欢迎访问作物学报，今天是
作物学报

作物学报 ›› 2018, Vol. 44 ›› Issue (9): 1311-1319.doi: 10.3724/SP.J.1006.2018.01311

• 研究论文 • 上一篇    下一篇

油菜种子含油量GWAS分析及位点整合系统构建

魏大勇1,2,3(),崔艺馨3,4,梅家琴3,4,汤青林1,2,李加纳3,4,钱伟3,4,*()   

  1. 1 西南大学园艺园林学院, 重庆 400715
    2 南方山地园艺学教育部重点实验室, 重庆 400715
    3 西南大学农学与生物科技学院, 重庆 400715
    4 西南大学现代农业科学研究院, 重庆 400715
  • 收稿日期:2018-01-30 接受日期:2018-06-09 出版日期:2018-09-10 网络出版日期:2018-09-12
  • 通讯作者: 钱伟
  • 基金资助:
    本研究由西南大学博士基金项目(SWU118010);国家自然科学基金项目(31601333);国家重点基础研究发展计划(973计划)项目(973 Program 2015CB150201);中央高校基本科研业务专项(XDJK2017B036)

Genome-wide Association Study on Seed Oil Content in Rapeseed and Construction of Integration System for Oil Content Loci

Da-Yong WEI1,2,3(),Yi-Xin CUI3,4,Jia-Qin MEI3,4,Qing-Lin TANG1,2,Jia-Na LI3,4,Wei QIAN3,4,*()   

  1. 1 College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
    2 Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing 400715, China
    3 College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
    4 Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China
  • Received:2018-01-30 Accepted:2018-06-09 Published:2018-09-10 Published online:2018-09-12
  • Contact: Wei QIAN
  • Supported by:
    This study was supported by the Doctoral Fund of Southwest University(SWU118010);the National Natural Science Foundation of China(31601333);the National Basic Research Program of China(973 Program 2015CB150201);the Fundamental Research Funds for Central Universities(XDJK2017B036)

RichHTML

34

PDF

871

摘要：

含油量是油菜最重要的性状之一, 目前已有较多的油菜种子含油量定位研究, 然而各研究系统相对独立, 群体与标记的差别使得难以比较不同研究结果。本研究连续4年种植了一个含308份材料的油菜自然群体, 结合60K SNP芯片数据对种子含油量进行了全基因组关联分析(GWAS), 并将所鉴定的显著位点与早前2个自然群体及10个分离群体鉴定到的位点进行全基因组比较与整合。结果显示, 通过GWAS共检测到8个与种子含油量显著关联的位点, 单个位点解释的表型变异度为3.22%~5.13%; 结合其他12个群体的定位结果, 共获得193个油菜含油量整合位点, 分布于油菜的所有19条染色体, A亚基因组平均每条染色体有13个位点, 显著高于C亚基因组(7个)。对不同群体鉴定结果的比较发现, 7个整合区间能在至少3个群体中被检测到, 均位于A亚基因组染色体(A01、A02、A03、A06、A08、A09和A10)上, 其中有3个与C亚基因组上的区间存在同源性, 在这3个区间中共鉴定到26个已知的油脂代谢相关基因。本研究将193个位点锚定到法国公布的甘蓝型油菜参考基因组, 构建了一个可视的油菜种子含油量位点全基因组整合系统, 可为油菜种子含油量重要位点的确定提供帮助, 并为制定提高油菜种子含油量的育种方案提供参考。

关键词: 甘蓝型油菜, 种子含油量, 全基因组关联分析, QTL, 整合系统

Abstract:

Genetic loci for oil content, one of the most important traits of rapeseed (Brassica napus L.), have been widely studied, however, comparisons were difficult to be carried out among studies due to different mapping populations and molecular marker systems. In the present study, a 60K Brassica SNP array was applied in the genome-wide association study (GWAS) using a natural rapeseed population which was comprised of 308 accessions and grown for four consecutive years to identify loci for seed oil content. An integration system was built by anchoring the present loci and previous loci that identified onto the rapeseed genome in other studies using ten segregation populations and two natural populations. A total of eight SNPs significantly associated with seed oil contents of rapeseed were detected in our study, explaining 3.22%-5.13% of the phenotypic variance each SNP. Combining the data from other 12 populations, 193 integrated loci were identified, spreading on all 19 chromosomes of B. napus with more loci distributed on A subgenome (13 loci/chromosome) than C subgenome (seven loci/chromosome). Seven integrated intervals from A subgenome (chromosome A01, A02, A03, A06, A08, A09, and A10) were identified in at least three populations, of which three were homologous to intervals on C subgenome, with 26 known genes associated with seed oil metabolism. The 193 loci were anchored to the reference genome of B. napus var. Darmor-Bzh, resulting in a visualized genome-wide integrated system for seed oil content loci. This study is helpful to determine the important seed oil content loci and to make the optimal breeding strategy to increase oil content in rapeseed.

