Welcome to Acta Agronomica Sinica,

Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (4): 587-598.doi: 10.3724/SP.J.1006.2021.04115


Construction of a high-density genetic map using genotyping by sequencing (GBS) for quantitative trait loci (QTL) analysis of pink petal trait in Brassica napus L.

ZHOU Xin-Tong1,2(), GUO Qing-Qing1,2,*(), CHEN Xue1,2, LI Jia-Na1,2, WANG Rui1,2,*()   

  1. 1Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
    2College of Agronomy and Biotechnology, Southwest University / Chongqing Engineering Research Center for Rapeseed, Chongqing 400715, China
  • Received:2020-05-30 Accepted:2020-09-13 Online:2021-04-12 Published:2020-12-01
  • Contact: GUO Qing-Qing,WANG Rui E-mail:wjzxt22@163.com;1833266719@qq.com;ruiwang71@163.com
  • Supported by:
    Innovation Project of Southwest University Students(106352020478)


Petal color is an important ornamental trait in B. napus, and the breeding and improvement of petal color have become the main goal in breeding and genetic research. To date, the research about interval location of pink petal trait in B. napus is very less yet. In this study, the genetic basis of petal phenotype was examined in the 62 (yellow petal) and 77 (pink petal) parents as well as 114 individuals comprising the doubled haploid (DH) mapping population. This DH population was examined using genotyping by sequencing (GBS) with 6065 high-density polymorphism single nucleotide polymorphism (SNP) markers to construct a genetic linkage map comprised of 3253 polymorphic markers. The genetic map spanned 1766.06 cM, with an average distance of 0.54 cM between markers. The complete interval mapping method identified two quantitative trait loci (QTL) for petal color located on chromosomes A07 and C03, respectively. Synteny analysis showed that some homologous genes in the interval of B. napus were located in Brassica rapa and Brassica oleracea. Also, eight genes related to flower color were analyzed between inbred line 77 and inbred line 62, the splice junctions of BnaA07g15980D and BnaA07g17500D were belong to intron retention type in pink petal of 77 parent. This study lays a foundation for further research on fine mapping of pink petal trait and molecular marker-assisted selection in Brassica napus L.

Key words: Brassica napus L., pink petal trait, genetic linkage map, QTL mapping

Table 1

Information statistics of genetic linkage groups"

Linkage groups
Number of markers
Genetic distance
Average genetic distance
Maximum spacing between markers (cM)
lg1 69 93.50 1.36 15.24
lg2 217 97.00 0.45 18.52
lg3 146 150.84 1.03 9.17
lg4 153 99.61 0.65 6.43
lg5 220 141.07 0.64 6.66
lg6 256 101.53 0.40 5.51
lg7 160 131.66 0.82 18.37
lg8 275 133.58 0.49 6.73
lg9 222 77.51 0.35 10.69
lg10 78 84.29 1.08 13.89
lg11 63 76.21 1.21 12.50
lg12 349 42.19 0.12 5.53
lg13 214 88.18 0.41 4.97
lg14 410 118.09 0.29 11.33
lg15 72 57.28 0.80 16.00
lg16 147 97.54 0.66 9.47
lg17 103 102.42 0.99 6.44
lg18 66 53.73 0.81 16.87

Fig. 1

Distribution map of linkage group markers X-axis represents linkage groups; Y-axis represents genetic distance (cM); blue is a valid SNP marker."

Fig. 2

Parental phenotype of pink petal and yellow petal in B. napus A1 and A2: female parent 62; B1 and B2: male parent 77."

Fig. 3

Phenotype of doubled haploid population for petal color in B. napus"

Table 2

Statistical parameters of petal color (PC) trait in B. napus"

Standard deviation
Interquartile range
花色PC 24.47 22.89 11.28 6.21 53.04 46.83 12.78 0.85 0.09 0.00

Fig. 4

Density distribution histogram of petal color trait X-axis represents the petal color phenotype; Y-axis represents the distribution density."

