用全基因组关联分析筛选甘蓝型油菜叶片叶绿素含量候选基因

doi:10.3724/SP.J.1006.2020.04007

Abstract

Abstract:

Increasing rapeseed production is important to ensure the national food and oil security. According to the theory of crop source and sink, sufficient photosynthate (sources) is the premise of high yield, and chlorophyll is the important substance for photosynthesis. Therefore, breeding high chlorophyll content Brassica napus is an important way to ensure high yield. In our previous study, 588 excellent germplasm resources collected worldwide were re-sequenced with 5x and 385,692 high-quality SNP markers were obtained. SPAD-502 chlorophyll meter was used to measure the total chlorophyll content of mature leaves in 2018-2019. Genome wide association study (GWAS) was conducted to screen SNP sites significantly related to chlorophyll content. Five SNP loci were identified in 2018, with a contribution rate of 5.51%-7.89%, of which S6_3493805 had the largest contribution. 46 SNP loci were detected in 2019, with a contribution rate of 7.29%-10.34%, of which S13_11413088 had the largest contribution. In total, 2022 rapeseed genes were screened out by comparing the reference genome with genes in the regions of the 500 kb before and after the SNP. Based on the function of Arabidopsis homologous genes previously reported, screened 23 candidate genes, among which five were homologous genes in chlorophyll synthesis pathway. These results lay a foundation for the genetic improvement of chlorophyll content in leaves of B. napus in future.

Key words: Brassica napus, chlorophyll content, GWAS, candidate genes

JIAN Hong-Ju, HUO Qiang, GAO Yu-Min, LI Yang-Yang, XIE Ling, WEI Li-Juan, LIU Lie-Zhao, LU Kun, LI Jia-Na. Selection of candidate genes for chlorophyll content in leaves of Brassica napus using genome-wide association analysis[J].Acta Agronomica Sinica, 2020, 46(10): 1557-1565.

Figures/Tables 8

Table 1

Table 2

Fig. 1

Fig. 2

Fig. 3

Table 3

Summary of significant SNPs for chlorophyll content by using the best model"

环境Environment		位点 SNP		染色体 Chr.		位置 Position		阈值 lg (P-value)	贡献率 R² (%)
2018		S1_12845378		A03		12,845,378		5.73	5.51
		S6_3493805		A06		3,493,805		7.49	7.89
		S6_3812220		A06		3,812,220		6.05	6.10
		S10_4969863		A10		4,969,863		6.25	6.23
		S14_37741561		C04		37,741,561		5.69	5.67
2019		S1_12688640		A01		12,688,640		6.39	8.42
		S1_12540615		A01		12,540,615		6.10	8.24
		S1_10570293		A01		10,570,293		5.93	8.51
		S1_12628926		A01		12,628,926		5.86	8.28
		S1_12540545		A01		12,540,545		5.84	7.67
		S1_12540622		A01		12,540,622		5.83	7.66
环境Environment	位点 SNP			染色体 Chr.		位置 Position		域值 lg (P-value)	贡献率 R² (%)
2019	S1_12628563		A01		12,628,563		5.79		9.76
	S1_12568566		A01		12,568,566		5.78		7.55
	S2_17839296		A02		17,839,296		6.91		9.73
	S3_13514793		A03		13,514,793		5.73		7.72
	S4_547942		A04		547,942		5.93		8.08
	S8_16108365		A08		16,108,365		6.46		8.44
	S8_16192480		A08		16,192,480		5.88		7.80
	S8_16181282		A08		16,181,282		5.78		7.85
	S8_16103637		A08		16,103,637		5.61		7.97
	S8_16181355		A08		16,181,355		5.60		7.29
	S9_10532790		A09		10,532,790		6.18		8.70
	S10_14050715		A10		14,050,715		5.61		7.72
	S12_20495602		C02		20,495,602		5.95		9.35
	S12_22225349		C02		22,225,349		5.74		8.76
	S13_11413088		C03		11,413,088		7.01		10.34
	S13_11423629		C03		11,423,629		6.95		9.31
	S13_11415175		C03		11,415,175		6.61		8.92
	S13_11433444		C03		11,433,444		6.39		8.88
	S13_11433450		C03		11,433,450		6.38		8.87
	S13_9816561		C03		9,816,561		6.06		8.70
	S13_48351338		C03		48,351,338		6.00		8.06
	S13_11249216		C03		11,249,216		5.97		8.22
	S14_7018412		C04		7,018,412		6.81		9.39
	S14_1487936		C04		1,487,936		5.73		7.96
	S14_5798300		C04		5,798,300		5.68		8.45
	S14_36521995		C04		36,521,995		5.60		7.95
	S15_6002527		C05		6,002,527		6.06		8.65
	S16_24042352		C06		24,042,352		6.55		9.94
	S16_14397036		C06		14,397,036		6.31		8.84
	S16_25797577		C06		25,797,577		6.25		8.34
	S16_25797598		C06		25,797,598		6.14		8.15
	S16_25233735		C06		25,233,735		6.14		8.09
	S16_25797558		C06		25,797,558		6.00		8.46
	S16_25234451		C06		25,234,451		5.97		8.45
	S16_25234262		C06		25,234,262		5.92		8.11
	S16_25797570		C06		25,797,570		5.89		8.06
	S16_25234230		C06		25,234,230		5.88		8.31
	S18_31711591		C08		31,711,591		6.32		8.85
	S18_28228959		C08		28,228,959		5.77		8.36
	S19_32818852		C09		32,818,852		5.62		8.15

