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作物学报 ›› 2019, Vol. 45 ›› Issue (9): 1303-1310.doi: 10.3724/SP.J.1006.2019.94021

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

甘蓝型油菜角果长度性状的全基因组关联分析

孙程明1,2,陈松1,彭琦1,张维1,易斌2,*(),张洁夫1,*(),傅廷栋2   

  1. 1 江苏省农业科学院经济作物研究所/农业部长江下游棉花与油菜重点实验室/江苏省现代作物生产协同创新中心, 江苏南京 210014
    2 华中农业大学植物科学技术学院/作物遗传改良国家重点实验室, 湖北武汉 430070
  • 收稿日期:2019-02-12 接受日期:2019-05-12 出版日期:2019-09-12 网络出版日期:2019-05-17
  • 通讯作者: 易斌,张洁夫
  • 作者简介:E-mail: suncm8331537@gmail.com
  • 基金资助:
    本研究由国家重点研发计划项目(2018YFD0100601);国家现代农业产业技术体系建设专项资助(CARS-12)

Genome-wide association study of silique length in rapeseed (Brassica napus L.)

SUN Cheng-Ming1,2,CHEN Song1,PENG Qi1,ZHANG Wei1,YI Bin2,*(),ZHANG Jie-Fu1,*(),FU Ting-Dong2   

  1. 1 Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences/Key Laboratory of Cotton and Rapeseed (Nanjing), Ministry of Agriculture/Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing 210014, Jiangsu, China
    2 National Key Laboratory of Crop Genetic Improvement/College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China;
  • Received:2019-02-12 Accepted:2019-05-12 Published:2019-09-12 Published online:2019-05-17
  • Contact: Bin YI,Jie-Fu ZHANG
  • Supported by:
    The study was supported by the National Key Research and Development Program of China(2018YFD0100601);the China Agriculture Research System(CARS-12)

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摘要：

角果长度是油菜重要的农艺性状, 适度增加角果长度有利于扩大角果库容量, 增加光合面积, 提高油菜的籽粒产量。本研究利用Illumina 60K SNP芯片对496份具有代表性的油菜资源进行基因型分析, 考察群体在4个环境中的角果长度表型, 利用MLM和GLM模型进行全基因组关联分析。结果表明, MLM模型检测到7个位点, 联合解释25.01%的表型变异; GLM模型检测到25个位点, 联合解释41.77%的表型变异。合并共同位点后得到27个位点, 其中7个与前人报道的QTL重叠, 其余20个是新鉴定的位点。效应最大的位点Bn-A09-p29991443位于A09染色体, 在MLM和GLM模型中分别解释13.89%和12.86%的表型变异, 携带其优异等位基因的材料平均角果长度增加0.89 cm。同时, 在该位点附近找到已克隆的油菜角果长度基因ARF18和BnaA9.CYP78A9。此外, 在5个位点附近发现拟南芥已知角果长度基因GID1b、FUL、EOD3、DOF4.4和GA20ox1的同源拷贝。本研究结果有助于解析角果长度的遗传基础, 为研究角果长度的调控机理, 指导角果长度的遗传改良打下基础。

关键词: 甘蓝型油菜, 产量, 角果长度, 关联分析, SNP标记

Abstract:

Silique length is a key agronomic trait of rapeseed. Moderately increasing silique length is conducive to high seed yield by enlarging photosynthetic area and seed volume. A collection of 496 representative rapeseed accessions was genotyped by the Illumina 60K SNP array, and phenotyped for silique length in four environments. The genome-wide association study (GWAS) of silique length was performed via the MLM (Mixed linear model) and GLM (General linear model). Seven loci and 25 loci were detected with MLM and GLM, which explained 25.01% and 41.77% of the phenotypic variance, respectively. Combining the common loci between two models, we finally got 27 unique loci, of which seven were overlapped with reported QTLs, and 20 were new one. Bn-A09-p29991443, the most effective locus, was located on chromosome A09, accounting for 13.89% and 12.86% of the phenotypic variance in MLM and GLM, respectively. Silique length of accessions with the favorable allele of Bn-A09-p29991443 was averagely 0.89 cm longer than that with the unfavorable allele. The cloned silique length genes ARF18 and BnaA9.CYP78A9 in rapeseed was found to be colocalized with Bn-A09-p29991443. Besides, five candidates including GID1b, FUL, EOD3, DOF4.4 and GA20ox1, orthologous to documented Arabidopsis silique length genes, were found near our GWAS loci. The results provide an insight into the genetic basis of silique length and lay a foundation for further mechanism exploration and breeding for this trait in B. napus.

Key words: Brassica napus L, yield, silique length, GWAS, SNP

表1

关联群体角果长度性状的统计分析"

环境
Environment		 最小值
Min.		 最大值
Max.		 平均值±标准差
Mean ± SD		 变异系数
CV
2013/2014 Nanjing 3.42 11.37 5.40±1.01 0.19
2013/2014 Nanjing 3.28 15.80 6.39±1.25 0.20
2014/2015 Taizhou 3.31 10.18 5.79±0.88 0.15
2015/2016 Taizhou 4.01 9.94 5.90±0.77 0.13

图1

关联群体在4个环境的角果长度分布 A和B分别指群体在南京和泰州2年的角果长度频数分布图。"

表2

4个环境的角果长度相关系数"

