| Literature DB >> 28018375 |
Xianjun Liu1, Ying Lu2, Mingli Yan3, Donghong Sun2, Xuefang Hu2, Shuyan Liu2, Sheyuan Chen2, Chunyun Guan2, Zhongsong Liu2.
Abstract
Proanthocyanidins (PA) is a type of prominent flavonoid compound deposited in seed coats which controls the pigmentation in all Brassica species. Annotation of Brassica juncea genome survey sequences showed 72 PA genes; however, a functional description of these genes, especially how their interactions regulate seed pigmentation, remains elusive. In the present study, we designed 19 primer pairs to screen a bacterial artificial chromosome (BAC) library of B. juncea. A total of 284 BAC clones were identified and sequenced. Alignment of the sequences confirmed that 55 genes were cloned, with every Arabidopsis PA gene having 2-7 homologs in B. juncea. BLAST analysis using the recently released B. rapa or B. napus genome database identified 31 and 58 homologous genes, respectively. Mapping and phylogenetic analysis indicated that 30 B. juncea PA genes are located in the A-genome chromosomes except A04, whereas the remaining 25 genes are mapped to the B-genome chromosomes except B05 and B07. RNA-seq data and Fragments Per Kilobase of a transcript per Million mapped reads (FPKM) analysis showed that most of the PA genes were expressed in the seed coat of B. juncea and B. napus, and that BjuTT3, BjuTT18, BjuANR, BjuTT4-2, BjuTT4-3, BjuTT19-1, and BjuTT19-3 are transcriptionally regulated, and not expressed or downregulated in yellow-seeded testa. Importantly, our study facilitates in better understanding of the molecular mechanism underlying Brassica PA profiles and accumulation, as well as in further characterization of PA genes.Entities:
Keywords: BAC library; Brassica spp.; gene cloning; proanthocyanidin biosynthesis; seed color
Year: 2016 PMID: 28018375 PMCID: PMC5145881 DOI: 10.3389/fpls.2016.01831
Source DB: PubMed Journal: Front Plant Sci ISSN: 1664-462X Impact factor: 5.753
Grouping of the PA gene carrier BAC clones screened by PCR from .
| Structural | STT4 | 5 | ZBjuH038D07, ZBjuH052L16, | |||
| – | 14 | ZBjuH036L22, ZBjuH062E10, ZBjuH068P04, ZBjuH090C04, ZBjuH103N17, ZBjuH115L06, ZBjuH117A13, ZBjuH125A20, ZBjuH130C13, ZBjuH167H05, ZBjuH167H11, ZBjuH167H12, | ||||
| 16 | ||||||
| 5 | ZBjuH031A21, ZBjuH031B12, | |||||
| 2 | ZBjuH044O21, | |||||
| 2 | ||||||
| – | 4 | ZBjuH049I15, ZBjuH049J15, | ||||
| STT5 | 1 | |||||
| 1 | ||||||
| 10 | ZBjuH027P19, ZBjuH036L22, ZBjuH041J15, ZBjuH058J20, ZBjuH066I18, ZBjuH066O10, | |||||
| 5 | ZBjuH096N21, | |||||
| STT6 | 7 | ZBjuH020C14, ZBjuH048G02, ZBjuH048M11, | ||||
| 5 | ZBjuH058P02, ZBjuH059D03, ZBjuH076G06, | |||||
| 1 | ||||||
| 8 | ||||||
| 6 | ZBjuH106N13, ZBjH131P01, | |||||
| STT7 | 9 | ZBjuH012H01, ZBjuH025M21, ZBjuH045C24, ZBjuH063G22, ZBjuH095P11, ZBjuH105C09, ZBjuH156A19, | ||||
| 4 | ||||||
| SDFR | 7 | |||||
| 3 | ZBjuH134O05, ZBjuH175D09, | |||||
| STT18 | 4 | |||||
| 3 | ZBjuH020C14, ZBjuH181I12, | |||||
| 3 | ||||||
| 5 | ZBjuH054H16, ZBjuH093H16, | |||||
| SANR | 3 | ZBjuH022P08, | ||||
| 2 | ||||||
| 4 | ZBjuH071P08, | |||||
| 1 | ||||||
