | Lus10000494 | flavin-binding monooxygenase family protein | AT4G2872, YUC8 | [73] | indole-3-pyruvate monooxygenase YUCCA8, responsible for auxin biosynthesis in leaves |
Chr9:20032070- Chr9:20032149 | Lus10011868 | CLAVATA3/ESR-RELATED 41 | AT3G24770, CLE41 | [74] | regulates vascular cell division, vascular organization and xylem differentiation in vascular tissue |
Lus10011858 | cytochrome B5 isoform B | AT2G32720, CB5-B | [75] | lignin biosynthesis | |
Chr12:16047776 | Lus10043075 | O-glycosyl hydrolase family 17 protein | AT5G20870 | [76] | hydrolytic activity towards different types of hemicelluloses or callose |
Chr13:1286479 | Lus10010665 | UDP-glycosyltransferase superfamily protein | AT1G2240, ATUGT85A1, UGT85A1 | [77,78] | cell cycle regulation, influences trans-zeatin (cytokinin) homeostasis likely through O-glycosylation |
Lus10010666 | annexin 8 | AT5G12380, ANNAT8 | [79] | cell wall protein | |
Chr13:3759775 | Lus10026123 | hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase | AT5G48930, HCT | [80] | lignin biosynthesis |
Chr15:1632466 | Lus10013935 | alpha/beta-hydrolases superfamily protein | AT4G18550 | [56] | breaking of carbon–carbon bonds |
Lus10013936 | alpha/beta-hydrolases superfamily protein | ||||
Lus10013945 | O-methyltransferase family protein | AT4G35160 | transfer of methyl groups to various biomolecules |
QTN | Gene | Functional Annotation | Arabidopsis Gene Name | Reference | Predicted Function |
---|---|---|---|---|---|
Chr2:734912 Chr2:748984 Chr2:752999 | Lus10019240 | glycosyl hydrolase family protein | AT5G10560 | [76] | hydrolysis of glycosidic bonds |
Lus10019273 | basic leucine-zipper 6 | AT2G22850, AtbZIP6, bZIP6 | transcription factor | ||
Chr2:3633762 Chr2:3633790 | Lus10003436 | glutamate receptor 2.7 | AT2G29120, GLR2.7 | [81] | non-selective cation channel |
Chr2:6831421 | Lus10038682 | major facilitator superfamily protein | AT2G39210 | [43] | facilitates movement of small solutes across cell membranes |
Chr2:17384359 Chr2:17384362 | Lus10033212 | RAD-like 6 | AT1G75250, RL6, RSM3 | MYB family TF | |
Chr3:12697091 | Lus10005850 | aldolase superfamily protein | AT4G26530 | [82] | modulates V-ATPase-dependent vesicular trafficking events and actin cytoskeleton remodeling |
Chr4:460524 | Lus10030216 | cytochrome P450, family 78, subfamily A, polypeptide 6 | AT2G46660, CYP78A6, EOD3 | [52,53,54] | cell expansion, enhancer of DA-1 3, seed and fruit development |
Chr4:2376445 | Lus10029458 | OBF-binding protein 3 | AT3G55370, OBP3 | [83] | TF, pays a role in plant growth and development, induced by SA and auxin |
Lus10029464 | nodulin MtN21/EamA-like transporter family protein | AT2G39510 | [84,85,86] | amino acid and auxin transporters | |
Chr4:9042565 | Lus10029065 | peroxidase superfamily protein, class III | AT5G05340, AtperoxP52 | [40,41] | cell wall localized proteins tightly associated to its loosening and stiffening |
Lus10029063 | major facilitator superfamily protein | AT2G40460 | [43] | facilitates movement of small solutes across cell membranes | |
Chr4:17106278 | Lus10004043 | myb domain protein 20 | AT1G66230 | [87] | activates lignin and phenylalanine biosynthesis genes during secondary wall formation |
Chr4:18493683 | Lus10030007 Lus10030008 | glycosyl hydrolase 9B8 | AT2G32990, GH9B8 | [88] | membrane endo (1→4)-β-D-glucanase (cellulase), wall assembly and cell elongation, fruit ripening and floral abscission |
Chr8:4371945 Chr8:4833196 | Lus10034491 | major facilitator superfamily protein | AT4G34950 | [43] | facilitates movement of small solutes across cell membranes |
Lus10023931 | plant regulator RWP-RK family protein | AT2G17150 | [89] | control of cell differentiation | |
Chr8:18364995 | Lus10007808, Lus10007809, Lus10007810, Lus10007811, Lus10007813, Lus10007814 | disease resistance protein (TIR-NBS-LRR class) family | AT5G36930 | [90] | plant immunity |