Fig. 5

Chromosomal location of QTL for petal color by WinQTL CIM X-axis represents 19 chromosomes, and Y-axis represents the LOD value and the additive effect a (H1) in Figure A; the horizontal line represents the LOD threshold line. Figure B, there is a represent QTL of petal color in figure C detected on chromosome 7 and chromosome 13, respectively; X-axis represents the genetic distance on the corresponding chromosome, and is marked with the corresponding linkage marker position, Y-axis represents the LOD value and the additive effect a (H1), respectively; the horizontal line indicates the LOD threshold line."

Table 3

QTLs related to petal color trair by WinQTL CIM in B. napus"

LOD peak
Position (cM)
Left marker
Right marker
99% CI (cM)
Additive effect
R2 (%)
Number of genes
qFC-chr7-1 6.62 23.8 mk2056 mk2036 8.383-42.019 4.58 14.29 287
qFC-chr13-1 14.01 30.8 mk4000 mk3898 20.305-41.353 6.61 34.02 308

Fig. 6

Synteny analysis of candidate interval for petal color between B. napus and B. oleracea or B. rapa by WinQTL CIM"

Table 4

Types of gene alternative splicing in location interval for petal color among parents in B. napus"

亲本Parent 染色体
Total number of genes in location interval
Number of genes with
alternative splicing
Number of the alternative splicings
WinQTL Cart 77 A07 287 26 26 2 5 0 33
62 A07 287 26 25 1 4 2 32
77 C03 308 14 10 0 5 1 16
62 C03 308 11 8 0 5 2 15

Fig. 7

Splice graphs for genes related to petal color between 77 and 62 A: splice graph for BnaA07g15980D in 62 petals; B: splice graph for BnaA07g15980D in 77 petals; C: splice graph for BnaA07g17500D in 62 petals; D: splice graph for BnaA07g17500D in 77 petals. The gray pentagons represent exons, the white region represent introns, the lines between them represent different ways of splicing. The picture is split into four parts, the first part is the gene model from the annotation file, the second part is the sequencing result, the third part is the gene splicing model between the sequencing result and the annotation file (with a representative protein isoform), the fourth part is the number of reads supporting each exon in the sequencing file. The numbers in the lower left and right corners represent the start and stop sites of the gene, respectively. "