| STT10-1 | 6 | ZBjuH003E23, BjuH033G01, ZBjuH048L18, ZBjuH057G09, | ||||
| STT10-2 | 9 | ZBjuH006C17, ZBjuH019G11, | ||||
| STT10-1 | 11 | |||||
| STT10-2 | 1 | |||||
| Regulatory | STT1 | 4 | ZBjuH021J20, ZBjuH036J21, ZBjuH157B22, | |||
| 3 | ZBjuH097N03, | |||||
| STT2 | 2 | |||||
| 7 | ZBjuH028M22, | |||||
| STT8-1 | 5 | |||||
| STT8-2 | 3 | |||||
| STT16-1 | 2 | ZBjuH051G23, | ||||
| STT16-1 | 6 | ZBjuH046H18, ZBjuH070H21, ZBjuH082B14, | ||||
| STT16-2 | 2 | |||||
| STT16-2 | – | 4 | ZBjuH057K05, ZBjuH057K06, | |||
| STT16-1 | 7 | ZBjuH061F23, ZBjuH064O06, ZBjuH070C13, ZBjuH094F17, | ||||
| STT16-1 | 11 | ZBjuH013K01, ZBjuH030F17, ZBjuH049C21, | ||||
| STTG1 | 2 | ZBjuH030O08, | ||||
| 6 | ||||||
| STTG2 | 1 | |||||
| 3 | ||||||
| 13 | ZBjuH025O05, ZBjuH032N08, ZBjuH039D04, | |||||
| 5 | ZBjuH028C13, | |||||
| Transporter | STT12 | 4 | ZBjuH046J03, | |||
| 3 | ||||||
| STT19 | 13 | ZBjuH006M03, ZBjuH037H06, ZBjuH061A09, ZBjuH064M21, ZBjuH066G20, ZBjuH092A06, ZBjuH093G08, | ||||
| 6 | ZBjuH062L17, ZBjuH120J17, ZBjuH143N08, | |||||
| 5 | ZBjuH021A20, ZBjuH070G12, |
The BAC clone in bold was used to sequence full-length sequence of the gene.
Proanthocyanidins-associated genes identified in .
| AtTT4/CHS (AT5G13930) | Bra020688(A02) | BnaA02g30320D /BnaC02g05070D | |
| Bra023441(A02) | BnaC02g38730D/ BnaCnng01290D | ||
| Bra006224(A03) | BnaA03g04590D/ BnaC03g06120D | ||
| Bra008792(A10) | BnaA10g19670D/ BnaC09g43250D | ||
| Bra036307(A09) | BnaA09g29340D | ||
| AtTTT5/CHI (AT3G55120) | Bra017728(A03) | BnaAnng08210D /BnaC07g45760D | |
| Bra003209(A07) | BnaA07g37900D/BnaCnng45660D | ||
| Bra007142(A09) | BnaA09g34840D/BnaC08g26010D | ||
| AtTT6/F3H (AT3G51240) | Bra012862(A03) | BnaA03g41250D/BnaC07g32140D | |
| Bra036828(A09) | BnaA09g31780D/BnaC08g22640D | ||
| Bra007813(A09) | BnaA09g55810D | ||
| AtTT7/F3′H (AT5G07990) | Bra009312(A10) | BnaA10g23330D/BnaC09g47980D | |
| AtTT3/DFR (AT5G42800) | Bra027457(A09) | BnaA09g15710D/BnaC09g17150D | |
| AtTT18/ANS (AT4G22880) | Bra013652(A01) | BnaA01g12530D/BnaC01g14310D | |
| Bra019350(A03) | BnaA03g45610D/BnaC07g37670D | ||
| AtANR (AT1G61720) | Bra021318(A01) | BnaA03g60670D/BnaC04g18950D | |
| Bra031403(A01) | BnaA01g36200D/BnaC01g29820D | ||
| AtTT10 (AT5G48100) | Bra020720(A02) | BnaAnng08030D /BnaC02g38340D | |
| Bra037510(A06) | BnaA06g30430D | ||
| AtTT1 (AT1G34790) | Bra028067(A09) | BnaAnng02100D/ BnaC06g08390D | |
| AtTT2 (AT5G35550) | Bra035532(A08) | BnaA08g29930D/BnaC08g07960D | |
| AtTT8 (AT4G09820) | Bra037887(A09) | BnaA09g22810D/BnaC09g24870D | |
| AtTT16 (AT5G23260) | Bra029365(A02) | BnaAnng30140D/ BnaC02g41690D | |
| Bra013028(A03) | BnaA03g39500D/BnaC02g42240D | ||
| Bra026507(A09) | BnaA09g05410D/BnaC09g04950D | ||
| AtTTG1 (AT5G24520) | Bra009770(A06) | BnaC07g29950D | |
| AtTTG2 (AT2G37260) | Bra023112(A03) | BnaA03g17120D/BnaC03g20650D | |
| Bra005210(A05) | BnaA05g07220D/BnaC04g08020D | ||
| AtTT12 (AT3G59030) | Bra003361(A07) | BnaA07g18120D/BnaC06g17050D | |
| AtTT19 (AT5G17220) | Bra023602(A02) | BnaA02g03440D/BnaC02g07090D | |
| Bra008570(A10) | BnaA10g17440D/BnaC09g40740D | ||
from http://brassicadb.org/brad/;
this study;
from .
