Rice Science ›› 2016, Vol. 23 ›› Issue (6): 287-296.DOI: 10.1016/j.rsci.2016.09.002
• • 下一篇
收稿日期:2016-07-25
接受日期:2016-09-22
出版日期:2016-12-12
发布日期:2016-08-10
. [J]. Rice Science, 2016, 23(6): 287-296.
Fig. 1. Conceivable biosynthetic pathways of phospholipids in cereals. Drawn based on Kinney (1993), D’Arrigo and Servi (2010) and Liu et al (2013). E, Ethanolamine; ME, Methylethanolamine; DME, Dimethylethanolamine; IP3, inositol 1,4,5-triphosphate; LPA, Lysophosphatidic acid; C, Choline; P, Phosphate; CDP, Cytidinediphosphate; PE, Phosphatidylethanolamine; PME, Phosphatidylmethylethanolamine; PDME, Phosphatidyldimethyle- thanolamine; PC, Phosphatidylcholine; PS, Phosphatidylserine; PI, Phosphatidylinositol; PIP, Phosphatidylinositol phosphate; PIP2, Phosphati- dylinositolbisphosphate; PGP, Phosphoglycerol phosphate; PG, Phosphatidylglycerol; DPG, Diphosphatidylglycerol; , Glycerol-3-phosphate acyltransferase; , 1-monoacylglycerol-3-phosphate acyltransferase; , CDP-diacylglycerol synthase (CTP: phosphatidatecytidylyltransferase); , Phosphatidatephosphohydrolase; , PI synthase (CDP-diacylglycerol: myo-inositol phosphatidyltransferase); , PI 4-kinase (ATP: phosphati- dylinositol-4-phosphotransferase); , PIP kinase (ATP: phosphatidylinositol 4-phosphate 5-phosphotransferase); , PGP synthase (CDP-diacylgly- cerolphosphatidyltransferase); , PGP phosphatase (phosphatidylglycerol-phosphate phosphohydrolase); , CDP diacylglycerolphosphatidly- transerase; , PS synthase (CDP-diacylglycerol: L-serine O-phosphatidyltransferase); , PS decarboxylase; , PE N-methyltransferase; , Phospholipid N-methyltransferase; , Aminoalcoholphosphotransferase; , Ethanolaminephosphotransferase (CDP-ethanolamine: 1,2-diacylglycerol cytidylyltransferase); , Ethanolamine phosphate cytidylyltransferase (CTP: ethanolamine phosphate cytidylyltransferase); , Ethanolamine kinase (ATP: ethanolamine phosphotransferase); , Cholinephosphotransferase (CDP-choline: 1,2-diacylglycerol cytidylyltransferase); , Choline phosphate cytidylyltransferase (CTP: choline phosphate cytidylyltransferase); , Choline kinase (ATP: choline phosphotransferase); , Phospholipase D (PLD) (Phosphatidylcholinephosphatidohydrolase); , Phospholipase C (PLC); , Diacylglycerol (DAG) kinase; , Phospholipase A2 (PLA2).
| Trait | Year | Model | QTL | Chr | Position a (bp) | P-value | Major allele | Minor allele | Minor allele frequency | Allelic effect (R2) | |
| LPC16:0 | 2011 | K | qC160-6-1 | 6 | 26 685 967 | 4.72 × 10-3 | C | T | 0.30 | 0.8011 | |
| 2012 | K | qC160-6-2 | 6 | 3 235 560 | 4.41 × 10-3 | G | A | 0.25 | 0.5573 | ||
| qC160-8 | 8 | 8 481 084 | 3.64 × 10-3 | A | G | 0.40 | 0.5872 | ||||
| LPC18:1 | 2012 | Q+K | qC181-2 | 2 | 14 522 544 | 3.15 × 10-3 | G | A | 0.20 | 0.8346 | |
| qC181-1 | 1 | 27 729 601 | 4.20 × 10-3 | C | T | 0.30 | 0.8107 | ||||
| LPC18:2 | 2011 | K | qC182-9 | 9 | 15 125 638 | 4.37 × 10-3 | C | T | 0.20 | 0.5585 | |
| 2012 | K | qC182-11 | 11 | 17 847 796 | 4.07 × 10-3 | A | T | 0.30 | 0.5698 | ||
