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作物学报 ›› 2018, Vol. 44 ›› Issue (04): 542-553.doi: 10.3724/SP.J.1006.2018.00542

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

草铵膦胁迫下油菜苗期叶片药害相关性状的全基因组关联分析

陈东亮1,2,**, 崔翠1,**, 任义英1, 王倩1, 李加纳1, 唐章林1, 周清元1,*()   

  1. 1西南大学农学与生物科技学院, 重庆 400715
    2贵州省农业科学院油料研究所, 贵州贵阳 550006
  • 收稿日期:2016-12-15 接受日期:2017-11-21 出版日期:2018-01-19 网络出版日期:2017-12-20
  • 通讯作者: 陈东亮,崔翠,周清元
  • 作者简介:

    hyj790124@163.com

  • 基金资助:
    本研究由国家科技支撑计划项目(2013BAD01B03-12), 国家现代农业产业技术体系建设专项(CARS-12), 重庆市社会事业与民生保障科技创新(cstc2016shmszx0756)和西南大学博士启动基金(swu113064)资助

Genome-wide Association Analysis of Some Phytotoxicity Related Traits at Seedling Stage in Rapeseed under Glufosinate Stress

Dong-Liang CHEN1,2,**, Cui CUI1,**, Yi-Ying REN1, Qian WANG1, Jia-Na LI1, Zhang-Lin TANG1, Qing-Yuan ZHOU1,*()   

  1. 1 College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
    2 Oil Research Institute in Guizhou Academy of Agricultural Sciences, Guiyan 550006, Guizhou, China
  • Received:2016-12-15 Accepted:2017-11-21 Published:2018-01-19 Published online:2017-12-20
  • Contact: Dong-Liang CHEN,Cui CUI,Qing-Yuan ZHOU
  • Supported by:
    This study was supported by the National Key Technology Support Program of China (2013BAD01B03-12), the China Agriculture Research System (CARS-12), the Science and Technology Committee of Chongqing (cstc2016shmszx0756), and the Doctoral Start-up Fund of Southwestern University (swu113064).

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摘要：

随着油菜大面积种植和田间草害的日益严重, 草铵膦近年来被尝试性地用于田间除草, 但草铵膦在杀除杂草的同时或轻或重会对油菜产生药害, 影响其正常生理活动, 甚至影响其产量。本研究通过比较, 选取最能体现油菜苗期耐药性差异的200 mg L-1作为胁迫浓度。以506份具有代表性的甘蓝型油菜品种(系)为材料, 利用芸薹属60k Illumina Infinium SNP芯片分析其基因型, 对油菜种质苗期的单位叶面积干重耐除草剂系数(CLW)、叶绿素含量耐除草剂系数(CCC)和综合药害指数(CPC)进行全基因组关联分析, 从基因组水平分析油菜在草铵膦胁迫下的生理和形态反应。关联分析中, 扫描到与单位叶面积干重耐除草剂系数显著相关的SNP位点6个, 表型贡献率在6.53%~10.04%之间; 与叶绿素含量耐除草剂系数相关的SNP位点共22个, 表型贡献率在4.97%~6.20%之间; 与综合药害指数相关的SNP位点98个, 覆盖了A、C基因组, 贡献率在3.25%~18.66%之间。通过对显著SNP位点对应的LD区间基因序列的分析, 共获得18个与草铵膦的灭生机制相关的候选基因。在叶绿素含量耐除草剂系数关联位点的LD区域发现11个候选基因, 其中9个参与酰基转移酶活性的调控, 2个与乙酰CoA转移酶活性有关。在与综合药害指数关联位点的LD区域发现7个候选基因, 其中1个与谷氨酰胺转移酶活性有关, 参与谷氨酰胺代谢, 其余6个和乙酰CoA转移酶活性有关。这些基因调控的生理生化过程均与叶片干重、叶绿素含量的变化及草铵膦的灭生机制有关。这些关联位点和候选基因的挖掘, 将为油菜在草铵膦逆境胁迫下的生理生态反应的基因调控机制研究提供参考。