Table 3

Table 4

Candidate genes for chlorophyll content"

基因名字 Gene name	物理位置 Physical position	拟南芥同源基因 Homologs in A. thaliana	功能注释 Functional annotation
BnaA01g20460D	A01:12331065-1233745	AT3G48740	Nodulin MtN3 family protein
BnaA02g24670D	A02:17989410-17990090	AT5G46780	VQ motif-containing protein
BnaA04g00500D	A04:365464-366530	AT3G61890	Homeobox 12 (HB-12)
BnaA04g00600D	A04:460722-461017	AT3G61640	Arabinogalactan protein 20 (AGP20)
BnaA05g01720D	A05:984996-986020	AT2G40490	HEME2
BnaA06g06000D	A06:3306811-3307795	AT1G10200	WLIM1
BnaA10g02050D	A10:1025298-1027102	AT1G03630	Protochlorophyllide oxidoreductase C (POR C)
BnaC02g01240D	C02:511615-513517	AT5G08280	Hydroxymethylbilane synthase (HEMC)
BnaC02g25030D	C02:22402218-22403498	AT1G07440	NAD(P)-binding Rossmann-fold superfamily protein
BnaC03g18820D	C03:9634933-9635479	AT2G33830	Dormancy/auxin associated family protein
BnaC03g20950D	C03:11192271-11192876	AT2G37970	SOUL-1
BnaC04g01850D	C04:1467437-1468078	AT2G41410	Calcium-binding EF-hand family protein
BnaC05g10770D	C05:6194068-6195531	AT1G14480	Ankyrin repeat family protein
基因名字 Gene name	物理位置 Physical position	拟南芥同源基因 Homologs in A. thaliana	功能注释 Functional annotation
BnaC05g38600D	C05:37280225-37281849	AT3G14930	HEME1
BnaC06g24160D	C06:25958767-25959390	AT1G72610	Germin-like protein 1 (GER1)
BnaC07g39280D	C07:40238482-40239858	AT4G25080	Magnesium-protoporphyrin IX methyltransferase (CH LM)
BnaC08g27000D	C08:28191454-28192970	AT3G56090	Ferritin 3 (FER3)
BnaC08g27310D	C08:28357417-28358091	AT3G56360	Unknown protein
BnaC09g05970D	C09:3640560-3642915	AT5G63570	Glutamate-1-semialdehyde-2,1-aminomutase (GSA1)
BnaC03g18980D	chrC03:9831772-9832572	AT2G34430	Light-harvesting chlorophyll-protein complex II subunit B1 (LHB1B1)
BnaC02g25060D	chrC02:22446772-22448037	AT1G78600	Light-regulated zinc finger protein 1 (LZF1)
BnaA04g00660D	chrA04:488057-489279	AT3G61470	Photosystem I light harvesting complex gene 2 (LHCA2)
BnaA08g22200D	chrA08:16221799-16222764	AT1G19150	Photosystem I light harvesting complex gene 6 (LHCA6)