| LPC18:3 | 2011 | K | qC183-1 | 1 | 23 517 183 | 3.27 × 10-3 | A | C | 0.25 | 0.6047 | |
| 2012 | K | qC183-1 | 1 | 23 517 183 | 4.89 × 10-3 | A | C | 0.25 | 0.5411 | ||
| TLPC | 2011 | ANOVA | qC-5 | 5 | 23 465 186 | 4.20 × 10-3 | G | A | 0.25 | 0.5647 | |
| qC-9 | 9 | 15 125 638 | 2.62 × 10-3 | C | T | 0.20 | 0.6409 | ||||
| qC-12 | 12 | 21 175 392 | 3.73 × 10-3 | T | A | 0.25 | 0.5835 | ||||
| 2012 | K | qC-10 | 10 | 5 339 258 | 4.36 × 10-3 | G | A | 0.25 | 0.5589 | ||
| LPE16:0 | 2011 | ANOVA | qE160-1 | 1 | 6 971 525 | 3.33 × 10-3 | G | A | 0.25 | 0.6016 | |
| LPE18:1 | 2011 | Q+K | qE181-2 | 2 | 14 522 544 | 3.26 × 10-3 | G | A | 0.20 | 0.7802 | |
| 2012 | Q+K | qE181-2 | 2 | 14 522 544 | 2.17 × 10-3 | G | A | 0.20 | 0.8364 | ||
| LPE18:2 | 2011 | K | qE182-1 | 1 | 23 585 360 | 3.23 × 10-3 | C | T | 0.25 | 0.6064 | |
| qE182-4 | 4 | 31 271 474 | 4.23 × 10-3 | T | C | 0.20 | 0.5637 | ||||
| qE182-11 | 11 | 17 943 118 | 3.82 × 10-3 | T | A | 0.35 | 0.5798 | ||||
| LPE18:3 | 2011 | K | qE183-1 | 1 | 23 517 183 | 4.27 × 10-3 | A | C | 0.25 | 0.5623 | |
| 2012 | K | qE183-1 | 1 | 23 517 183 | 4.33 × 10-3 | A | C | 0.25 | 0.5600 | ||
| TLPE | 2011 | ANOVA | qE-10 | 10 | 5 339 258 | 4.69 × 10-3 | G | A | 0.25 | 0.5477 | |
| TLPL | 2011 | ANOVA | qL-9 | 9 | 15 125 638 | 2.92 × 10-3 | C | T | 0.20 | 0.6229 | |
| qL-10 | 10 | 5 339 258 | 4.67 × 10-3 | G | A | 0.25 | 0.5482 | ||||
| qL-12 | 12 | 21 175 392 | 4.93 × 10-3 | T | A | 0.25 | 0.5399 | ||||
| 2012 | K | qL-10 | 10 | 5 339 258 | 4.19 × 10-3 | G | A | 0.25 | 0.5649 | ||
| LPC14:0, 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine; LPC16:0, 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine; LPC18:1, 1-oleoyl- 2-hydroxy-sn-glycero-3-phosphocholine; LPC18:2, 1-linoleoyl-2-hydroxy-sn-glycero-3-phosphocholine; LPC18:3, 1-linolenoyl-2-hydroxy-sn- glycero-3-phosphocholine; LPE14:0, 1-myristoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine; LPE16:0, 1-palmitoyl-2-hydroxy-sn-glycero-3- phosphoethanolamine; LPE18:1, 1-oleoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine; LPE18:2, 1-linoleoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine; LPE18:3, 1-linolenoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine; TLPC, Total lysophosphatidylcholine; TLPE, Total lysophosphatidylethanolamine; TLPL, Total lysophospholipid; Q, Population structure; K, Kinship; ANOVA, Analysis of variance; Chr, Chromosome. a, Position in base pairs for the leading SNP of rice sequence. | |||||||||||
Table 1 Genome-wide significantly associated QTLs for rice lysophospholipids (LPLs)
| Trait | Year | Model | QTL | Chr | Position a (bp) | P-value | Major allele | Minor allele | Minor allele frequency | Allelic effect (R2) | |
| LPC16:0 | 2011 | K | qC160-6-1 | 6 | 26 685 967 | 4.72 × 10-3 | C | T | 0.30 | 0.8011 | |
| 2012 | K | qC160-6-2 | 6 | 3 235 560 | 4.41 × 10-3 | G | A | 0.25 | 0.5573 | ||
| qC160-8 | 8 | 8 481 084 | 3.64 × 10-3 | A | G | 0.40 | 0.5872 | ||||
| LPC18:1 | 2012 | Q+K | qC181-2 | 2 | 14 522 544 | 3.15 × 10-3 | G | A | 0.20 | 0.8346 | |