关键词: 油菜, 苗期, 草铵膦, 全基因组关联分析

Abstract:

With planting rape in large area and weeds growing seriously in the field, glufosinate has been used in controlling field weeds tentatively. However glufosinate also produced phytotoxicity to the main cultivated rapeseed more or less, affecting the normal physiological and morphological activities, even yield. In this study, glufosinate of 200 mg L-1 was used at stress concentration 506 representative Brassica napus varieties (lines) were genotyped using the Brassica 60k Illumina Infinium SNP array by genome-wide association studies of herbicide resistance coefficient of dry weight per unit leaf area (CLW), herbicide resistance coefficient of chlorophyll content (CCC) and comprehensive phytotoxicity coefficient (CPC). A total of 16 SNP sites related to the killing mechanism of glufosinate were detected. Six SNP sites associated with CLW were detected, with phenotypic contribution rate ranging from 6.53% to 10.04%, and 22 SNP sites associated with CCC, with the phenotypic from 4.97% to 6.20%, 98 SNP sites associated with CPC over A subgenome and C subgenome, with the rate range from 3.25% to 18.66%. After analysising the genes in the linkage disequilibrium (LD) interval of significant SNP, we found 18 glufosinate tolerance related candidate genes. Eleven candidate genes were found in the LD interval of SNPs related to CCC, among them nine were involved in acyltransferase activity, two were involved in acetyl-CoA transferase activity, seven candidate genes were found in the LD interval of SNPs related to CPC, one of them was associated with glutamine transferase activity, participating in glutamine metabolism, and other six genes were involved in acetyl CoA transferase activity. The physiological and biochemical process regulated by these genes related to the changes of leaf dry weight, chlorophyll content and the killing mechanism of glufosinate. Mining association sites and candidate genes provides a reference for the research of gene regulation mechanism in the physiological and morphological process under glufosinate stress.

Key words: Brassica napus L., seedling stage, glufosinate, genome-wide association studies

图1

不同浓度草铵膦胁迫下油菜苗期的生理形态差异"

图2

相关性状频率分布图 CLW: 单位叶面积干重系数; CCC: 叶绿素含量系数; CPC: 综合药害指数。"

表1

相关性状的表型统计"

性状
Trait		 均值±标准差
Mean±SD		 变幅范围
Range (%)		 变异系数
CV (%)
单位叶面积干重系数CLW 37.30±6.210** 21.1-68.8 16.649
叶绿素含量系数CCC 80.24±8.323** 54.2-100.0 10.373
综合药害指数CPC 58.93±14.144** 0.490-95.000 24.001

表2

3个性状的相关性分析"

测定指标Index 单位叶面积干重系数CLW 综合药害指数CPC 叶绿素含量系数CCC
单位叶面积干重系数CLW 1.000
综合药害指数CPC -0.134** 1.000
叶绿素含量系数CCC 0.185** -0.314** 1.000

图3

自然群体的∆K值"

图4

自然群体内不同油菜品系两两之间的亲缘关系分布"

图5

甘蓝型油菜A和C基因组不同染色体的LD衰减"

图6

Q+K模型下甘蓝型油菜各耐药性性状曼哈顿图 a1、a2分别为单位叶面积干重系数的曼哈顿图和QQ图; b1、b2分别为叶绿素含量系数的曼哈顿图和QQ图; c1、c2分别为综合药害指数的曼哈顿图和QQ图。"

表3

相关性状的关联位点"