Mapping to the .
| ZBjuH187G14 | 1269 | A02(23204660-23205926) | 98.7 | 98.9 | A02 | Bra020688 | A02(21961707-21962975) | 100 | 99.2 | A02 | BnaA02g30320D | |
| ZBjuH175I06 | 1454 | A02(2357734-2359185) | 98.0 | 97.9 | A02 | Bra023441 | C02(2648298-2649755) | 99.7 | 96.6 | – | BnaC02g38730D | |
| ZBjuH037O10 | 1458 | A03(2596137-2597594) | 92.4 | 99.3 | A03 | Bra006224 | A03(2138849-2140306) | 100 | 99.8 | A03 | BnaA03g04590D | |
| ZBjuH036O12 | 1263 | A10(12657235-12655973) | 99.0 | 99.0 | A10 | Bra008792 | A10(13887677-13888939) | 100 | 99.3 | A10 | BnaA10g19670D | |
| ZBjuH053C09 | 1516 | B02(31676065-31677577) | 100 | 97.8 | B02 | – | C02(2648298-2649755) | 96.2 | 93.7 | – | BnaCnng01290D | |
| ZBjuH053C08 | 1352 | B03(41854375-41855800) | 94.8 | 96.2 | B03 | – | C03(2967996-2969460) | 92.3 | 94.3 | – | BnaC03g06120D | |
| ZBjuH090K23 | 1267 | B08(26615339-26614079) | 100 | 96.9 | B08 | – | A10(13887677-13888939) | 99.7 | 93.5 | – | BnaC09g43250D | |
| 1387 | B06(30337366-30338627) | 97.3 | 94.4 | B03 | – | A03(2138849-2140306) | 96.7 | 94.8 | – | BnaC02g05070D | ||
| ZBjuH186N11 | 1358 | A03(30108206-30109397) | 98.9 | 99.0 | A03 | Bra017728 | C07(43667810-43668920) | 93.2 | 95.5 | – | BnaC07g45760D | |
| ZBjuH181K10 | 1526 | A07(15175119-15173091) | 71.1 | 97.1 | A07 | Bra003209 | A07_random(1352839-1353912) | 70.4 | 100 | A07 | BnaA07g37900D | |
| ZBjuH080G05 | 1621 | A09(29057157-29055564) | 98.6 | 97.8 | A09 | Bra007142 | A09(25461126-25462763) | 99.0 | 98.7 | A09 | BnaA09g34840D | |
| ZBjuH106O08 | 1625 | scaffold_30.1(142586-144208) | 99.7 | 98.8 | B | – | C08(27510384-27511983) | 98.5 | 91.9 | – | BnaC08g26010D | |
| 1667 | B04(26277974-26279709) | 96.1 | 95.2 | B04 | – | Un_random(67254442-67255968) | 91.6 | 92.4 | – | BnaCnng45660D | ||
| ZBjuH058K21 | 1343 | A03(21908585-21910045) | 82.4 | 97.0 | A03 | Bra012862 | A03(20668741-20670084) | 99.9 | 99.4 | A03 | BnaA03g41250D | |
| ZBjuH087J23 | 1514 | A09(27095567-27097080) | 100.0 | 100.0 | A09 | Bra036828 | C08(25256551-25258093) | 98.1 | 97.6 | – | BnaA09g31780D | |
| ZBjuH031F14 | 2998 | A09(32529280-32526116) | 94.0 | 98.0 | A09 | Bra007813 | A09_random(3426703-3429867) | 94.7 | 99.8 | A09 | BnaA09g55810D | |
| ZBjuH022O18 | 1820 | B03(6099152-6097595) | 93.2 | 98.5 | B03 | – | A09(23688234-23689696) | 80.4 | 92.7 | – | BnaC07g32140D | |
| ZBjuH143I07 | 1454 | B08(40828252-40826791) | 99.1 | 98.1 | B08 | – | C07(35957629-35959030) | 96.4 | 91.9 | – | BnaC08g22640D | |
| ZBjuH159L04 | 2742 | A10(14358845-14356094) | 89.4 | 99.2 | A10 | Bra009312 | A10(15436550-15439304) | 99.5 | 98.8 | A10 | BnaA10g23330D | |
| ZBjuH080O14 | 2989 | B08(28566520-28563560) | 98.6 | 98.4 | B08 | – | C09(47019883-47026924) | 44.4 | 94.1 | – | BnaC09g47980D | |
