Table 1. Alleles of carotenogenesis genes in different tissues of ‘Chuhong’ and ‘Feicui’ pummelo (Citrus maxima) fruits.
| Genes | Alleles (pummelos) | Length of coding DNA sequence (CDS) bp (amino acid) |
Different sites of nucleotides (amino acids) (site bp) | ||||
|---|---|---|---|---|---|---|---|
| CmDXR | CmDXRa CH | 1422(473) | T(F) 20(7) | G(A) 430(145) | |||
| CmDXRb FC | 1422(473) | C(S) 20(7) | T(S) 430(145) | ||||
| CmPSY | CmPSYa CH, HR, HB, WS, FH, KP, T | 1317(438) | T(V) 74(25) | A(N) 178(60) | TAA(N) 183-185(61) | G(R) 644(215) | -- |
| CmPSYb HR, QDC, WBH, FC, FH | 1314(437) | T(V) 74(25) | A(N) 178(60) | --183-185(61) | A(Q) 644(215) | -- | |
| CmPSYc HR, WBH, KP | 1314(438) | T(V) 74(25) | A(N) 178(60) | --183-185(61) | G(R) 644(215) | -- | |
| CmPSYd QDC | 1314(437) | G(G) 74(25) | A(N) 178(60) | --183-185(61) | A(Q) 644(215) | -- | |
| CmPSYe HB, WS, T | 1314(438) | T(V)7 4(25) | G(D) 178(60) | --183-185(61) | G(R) 644(215) | -- | |
| CmPSYf WBH, FH, KP | 1402(397) | T(V) 74(25) | A(N) 178(60) | TAA(N) 183-185(61) | G(R) 644(215) | 1147-1231 (85-bp base insertion; causing premature termination in amino acids, see S2A Fig) | |
| CmPDS | CmPDS CH, FC | 1659(552) | |||||
| CmZISO | CmZISO CH, FC | 1125(374) | |||||
| CmCRTISO | CmCRTISOa CH | 2028(675) | C(L) 1360(454) | G(M) 1797(599) | |||
| CmCRTISOb FC | 2028(675) | A(I) 1360(454) | A(I) 1797(599) | ||||
| CmLCYb1 | CmLCYb1a CH, FC | 1515(504) | G(G) 323(108) | ||||
| CmLCYb1b FC | 1515(504) | A(E) 323(108) | |||||
| CmLCYb2 | CmLCYb2a CH, FC | 1512(503) | C(S) 968(323) | ||||
| CmLCYb2b FC | 1512(503) | T(L) 968(323) | |||||
| CmLCYe | CmLCYea CH, FC | 1590(529) | A(I) 307(103) | ||||
| CmLCYeb CH, FC | 1590(529) | T(F) 307(103) | |||||
| CmBCH | CmBCH CH, FC | 936(309) | |||||
| CmZEP | CmZEPa CH | 1995(664) | C(H) 916(306) | T(L) 937(313) | A(D) 944(315) | G(R) 1538(513) | T(V) 1647(549) |
| CmZEPb FC | 1995(664) | A(N) 916(306) | G(V) 937(313) | G(G) 944(315) | A(Q) 1538(513) | G(G) 1647(549) | |
| CmNSY | CmNSY CH, FC | 747(248) | |||||
Note: The numbers and letters under ‘Different sites of nucleotides (amino acid) (site bp)’ means the number of sites and different nucleotides (amino acids) among the alleles of each gene. --: deletion/no insertion. All single nucleotide polymorphisms shown above are nonsynonymous different sites. At least 10 clones for each carotenogenesis gene were sequenced from the cDNA mainly from the JS of each pummelo fruit. In particular, for CmPSY, CmLCYb1, CmLCYb2, CmLCYe and CmNSY, nearly 50 clones of each gene in each pummelo fruit were obtained. CmDXR: 1-deoxy-D-xylulose-5-phosphate reductoisomerase gene. CmPSY: phytoene synthase gene. CmPDS: phytoene desaturase gene. CmCRTISO: carotenoid isomerase gene. CmZISO: 15-cis-ζ-carotene isomerase gene. CmLCYb1: lycopene β-cyclase gene 1. CmLCYb2: lycopene β-cyclase gene 2. CmLCYe: lycopene ε-cyclase gene. CmBCH: β-carotenoid hydroxylase gene. CmZEP: zeaxanthin epoxidase gene. CmNSY: neoxanthin synthase gene. CH: ‘Chuhong’ pummelo (red-fleshed). FC: ‘Feicui’ pummelo (pale green-fleshed). HR: Huanong Red pummelo (red-fleshed). QDC: Chandler pummelo (red-fleshed). HB: Hirado Buntan pummelo (pink-fleshed). WBH: Wubu Red-fleshed pummelo (red-fleshed). T: Thai pummelo (pale yellow-fleshed). KP: Kao Pan (pale green-fleshed). FH: Fenghuang pummelo (pale green-fleshed). WS: Acidless pummelo (pale green-fleshed).