中国农业科学 ›› 2019, Vol. 52 ›› Issue (3): 399-413.doi: 10.3864/j.issn.0578-1752.2019.03.002
周清元,王倩,叶桑,崔明圣,雷维,郜欢欢,赵愉风,徐新福,唐章林,李加纳,崔翠()
收稿日期:
2018-09-17
接受日期:
2018-11-17
出版日期:
2019-02-01
发布日期:
2019-02-14
通讯作者:
崔翠,Tel:13883787860;
作者简介:
周清元,Tel:13883388890;E-mail: 基金资助:
ZHOU QingYuan,WANG Qian,YE Sang,CUI MinSheng,LEI Wei,GAO HuanHuan,ZHAO YuFeng,XU XinFu,TANG ZhangLin,LI JiaNa,CUI Cui()
Received:
2018-09-17
Accepted:
2018-11-17
Online:
2019-02-01
Published:
2019-02-14
摘要:
目的 研究苯磺隆残留对油菜种子萌发的影响,运用全基因组关联分析(genome-wide association analysis,GWAS)揭示苯磺隆胁迫下油菜萌发期相关性状的遗传因子和候选基因,探究油菜在苯磺隆逆境胁迫下的生理形态所反映的基因调控机制,为耐苯磺隆油菜品种的研究提供参考。方法 以241份甘蓝型油菜品种(系)为材料、25 mg·L -1苯磺隆溶液为处理液、蒸馏水为对照进行发芽试验。发芽7 d测定并计算相对发芽率、相对根长和相对鲜重。结合芸薹属60K SNP芯片分析群体基因型,通过STRUCTURE软件和TASSEL软件分别对该群体进行群体结构分析以及亲缘关系和LD衰减分析。为有效排除假关联的影响,采用一般线性模型(GLM)和混合线性模型(MLM)中的6种模型进行比较,确定每个性状GWAS分析的最优模型。同时,利用TASSEL软件在最优模型下对241份材料的3个性状分别进行全基因组关联分析,根据关联SNP位点的LD区间序列预测候选基因。 结果 241份品种(系)群体可分为P1(94份材料)和P2(147份材料)2个亚群,其中约56.28%的材料之间的亲缘关系值为0。全基因组关联分析(K+PCA模型)共检测到16个与性状显著关联的SNP位点,这些位点可解释9.42%—13.14%的表型变异率。通过分析显著SNP位点的LD区间与甘蓝型油菜对应的区间序列,筛选出25个候选基因可能与油菜耐苯磺隆有关,其中9个为细胞色素P450家族基因,5个参与谷胱甘肽合成或代谢过程,2个为多药耐药相关蛋白基因。同时发现与相对发芽率显著相关的基因ATGSTU19编码谷胱甘肽转移酶,参与毒素分解过程,在各种胁迫反应中起重要作用。在相对根长和相对鲜重共同鉴定到的候选基因BnaC02g27690D功能未知。结论 共检测到16个SNP位点与耐苯磺隆性状显著关联,筛选出25个候选基因可能与油菜耐苯磺隆有关。
周清元, 王倩, 叶桑, 崔明圣, 雷维, 郜欢欢, 赵愉风, 徐新福, 唐章林, 李加纳, 崔翠. 苯磺隆胁迫下油菜萌发期相关性状的全基因组关联分析[J]. 中国农业科学, 2019, 52(3): 399-413.
ZHOU QingYuan, WANG Qian, YE Sang, CUI MinSheng, LEI Wei, GAO HuanHuan, ZHAO YuFeng, XU XinFu, TANG ZhangLin, LI JiaNa, CUI Cui. Genome-Wide Association Analysis of Tribenuron-Methyl Tolerance Related Traits in Brassica napus L. Under Germination[J]. Scientia Agricultura Sinica, 2019, 52(3): 399-413.