[1] 王汉中, 殷艳. 我国油料产业形势分析与发展对策建议. 中国油料作物学报, 2014,36:414-421.
doi: 10.7505/j.issn.1007-9084.2014.03.020
Wang H Z, Yin Y. Analysis and strategy for oil crop industry in China. Chin J Oil Crop Sci, 2014,36:414-421 (in Chinese with English abstract).
[2] Chen B, Heneen W, Jonsson R. Independent inheritance of erucic acid content and flower colour in the C-genome of Brassica napus L. Plant Breed, 1988,100:147-149.
doi: 10.1111/pbr.1988.100.issue-2
[3] 戚存扣, 傅寿仲. 甘蓝型油菜白花性状的遗传. 中国油料作物学报, 1992,1(3):60-62.
Qi C K, Fu S Z. Genetic studies of white petals in Brassica napus L. Chin J Oil Crop Sci, 1992,1(3):60-62 (in Chinese with English abstract).
[4] 董育红, 田建华, 李殿荣. 甘蓝型油菜白花基因的RAPD标记. 西北农林科技大学学报, 2005,33(10):57-61.
Dong Y H, Tian J H, Li D R. RAPD markers linked to white-petal gene in Brassica napus L. J Northwest A&F Univ, 2005,33(10):57-61 (in Chinese with English abstract).
[5] 刘雪平, 涂金星, 刘志文, 陈宝元, 傅廷栋. 甘蓝型油菜遗传图谱的构建及芥酸含量的QTL分析. 作物学报, 2005,31:275-282.
Liu X P, Tu J X, Liu Z W, Chen B Y, Fu T D. Construction of a molecular marker linkage map and its use for QTL analysis of erucic acid content in Brassica napus L. Acta Agron Sin, 2005,31:275-282 (in Chinese with English abstract).
[6] Huang Z, Ban Y Y, Bao R, Zhang X X, Xu A X, Ding J. Inheritance and gene mapping of the white flower in Brassica napus L. New Zealand J Crop Hortic Sci, 2014,42:111-117.
doi: 10.1080/01140671.2013.863211
[7] 黄镇, 许婷, 班元元, 刘欢, 范胜栩, 杨丽, 徐爱遐. 甘蓝型油菜白花性状的遗传及AFLP标记. 华北农学报, 2012,27(1):98-101.
doi: 10.3969/j.issn.1000-7091.2012.01.018
Huang Z, Xu T, Ban Y Y, Liu H, Fan S X, Yang L, Xu A X. Genetic studies of white petals and AFLP markers linked to white petal gene in Brassica napus L. Acta Agric Boreali-Sin, 2012,27(1):98-101 (in Chinese with English abstract).
[8] 张豹. 甘蓝型油菜导入系构建、重要农艺性状QTL分析和白花基因克隆. 华中农业大学博士学位论文, 湖北武汉, 2015.
Zhang B. Development of Chromosome Segment Substitution Lines for QTL Analysis of Important Agronomic Traits and Cloning the White-Flowered Gene in Brassica napus L. PhD Dissertation of Huazhong Agricultural University, Wuhan, Hubei, China, 2015 (in Chinese with English abstract).
[9] 赵君伟. 白菜型油菜花色遗传及花色基因精细定位. 华中农业大学硕士学位论文, 湖北武汉, 2017.
Zhao J W. Genetic Analysis and Fine Mapping of the Flower Color Gene in Brassica napus L. MS Thesis of Huazhong Agricultural University, Wuhan, Hubei, China, 2017 (in Chinese with English abstract).
[10] 淡亚彬. 甘蓝型油菜桔红花色基因和心叶紫色基因的初步定位. 青海大学硕士学位论文, 青海西宁, 2016.
Dan Y B. Primary Mapping of the Orange Flower Gene and Central Leaf Color Gene in Brassica napus L. MS Thesis of Qinghai University, Xining, Qinghai, China, 2016 (in Chinese with English abstract).
[11] Yao Y M, Li K X, Liu H D, Duan R W, Guo S M, Xiao L, Du D Z. Whole-genome re-sequencing and fine mapping of an orange petal color gene ( Bnpe 1) in spring Brassica napus L. to a 151-kb region. Euphytica, 2017,213:165.
doi: 10.1007/s10681-017-1959-4
[12] Zhang N, Zhang H M, Ren Y J, Chen L, Zhang J, Zhang L G. Genetic analysis and gene mapping of the orange flower trait in Chinese cabbage ( Brassica rapa L.). Mol Breed, 2019,39:1-11.
