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Acta Agronomica Sinica ›› 2020, Vol. 46 ›› Issue (6): 832-843.doi: 10.3724/SP.J.1006.2020.94154


QTL mapping of seed germination-related traits in Brassica napus L. under aluminum toxicity stress

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()   

  1. College of Agronomy and Biotechnology, Southwestern University, Chongqing 400715, China
  • Received:2019-10-16 Accepted:2020-01-15 Online:2020-06-12 Published:2020-02-19
  • Contact: Qing-Yuan ZHOU,Cui CUI E-mail:qingyuan@swu.edu.cn;cuicui@swu.edu.cn
  • Supported by:
    National Key Research and Development Program of China(2018YFD0100500);China Agriculture Research System(CARS-12);Technological Innovation and Application Development in Chongqing(cstc2019jscx-msxmX0383)


With the aggravation of soil acidification, aluminum toxicity has become one of the important stress factors that affect crop seed germination quality and crop yield. There have been many reports on QTL mapping and candidate gene screening for aluminum tolerance related traits in crops, but few reports on QTL mapping for aluminum tolerance during germination in Brassica napus L. The seed germination test was conducted on the recombinant inbred line population treated with 80 μg mL -1 aluminum solution and with distilled water as control. Germination potential was investigated at 3 d, germination rate was investigated at 7 d, root length, bud length and dry weight were measured, and the relative values of various characters were calculated. Based on 6K SNP chip and combined with high density genetic linkage map, we detected 23 QTLs for five traits in rape germination period. QTLs for relative germination potential, relative germination rate, relative root length, relative bud length and relative dry weight were 9, 1, 4, 5, and 4 respectively, covering A and C genomes, with LOD values from 3.00 to 5.26, and interpretable phenotypic variation from 7.70% to 13.10%. According to the confidence interval sequence of each QTL, 30 candidate genes related to aluminum stress were screened. ALMT1 gene and MATE gene are related to the synthesis and secretion of organic acids, which mainly enhance the aluminum tolerance of plants through the secretion of organic acids such as malic acid, citric acid and oxalic acid. STOP1 gene, NAC gene and RAP2.4 gene all belong to transcription activation factors, which enhance the resistance of plants by inducing the expression of aluminum tolerance genes. ABC transporter, membrane protein transporter, GDSL lipase enhance aluminum tolerance of plants by reducing accumulation of toxic substances on plasma membrane or discharging toxic substances out of body. Peroxidase and cytochrome P450 are genes related to oxidative stress, which have the functions of preventing oxidative damage of plant cells and resisting stress. At the same time, many genes encoding stress proteins were found, which play an important role in various stress reactions. The results of this study provide a theoretical basis for the cultivation of aluminum-tolerant rape varieties and the functional research of subsequent genes.

Key words: Brassica napus L., germination, single nucleotide polymorphism, aluminum stress, QTL, candidate gene

Fig. 1

Effects of different concentrations of aluminum on root length of rapeseed"

Table 1

Distribution characteristics of relative traits in recombinant inbred lines and their parents rape under aluminum stress"

Relative trait
亲本 Parents RIL群体 RIL population
ZS11 10D130 均值Mean 极差Range 标准差SD 变异系CV(%)
相对发芽势 RGV 0.982 0.967 1.032** 1.667 0.230 22.3
相对发芽率 RGR 0.983 0.982 1.043** 1.030 0.140 13.4
相对根长 RRL 0.621 0.472 0.465** 0.733 0.146 31.3
相对芽长 RBL 0.955 0.987 0.994** 1.158 0.178 17.9
相对干重 RDW 0.987 0.990 0.920** 1.125 0.175 19.0

Fig. 2

Frequency distribution of relative values of various characters of rape lines under optimum aluminum stress RGV: relative germination vigor; RGR: relative germination rate; RRL: relative root length; RBL: relative bud length; RDW: relative dry weight. "

Table 2

Correlation analysis of various characters of rape seeds treated by aluminum stress"

测定指标Index 相对发芽势RGV 相对发芽率RGR 相对根长RRL 相对芽长RBL 相对干重RDW
相对发芽势RGV 1
相对发芽率RGR 0.404** 1
相对根长RRL 0.101 0.053 1
相对芽长RBL -0.108 -0.109 0.062 1
相对干重RDW -0.148* -0.252** -0.075 -0.020 1

Fig. 3

Distribution of QTL for aluminum tolerance in Brassica napus on SNP genetic map RGV: relative germination vigor; RGR: relative germination rate; RRL: relative root length; RBL: relative bud length; RDW: relative dry weight. "

Table 3

QTL for rape germination under aluminum stress detected by composite interval mapping"