| ZBjuH029J10 | 1556 | A09(10927890-10926334) | 98.3 | 98.3 | A09 | Bra027457 | A09(9168455-9170011) | 99.9 | 100 | A09 | BnaA09g15710D | |
| ZBjuH183H13 | 1689 | B06(24256936-24255214) | 96.1 | 99.5 | B06 | – | C09(10927890-10926334) | 92.5 | 94.2 | – | BnaC09g17150D | |
| ZBjuH054O02 | 1422 | A01(6887113-6885692) | 98.5 | 98.5 | A01 | Bra013652 | A01(6294305-6295726) | 100 | 100 | A01 | BnaA01g12530D | |
| ZBjuH181K08 | 1161 | A03(24797395-24796232) | 96.3 | 96.2 | A03 | Bra019350 | A03(23215394-23216555) | 99.9 | 97.3 | A03 | BnaA03g45610D | |
| ZBjuH091K10 | 1143 | B02(37385323-37384165) | 99.2 | 95.3 | B02 | – | C01(9585700-9587061) | 83.9 | 93.8 | – | BnaC01g14310D | |
| ZBjuH177N08 | 1152 | B08(43361751-43360600) | 98.1 | 95.8 | B08 | – | C07(39327212-39328382) | 98.4 | 94.2 | – | BnaC07g37670D | |
| ZBjuH082J01 | 1433 | A01(21514882-21513450) | 99.2 | 99.2 | A01 | Bra021318 | A03_random(5666520-5667956) | 99.7 | 99.2 | A03 | BnaA03g60670D | |
| ZBjuH148I16 | 1466 | A01(17603658-17602193) | 99.3 | 99.3 | A01 | Bra031403 | A01(1630437-1631902) | 100 | 100 | A01 | BnaA01g36200D | |
| ZBjuH116E04 | 1499 | B01(22657990-22659506) | 98.6 | 96.8 | B01 | – | C01(28124388-28125894) | 99.5 | 90.5 | – | BnaC01g29820D | |
| ZBjuH034P21 | 1400 | B08(31434047-31435447) | 99.9 | 99.1 | B08 | – | C04(18894005-18895401) | 99.8 | 94.6 | – | BnaC04g18950D | |
| ZBjuH083G18 | 3491 | A02(22971851-22968361) | 99.9 | 98.8 | A02 | Bra020720 | Un_random(41316930-41322490) | 62.8 | 94.9 | – | BnaAnng08030D | |
| ZBjuH055H16 | 2297 | A06(20410060-20412553) | 91.3 | 99.7 | A06 | Bra037510 | A06(20553612-20555918) | 99.6 | 99.2 | A06 | BnaA06g30430D | |
| ZBjuH021A16 | 2838 | B06(30198717-30195455) | 87.0 | 97.4 | B06 | – | C02(41316930-41322490) | 51.0 | 91.5 | – | BnaC02g38340D | |
| ZBjuH176D10 | 2293 | B08(38281497-20412553) | 98.9 | 99.0 | B08 | – | A06(20553612-20555918) | 99.4 | 93.1 | – | – | |
| ZBjuH180A05 | 1761 | A09(18767007-18765243) | 99.8 | 97.5 | A09 | Bra028067 | Un_random(4808305-4809953) | 93.6 | 97.9 | – | BnaAnng02100D | |
| ZBjuH147E23 | 1707 | B06(8841257-8839558) | 100 | 97.4 | B06 | – | C06(9366519-9368246) | 98.8 | 93.2 | – | BnaC06g08390D | |
| ZBjuH085H24 | 945 | A08(8306171-8305232) | 96.5 | 98.9 | A08 | Bra035532 | A08_random(1033684-1034627) | 100 | 99.5 | A08 | BnaA08g29930D | |
| ZBjuH034J15 | 944 | scaffold_500.1(70364-69421) | 100 | 100 | B | – | C08(11760224-11761157) | 98.9 | 93.3 | – | BnaC08g07960D | |
| ZBjuH004L18 | 3551 | A09(15769736-15773288) | 80.2 | 97.7 | A09 | Bra037887 | A09(15413735-15417282) | 99.9 | 99.3 | A09 | BnaA09g22810D | |