| qC181-1 | 1 | 27 729 601 | 4.20 × 10-3 | C | T | 0.30 | 0.8107 | ||||
| LPC18:2 | 2011 | K | qC182-9 | 9 | 15 125 638 | 4.37 × 10-3 | C | T | 0.20 | 0.5585 | |
| 2012 | K | qC182-11 | 11 | 17 847 796 | 4.07 × 10-3 | A | T | 0.30 | 0.5698 | ||
| LPC18:3 | 2011 | K | qC183-1 | 1 | 23 517 183 | 3.27 × 10-3 | A | C | 0.25 | 0.6047 | |
| 2012 | K | qC183-1 | 1 | 23 517 183 | 4.89 × 10-3 | A | C | 0.25 | 0.5411 | ||
| TLPC | 2011 | ANOVA | qC-5 | 5 | 23 465 186 | 4.20 × 10-3 | G | A | 0.25 | 0.5647 | |
| qC-9 | 9 | 15 125 638 | 2.62 × 10-3 | C | T | 0.20 | 0.6409 | ||||
| qC-12 | 12 | 21 175 392 | 3.73 × 10-3 | T | A | 0.25 | 0.5835 | ||||
| 2012 | K | qC-10 | 10 | 5 339 258 | 4.36 × 10-3 | G | A | 0.25 | 0.5589 | ||
| LPE16:0 | 2011 | ANOVA | qE160-1 | 1 | 6 971 525 | 3.33 × 10-3 | G | A | 0.25 | 0.6016 | |
| LPE18:1 | 2011 | Q+K | qE181-2 | 2 | 14 522 544 | 3.26 × 10-3 | G | A | 0.20 | 0.7802 | |
| 2012 | Q+K | qE181-2 | 2 | 14 522 544 | 2.17 × 10-3 | G | A | 0.20 | 0.8364 | ||
| LPE18:2 | 2011 | K | qE182-1 | 1 | 23 585 360 | 3.23 × 10-3 | C | T | 0.25 | 0.6064 | |
| qE182-4 | 4 | 31 271 474 | 4.23 × 10-3 | T | C | 0.20 | 0.5637 | ||||
| qE182-11 | 11 | 17 943 118 | 3.82 × 10-3 | T | A | 0.35 | 0.5798 | ||||
| LPE18:3 | 2011 | K | qE183-1 | 1 | 23 517 183 | 4.27 × 10-3 | A | C | 0.25 | 0.5623 | |
| 2012 | K | qE183-1 | 1 | 23 517 183 | 4.33 × 10-3 | A | C | 0.25 | 0.5600 | ||
| TLPE | 2011 | ANOVA | qE-10 | 10 | 5 339 258 | 4.69 × 10-3 | G | A | 0.25 | 0.5477 | |
| TLPL | 2011 | ANOVA | qL-9 | 9 | 15 125 638 | 2.92 × 10-3 | C | T | 0.20 | 0.6229 | |
| qL-10 | 10 | 5 339 258 | 4.67 × 10-3 | G | A | 0.25 | 0.5482 | ||||
| qL-12 | 12 | 21 175 392 | 4.93 × 10-3 | T | A | 0.25 | 0.5399 | ||||
| 2012 | K | qL-10 | 10 | 5 339 258 | 4.19 × 10-3 | G | A | 0.25 | 0.5649 | ||
| LPC14:0, 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine; LPC16:0, 1-palmitoyl-2-hydroxy-sn-glycero-3-phosphocholine; LPC18:1, 1-oleoyl- 2-hydroxy-sn-glycero-3-phosphocholine; LPC18:2, 1-linoleoyl-2-hydroxy-sn-glycero-3-phosphocholine; LPC18:3, 1-linolenoyl-2-hydroxy-sn- glycero-3-phosphocholine; LPE14:0, 1-myristoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine; LPE16:0, 1-palmitoyl-2-hydroxy-sn-glycero-3- phosphoethanolamine; LPE18:1, 1-oleoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine; LPE18:2, 1-linoleoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine; LPE18:3, 1-linolenoyl-2-hydroxy-sn-glycero-3-phosphoethanolamine; TLPC, Total lysophosphatidylcholine; TLPE, Total lysophosphatidylethanolamine; TLPL, Total lysophospholipid; Q, Population structure; K, Kinship; ANOVA, Analysis of variance; Chr, Chromosome. a, Position in base pairs for the leading SNP of rice sequence. | |||||||||||
Fig. 2. Location of QTLs for rice starch lysophospholipids (LPLs) on chromosomes (Chr). C160, C181, C182, C183, E160, E181, E182, E183, C, E and L in the QTLs represent LPC16:0, LPC18:1, LPC18:2, LPC18:3, LPE16:0, LPE18:1, LPE18:2, LPE18:3, total lysophosphatidylcholine, total lysophosphatidylethanolamine and total lysophospholipid, respectively.