Key words: Brassica napus, seed oil content, genome-wide association study, QTL, integrated system

表1

308份自然群体中油菜种子含油量的表型变异"

年份 Year 范围 Range (%) 平均值±标准偏差 Mean±SD (%) 变异系数CV (%)
2013 24.50-48.46 37.01±3.79 10.24
2014 27.47-47.35 36.82±3.45 9.37
2015 25.27-44.43 34.99±3.07 8.79
2016 25.21-49.91 38.54±3.88 10.06

图1

种子含油量的频率分布"

表2

GWAS结果和候选基因预测"

染色体
Chr.		 位置
Position (bp)		 贡献率
R2 (%)		 假阳性率
FDR		 候选基因
Candidate gene		 拟南芥同源基因
Arabidopsis homologue		 基因注释
Gene annotation
A02 20818388 3.22 3.85E-05 BnaA02g28280D AT3G26790 B3类转录因子
B3 transcription factor
A03 6727279 4.56 3.18E-05 BnaA03g14670D AT2G31690 三酰甘油酯的降解
Involved in the degradation of triacylglycerol
A05 15959252 3.51 3.45E-05 — — —
A05 18730739 4.29 2.44E-05 BnaA05g25260D AT3G14205 磷酸肌醇磷酸酯酶家族蛋白
Phosphoinositide phosphatase family protein
A05 19407850 3.26 7.52E-06 BnaA05g26510D AT3G12680 C3H类转录因子
C3H transcription factor
A05 19483554 5.13 6.52E-06 BnaA05g26900D AT3G12120 bZIP类转录因子
bZIP transcription factor
C02 45446662 3.71 2.46E-05 — — —
C02 45458214 4.22 1.65E-05 BnaC02g43130D AT5G64440 肪酸酰胺水解酶
Fatty acid amide hydrolase

图2

种子含油量的全基因组关联分析 a: 种子含油量的曼哈顿图, 水平黑色虚线表示阈值(1/23490, -lg P= 4.37); b: 估计阈值的Q-Q图。"

Table 3

Summary of known sites associated with seed oil content in B.napus"

图3

全基因组组水平展示不同油菜群体种子含油量的定位结果(a)染色体数目; (b)参考基因组所有基因的热图(窗口大小为500 kb); (c)已知的1663个油分代谢相关基因; (1) DY-DH群体; (2) RNSL-DH群体; (3) GP-RIL群体; (4) RC-F2群体; (5) SG-DH群体; (6) Z5-DH群体; (7) KN-DH群体; (8) TN-DH群体; (9)PT-DH群体; (10) 521份自然群体1; (11) 521份自然群体2; (12) 521份自然群体3; (13) ES-DH群体; (14) 142份自然群体4; (15) 308份自然群体。中间不同颜色线条表示A和C亚基因组上存在同源关系的12组整合区间。"

表4

甘蓝型油菜遗传稳定的种子含油量位点染色体分布及油脂代谢相关基因"