Table 4

Fig. 4

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基因Gene	引物序列Primer sequence (5°-3°)
BnaA04g00600D	F: AAATGTCGTTGAGGAATTACGC; R: TGAATGATATACGTCAGCACCA
BnaC09g54390D	F: AAGGAGCTAACACAATGACTGA; R: GGTATCATCACAGGTAACCCAT
BnaC03g18820D	F: AATCATGTTTCCATTAGCCACG; R: CATTACCACCGTTGAAAACCAA
BnaC06g24160D	F: AATGTTGCGCATTATCTTCCTC; R: TGTTTGTAGTGTTTCCAGGAGT
BnaC07g39280D	F: AGAAAACGATGCTTATGCTGAC; R: CATAGCTGCAGAGATATCGCTA
BnaA04g00500D	F: AGCTCATATACATTGTGGAGCA; R: TGCTGCTAGATTGGTCTAAGAG
BnaA02g24670D	F: CTAATCGAATCAAGCCCTGTTG; R: GGTGAAAACGCAAAGAAATTGG
BnaC02g01240D	F: CTCAAGGAGCTATTGGAATTGC; R: TATCCAGCAATAGGTGTACGAC
BnaC03g20950D	F: CTTTATGGTGTTGGCCAAGTAC; R: AACTTTACCACGCCGTATTTTC
BnaC05g38600D	F: GACTCTCTGAAGATACTGAGGC; R: ACTCTTGATCACCGTATACGTC
BnaA10g02050D	F: GAGCTGGAACAATAACTCCTCT; R: CACAGTTTCTTTGCCTTCTCTG
BnaC05g10770D	F: GAGTGTTCCTGATTGTATGCAC; R: AGATGTGCCAATCCAAAAGAAC
BnaC04g01850D	F: GATAGGAACGGTGATGGTTTTG; R: TTCCGTCACGAAATTAAAACCC
BnaC02g25030D	F: GTAAATGTGCCTGATGAGGTTG; R: TGAACAATCTCTTCGTCAAGGA
BnaA06g06000D	F: GTCGCTGCTTAAACAGTTACAA; R: GAAACCCAACAAAGAGTGAACA
BnaA05g01720D	F: GTTCACAACGTCAATGATCACA; R: GTGGCCCAAGAATCAAAGATTT
BnaC08g27000D	F: GTTTCTGAACGAACAGGTTGAA; R: ATTTAAGCAGCAGCAGAAGTTC
BnaC09g05970D	F: TTACTAGCTTGGCTCACACTAC; R: CGTTCTCATCAACAACACTCAG
BnaC09g05970D	F: TTACTAGCTTGGCTCACACTAC; R: CGTTCTCATCAACAACACTCAG
BnaA01g20460D	F: TTATCAAGCGTGCGAAGTAAAG; R: CGCGCTGATCTTAACCTAGTTA
BnaC08g27310D	F: TTTGCTACCTGTTGAAAACGAC; R: TTATTCAACTGTGACAAAGCCG

性状 Trait	环境 Environment	均值±标准差 Mean ± SD	范围 Range	变异系数 CV (%)
叶绿素含量	2018	47.79±5.39	33.44-65.82	11.27
Chlorophyll content	2019	46.37±5.90	32.92-72.04	12.73

Selection of candidate genes for chlorophyll content in leaves of Brassica napus using genome-wide association analysis