性状
Trait		 位点名称
SNP		 染色体
Chr.		 P值
P-value		 贡献率
R2 (%)		 位点名称
SNP		 染色体
Chr.		 P 值
P-value		 贡献率
R2 (%)
单位叶面积干重系数
CLW		 Bn-A01-p1704123 A01 2.36×10-6 5.362 Bn-A07-p593034 A07 2.45×10-5 6.526
Bn-A01-p4549945 A01 3.86×10-6 7.723 Bn-C01-p38105098 C01 1.35×10-6 8.348
Bn-A01-p5849310 A01 1.94×10-5 6.766 Bn-C06-p17529141 C06 2.90×10-5 6.526
叶绿素含量系数
CCC		 Bn-A01-p21360797 A01 4.25×10-6 5.418 Bn-A06-p20421942 A06 1.83×10-5 5.179
Bn-A02-p4940608 A02 1.35×10-5 5.313 Bn-A07-p3477622 A07 3.81×10-6 5.883
Bn-A03-p21755979 A03 9.06×10-6 5.493 Bn-A08-p9184409 A08 1.90×10-6 6.195
Bn-A03-p4171667 A03 2.37×10-5 5.063 Bn-A08-p984273 A08 5.34×10-6 5.730
Bn-A04-p16495266 A04 1.06×10-5 5.423 Bn-A09-p16498800 A09 2.14×10-6 6.142
Bn-A04-p7873782 A04 1.64×10-5 5.228 Bn-A09-p15859343 A09 5.27×10-6 5.737
Bn-A05-p10742077 A05 1.52×10-5 5.261 Bn-A09-p4171667 A09 1.77×10-5 5.193
Bn-A06-p20575568 A06 4.27×10-6 5.831 Bn-C01-p25343230 C01 9.59×10-6 5.468
Bn-A06-p20526477 A06 4.78×10-6 5.780 Bn-C07-p41693853 C07 1.41×10-5 5.294
Bn-A06-p20546803 A06 4.83×10-6 5.775 Bn-C08-p32299051 C08 2.55×10-5 5.030
Bn-A06-p20602779 A06 1.79×10-5 5.187 Bn-C09-p40117533 C09 2.89×10-5 4.974
综合药
害指数
CPC		 Bn-A01-p986711 A01 2.30×10-5 9.031 Bn-A09-p6931495 A09 1.41×10-7 7.465
Bn-A01-p994322 A01 3.35×10-5 4.360 Bn-A10-p12019156 A10 2.21×10-6 7.783
Bn-A02-p6931495 A02 2.75×10-5 12.645 Bn-A10-p19586200 A10 6.82×10-6 4.996
Bn-A02-p6901239 A02 1.11×10-6 5.712 Bn-A10-p10124750 A10 2.88×10-6 5.236
Bn-A02-p6976201 A02 2.36×10-7 18.659 Bn-A10-p14852876 A10 1.28×10-7 5.632
Bn-A02-p6371001 A02 8.58×10-6 4.896 Bn-A10-p15935269 A10 3.45×10-5 7.852
Bn-A02-p8005692 A02 1.39×10-9 10.455 Bn-A10-p15524190 A10 1.86×10-5 4.891
Bn-A02-p8945120 A02 4.27×10-9 7.960 Bn-C01-p9201350 C01 1.84×10-7 8.123
Bn-A02-p145473 A02 1.75×10-5 4.513 Bn-C01-p9611053 C01 9.24×10-6 4.866
Bn-A02-p121255 A02 1.01×10-5 4.838 Bn-C01-p9965323 C01 2.01×10-6 5.624
Bn-A02-p9652140 A02 4.23×10-6 4.020 Bn-C01-p9604036 C01 5.12×10-6 5.108
Bn-A02-p9570320 A02 3.69×10-5 4.181 Bn-C01-p32514001 C01 2.32×10-10 8.583
Bn-A02-p965241 A02 2.06×10-5 5.342 Bn-C01-p33876059 C01 9.97×10-7 5.798
Bn-A02-p974395 A02 1.02×10-6 5.745 Bn-C02-p41927269 C02 8.48×10-5 4.122
Bn-A02-p3483764 A02 1.87×10-5 4.337 Bn-C02-p41639953 C02 9.25×10-9 8.390
Bn-A02-p3546981 A02 3.69×10-5 4.321 Bn-C03-p55465412 C03 5.56×10-5 4.391
Bn-A02-p6627159 A02 5.02×10-7 12.607 Bn-C03-p57991205 C03 4.04×10-6 5.938