Chr8:19022659 | Lus10002243 | subtilase family protein | AT1G04110, SDD1 | [91] | cell wall enzyme |
Chr9:971861 | Lus10007528, Lus10007529 | TRICHOME BIREFRINGENCE-LIKE 33 | AT2G40320, TBL33 | [92] | contribute to the synthesis and deposition of secondary wall cellulose, presumably by influencing the esterification state of pectic polymers |
Lus10007532 | laccase 5 | AT2G40370, LAC5 | [93] | lignin degradation and detoxification of lignin-derived product | |
Chr9:7152630 | Lus10000957 | expansin-like B1 | AT4G17030, ATEXLB1, ATEXPR1, ATHEXPBETA 3.1, EXLB1, EXPR | [79] | cell wall loosening |
Chr9:7487990 Chr9:7488554 | Lus10024499 | IQ-domain 22 | AT4G23060, IQD22 | [94,95] | Ca2+/CaM-regulated scaffold for cellular transport of specific cargo along microtubules |
Lus10024485 | KNOTTED-like homeobox of Arabidopsis thaliana 7 | AT1G62990, IXR11, KNAT7 | [96] | Secondary-wall-associated transcription factor | |
Chr9:8240615 Chr9:8240618 | Lus10007455 | disease resistance protein (TIR-NBS-LRR class) family | AT3G44480, cog1, RPP1 | [90] | plant immunity |
Chr9:9241973 | Lus10006152 | cytochrome P450, family 90, subfamily D, polypeptide 1 | AT3G13730, CYP90D1 | [72] | modification of cyclic terpenes and sterols in the brassinosteroid, abscisic acid and gibberellin pathways |
Chr9:17172377 Chr9:17190919 | Lus10042571 | aluminum-activated malate transporter family protein | AT5G46600 | [68] | transporter |
Chr9:17511839 Chr9:17513033 | Lus10042531 | NAC domain-containing protein 47 | AT3G04070, anac047, NAC047 | [69] | transcription factor |
Lus10042516 | sugar transporter 1 | AT1G11260, STP1 | [97] | H+/monosaccharide cotransporter | |
Chr9:18121668 | Lus10029638 Lus10029639 | GDSL-like lipase/acylhydrolase superfamily protein | AT1G54790 | [98,99,100] | growth, biotic stress response, in cotton the GDSL (GhGDSL) li pase/hydrolase gene (CotAD_74480) is expressed during SCW biosynthesis |
Chr11:11843614 | Lus10021553 | auxin-responsive family protein | AT3G25290 | [101] | TF, bind to AuxRE in the promoters of auxin-regulated genes |
Chr12:16474392 | Lus10027867 | reticulon family protein | AT3G19460 | [102] | endoplasmic reticulum-Golgi trafficking, vesicle formation and membrane morphogenesis |
Chr13:12832925 | Lus10010638 | basic helix-loop-helix (bHLH) DNA-binding superfamily protein | AT1G27660, PFA5 | [103] | governs the competence of pericycle cells to initiate lateral root primordium formation |
Chr13:18496268 | Lus10030901 | cysteine-rich RLK (RECEPTOR-like protein kinase) 2 | AT1G70520, CRK2 | [104] | plant immunity |
Chr14:3502060 | Lus10020525 | disease resistance protein (TIR-NBS-LRR class) family | AT4G16950, RPP5 | [105] | plant immunity |
Chr14:13328874 | Lus10032902 | HSP20-like chaperones superfamily protein | AT1G54400 | [42] | enhances membrane stability and detoxifies ROS by regulating the antioxidant enzymes system |
Chr15:124776 | Lus10007632 Lus10007633 | cysteine-rich RLK (RECEPTOR-like protein kinase) 25 | AT4G05200, CRK25 | [106] | plant immunity |
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Kanapin, A.; Rozhmina, T.; Bankin, M.; Surkova, S.; Duk, M.; Osyagina, E.; Samsonova, M. Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration. Int. J. Mol. Sci. 2022, 23, 14536. https://doi.org/10.3390/ijms232314536
Kanapin A, Rozhmina T, Bankin M, Surkova S, Duk M, Osyagina E, Samsonova M. Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration. International Journal of Molecular Sciences. 2022; 23(23):14536. https://doi.org/10.3390/ijms232314536
Chicago/Turabian StyleKanapin, Alexander, Tatyana Rozhmina, Mikhail Bankin, Svetlana Surkova, Maria Duk, Ekaterina Osyagina, and Maria Samsonova. 2022. "Genetic Determinants of Fiber-Associated Traits in Flax Identified by Omics Data Integration" International Journal of Molecular Sciences 23, no. 23: 14536. https://doi.org/10.3390/ijms232314536