表2
SNP在染色体上的分布"
染色体 Chr. | SNP数目 No. | 长度 Length (bp) | SNP密度 SNP density (1 SNP/kb) | 染色体 Chr. | SNP数目 No. | 长度 Length (bp) | SNP密度 SNP density (1 SNP/kb) | |
---|---|---|---|---|---|---|---|---|
A01 | 1533 | 23213190 | 15.14 | C01 | 2321 | 38751959 | 16.70 | |
A02 | 1266 | 24751063 | 19.55 | C02 | 2225 | 46171227 | 20.75 | |
A03 | 2206 | 29727584 | 13.48 | C03 | 2707 | 60554466 | 22.37 | |
A04 | 1444 | 19097304 | 13.23 | C04 | 3005 | 48891192 | 16.27 | |
A05 | 1623 | 22986419 | 14.16 | C05 | 1011 | 43165527 | 42.70 | |
A06 | 1519 | 24371484 | 16.04 | C06 | 1287 | 37161109 | 28.87 | |
A07 | 1882 | 23921822 | 12.71 | C07 | 1683 | 44305541 | 26.33 | |
A08 | 1085 | 18658096 | 17.20 | C08 | 1527 | 38226084 | 25.03 | |
A09 | 1637 | 33803997 | 20.65 | C09 | 1006 | 48440856 | 48.15 | |
A10 | 1526 | 17348295 | 11.37 | |||||
A染色体SNP 的平均分布 Mean A genome | 1572 | 23787925 | 15.13 | C染色体SNP 的平均分布 Mean C genome | 1864 | 45074218 | 24.19 |
表3
连锁不平衡在A、C基因组中的衰减距离"
染色体 Chr. | A基因组LD衰减距离 A genome LD attenuation distance (kb) | 染色体 Chr. | C基因组LD衰减距离 C genome LD attenuation distance (kb) | |
---|---|---|---|---|
A01 | 150 | C01 | 750 | |
A02 | 130 | C02 | 1150 | |
A03 | 130 | C03 | 370 | |
A04 | 150 | C04 | 560 | |
A05 | 150 | C05 | 270 | |
A06 | 150 | C06 | 370 | |
A07 | 140 | C07 | 350 | |
A08 | 550 | C08 | 640 | |
A09 | 370 | C09 | 760 | |
A10 | 240 | |||
A基因组 A genome | 170 | C基因组 C genome | 650 |
表4
苯磺隆胁迫下相关性状的显著关联标记"
性状 Trait | 标记 Marker | 等位基因 Allele | 染色体 Chr. | 位置 Position (bp) | 阈值 P-value | 贡献率 R2(%) |
---|---|---|---|---|---|---|
相对根长 Relative root length | Bn-A03-p21744993 | A/G | A03 | 20527711 | 4.37×10-6 | 12.19 |
Bn-A05-p23188406 | A/C | A05 | 21346681 | 1.18×10-5 | 11.22 | |
Bn-A02-p5442618 | A/G | C02 | 5190991 | 4.35×10-6 | 12.20 | |
Bn-A05-p9277011 | A/C | C02 | 26364667 | 2.94×10-5 | 10.35 | |
Bn-scaff_18322_1-p2518158 | T/C | C03 | 6708755 | 4.26×10-6 | 12.22 | |
Bn-scaff_17799_1-p1082380 | A/G | C06 | 35520328 | 9.75×10-6 | 11.42 | |
相对鲜重 Relative fresh weight | Bn-A01-p11163980 | A/G | A01 | 9233493 | 1.48×10-5 | 11.12 |
Bn-scaff_22749_1-p462527 | T/C | C02 | 25111534 | 8.44×10-6 | 11.66 | |
Bn-scaff_17457_1-p187316 | A/G | C03 | 54357603 | 1.34×10-5 | 11.22 | |
Bn-scaff_17457_1-p82664 | T/G | C03 | 54463472 | 2.31×10-5 | 10.69 | |
Bn-scaff_15798_1-p152131 | T/G | C04 | 36758548 | 2.28×10-5 | 9.42 | |
Bn-scaff_15794_3-p286350 | A/C | C03 | 55318298 | 3.12×10-5 | 10.40 | |