Fig. 3. Manhattan plots of association test for total lysophospholipid.
Fig. 4. Part sequence alignments of AAPT and PLA2 genes. A, InDel found in AAPT gene among G01-G20; B, Single nucleotide polymorphism found in PLA2 gene among G01-G20. AAPT, Aminoalcoholphosphotransferase; PLA2, Phospholipase A2.
| Primer | Type | Sequence (5′-3′) | PCR product (bp) | Restriction enzyme | Enzyme digestion product (bp) |
| AAPT1-F | InDel | CCAGCCTTGTTTCAATACCTG | 134/127 | - | - |
| AAPT1-R | AAATGTAGGAAGTTTTTACTTGC | ||||
| AAPT2-F | dCAPS | AAGAGCAAGTAAAAACTTCCTAAATT | 222 | ApoI | 22, 200 |
| AAPT2-R | GATACAAATGCCCAAATACCA | ||||
| AAPT3-F | dCAPS | CAAAGATCAATGCTGGGTAATTTC | 184 | SphI | 22, 162 |
| AAPT3-R | AGGTAAATCAGTTCACCTGTGCA | ||||
| PLD1-F | dCAPS | CATCCTGCACTAAAAACAGTTGAAT | 214 | HinfI | 22, 192 |
| PLD1-R | TGCACAACACCAGAGCCCCACC | ||||
| PLD2-F | dCAPS | CCTCCCAAAGTTTAGGCGGAAAAGGCC | 187 | HpaII | 27, 160 |
| PLD2-R | TCAAAGCTCACAATAGCAGAATA | ||||
| PLA21-F | dCAPS | TTCCTATTGTTTCTTCCTCCCTCTT | 230 | HinfI | 20, 210 |
| PLA21-R | GAAAAAACAAAATTAAAAAAGAGT | ||||
| dCAPS, Development of derived cleaved amplified polymorphic sequences. Underlined letter means the mismatch base. | |||||
Table 2 Primers for enzyme digestion of several single nucleotide polymorphisms
| Primer | Type | Sequence (5′-3′) | PCR product (bp) | Restriction enzyme | Enzyme digestion product (bp) |
| AAPT1-F | InDel | CCAGCCTTGTTTCAATACCTG | 134/127 | - | - |
| AAPT1-R | AAATGTAGGAAGTTTTTACTTGC | ||||
| AAPT2-F | dCAPS | AAGAGCAAGTAAAAACTTCCTAAATT | 222 | ApoI | 22, 200 |
| AAPT2-R | GATACAAATGCCCAAATACCA | ||||
| AAPT3-F | dCAPS | CAAAGATCAATGCTGGGTAATTTC | 184 | SphI | 22, 162 |
| AAPT3-R | AGGTAAATCAGTTCACCTGTGCA | ||||
| PLD1-F | dCAPS | CATCCTGCACTAAAAACAGTTGAAT | 214 | HinfI | 22, 192 |
| PLD1-R | TGCACAACACCAGAGCCCCACC | ||||
| PLD2-F | dCAPS | CCTCCCAAAGTTTAGGCGGAAAAGGCC | 187 | HpaII | 27, 160 |
| PLD2-R | TCAAAGCTCACAATAGCAGAATA | ||||
| PLA21-F | dCAPS | TTCCTATTGTTTCTTCCTCCCTCTT | 230 | HinfI | 20, 210 |
| PLA21-R | GAAAAAACAAAATTAAAAAAGAGT | ||||
| dCAPS, Development of derived cleaved amplified polymorphic sequences. Underlined letter means the mismatch base. | |||||
| Accession | AAPT1 | AAPT2 | AAPT3 | PLD1 | PLD2 | PLA21 | Accession | AAPT1 | AAPT2 | AAPT3 | PLD1 | PLD2 | PLA21 |
| G01 | D | T | A | C | G | G | G18 | I | A | G | C | C | G |
| G02 | D | T | A | C | G | G | G19 | D | T | A | C | G | T |
| G03 | D | T | A | A | C | T | G20 | I | A | G | A | C | T |
| G04 | D | T | A | A | C | G | R01 | D | T | A | C | C | G |
| G05 | D | T | A | C | C | T | R02 | D | T | A | C | C | G |
| G06 | D | T | A | C | G | G | R03 | D | T | A | C | G | T |
| G07 | D | T | A | C | G | G | R04 | D | T | A | C | C | G |
| G08 | D | T | A | C | C | T | R05 | D | T | A | C | C | T |
| G09 | D | T | A | C | G | G | R06 | D | T | A | C | C | G |
| G10 | D | T | A | A | C | T | R07 | D | T | A | C | G | G |
| G11 | D | T | A | C | G | G | R08 | I | A | G | C | C | G |
| G12 | D | T | A | C | C | T | R09 | D | T | A | C | C | T |
| G13 | D | T | A | C | C | T | R10 | I | A | G | C | C | T |
| G14 | I | A | G | C | C | T | R11 | D | T | A | C | C | T |
| G15 | D | T | A | C | C | G | R12 | D | T | A | C | C | T |
| G16 | D | T | A | C | G | G | R13 | I | A | G | C | C | T |
| G17 | I | A | G | C | C | G | |||||||
| AAPT, Aminoalcoholphosphotransferase; PLD, Phospholipase D; PLA2, Phospholipase A2; I, Insertion; D, Deletion. | |||||||||||||
Table 3 Summary of alleles of three candidate genes.