QTL 标记区间
Marker interval
LOD 表观贡献率
PVE (%)
Additive effect
Confidence interval (cM)
相对发芽势RGV qRGV-A01-1 AX-177912497-AX-179306831 4.33 10.90 -0.0282 37.410-43.975
qRGV-A01-2 AX-182171878-AX-182150271 3.90 9.90 -0.0217 141.657-155.683
qRGV-A03-1 AX-95507427-AX-177832788 4.20 10.60 0.0064 179.611-222.454
qRGV-A03-2 AX-95504605-AX-177831059 3.74 9.50 0.0033 93.552-97.113
qRGV-A03-3 AX-95681175-AX-95665748 3.23 8.20 -0.0236 121.496-124.157
qRGV-A08 AX-95506362-AX-182175648 5.26 13.10 -0.0402 8.146-12.834
qRGV-C01-1 AX-182087666-AX-95638042 3.43 8.70 -0.0123 160.226-163.199
qRGV-C01-2 AX-177910610-AX86223402 3.00 7.70 -0.0072 1.826-6.674
qRGV-C03 AX-95665064-AX-105309102 4.17 10.50 -0.0022 6.340-10.132
相对发芽率RGR qRGR-C04 AX-95636072-AX-182161180 3.12 8.00 0.0329 34.378-38.45
相对根长RRL qRRL-A03-1 AX-182087696-X-182147367 3.14 8.00 -0.0349 144.851-146.986
qRRL-A03-2 AX-95509347-AX-95509401 3.11 8.00 -0.0366 207.579-211.5
qRRL-A09 AX-95635531-AX-182177329 3.36 8.60 -0.0348 59.898-79.773
qRRL-C03 AX-95662770-AX-177910217 3.23 8.20 -0.0274 218.487-221.508
相对芽长RBL qRBL-A03 AX-95636441-AX-177911244 3.12 8.00 -0.0038 32.513-47.814
qRBL-A08-1 AX-95663434-AX-95506362 3.34 8.50 -0.0158 2.275-8.146
qRBL-A09-1 AX-177912380-AX-177829538 4.07 10.30 0.0216 178.878-188.216
qRBL-A09-2 AX-177832428-AX-182127697 3.53 9.00 0.0224 6.106-15.138
qRBL-C08 AX-95665611-AX-86227922 4.75 11.90 0.0115 94.661-132.074
相对干重RDW qRDW-A09-1 AX-182158057-AX-182154686 3.60 7.80 0.0196 127.938-128.931
qRDW-A09-2 AX-95682972-AX-182133711 3.05 9.10 0.0067 275.002-280.965
qRDW-A10-1 AX-182087443-AX-65636575 4.09 10.30 0.0050 129.25-131.783
qRDW-A10-2 AX-177829985-AX-182146546 3.90 9.90 0.0036 160.157-160.711

Table 4

Comparison between QTL confidence interval candidate genes in Brassica napus genome and Arabidopsis stress related genes"

Physical interval
Gene ID in B. napus
Gene accession
Gene annotation
相对发芽势RGV 18835423-22795371 BnaA01g26740D AT3G18440 Aluminum-activated malate transporter 9 (ALMT9) [14]
20061150-26605700 BnaA03g57410D AT3G06130 Heavy metal-associated domain (HMA) [23]
BnaA03g39800D AT5G61240 Leucine-rich repeat (LRR) family protein [24]
14408144-15038093 BnaA03g03270D AT5G11250 Disease resistance protein (TIR-NBS-LRR class)
BnaA03g14650D AT2G31660 Super sensitive to ABA and drought2 (SAD2) [25]
11435749-11630658 BnaA03g13730D AT2G30140 UDP-Glycosyltransferase superfamily protein [26]
1012939-2022032 BnaA08g30510D AT4G19960 K+ uptake permease 9 (KUP9) [27]
BnaA08g19190D AT1G24620 EF hand calcium-binding protein family (CML25) [28]
BnaA08g26970D AT1G08430 Aluminum-activated malate transporter 1 (ALMT1)
676816-1129401 BnaC01g23380D AT3G51490 Metallothionein 3 (MT3) [29]
BnaC01g01650D AT4G37270 Response to toxic substance (HMA)
3925832-4284222 BnaC03g08920D AT5G18370 Disease resistance protein (TIR-NBS-LRR class) family [30]
相对发芽率RGR 3627529-9882343 BnaC04g12580D AT2G27780 Transcription factor IIS family protein [31]
相对根长RRL 17577932-2005963 BnaA03g35920D AT3G20750 Zinc ion binding (GATA) [32]
24406111-29734315 BnaA03g35900D AT5G26717 Putative membrane lipoprotein [33]
BnaA03g54580D AT1G34370 Sensitive to proton rhizotoxicity 1 (STOP1) [15]
866809-2227131 BnaA09g11920D AT1G64065 Late embryogenesis abundant (LEA) [34]
BnaA09g14610D AT3G43570 GDSL-like Lipase/Acylhydrolase superfamily protein [35]
51210223-55837858 BnaC03g04310D AT5G44050 MATE efflux family protein [16]
BnaC03g65810D AT4G34710 Response to osmotic stress (ADC2) [36]
相对芽长RBL 3249677-4604524 BnaA03g39360D AT5G02490 Heat shock protein 70 (Hsp 70) family protein [37]
598224-1012939 BnaA08g01480D AT1G52490 F-box associated interaction domain [38]
22081699-23394648 BnaA09g02290D AT3G28415 ABC transporter family protein [39]
BnaA09g30790D AT1G22220 F-box family protein
BnaA09g30810D AT1G22190 Response to toxic substance (RAP2.4) [40]
575326-705822 BnaA08g28220D AT1G05250 Peroxidase superfamily protein [41]
19580994-23049951 BnaC08g07240D AT1G33110 MATE efflux family protein
相对干重RDW 32408555-33029777 BnaA09g48330D AT1G49360 F-box family protein
16531371-16654826 BnaA10g24620D AT3G26180 Cytochrome P450 proteins [42]
BnaA10g25760D AT5G04410 Regulation of flavonoid biosynthetic process (NAC) [43]
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