染色体
Chr.		 群体编号
ID		 区间
Region (Mb)		 已知的油脂代谢相关基因1)
Known genes related to oil metabolism1)
A01 3, 4, 5, 8 7.23-7.49 BnaA01g14400D, BnaA01g14480D
A02 6, 8, 11 8.09-10.25 BnaA02g14460D, BnaA02g15090D, BnaA02g15290D, BnaA02g15690D, BnaA02g15770D, BnaA02g16020D, BnaA02g16070D, BnaA02g16200D, BnaA02g16260D, BnaA02g16470D, BnaA02g16520D, BnaA02g16570D, BnaA02g17050D
A03 1, 2, 8, 9 16.53-17.65 BnaA03g34340D, BnaA03g34830D, BnaA03g34980D, BnaA03g35170D,
A06 1, 10, 14 21.5-21.7 BnaA06g32660D
A08 2, 3, 4, 7, 8 10.85-12.17 BnaA08g12720D, BnaA08g12780D, BnaA08g12850D, BnaA08g13370D, BnaA08g13410D, BnaA08g13530D, BnaA08g13870D, BnaA08g14190D
A09 8, 10, 11, 12, 13 30.49-31.23 BnaA09g44630D, BnaA09g44650D, BnaA09g44980D, BnaA09g45010D, BnaA09g45250D, BnaA09g45720D
A10 10, 11, 12, 13, 14 14.35-16.06 BnaA10g20920D, BnaA10g21350D, BnaA10g21780D, BnaA10g22070D, BnaA10g23290D, BnaA10g23670D, BnaA10g23790D, BnaA10g23950D, BnaA10g24440D, BnaA10g24560D
[1] 王汉中 . 我国油菜产业发展的历史回顾与展望. 中国油料作物学报, 2010,32:300-302
Wang H Z . Review and future development of rapeseed industry in China. Chin J Oil Crop Sci, 2010,32:300-302 (in Chinese with English abstract)
[2] 李殿荣, 郑磊, 李少钦 . 近十三年我国冬油菜新品种单产与含油量的变化分析. 种子, 2014,33:96-100
Li D R, Zheng L, Li S Q . The development analysis on yield and oil content of winter rapeseed varieties in Brassica napus L.. from 2000 to 2012 in China. Seed, 2014,33:96-100 (in Chinese with English abstract)
[3] Hu Q, Hua W, Yin Y, Zhang X, Liu L, Shi J, Zhao Y, Qin L, Chen C, Wang H . Rapeseed research and production in China. Crop J, 2017,5:127-135
[4] 李超, 李波, 曲存民, 阎星颖, 付福友, 刘列钊, 谌利, 李加纳 . 两种环境下甘蓝型油菜含油量的差值QTL分析. 作物学报, 2011,37:249-254
Li C, Li B, Qu C M, Yan X Y, Fu F Y, Liu L Z, Chen L, Li J N . Analysis of difference QTLs for oil content between two environments in Brassica napus L.. Acta Agron Sin, 2011,37:249-254 (in Chinese with English abstract)
[5] 刘后利 . 油菜遗传育种学 . 北京: 中国农业大学出版社, 2000. pp 146-154
Liu H L. Genetics and Breeding in Rrapeseed. Beijing: Chinese Agricultural Universitatis Press, 2000. pp 146-154(in Chinese with English abstract)
[6] 马珍珍, 李加纳 Wittkop B, Frauen M, 阎星颖, 刘列钊, 肖阳. 甘蓝型油菜籽粒含油量、蛋白质、纤维素及半纤维素含量QTL分析. 作物学报, 2013,39:1214-1222
Ma Z Z, Li J N, Wittkop B, Frauen M, Yan X Y, Liu L Z, Xiao Y . QTL mapping for oil, protein, cellulose, and hemicellulose contents in seeds of Brassica napus L. Acta Agron Sin, 2013,39:1214-1222 (in Chinese with English abstract)
[7] Yan R, Falentin C, Huteau V, Clouet V, Horvais R, Gandon B, Specel S, Hanneton L, Dheu J E, Deschamps M, Margale E, Vincourt P, Renard M . Genetic control of oil content in oilseed rape ( Brassica napus L.). Theor Appl Genet, 2006,113:1331-1345
[8] Yan X Y, Li J N, Fu F Y, Jin M Y, Chen L, Liu L Z . Co-location of seed oil content, seed hull content and seed coat color QTL in three different environments in Brassica napus L. Euphytica, 2009,170:355-364
[9] Shi J, Li R, Zou J, Yan L, Meng J . A dynamic and complex network regulates the heterosis of yield-correlated traits in rapeseed (Brassica napus L.). PLoS One, 2011,6:e21645