Bn-A03-p9845120 A03 1.96×10-8 16.363 Bn-C03-p57106187 C03 2.87×10-9 8.559
Bn-A03-p9468697 A03 1.39×10-5 4.706 Bn-C03-p57326280 C03 1.52×10-8 7.918
Bn-A03-p9999846 A03 4.75×10-7 4.842 Bn-C04-p6292605 C04 2.30×10-6 5.720
Bn-A03-p9451200 A03 2.96×10-5 3.958 Bn-C04-p6200125 C04 5.97×10-6 5.387
Bn-A03-p21867237 A03 8.88×10-6 4.472 Bn-C04-p6312067 C04 5.11×10-6 5.460
Bn-A04-p16524169 A04 2.94×10-5 4.735 Bn-C04-p621851 C04 5.98×10-6 5.426
Bn-A04-p16714914 A04 3.05×10-8 7.548 Bn-C04-p6313229 C04 5.51×10-5 4.388
Bn-A04-p16732201 A04 4.77×10-6 5.505 Bn-C04-p6985469 C04 4.38×10-6 5.512
Bn-A04-p1983502 A04 3.09×10-8 7.544 Bn-C04-p20152051 C04 3.48×10-5 4.623
Bn-A04-p1945120 A04 1.24×10-6 6.115 Bn-C04-p9140899 C04 2.70×10-5 4.689
Bn-A04-p9002613 A04 1.03×10-8 8.011 Bn-C05-p7747904 C05 8.26×10-7 6.148
性状
Trait		 位点名称
SNP		 染色体
Chr.		 P值
P-value		 贡献率
R2 (%)		 位点名称
SNP		 染色体
Chr.		 P 值
P-value		 贡献率
R2 (%)
综合药
害指数
CPC		 Bn-A05-p19765662 A05 2.77×10-5 4.675 Bn-C05-p7765985 C05 1.89×10-10 9.835
Bn-A05-p19693221 A05 7.18×10-5 4.364 Bn-C05-p3235412 C05 8.74×10-5 4.207
Bn-A06-p15660438 A06 3.14×10-5 4.626 Bn-C05-p3698257 C05 3.25×10-5 4.656
Bn-A06-p14512365 A06 5.24×10-6 5.467 Bn-C05-p36474843 C05 5.81×10-5 4.140
Bn-A06-p15261863 A06 2.47×10-5 4.741 Bn-C05-p21774776 C05 2.47×10-6 18.623
Bn-A06-p15365248 A06 4.82×10-7 6.452 Bn-C05-p2564789 C05 6.21×10-5 4.119
Bn-A07-p23001203 A07 1.00×10-8 8.026 Bn-C06-p24235721 C06 7.16×10-5 4.061
Bn-A07-p23418663 A07 2.23×10-5 4.812 Bn-C06-p32728327 C06 4.25×10-5 4.069
Bn-A07-p4480260 A07 2.25×10-6 4.260 Bn-C07-p22140411 C07 5.55×10-7 10.771
Bn-A07-p20935217 A07 2.44×10-6 5.263 Bn-C07-p12256348 C07 2.45×10-5 4.487
Bn-A07-p23340612 A07 7.48×10-5 4.260 Bn-C07-p22118892 C07 2.87×10-7 6.745
Bn-A07-p28542122 A07 2.77×10-5 4.865 Bn-C07-p20147854 C07 1.33×10-5 4.756
Bn-A08-p10182282 A08 1.81×10-5 4.869 Bn-C08-p13638153 C08 2.39×10-9 5.369
Bn-A08-p13250140 A08 7.39×10-5 4.362 Bn-C08-p12356824 C08 8.26×10-6 4.912
Bn-A08-p7652410 A08 2.12×10-7 6.728 Bn-C08-p19139658 C08 3.25×10-8 6.952
Bn-A08-p7505807 A08 7.75×10-8 7.289 Bn-C08-p19568928 C08 1.37×10-6 5.627
Bn-A09-p2201470 A09 1.12×10-7 7.154 Bn-C09-p40117533 C09 4.16×10-7 6.356
Bn-A09-p2176198 A09 9.27×10-6 5.182 Bn-C09-p46985366 C09 6.42×10-5 5.632
Bn-A09-p16521452 A09 7.81×10-6 5.211 Bn-C09-p12891995 C09 2.99×10-5 3.265
Bn-A09-p15882405 A09 2.91×10-5 4.721 Bn-C09-p12356923 C09 3.54×10-5 4.631
Bn-A09-p6598420 A09 1.90×10-5 5.304 Bn-C09-p13003243 C09 1.67×10-5 4.365

