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

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

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)

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Abstract:

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"

连锁群
Linkage groups		 标记数量
Number of markers		 遗传距离
Genetic distance
(cM)		 平均遗传距离
Average genetic distance
(cM)		 标记间最大间隔
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
lg19
总计Total		 33
3253		 19.83
1766.06		 0.60
0.54		 9.65
18.52

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"

性状
Trait		 平均数
Average		 中位数
Median		 标准偏差
Standard deviation		 最小值
Minimum		 最大值
Maximum		 范围
Range		 四分位距
Interquartile range		 偏斜度
Skewness		 峰度
Kurtosis		 显著性
Significance
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"

QTL LOD峰值
LOD peak		 位置
Position (cM)		 左端标记
Left marker		 右端标记
Right marker		 99%置信
区间范围
99% CI (cM)		 加性效应
Additive effect		 贡献率
R2 (%)		 区间基因数量
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"

方法
Method		 亲本Parent 染色体
Chromosome		 定位区间内基因总数
Total number of genes in location interval		 发生可变剪切基因总数
Number of genes with
alternative splicing		 可变剪切出现次数
Number of the alternative splicings
IR ES A3SS A5SS 总计
Total
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. "

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