[10] Sun M, Hua W, Liu J, Huang S, Wang X, Liu G, Wang H . Design of new genome- and gene-sourced primers and identification of QTL for seed oil content in a specially high-oil Brassica napus cultivar. PLoS One, 2012,7:e47037
[11] Zhao J, Huang J, Chen F, Xu F, Ni X, Xu H, Wang Y, Jiang C, Wang H, Xu A, Huang R, Li D, Meng J . Molecular mapping of Arabidopsis thaliana lipid-related orthologous genes in Brassica napus. Theor Appl Genet, 2012,124:407-421
[12] Wang X, Hao W, Yan L, Li D, Yin Y, Tian J, Li C, Liu L, Zhao W, Zhao Y . Identification of QTLs associated with oil content in a high-oil Brassica napus cultivar and construction of a high-density consensus map for QTLs comparison in B. napus. PLoS One, 2013,8:e80569
[13] Jiang C, Shi J, Li R, Long Y, Wang H, Li D, Zhao J, Meng J . Quantitative trait loci that control the oil content variation of rapeseed ( Brassica napus L.). Theor Appl Genet, 2014,127:957-968
doi: 10.1007/s00122-014-2271-5 pmid: 24504552
[14] Javed N, Geng J, Tahir M, McVetty P B E, Li G, Duncan R W. , Identification of QTL influencing seed oil content, fatty acid profile and days to flowering in Brassica napus L. Euphytica, 2015,207:191-211
[15] Liu S, Fan C, Li J, Cai G, Yang Q, Wu J, Yi X, Zhang C, Zhou Y . A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus. Theor Appl Genet, 2016,129:1203-1215
[16] Fu Y, Zhang D, Gleeson M, Zhang Y, Lin B, Hua S, Ding H, Frauen M, Li J, Qian W, Yu H . Analysis of QTL for seed oil content in Brassica napus by association mapping and QTL mapping. Euphytica, 2017,213:17
[17] Chalhoub B, Denoeud F, Liu S, Parkin I A, Tang H, Wang X, Chiquet J, Belcram H, Tong C, Samans B, Correa M, Da Silva C, Just J, Falentin C, Koh C S, Le Clainche I, Bernard M, Bento P, Noel B, Labadie K, Alberti A, Charles M, Arnaud D, Guo H, Daviaud C, Alamery S, Jabbari K, Zhao M, Edger P P, Chelaifa H, Tack D, Lassalle G, Mestiri I, Schnel N ,Le Paslier M C, Fan G, Renault V, Bayer P E, Golicz A A, Manoli S, Lee T H, Thi V H, Chalabi S, Hu Q, Fan C, Tollenaere R, Lu Y, Battail C, Shen J, Sidebottom C H, Wang X, Canaguier A, Chauveau A, Berard A, Deniot G, Guan M, Liu Z, Sun F, Lim Y P, Lyons E, Town C D, Bancroft I, Wang X, Meng J, Ma J, Pires J C, King G J, Brunel D, Delourme R, Renard M, Aury J M, Adams K L, Batley J, Snowdon R J, Tost J, Edwards D, Zhou Y, Hua W, Sharpe A G, Paterson A H, Guan C, Wincker P., Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome. Science, 2014,345:950-953
[18] Li F, Chen B Y, Xu K, Wu J F, Song W L, Bancroft I, Harper A L, Trick M, Liu S Y, Gao G Z, Wang N, Yan G X, Qiao J W, Li J, Li H, Xiao X, Zhang T Y, Wu X M . Genome-wide association sudy dissects the genetic architecture of seed weight and seed quality in rapeseed ( Brassica napus L.). DNA Res, 2014,21:355-367
[19] Wei D, Cui Y, He Y, Xiong Q, Qian L, Tong C, Lu G, Ding Y, Li J, Jung C, Qian W . A genome-wide survey with different rapeseed ecotypes uncovers footprints of domestication and breeding. J Exp Bot, 2017,68:4791-4801
[20] Wei L, Jian H, Lu K, Filardo F, Yin N, Liu L, Qu C, Li W, Du H, Li J . Genome-wide association analysis and differential expression analysis of resistance to Sclerotinia stem rot in Brassica napus. Plant Biotechnol J, 2015: 1-13