| ZBjuH005J18 | 2768 | B03(8122342-8125109) | 100 | 99.7 | B03 | – | C09(23189158-23191902) | 99.1 | 94.1 | – | BnaC09g24870D | |
| ZBjuH130K12 | 1954 | A02(25055704-25053743) | 98.3 | 99.5 | A02 | Bra029365 | Un_random(101450485-101452437) | 99.9 | 99.6 | – | BnaAnng30140D | |
| ZBjuH099A21 | 2258 | A03(20961426-20959132) | 92.9 | 99.4 | A03 | Bra013028 | A03(19707165-19709160) | 88.4 | 98.5 | A03 | BnaA03g39500D | |
| ZBjuH091L03 | 2004 | A09(3307401-3305402) | 45.1 | 97.6 | A09 | Bra026507 | A09(2642192-2644190) | 99.7 | 98.9 | A09 | BnaA09g05410D | |
| ZBjuH098G12 | 1981 | B01(19554897-19552670) | 89.0 | 96.9 | B01 | C09(2859965-2861956) | 99.4 | 91.3 | – | BnaC09g04950D | ||
| ZBjuH094N07 | 2129 | B06(30711288-30713462) | 97.5 | 97.6 | B06 | – | Un_random(101450485-101452437) | 91.7 | 92.1 | – | BnaC02g41690D | |
| ZBjuH077C18 | 1980 | B08(41662625-41664607) | 99.8 | 98.1 | B08 | – | C02(44915780-44917790) | 98.5 | 92.6 | – | BnaC02g42240D | |
| ZBjuH130K10 | 1582 | A06(17740552-17739539) | 99.7 | 98.8 | A06 | Bra009770 | A06(18525005-18526105) | 69.6 | 93.9 | A06 | – | |
| ZBjuH129A18 | 1014 | B08(42051009-42049996) | 100 | 98.6 | B08 | – | C07(34623713-34624389) | 66.8 | 92.8 | – | BnaC07g29950D | |
| ZBjuH088A24 | 1516 | A03(8752727-8754251) | 96.4 | 96.0 | A03 | Bra023112 | A03(8032043-8033567) | 99.4 | 97.5 | A03 | BnaA03g17120D | |
| ZBjuH101A24 | 1466 | A05(4037093-4035604) | 96.5 | 97.2 | A05 | Bra005210 | A05(3894221-3895658) | 99.4 | 96.3 | A05 | BnaA05g07220D | |
| ZBjuH063L13 | 1528 | B03(32083362-32081848) | 100 | 97.2 | B03 | – | C03(10964876-10966395) | 99.2 | 93.1 | – | BnaC03g20650D | |
| ZBjuH043G17 | 1501 | B04(5191336-5189901) | 100 | 95.1 | B04 | – | C04(6027042-6028503) | 97.4 | 90.9 | - | BnaC04g08020D | |
| ZBjuH047J16 | 2487 | A07(16102336-16104823) | 95.1 | 95.5 | A07 | Bra003361 | A07(14915288-14917797) | 99.1 | 96.9 | A07 | BnaA07g18120D | |
| ZBjuH124J12 | 2505 | B04(25039840-25037376) | 98.4 | 92.8 | B04 | – | C06(19784039-19786887) | 87.9 | 94.1 | – | BnaC06g17050D | |
| ZBjuH095N01 | 808 | A02(3117740-3118547) | 98.6 | 98.6 | A02 | Bra023602 | A02(1531517-1532324) | 100 | 99.9 | A02 | BnaA02g03440D | |
| ZBjuH170C22 | 800 | A10(11678470-11677671) | 99.9 | 99.9 | A10 | Bra008570 | A10(12914260-12915058) | 99.9 | 99.7 | A10 | BnaA10g17440D | |
| ZBjuH122M08 | 1030 | B02(33205499-33206525) | 100 | 96.7 | B02 | – | C02(3777795-3778584) | 85.6 | 95.2 | – | BnaC02g07090D | |
| 825 | B08(25314277-25313454) | 100 | 99.4 | B08 | – | A10(12914260-12915058) | 96.4 | 91.1 | – | – |
Figure 1Putative chromosomal positions of cloned proanthocyanidins-associated genes in . BjuTT5-4 and BjuTT2-2 were not located on the chromosome in B. juncea.