doi: 10.1007/s11032-018-0907-x
[13] 丁戈, 陈伦林, 邹小云, 李书宇, 熊洁, 邹晓芬, 宋来强. 甘蓝型油菜桔黄花色基因的QTL-seq遗传分析及InDel分子标记开发. 分子植物育种, 2019,17:3983-3992.
Ding G, Chen L L, Zou X Y, Li S Y, Xiong J, Zou X F, Song L Q. QTL-seq genetic analysis and InDel marker development of orange petal colour gene in Brassica napus. Mol Plant Breed, 2019,17:3983-3992 (in Chinese with English abstract).
[14] 陈雪, 王瑞, 井付钰, 张胜森, 贾乐东, 段谋正, 吴宇. 基于二代测序的甘蓝型油菜白花基因候选区间定位及连锁标记验证. 中国农业科学, 2020,53:1108-1117.
doi: 10.3864/j.issn.0578-1752.2020.06.003
Chen X, Wang R, Jing F Y, Zhang S S, Jia L D, Duan M Z, Wu Y. Location and linkage markers for candidate interval of the white petal gene in Brassica napus L. by Next Generation Sequencing. Sci Agric Sin, 2020,53:1108-1117 (in Chinese with English abstract).
[15] 王小柯, 江东, 孙珍珠. 利用GBS技术研究240份宽皮柑橘的系统演化. 中国农业科学, 2017,50:1666-1673.
doi: 10.3864/j.issn.0578-1752.2017.09.012
Wang X K, Jiang D, Sun Z Z. Study on phylogeny of 240 mandarin accessions with genotyping-by-sequencing technology. Sci Agric Sin, 2017,50:1666-1673 (in Chinese with English abstract).
[16] 蔡露, 杨欢, 王勇, 李廷轩, 陈光登. 利用GBS技术开发烟草SNP标记及遗传多样性分析. 中国烟草科学, 2018,39(5):17-24.
Cai L, Yang H, Wang Y, Li Y X, Chen G D. Analysis of genetic diversity of tobacco germplasm resources based on SNP markers via genotyping-by-sequencing technology. Chin Tob Sci, 2018,39(5):17-24 (in Chinese with English abstract).
[17] 刘作铭. 基于GBS测序的玉米苗期耐旱相关性状QTL定位. 四川农业大学硕士学位论文, 四川雅安, 2017.
Liu Z M. QTL Mapping of Maize Drought Tolerance Related Traits at Seeding Stage by Genotyping-by-Sequencing. MS Thesis of Sichuan Agricultural University, Ya’an, Sichuan, China, 2017 (in Chinese with English abstract).
[18] Hai K Q, Ning W, Wen Q Q, Qing H X, Hong Z, Jian B S, Gen T Y, Qun H. Construction of a high-density genetic map using genotyping by sequencing (GBS) for quantitative trait loci (QTL) analysis of three plant morphological traits in upland cotton ( Gossypium hirsutum L.). Euphytica, 2017,213:1-17.
doi: 10.1007/s10681-016-1788-x
[19] Zhong Z, Tian J W, Ying Z, Xin G L, Jian H. Construction of a high-density genetic map of Ziziphus jujuba Mill. using genotyping by sequencing technology. Tree Genet Genomes, 2016,12:76-80.
doi: 10.1007/s11295-016-1032-9
[20] Melo A T O, Bartaula R, Hale I. GBS-SNP-CROP: a reference- optional pipeline for SNP discovery and plant germplasm characterization using variable length, paired-end genotyping- by-sequencing data. BMC Bioinf, 2016,17:29-33.
doi: 10.1186/s12859-016-0879-y
[21] Stam P. Construction of integrated genetic linkage maps by means of a new computer package: Join Map. Plant J, 1993,3:739-744.
doi: 10.1111/j.1365-313X.1993.00739.x
[22] Rogers M F, Julie T, Anireddy S N R, Asa B. SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data. Genome Biol, 2012,13:1-17.
[23] 罗昕. 基于下一代测序的玉米高通量SNP开发及关联分析. 华中农业大学硕士学位论文, 湖北武汉, 2015.
Luo X. High-Throughput SNP Development and Genome-Wide Association Study in Maize Based on Next-Generation Sequencing. MS Thesis of Huazhong Agricultural University, Wuhan, Hubei, China, 2015 (in Chinese with English abstract).
