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Acta Agronomica Sinica ›› 2019, Vol. 45 ›› Issue (9): 1303-1310.doi: 10.3724/SP.J.1006.2019.94021

• CROP GENETICS & BREEDING · GERMPLASM RESOURCES · MOLECULAR GENETICS • Previous Articles     Next Articles

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 Online:2019-09-12 Published:2019-05-17
  • Contact: Bin YI,Jie-Fu ZHANG E-mail:yibin@mail.hzau.edu.cn;jiefu_z@163.com
  • 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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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

Table 1

Statistical analysis of silique length of the association panel"

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

Fig. 1

Distribution of silique length of the association panel in four environments A and B, histogram of silique length in Nanjing and Taizhou in two years, respectively."

Table 2

Correlation coefficients of silique length among four environments"

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***

Table 3

Significant GWAS loci of silique length in MLM (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

Fig. 2

Genome-wide association study of rapeseed silique length (BLUP) A: Manhattan plot of MLM for silique length; B: Quantile-quantile plot of MLM for silique length; C: Manhattan plot of GLM for silique length; D: Quantile-quantile plot of GLM for silique length. The dashed horizontal line depicts the Bonferroni significance threshold."

Table 4

Significant GWAS loci of silique length in GLM (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

Table 5

Information of candidate genes of silique length GWAS loci"

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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