Mapping to the .
| BjuTT4-1 | ZBjuH187G14 | 1048 | A02(23296428-23295380) | 98.9 | 1113 | A02(23152779-23153899) | 97.7 | A02 |
| A02(22075270-22077756) | 99.5 | A02 (21892025-21893145) | 99.6 | |||||
| BjuTT4-2 | ZBjuH175I06 | 1071 | A02(2363318-2361982) | 97.5 | 964 | A02(2240655-2241616) | 96.1 | A02 |
| A02 (887331-888410) | 99.6 | A02 (755926-756886) | 99.2 | |||||
| BjuTT4-3 | ZBjuH037O10 | 1080 | A03(2659211-2658129) | 99.0 | 587 | A03(2525990-2526576) | 99.1 | A03 |
| A03(2210720-2211802) | 100 | A03(2079518-2080104) | 97.5 | |||||
| BjuTT4-4 | ZBjuH036O12 | 1031 | A10(12537033-12538063) | 97.4 | 1059 | A10(12660016-12659255) | 97.8 | A10 |
| A10(13765877-13766904) | 98.1 | A10(13890039-13890915) | 98.2 | |||||
| BjuTT4-5 | ZBjuH053C09 | 1062 | B02(31653057-31654113) | 94.2 | 994 | B02(31799935-31798937) | 95.2 | B02 |
| BjuTT4-6 | ZBjuH053C08 | 1110 | B03(41773983-41775087) | 97.5 | 1097 | Repeat sequence | – | B03 |
| BjuTT4-7 | ZBjuH090K23 | 1065 | B08(26731199-26730093) | 93.2 | 1111 | B08(26612733-26613845) | 92.3 | B08 |
| BjuTT5-1 | ZBjuH186N11 | 1023 | A03(30133579-30132560) | 98.0 | 1112 | A03(30031062-30032157) | 98.3 | A03 |
| Un_random(22402145-22403163) | 98.6 | A03(28012499-28013608) | 97.6 | |||||
| BjuTT5-2 | ZBjuH181K10 | 1071 | A07(15073257-15074276) | 97.0 | 926 | A09(31899835-31899128) | 97.4 | A07 |
| A07(13943509-13944466) | 95.7 | A06(7618337-7619247) | 97.5 | |||||
| BjuTT5-3 | ZBjuH080G05 | 997 | A09(29107181-29106192) | 99.0 | 948 | A09(28952074-28953021) | 97.3 | A09 |
| A09(25510915-25511912) | 98.2 | A09_random(28952074-28953021) | 99.1 | |||||
| BjuTT5-4 | ZBjuH106O08 | 1233 | scaffold_30.1(166852-165708) | 92.5 | 930 | scaffold_30.1(64946-65862) | 94.8 | B |
| BjuTT6-1 | ZBjuH058K21 | 1177 | A07(2473977-2472803) | 96.2 | 1179 | A03(21939848-21938684) | 97.7 | A03 |
| A07(2765573-2766747) | 98.0 | A03(20708198-20709378) | 98.9 | |||||
| BjuTT6-2 | ZBjuH087J23 | 863 | A09(27193799-27193372) | 96.4 | 1002 | A09(27076762-27077609) | 98.9 | A09 |
| Un_random(93706755-93707622) | 96.9 | A09(23672668-23672668) | 92.7 | |||||
| BjuTT6-3 | ZBjuH031F14 | 1036 | A09(32538591-32537560) | 97.4 | 963 | A09(32402616-32403171) | 98.6 | A09 |
| A09_random(3439921-3440956) | 98.7 | A09(28629617-28630172) | 99.1 | |||||
| BjuTT6-4 | ZBjuH022O18 | 1051 | B03(6156413-6155347) | 97.2 | 1068 | B03(6011976-6012882) | 99.1 | B03 |
| BjuTT6-5 | ZBjuH143I07 | 1034 | B08(40752199-40753230) | 96.6 | 1115 | B08(40891718-40890578) | 95.6 | B08 |
| BjuTT7-1 | ZBjuH159L04 | 950 | A10(14281026-14287855) | 94.3 | 875 | A10(14428932-14428063) | 99.2 | A10 |
| A10(15377459-15378411) | 95.4 | Un_random(110160592-110161461) | 99.1 | |||||
| BjuTT7-2 | ZBjuH080O14 | 1072 | B08(28651670-28650600) | 94.8 | 1084 | B05(13990978-13992051) | 97.5 | B08 |
| BjuTT3-1 | ZBjuH029J10 | 952 | A09(10801814-10802675) | 99.1 | 902 | A09(10945043-10944178) | 96.0 | A09 |
| A09_random(1204329-1205280) | 99.7 | A09(9183884-9184783) | 97.5 | |||||