[24] Landry B S, Hubert N, Etoh T, Harada J J, Lincoin S E. A genetic map for Brassica napus based on restriction fragment length polymorphisms detected with expressed DNA sequences. Genome, 1991,34:543-552.
doi: 10.1139/g91-084
[25] Mahmood S, Li Z, Yue X P, Wang B, Chen J, Liu K D. Development of INDELs markers in oilseed rape (Brassica napus L.) using re-sequencing data. Mol Breed, 2016,36:79-84.
doi: 10.1007/s11032-016-0501-z
[26] 刘雪平. 人工合成甘蓝型油菜种皮色泽、芥酸含量和花色的遗传研究. 华中农业大学博士学位论文, 湖北武汉, 2005.
Liu X P. Inheritance of Seed Colour, Erucic, Acid Content and Flower Colour in Artificially Resynthesized Brassica napus L. PhD Dissertation of Huazhong Agricultural University, Wuhan, Hubei, China, 2005 (in Chinese with English abstract) .
[27] Wang X D, Yu K J, Li H, Peng Q, Chen F, Zhang W, Chen S, Hu M L, Zhang J F. High-density SNP map construction and QTL identification for the apetalous character in Brassica napus L. Front Plant Sci, 2015,6:1164.
doi: 10.3389/fpls.2015.01164 pmid: 26779193
[28] Zhang B, Liu C, Wang Y Q, Yao X, Wang F, Wu J S, King G J, Liu K D. Disruption of a CAROTENOID CLEAVAGE DIOXYGENASE 4 gene convents flower colour from white to yellow in Brassica species. New Phytol, 2015,206:1513-1526.
doi: 10.1111/nph.13335 pmid: 25690717
[29] 杨晓刚. 大白菜遗传图谱的构建及花色性状基因的遗传定位. 曲阜师范大学硕士学位论文, 山东曲阜, 2018.
Yang X G. Construction of Genetic Map of Chinese Cabbage and Genetic Location of Flower Color Trait Gene. MS Thesis of Qufu Normal University, Qufu, Shandong, China, 2018 (in Chinese with English abstract).
[30] 杨茹涵, 刘进, 李加纳, 钱伟, 梅家琴. 甘蓝花色性状QTL定位及候选基因变异分析. 植物遗传资源学报, 2019,20:1271-1277.
Yang R H, Liu J, Li J N, Qian W, Mei J Q. QTL mapping and variation analysis of candidate gene for flower color in Brassica oleracea L. J Plant Genet Resour, 2019,20:1271-1277 (in Chinese with English abstract).
[1] YU Chun-Miao, ZHANG Yong, WANG Hao-Rang, YANG Xing-Yong, DONG Quan-Zhong, XUE Hong, ZHANG Ming-Ming, LI Wei-Wei, WANG Lei, HU Kai-Feng, GU Yong-Zhe, QIU Li-Juan. Construction of a high density genetic map between cultivated and semi-wild soybeans and identification of QTLs for plant height [J]. Acta Agronomica Sinica, 2022, 48(5): 1091-1102.
[2] WANG Rui, CHEN Xue, GUO Qing-Qing, ZHOU Rong, CHEN Lei, LI Jia-Na. Development of linkage InDel markers of the white petal gene based on whole-genome re-sequencing data in Brassica napus L. [J]. Acta Agronomica Sinica, 2022, 48(3): 759-769.
[3] ZHANG Bo, PEI Rui-Qing, YANG Wei-Feng, ZHU Hai-Tao, LIU Gui-Fu, ZHANG Gui-Quan, WANG Shao-Kui. Mapping and identification QTLs controlling grain size in rice (Oryza sativa L.) by using single segment substitution lines derived from IAPAR9 [J]. Acta Agronomica Sinica, 2021, 47(8): 1472-1480.
[4] LI Shu-Yu, HUANG Yang, XIONG Jie, DING Ge, CHEN Lun-Lin, SONG Lai-Qiang. QTL mapping and candidate genes screening of earliness traits in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(4): 626-637.