| Accession | AAPT1 | AAPT2 | AAPT3 | PLD1 | PLD2 | PLA21 | Accession | AAPT1 | AAPT2 | AAPT3 | PLD1 | PLD2 | PLA21 |
| G01 | D | T | A | C | G | G | G18 | I | A | G | C | C | G |
| G02 | D | T | A | C | G | G | G19 | D | T | A | C | G | T |
| G03 | D | T | A | A | C | T | G20 | I | A | G | A | C | T |
| G04 | D | T | A | A | C | G | R01 | D | T | A | C | C | G |
| G05 | D | T | A | C | C | T | R02 | D | T | A | C | C | G |
| G06 | D | T | A | C | G | G | R03 | D | T | A | C | G | T |
| G07 | D | T | A | C | G | G | R04 | D | T | A | C | C | G |
| G08 | D | T | A | C | C | T | R05 | D | T | A | C | C | T |
| G09 | D | T | A | C | G | G | R06 | D | T | A | C | C | G |
| G10 | D | T | A | A | C | T | R07 | D | T | A | C | G | G |
| G11 | D | T | A | C | G | G | R08 | I | A | G | C | C | G |
| G12 | D | T | A | C | C | T | R09 | D | T | A | C | C | T |
| G13 | D | T | A | C | C | T | R10 | I | A | G | C | C | T |
| G14 | I | A | G | C | C | T | R11 | D | T | A | C | C | T |
| G15 | D | T | A | C | C | G | R12 | D | T | A | C | C | T |
| G16 | D | T | A | C | G | G | R13 | I | A | G | C | C | T |
| G17 | I | A | G | C | C | G | |||||||
| AAPT, Aminoalcoholphosphotransferase; PLD, Phospholipase D; PLA2, Phospholipase A2; I, Insertion; D, Deletion. | |||||||||||||
Fig. 5. Polymorphism of InDel and simple nucleotide polymorphisms in AAPT, PLD and PLA2 genes in rice accessions G01-G20 and R01-R13. AAPT, Aminoalcoholphosphotransferase; PLD, Phospholipase D; PLA2, Phospholipase A2. Lanes from left to right in each part are marker, G01-G20 and R01-R13, respectively.
| Gene | Marker | Trait | Non-waxy accession (31) | All rice accession (33) | QTL | |||
| p_Marker | R2_Marker | p_Marker | R2_Marker | |||||
| PLD | PLD1 | LPC16:0 | 0.0149 | 0.1876 | 0.0984 | 0.0856 | qC160-6-1 | |
| PLA2 | PLA21 | LPC18:2 | 0.0902 | 0.0958 | 0.0277 | 0.1468 | qC182-11, qE182-11 | |
| PLD, Phospholipase D; PLA2, Phospholipase A2. | ||||||||
Table 4 Marker loci associated with starch lysophospholipids (LPLs) traits detected with analysis of variance (ANOVA) model in 31 non-waxy and all the 33 rice accessions.
| Gene | Marker | Trait | Non-waxy accession (31) | All rice accession (33) | QTL | |||
| p_Marker | R2_Marker | p_Marker | R2_Marker | |||||
| PLD | PLD1 | LPC16:0 | 0.0149 | 0.1876 | 0.0984 | 0.0856 | qC160-6-1 | |
| PLA2 | PLA21 | LPC18:2 | 0.0902 | 0.0958 | 0.0277 | 0.1468 | qC182-11, qE182-11 | |
| PLD, Phospholipase D; PLA2, Phospholipase A2. | ||||||||
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| 39 | (Managing Editor: Li Guan) |
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