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[4]	YUAN Da-Shuang, DENG Wan-Yu, WANG Zhen, PENG Qian, ZHANG Xiao-Li, YAO Meng-Nan, MIAO Wen-Jie, ZHU Dong-Ming, LI Jia-Na, LIANG Ying. Cloning and functional analysis of BnMAPK2 gene in Brassica napus [J]. Acta Agronomica Sinica, 2022, 48(4): 840-850.
[5]	HUANG Cheng, LIANG Xiao-Mei, DAI Cheng, WEN Jing, YI Bin, TU Jin-Xing, SHEN Jin-Xiong, FU Ting-Dong, MA Chao-Zhi. Genome wide analysis of BnAPs gene family in Brassica napus [J]. Acta Agronomica Sinica, 2022, 48(3): 597-607.
[6]	WANG Rui, CHEN Xue, GUO Qing-Qing, ZHOU Rong, CHEN Lei, LI Jia-Na. Development of linkage InDel markers of the white petal gene based on whole-genome re-sequencing data in Brassica napus L. [J]. Acta Agronomica Sinica, 2022, 48(3): 759-769.
[7]	ZHAO Hai-Han, LIAN Wang-Min, ZHAN Xiao-Deng, XU Hai-Ming, ZHANG Ying-Xin, CHENG Shi-Hua, LOU Xiang-Yang, CAO Li-Yong, HONG Yong-Bo. Genetic dissection of the bacterial blight disease resistance in super hybrid rice RILs using genome-wide association study [J]. Acta Agronomica Sinica, 2022, 48(1): 121-137.
[8]	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.
[9]	ZENG Wei-Ying, LAI Zhen-Guang, SUN Zu-Dong, YANG Shou-Zhen, CHEN Huai-Zhu, TANG Xiang-Min. Identification of the candidate genes of soybean resistance to bean pyralid (Lamprosema indicata Fabricius) by BSA-Seq and RNA-Seq [J]. Acta Agronomica Sinica, 2021, 47(8): 1460-1471.
[10]	MA Juan, CAO Yan-Yong, LI Hui-Yong. Genome-wide association study of ear cob diameter in maize [J]. Acta Agronomica Sinica, 2021, 47(7): 1228-1238.
[11]	GENG La, HUANG Ye-Chang, LI Meng-Di, XIE Shang-Geng, YE Ling-Zhen, ZHANG Guo-Ping. Genome-wide association study of β-glucan content in barley grains [J]. Acta Agronomica Sinica, 2021, 47(7): 1205-1214.
[12]	CHEN Can, NONG Bao-Xuan, XIA Xiu-Zhong, ZHANG Zong-Qiong, ZENG Yu, FENG Rui, GUO Hui, DENG Guo-Fu, LI Dan-Ting, YANG Xing-Hai. Genome-wide association study of blast resistance loci in the core germplasm of rice landraces from Guangxi [J]. Acta Agronomica Sinica, 2021, 47(6): 1114-1123.
[13]	LI Jie-Hua, DUAN Qun, SHI Ming-Tao, WU Lu-Mei, LIU Han, LIN Yong-Jun, WU Gao-Bing, FAN Chu-Chuan, ZHOU Yong-Ming. Development and identification of transgenic rapeseed with a novel gene for glyphosate resistance [J]. Acta Agronomica Sinica, 2021, 47(5): 789-798.
[14]	TANG Xin, LI Yuan-Yuan, LU Jun-Xing, ZHANG Tao. Morphological characteristics and cytological study of anther abortion of temperature-sensitive nuclear male sterile line 160S in Brassica napus [J]. Acta Agronomica Sinica, 2021, 47(5): 983-990.
[15]	ZHOU Xin-Tong, GUO Qing-Qing, CHEN Xue, LI Jia-Na, WANG Rui. Construction of a high-density genetic map using genotyping by sequencing (GBS) for quantitative trait loci (QTL) analysis of pink petal trait in Brassica napus L. [J]. Acta Agronomica Sinica, 2021, 47(4): 587-598.