2012/2013 Nanjing 2013/2014
Nanjing		 2014/2015 Taizhou
2013/2014 Nanjing 0.57***
2014/2015 Taizhou 0.64*** 0.70***
2015/2016 Taizhou 0.56*** 0.57*** 0.75***

表3

MLM角果长度显著关联位点(BLUP) "

标记
Marker		 染色体
Chr.		 位置
Position		 -lg (P) 表型变异
R2 (%)		 环境
Environment		 已报道QTL
Reported QTL
Bn-A07-p8572785 A07 10,018,929 5.80 5.10 13NJ/15TZ
Bn-A09-p28925363 A09 26,858,796 5.15 4.92 13NJ/15TZ [8, 22]
Bn-A09-p29991443 A09 27,815,620 13.59 13.89 13NJ/14NJ/15TZ [6, 8, 22, 23]
Bn-scaff_15712_2-p492440 C02 38,697,584 4.67 3.54
Bn-scaff_17869_1-p813291 C04 9,884,407 5.41 4.73 14NJ /15TZ
Bn-scaff_20817_1-p60579 C04 48,635,772 4.56 4.27 15TZ
Bn-scaff_15576_1-p68473 C09 41,121,951 4.29 3.21 13NJ/15TZ

图2

油菜角果长度全基因组关联分析(BLUP) A: 角果长度MLM曼哈顿图; B: 角果长度MLM QQ图; C: 角果长度GLM曼哈顿图; D: 角果长度GLM QQ图。水平线代表Bonferroni阈值。"

表4

GLM角果长度显著关联位点(BLUP) "

标记
Marker		 染色体
Chr.		 位置
Position		 -lg (P) 表型变异
R2 (%)		 环境
Environment		 已报道QTL
Reported QTL
Bn-A02-p11454573 A02 8,166,563 4.61 3.72 13NJ/14NJ/15TZ
Bn-A03-p4408895 A03 3,938,915 4.39 2.91
Bn-scaff_16092_1-p866917 A03 18,418,252 4.74 4.66 13NJ/15TZ
Bn-scaff_27914_1-p34836 A06 15,544,511 6.21 5.30 15TZ/16TZ
Bn-A06-p23042849 A06 22,092,944 4.72 3.85 15TZ/16TZ
Bn-A07-p1228602 A07 860,252 4.51 3.76 16TZ
Bn-A10-p12099059 A07 2,762,935 5.02 3.38 15TZ/16TZ
Bn-A07-p7606228 A07 9,162,030 6.03 4.90 13NJ/15TZ/16TZ [23]
Bn-A07-p8572785 A07 10,018,929 9.38 7.76 13NJ/15TZ/16TZ
Bn-A07-p10340211 A07 11,509,208 4.45 3.70 15TZ/16TZ
Bn-A07-p13957160 A07 15,884,413 5.18 4.20 15TZ/16TZ [23]
Bn-A07-p18319586 A07 20,221,220 5.14 4.33 14NJ/15TZ [6, 23]
Bn-A09-p3051349 A09 2,971,335 4.31 3.32 15TZ
Bn-A09-p28925363 A09 26,858,796 6.08 4.89 13NJ/15TZ/16TZ [8, 22]
Bn-A09-p29991443 A09 27,815,620 16.27 12.86 13NJ/14NJ/15TZ/16TZ [6, 8, 22, 23]
Bn-A10-p3966740 A10 885,133 6.47 4.46 13NJ/14NJ/15TZ/16TZ [6]
Bn-A10-p15793623 A10 15,756,213 4.60 3.65
Bn-scaff_17177_1-p381225 C02 44,843,894 5.12 4.13 15TZ
Bn-A05-p4304172 C04 6,449,454 6.96 5.75 14NJ/15TZ/16TZ
Bn-scaff_27914_1-p9919 C04 28,255,420 7.06 6.09 13NJ/14NJ/15TZ/16TZ
Bn-scaff_20817_1-p60579 C04 48,635,772 7.98 6.89 13NJ/14NJ/15TZ/16TZ
Bn-scaff_16069_1-p1668600 C07 38,086,007 6.38 5.29 15TZ/16TZ
Bn-scaff_16069_1-p3731985 C07 40,142,298 5.92 4.63 13NJ/14NJ/15TZ/16TZ
Bn-scaff_16361_1-p241830 C08 27,753,144 4.34 3.48 13NJ [9]
Bn-scaff_15576_1-p68473 C09 41,121,951 5.47 3.72 14NJ/15TZ/16TZ

表5

角果长度关联位点候选基因信息"

标记
Marker		 油菜基因
Rapeseed gene		 染色体
Chr.		 位置
Position		 拟南芥同源基因
Ar. homolog		 参考基因组
Ref. genome
Bn-A07-p13957160 BnaA07g19530 A07 15,590,253 GID1b Darmor-bzh
Bn-A09-p3051349 BnaA09g05500 A09 2,718,832 FUL Darmor-bzh
Bn-scaff_20817_1-p60579 BnaC04g50960 C04 48,343,005 EOD3 Darmor-bzh
Bn-scaff_16069_1-p1668600 BnaC07g36530 C07 38,575,790 DOF4.4 Darmor-bzh
Bn-scaff_16069_1-p3731985 BnaC07g39650 C07 40,392,394 GA20ox1 Darmor-bzh
Bn-A09-p29991443 BnA09g0377700 A09 36,712,502 ARF18 ZS11
Bn-A09-p29991443 BnA09g0377760 A09 36,740,578 CYP78A9 ZS11
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