[5] SHEN Wen-Qiang, ZHAO Bing-Bing, YU Guo-Ling, LI Feng-Fei, ZHU Xiao-Yan, MA Fu-Ying, LI Yun-Feng, HE Guang-Hua, ZHAO Fang-Ming. Identification of an excellent rice chromosome segment substitution line Z746 and QTL mapping and verification of important agronomic traits [J]. Acta Agronomica Sinica, 2021, 47(3): 451-461.
[6] MENG Jiang-Yu, LIANG Guang-Wei, HE Ya-Jun, QIAN Wei. QTL mapping of salt and drought tolerance related traits in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(3): 462-471.
[7] WANG Rui-Li, WANG Liu-Yan, LEI Wei, WU Jia-Yi, SHI Hong-Song, LI Chen-Yang, TANG Zhang-Lin, LI Jia-Na, ZHOU Qing-Yuan, CUI Cui. Screening candidate genes related to aluminum toxicity stress at germination stage via RNA-seq and QTL mapping in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(12): 2407-2422.
[8] GUO Qing-Qing, ZHOU Rong, CHEN Xue, CHEN Lei, LI Jia-Na, WANG Rui. Location and InDel markers for candidate interval of the orange petal gene in Brassica napus L. by next generation sequencing [J]. Acta Agronomica Sinica, 2021, 47(11): 2163-2172.
[9] LEI Wei, WANG Rui-Li, WANG Liu-Yan, YUAN Fang, MENG Li-Jiao, XING Ming-Li, XU Lu, TANG Zhang-Lin, LI Jia-Na, CUI Cui, ZHOU Qing-Yuan. Genome-wide association study of seed density and its related traits in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(11): 2099-2110.
[10] WANG Rui-Li,WANG Liu-Yan,YE Sang,Gao Huan-Huan,LEI Wei,WU Jia-Yi,YUAN Fang,MENG Li-Jiao,TANG Zhang-Lin,LI Jia-Na,ZHOU Qing-Yuan,CUI Cui. QTL mapping of seed germination-related traits in Brassica napus L. under aluminum toxicity stress [J]. Acta Agronomica Sinica, 2020, 46(6): 832-843.
[11] Dai-Ling LIU,Jun-Feng XIE,Qian-Rui HE,Si-Wei CHEN,Yue HU,Jia ZHOU,Yue-Hui SHE,Wei-Guo LIU,Wen-Yu YANG,Xiao-Ling WU. QTL analysis for relative contents of glycinin and β-conglycinin fractions from storage protein in soybean seeds under monoculture and relay intercropping [J]. Acta Agronomica Sinica, 2020, 46(3): 341-353.
[12] WU Hai-Tao, ZHANG Yong, SU Bo-Hong, Lamlom F Sobhi, QIU Li-Juan. Development of molecular markers and fine mapping of qBN-18 locus related to branch number in soybean (Glycine max L.) [J]. Acta Agronomica Sinica, 2020, 46(11): 1667-1677.
[13] LYU Wei-Sheng, XIAO Fu-Liang, ZHANG Shao-Wen, ZHENG Wei, HUANG Tian-Bao, XIAO Xiao-Jun, LI Ya-Zhen, WU Yan, HAN De-Peng, XIAO Guo-Bin, ZHANG Xue-Kun. Effects of sowing and fertilizing methods on yield and fertilizer use efficiency in red-soil dryland rapeseed (Brassica napus L.) [J]. Acta Agronomica Sinica, 2020, 46(11): 1790-1800.
[14] LIU Rong, WANG Fang, FANG Li, YANG Tao, ZHANG Hong-Yan, HUANG Yu-Ning, WANG Dong, JI Yi-Shan, XU Dong-Xu, LI Guan, GUO Rui-Jun, ZONG Xu-Xiao. An integrated high-density SSR genetic linkage map from two F2 population in Chinese pea [J]. Acta Agronomica Sinica, 2020, 46(10): 1496-1506.
[15] HU Mao-Long, CHENG Li, GUO Yue, LONG Wei-Hua, GAO Jian-Qin, PU Hui-Ming, ZHANG Jie-Fu, CHEN Song. Development and application of the marker for imidazolinone-resistant gene in Brassica napus [J]. Acta Agronomica Sinica, 2020, 46(10): 1639-1646.
Full text



No Suggested Reading articles found!