表4

耐药性相关性状的候选基因"

性状
Trait		 位点
Site		 染色体
Chr.		 物理位置
Physical interval
(bp)		 拟南芥基因
Arabidopisis genes		 候选基因
Candidate genes
in the LD interval
单位叶面积干重系数 Bn-A01-p1704123 A01 1633033-1633658 AT4G33467 BnaA01g03470D
CWL Bn-A01-p4549945 A01 4548199-4552433 AT4G18490 BnaA01g09330D
叶绿素含量系数 Bn-A01-p21360797 A01 21153560-21155842 AT3G11290 BnaA01g31070D
CCC Bn-A02-p4940608 A02 4607681-4610486 AT5G55050 BnaA02g09320D
Bn-A02-p4940608 A02 459901-4602406 AT5G55070 BnaA02g09300D
Bn-A02-p4940608 A02 5204578-5206797 AT5G53470 ACBP1
Bn-A03-p21755979 A03 21582364-21584595 AT4G17250 BnaA03g42990D
Bn-A03-p21755979 A03 21958105-21965340 AT2G07680 ATABCC13
Bn-A03-p21755979 A03 21953245-21955187 AT4G18070 BnaA03g43580D
Bn-A03-p4171667 A03 4122660-4124952 AT5G59960 BnaA03g09150D
Bn-A04-p16495266 A04 16368845-16371398 AT2G37500 BnaA04g21470D
Bn-A04-p16495266 A04 16372246-16376604 AT2G37520 BnaA04g21480D
Bn-A04-p16495266 A04 16498173-16499643 AT2G20625 BnaA04g21710D
Bn-A04-p16495266 A04 16508877-16511523 AT2G37960 BnaA04g21730D
Bn-A04-p7873782 A04 7808158-7809504 AT5G67150 BnaA04g08790D
Bn-A05-p10742077 A05 10774154-10779061 LACS2 BnaA05g16170D
Bn-A07-p3477622 A07 3235720-3238222 AT2G16270 BnaA07g03580D
Bn-A09-p16498800 A09 16425283-16427170 AT1G33270 BnaA09g23800D
Bn-C07-p41693853 C07 41701416-41703232 AT2G25150 BnaC07g42100D
Bn-C07-p41693853 C07 41797435-41799523 AT4G30060 BnaC07g42290D
综合药害指数 Bn-A02-p6901239 A02 6771193-6774102 AT1G66860 BnaA02g12600D
CPC Bn-A04-p1983502 A04 2101543-2102589 AT2G23060 BnaA04g03220D
Bn-A04-p1983502 A04 2110543-2111592 AT3G57100 BnaA04g03240D
Bn-A07-p4480260 A07 4562018-4563915 AT2G06025 BnaA07g04340D
Bn-A08-p10182282 A08 10187701-10189221 AT4G34520 BnaA08g11130D
Bn-A08-p13250140 A08 13047661-13049407 AT4G37580 BnaA08g15700D
Bn-C07-p22140411 C07 22179972-22180303 AT5G67160 EPS1
Bn-C07-p22140411 C07 22181878-22183299 AT5G67150 BnaC07g16220D
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