整合GWAS和WGCNA筛选鉴定甘蓝型油菜生物产量候选基因

doi:10.3724/SP.J.1006.2021.04175

Abstract

Abstract:

Biomass yield is especially important for Brassica napus, as it is the basis for high yields of crops. In this study, the phenotypic data of the natural populations composed of 588 materials were used for genome-wide association analysis (GWAS). We performed the transcriptome sequencing (RNA-seq) of biomass yield using ‘CQ45’ (high biological yield material) and ‘CQ46’ (low biological yield material). A weighted gene co-expression network analysis (WGCNA) network was constructed by integrating transcriptome data of six tissues of the extreme materials, such as stalks, leaves, 30 day after flowering (DAF) seeds of main inflorescence and lateral branch, 30 DAF pod keratin of main branch and lateral branch. We finally screened the candidate genes related to biomass yield. The main results are as follows: Biomass yields in B. napus had positive effects on most yield-related traits; K + PCA model was the best model for biomass analysis of the natural population, and nine significant loci were detected in the best model (P < 1/385691 or P < 0.05/385691); according to 36 groups of transcriptome data, MAD value of each gene was calculated. A total of 5052 genes with MAD value of the top 5% were selected to construct WGCNA. Fifteen gene modules were obtained, among which, five genes co-expression modules were significantly correlated with leaves, stems, and seeds of 30 DAF. The hub genes of the key modules in WGCNA, the significant SNP loci obtained from GWAS, and the extreme phenotypic differential genes were integrated to identify the candidate genes. Their Arabidopsis homologous genes were HCEF1, HOG1, SBPASE, and ACT2, which played the important roles in the Calvin cycle, carbon assimilation, and material accumulation of photosynthesis.

Key words: GWAS, WGCNA, RNA seq, Brassica napus

WANG Yan-Hua, LIU Jing-Sen, LI Jia-Na. Integrating GWAS and WGCNA to screen and identify candidate genes for biological yield in Brassica napus L.[J].Acta Agronomica Sinica, 2021, 47(8): 1491-1510.

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性状 Trait	环境Environment	粒果比SWSI	千粒重TSW	每角粒数SNPS	茎秆干重ST	上部生物产量CBY	籽粒产量SY	收获指数HI	生物产量BY
SWSI SWSI	2017CQ	1
SWSI SWSI	2019CQ	1
TSW	2017CQ	0.506^**	1
TSW	2019CQ	-0.008	1
SNPS	2017CQ	0.513^**	0.156^**	1
SNPS	2019CQ	0.284	0.056^**	1
ST	2017CQ	-0.023	0.108^*	0.104^*	1
ST	2019CQ	-0.055^**	0.213^**	0.198^**	1
CBY	2017CQ	0.0247	0.106^*	0.072	0.682^**	1
CBY	2019CQ	-0.037	0.249^**	0.171^**	0.567^**	1
SY	2017CQ	0.204^**	0.155^**	0.210^**	0.524^**	0.773^**	1
SY	2019CQ	0.179	0.327^**	0.409^**	0.424^**	0.726^**	1
HI	2017CQ	0.308^**	0.127^**	0.232^**	-0.099^*	0.142^**	0.687^**	1
HI	2019CQ	0.033^**	0.292^**	0.262^**	0.556^**	0.972^**	0.866^**	1
BY	2017CQ	0.007	0.117^*	0.089	0.861^**	0.957^**	0.738^**	0.056	1
BY	2019CQ	-0.042	0.313^**	0.265^**	0.752^**	0.905^**	0.718^**	0.901	1

染色体 Chr.	物理位置 Position	位点 SNP	P值 P-value	贡献率 R² (%)	置信区间 Confidence interval (250 kb up/downstream)
A3	7901059	S3_7901059	9.91E-07	7.25	7651059-8151059
A7	15487057	S7_15487057	1.06E-06	7.70	15237057-15737057
A7	16899362	S7_16899362	1.46E-06	7.43	16649362-17149362
A7	19665408	S7_19665408	1.73E-06	5.99	19415408-19915408
C1	3258674	S11_3258674	1.46E-06	7.65	3008674-3508674
C3	20691876	S13_20691876	1.87E-06	5.64	20441876-20941876
C4	34485253	S14_34485253	1.39E-06	7.51	34174883-34735253
C6	26169577	S16_26169577	2.87E-07	7.98	25919577-26419577
C9	23643765	S19_23643765	1.14E-06	7.61	23393765-23893765

基因 Genes	染色体 Chromosome	物理位置 Physical position	拟南芥同源基因 Homologs in A. thaliana	功能注释 Functional annotation
BnaA04g04350D	A04	3211999-3214328	AT3G54050	高循环电子流 High cyclic electron flow 1 (HCEF1)
BnaA04g06420D	A04	5053017-5055052	AT4G13940	同源依赖性的基因沉默 HOMOLOGY-DEPENDENT GENE SILENCING 1 (HOG1)
BnaA07g19320D	A07	15496197-15496586	AT3G62410	CP12含域蛋白2 CP12 domain-containing protein 2 (CP12-2)
BnaA09g35380D	A09	25808955-25811193	AT3G55800	景天庚酮糖二磷酸酶 Sedoheptulose-bisphosphatase (SBPASE)
BnaC03g33610D	C03	20464104-20466211	AT3G04120	甘油醛-3-磷酸脱氢酶C亚基1 Glyceraldehyde-3-phosphate dehydrogenase C subunit 1 (GAPC1)
BnaC03g73810D	C03	1811021-1813439	AT3G18780	肌动蛋白2 Actin 2 (ACT2)
BnaC08g48810D	C08	3782204-3784813	AT3G54050	高循环电子流 High cyclic electron flow 1 (HCEF1)

Integrating GWAS and WGCNA to screen and identify candidate genes for biological yield in Brassica napus L.

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