相对发芽率 Relative germination rate | Bn-A04-p10628643 | T/C | A04 | 11766577 | 1.88×10-6 | 13.14 |
Bn-A07-p5710530 | T/G | A07 | 7686960 | 2.52×10-6 | 12.85 | |
Bn-scaff_16300_1-p1228965 | A/C | C02 | 22565646 | 1.75×10-5 | 10.95 | |
Bn-A09-p9040117 | A/C | C09 | 11435455 | 1.28×10-5 | 11.26 |
表5
苯磺隆耐性相关性状的候选基因"
性状 Trait | 标记 Marker | 染色体 Chr. | LD区间 LD interval (bp) | 候选基因 Candidate gene | 拟南芥基因 Arabidopsis gene | 基因 Gene | 参考文献 Reference |
---|---|---|---|---|---|---|---|
相对根长 Relative root length | Bn-A03-p21744993 | A03 | 20397711-20657711 | BnaA03g40900D | AT3G50740 | UGT72E1 | [33] |
Bn-A05-p23188406 | A05 | 21196681-21496681 | BnaA05g30790D | AT3G06590 | AIF2 | [34] | |
Bn-A02-p5442618 | C02 | 4040991-6340991 | BnaC02g07650D | AT5G17960 | 未知Unknown | ||
BnaC02g08720D | AT5G19450 | CDPK19 | [35] | ||||
BnaC02g10110D | AT1G01190 | CYP78A8 | [36] | ||||
BnaC02g10430D | AT5G58860 | CYP86A1 | [37] | ||||
Bn-A05-p9277011 | C02 | 25214667-27514667 | BnaC02g27690D | AT4G01210 | 未知Unknown | ||
BnaC02g28290D | AT4G12320 | CYP706A6 | |||||
Bn-scaff_17799_ 1-p1082380 | C06 | 35150328-35890328 | BnaC06g38000D | AT1G77290 | 未知Unknown | ||
相对鲜重 Relative fresh weight | Bn-A01-p11163980 | A01 | 9083493-9383493 | BnaA01g17570D | AT4G16190 | 未知Unknown | |
Bn-scaff_22749 _1-p462527 | C02 | 23961534-26261534 | BnaC02g27690D | AT4G01210 | 未知Unknown | ||
BnaC02g27750D | AT4G01070 | GT72B1 | [38] | ||||
Bn-scaff_17457 _1-p187316 | C03 | 53987603-54727603 | BnaC03g64930D | AT4G12560 | CPR1 | [39] | |
BnaC03g65100D | AT4G22690 | CYP706A1 | [40] | ||||
BnaC03g65140D | AT4G23100 | GSH1 | [41] | ||||
Bn-scaff_17457 _1-p82664 | C03 | 54093472-54833472 | BnaC03g65260D | AT1G49860 | GSTF14 | [42] | |
Bn-scaff_15798 _1-p152131 | C04 | 36198548-37318548 | BnaC04g35220D | AT1G13080 | CYP71B2 | [43] | |
BnaC04g35620D | AT1G78490 | CYP708A3 | |||||
相对发芽率 Relative germination rate | Bn-A07-p5710530 | A07 | 7546960-7826960 | BnaA07g07310D | AT1G30410 | ATMRP13 | [41] |
BnaA07g07330D | AT1G30420 | ATMRP12 | [44] | ||||
Bn-scaff_16300 _1-p1228965 | C02 | 21415646-23715646 | BnaC02g24410D | AT1G47620 | CYP96A8 | [45] | |
BnaC02g24920D | AT1G78270 | UGT85A4 | [46] | ||||
BnaC02g24980D | AT1G78380 | ATGSTU19 | [47] | ||||
Bn-A09-p9040117 | C09 | 10675455-12195455 | BnaC09g14070D | AT3G26160 | CYP71B17 | [48] | |
BnaC09g14150D | AT3G26170 | CYP71B19 | [49] | ||||
BnaC09g15080D | AT1G59700 | GSTU16 | [50] |
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