整合GWAS和WGCNA分析挖掘甘蓝型油菜黄籽微效作用位点

doi:10.3724/SP.J.1006.2018.01105

Abstract

Abstract:

Brassica napus is one of the most important oil crops in the world, and developing yellow-seeded B. napus with improved qualities is a major breeding goal. The yellow-seeded minor genes were mined by genome-wide association study (GWAS) and weighted gene co-expression network analysis (WGCNA) with 520 representative varieties (or lines) and the transcriptional data at eight time points during the seed development. The 199 SNPs and 1826 nominally significant GWAS candidate genes were detected. Weighted gene co-expression network analysis was performed using the WGCNA R package to construct the resulting network composing eight distinct gene modules. Among them, the turquoise module and the blue module were related to the seed coat color based on gene function enrichment analysis. BnATCAD4, BnF3H, and BnANS, the key enzymes genes of phenylpropane metabolic pathway and flavonoid metabolic pathway were found in turquoise module. Through the characterization of module content and topology, we mined a number of micro effect genes based on known yellow-seed related genes mainly involved in the phenylpropanoid metabolic process, flavonoid metabolic process and proanthocyanidin biosynthetic process. This information of minor loci and candidate genes should be useful in the breeding for yellow-seeded B. napus.

Key words: Brassica napus, yellow-seeded, GWAS, WGCNA

Xiao-Hua XIAN,Jia WANG,Xin-Fu XU,Cun-Min QU,Kun LU,Jia-Na LI,Lie-Zhao LIU. Mining Yellow-seeded Micro Effect Loci in B. napus by Integrated GWAS and WGCNA Analysis[J].Acta Agronomica Sinica, 2018, 44(8): 1105-1113.

Figures/Tables 6

Fig. 1

Fig. 2

Table 1

GO enrichments of network modules (part)"

模块 Module	基因数目 Number of genes	GO	每个模块显著富集的term Top term for each module	P值 P-value	FDR
Black	68	GO:0004499	N,N-二甲基苯胺单加氧酶活性 N,N-dimethylaniline monooxygenase activity	2.38E-03	1.26E-01
Blue	303	GO:0045551	肉桂醇脱氢酶活性 Cinnamyl-alcohol dehydrogenase activity	1.53E-04	3.37E-02
		GO:0052747	芥子醇脱氢酶活性 Sinapyl alcohol dehydrogenase activity	1.53E-04	3.37E-02
		GO:0009698	苯丙烷代谢过程 Phenylpropanoid metabolic process	1.40E-06	2.01E-03
		GO:0009699	苯丙烷生物合成过程 Phenylpropanoid biosynthetic process	4.27E-06	3.06E-03
		GO:0019748	次生代谢过程 Secondary metabolic process	9.92E-05	3.56E-02
Brown	157	GO:0044699	单一的生物过程 Single-organism process	4.78E-05	5.30E-02
Green	82	GO:0008107	α-1,2岩藻糖基转移酶活性 Galactoside 2-alpha-L-fucosyltransferase activity	4.89E-04	4.74E-02
Pink	49	GO:0016886	形成磷酸酯键的连接酶活性 Ligase activity, forming phosphoric ester bonds	4.32E-05	7.04E-03
Red	79	GO:0043170	大分子代谢过程 Macromolecule metabolic process	3.86E-05	2.51E-02
Turquoise	473	GO:0009699	苯丙烷生物合成过程 Phenylpropanoid biosynthetic process	6.06E-07	1.47E-04
		GO:0010023	原花青素的生物合成过程 Proanthocyanidin biosynthetic process	1.11E-04	7.92E-03
		GO:0009809	木质素的生物合成过程 Lignin biosynthetic process	1.23E-04	8.13E-03
		GO:0009698	苯丙烷代谢过程 Phenylpropanoid metabolic process	2.90E-04	1.36E-02
		GO:0009808	木质素代谢过程 Lignin metabolic process	3.68E-04	1.65E-02
		GO:0009812	类黄酮代谢过程 Flavonoid metabolic process	5.93E-04	2.18E-02
		GO:0009813	类黄酮生物合成过程 Flavonoid biosynthetic process	6.35E-04	2.27E-02
Yellow	142	GO:0050619	还原酶活性 Phytochromobilin: ferredoxin oxidoreductase activity	5.33E-03	2.78E-01

Table 1

Fig. 3

Fig. 4

Fig. 5

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