| BjuTT3-2 | ZBjuH183H13 | 973 | B06(24254316-24255289) | 99.9 | 984 | B06(24372970-24371986) | 99.9 | B06 |
| BjuTT18-1 | ZBjuH054O02 | 1063 | A01(6900126-6899636) | 97.6 | 896 | A01(6775183-6775797) | 94.7 | A01 |
| A04 (19187764-19188396) | 97.2 | A01_random(376002-376873) | 96.3 | |||||
| BjuTT18-2 | ZBjuH181K08 | 1071 | A03(24832511-24831559) | 93.6 | 928 | A03(24707499-24708449) | 98.2 | A03 |
| A03(23248562-23249571) | 95.6 | A03_random(1774070-1775012) | 96.3 | |||||
| BjuTT18-3 | ZBjuH091K10 | 1151 | B02(37271971-37273119) | 99.5 | 1033 | B02(36953007-36952312) | 92.9 | B02 |
| BjuTT18-4 | ZBjuH177N08 | 1179 | B08(43363553-43362571) | 94.8 | 1036 | Scaffold_215.1 (85454-84890) | 99.1 | B08 |
| BjuANR-1 | ZBjuH082J01 | 981 | A01(21610018-21609039) | 100 | 890 | A01(21496749-21497598) | 93.7 | A01 |
| A03_random(5751842-5752821) | 98.8 | A03_random(5650455-5651236) | 98.1 | |||||
| BjuANR-2 | ZBjuH148I16 | 1088 | A01(17599566-17600642) | 98.5 | 996 | A05(6382585-6383570) | 96.7 | A01 |
| A01_random(1627810-1628889) | 97.7 | C06(11884727-11885709) | 94.0 | |||||
| BjuANR-3 | ZBjuH116E04 | 1136 | B01(23295810-23295103) | 96.8 | 1143 | B01(22662292-22661178) | 93.5 | B01 |
| BjuANR-4 | ZBjuH034P21 | 1015 | B08(31415998-31416996) | 95.1 | 996 | B08(31573791-31572839) | 99.6 | B08 |
| BjuTT10-1 | ZBjuH083G18 | 895 | A02(22936601-22937747) | 96.8 | 926 | A07(287213-288132) | 82.6 | A02 |
| Un_random(20422597-20428316) | 99.7 | A10(7084906-7085831) | 99.4 | |||||
| BjuTT10-2 | ZBjuH055H16 | 998 | A06(20316953-20317946) | 95.7 | 974 | A06(20441440-20440468) | 99.6 | A06 |
| A06(20471573-20472569) | 96.0 | A06 (20582545-20583508) | 96.9 | |||||
| BjuTT10-3 | ZBjuH021A16 | 1006 | B06(30166234-30167223) | 92.7 | 988 | B06(30284319-30283311) | 93.7 | B06 |
| BjuTT10-4 | ZBjuH176D10 | 1037 | B07(12155684-12156717) | 99.0 | 1008 | B07(12306990-12305968) | 98.1 | B07 |
| BjuTT1-1 | ZBjuH180A05 | 1064 | A09(18800232-18799233) | 96.8 | 888 | A09(18714197-18714808) | 95.7 | A09 |
| Un_random(4883830-4884831) | 96.2 | Un_random(4606100-4606768) | 95.5 | |||||
| BjuTT1-2 | ZBjuH147E23 | 1021 | Scaffold_312.1 (121001-121983) | 97.7 | 880 | Repeat Sequence | – | B06 |
| BjuTT2-1 | ZBjuH085H24 | 1008 | Scaffold000519(4310-5318) | 99.2 | 933 | A08(8207949-8208882) | 99.3 | A08 |
| Un_random(53133429-53134437) | 99.8 | A08(7146333-7147266) | 99.7 | |||||
| BjuTT2-2 | ZBjuH034J15 | 1041 | Scaffold_500.1 (142630-141751) | 98.1 | 974 | Scaffold_1045.1 (32982-32009) | 99.2 | B |
| BjuTT8-1 | ZBjuH004L18 | 926 | Repeat sequence | – | 962 | A09(15796870-15796730) | 91.4 | A09 |
| A09_random(2192731-2193692) | 98.7 | A09(15375879-15376928) | 99.4 | |||||
| BjuTT8-2 | ZBjuH005J18 | 923 | B03(8048419-8049250) | 98.0 | 729 | B03(8126536-8125803) | 98.5 | B03 |
| BjuTT16-1 | ZBjuH130K12 | 1069 | A02(25075678-25075282) | 84.8 | 1046 | A02(24938143-24939195) | 97.8 | A02 |
| A02(23647099-23647956) | 95.6 | A02(23509181-23510233) | 98.7 | |||||