[21] SASV9.13 software . SAS Institute, Cary, NC, USA, 2005
[22] 魏大勇, 谭传东, 崔艺馨, 吴道明, 李加纳, 梅家琴, 钱伟 . 甘蓝型油菜pol CMS育性恢复位点的全基因组关联分析. 中国农业科学, 2017,50:802-819
Wei D Y, Tan C D, Cui Y X, Wu D M, Li J N, Mei J Q, Qian W . Genome-wide association study of the fertility restorer loci for pol CMS in rapeseed( Brassica napus L.).. Sci Agric Sin, 2017,50:802-819 (in Chinese with English abstract)
[23] Aulchenko Y S, Ripke S, Isaacs A , Van Duijn C M. GenABEL: an R library for genome-wide association analysis. Bioinformatics, 2007,23:1294-1296
[24] Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones S J, Marra M A . Circos: an information aesthetic for comparative genomics. Genome Res, 2009,19:1639-1645
[25] Merk H L, Yarnes S C, Van Deynze A, Tong N K, Menda N, Mueller L A, Mutschler M A, Loewen S A, Myers J R, Francis D M . Trait diversity and potential for selection indices based on variation among regionally adapted processing tomato germplasm. J Am Soc Hort Sci, 2012,137:427-437
[26] NU. Genomic analysis in Brassica with special reference to the experimental formation of B. napus and peculiar bode of fertilization. Jpn J Bot, 1935,7:389-452
[27] Qian L, Qian W, Snowdon R J . Sub-genomic selection patterns as a signature of breeding in the allopolyploid Brassica napus genome. BMC Genomics, 2014,15:1170
[28] Wang N, Li F, Chen B, Xu K, Yan G, Qiao J, Li J, Gao G, Bancroft I, Meng J, King G J, Wu X . Genome-wide investigation of genetic changes during modern breeding of Brassica napus. Theor Appl Genet, 2014,127:1817-1829
[1] 陈玲玲, 李战, 刘亭萱, 谷勇哲, 宋健, 王俊, 邱丽娟. 基于783份大豆种质资源的叶柄夹角全基因组关联分析[J]. 作物学报, 2022, 48(6): 1333-1345.
[2] 胡文静, 李东升, 裔新, 张春梅, 张勇. 小麦穗部性状和株高的QTL定位及育种标记开发和验证[J]. 作物学报, 2022, 48(6): 1346-1356.
[3] 陈松余, 丁一娟, 孙峻溟, 黄登文, 杨楠, 代雨涵, 万华方, 钱伟. 甘蓝型油菜BnCNGC基因家族鉴定及其在核盘菌侵染和PEG处理下的表达特性分析[J]. 作物学报, 2022, 48(6): 1357-1371.
[4] 秦璐, 韩配配, 常海滨, 顾炽明, 黄威, 李银水, 廖祥生, 谢立华, 廖星. 甘蓝型油菜耐低氮种质筛选及绿肥应用潜力评价[J]. 作物学报, 2022, 48(6): 1488-1501.
[5] 孙思敏, 韩贝, 陈林, 孙伟男, 张献龙, 杨细燕. 棉花苗期根系分型及根系性状的关联分析[J]. 作物学报, 2022, 48(5): 1081-1090.
[6] 于春淼, 张勇, 王好让, 杨兴勇, 董全中, 薛红, 张明明, 李微微, 王磊, 胡凯凤, 谷勇哲, 邱丽娟. 栽培大豆×半野生大豆高密度遗传图谱构建及株高QTL定位[J]. 作物学报, 2022, 48(5): 1091-1102.
[7] 袁大双, 邓琬玉, 王珍, 彭茜, 张晓莉, 姚梦楠, 缪文杰, 朱冬鸣, 李加纳, 梁颖. 甘蓝型油菜BnMAPK2基因的克隆及功能分析[J]. 作物学报, 2022, 48(4): 840-850.
[8] 黄成, 梁晓梅, 戴成, 文静, 易斌, 涂金星, 沈金雄, 傅廷栋, 马朝芝. 甘蓝型油菜BnAPs基因家族成员全基因组鉴定及分析[J]. 作物学报, 2022, 48(3): 597-607.
[9] 王瑞, 陈雪, 郭青青, 周蓉, 陈蕾, 李加纳. 甘蓝型油菜白花基因InDel连锁标记开发[J]. 作物学报, 2022, 48(3): 759-769.
[10] 渠建洲, 冯文豪, 张兴华, 徐淑兔, 薛吉全. 基于全基因组关联分析解析玉米籽粒大小的遗传结构[J]. 作物学报, 2022, 48(2): 304-319.
[11] 张艳波, 王袁, 冯甘雨, 段慧蓉, 刘海英. 棉籽油分和3种主要脂肪酸含量QTL分析[J]. 作物学报, 2022, 48(2): 380-395.
[12] 赵海涵, 练旺民, 占小登, 徐海明, 张迎信, 程式华, 楼向阳, 曹立勇, 洪永波. 水稻协优9308重组自交系群体白叶枯病抗性的全基因组关联分析[J]. 作物学报, 2022, 48(1): 121-137.
[13] 王艳花, 刘景森, 李加纳. 整合GWAS和WGCNA筛选鉴定甘蓝型油菜生物产量候选基因[J]. 作物学报, 2021, 47(8): 1491-1510.
[14] 张波, 裴瑞琴, 杨维丰, 朱海涛, 刘桂富, 张桂权, 王少奎. 利用单片段代换系鉴定巴西陆稻IAPAR9中的粒型基因[J]. 作物学报, 2021, 47(8): 1472-1480.
[15] 马娟, 曹言勇, 李会勇. 玉米穗轴粗全基因组关联分析[J]. 作物学报, 2021, 47(7): 1228-1238.
Viewed
Full text


Abstract

Cited
  Shared   
  Discussed   
No Suggested Reading articles found!
京ICP备15008789号-2