| BjuTT16-2 | ZBjuH099A21 | 973 | A03(20916287-20917258) | 100 | 971 | A03(21065354-21064524) | 98.1 | A03 |
| Un_random(122117253-122118230) | 99.1 | A03(19805901-19806859) | 96.9 | |||||
| BjuTT16-3 | ZBjuH091L03 | 1089 | A09(3425481-3424388) | 96.9 | 1096 | Repeat sequence | – | A09 |
| A09(2759676-2760769) | 97.5 | A04(12367561-12368716) | 95.1 | |||||
| BjuTT16-4 | ZBjuH098G12 | 1116 | B01(19570278-19569159) | 95.7 | 1094 | B01(19452807-19453868) | 93.9 | B01 |
| BjuTT16-5 | ZBjuH094N07 | 1014 | B06(30590171-30591180) | 98.3 | 998 | B06(30721361-30720370) | 95.9 | B06 |
| BjuTT16-6 | ZBjuH077C18 | 1022 | B08(41697103-41696075) | 97.8 | 1076 | B08(41543305-41544388) | 97.4 | B08 |
| BjuTTG1-1 | ZBjuH130K10 | 1077 | A06(17786017-17784921) | 96.1 | 1073 | Scaffold000172(118821-119882) | 96.3 | A06 |
| A06(18565145-18566064) | 94.5 | Un_random(101024139-101025200) | 96.8 | |||||
| BjuTTG1-2 | ZBjuH129A18 | 1083 | B08(41995537-41996211) | 93.2 | 1087 | B08(42142183-42141110) | 97.3 | B08 |
| BjuTTG2-1 | ZBjuH088A24 | 1139 | A01(12598037-12597696) | 78.9 | 1145 | A03(8757693-8756631) | 96.4 | A03 |
| C07(33256608-33257744) | 92.1 | A03(8043552-8044706) | 99.1 | |||||
| BjuTTG2-2 | ZBjuH101A24 | 1047 | A05(4101759-4100924) | 98.8 | 1074 | A05(3964877-3966181) | 90.9 | A05 |
| A05(3967225-3968262) | 97.6 | A05(3832372-3833452) | 98.6 | |||||
| BjuTTG2-3 | ZBjuH063L13 | 1099 | B03(32169026-32168705) | 82.7 | 1080 | B03(32059185-32060257) | 96.2 | B03 |
| BjuTTG2-4 | ZBjuH043G17 | 1094 | B04(5231833-5230759) | 96.8 | 1118 | B04(5118011-5119109) | 94.9 | B04 |
| BjuTT12-1 | ZBjuH047J16 | 1005 | A07(16179990-16178972) | 96.9 | 1010 | A07(16062416-16062903) | 98.6 | A07 |
| A07(14996804-14997785) | 96.6 | A07(14870425-14871409) | 98.6 | |||||
| BjuTT12-2 | ZBjuH124J12 | 1057 | B04(24922182-24923204) | 90.5 | 1030 | B04(25075022-25073994) | 97.8 | B04 |
| BjuTT19-1 | ZBjuH095N01 | 1093 | Repeat sequence | – | 969 | A02(3047112-3048020) | 96.7 | A02 |
| Repeat sequence | – | A02(1465948-1468567) | 96.5 | |||||
| BjuTT19-2 | ZBjuH170C22 | 1054 | A10(11649528-11650476) | 94.0 | 985 | A10(11804011-11803026) | 99.8 | A10 |
| A10(12892359-12893412) | 100 | C09(43030716-43031727) | 93.4 | |||||
| BjuTT19-3 | ZBjuH122M08 | 1033 | B02(33362984-33362101) | 92.3 | 888 | B02(33197233-33197697) | 98.5 | B02 |
Position in B. rapa reference genome is listed in the first line.
Position in B. napus reference genome is listed in the second line.
Figure 2Expession heatmap of gene expression based on FPKM data. NILA, NILB, SY represent the seed coat of B.juncea, and XY15, RIL52, RIL55 represent the seed coat of B.nupus. The color key represents FPKM normalized log2 transformed counts.
Figure 3RT-PCR analysis of genes for proanthocyanidin biosynthesis in the seed coats of . SY, Sichuan Yellow; NILA and NILB, Near-Isogenic Lines A and B. Seed coats were separated from seeds at 15 days after pollination.