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

作物学报 ›› 2020, Vol. 46 ›› Issue (10): 1557-1565.doi: 10.3724/SP.J.1006.2020.04007

• 作物遗传育种·种质资源·分子遗传学 • 上一篇下一篇

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

荐红举¹^,²(), 霍强¹^,²(), 高玉敏¹^,², 李阳阳¹^,², 谢玲¹^,², 魏丽娟¹^,², 刘列钊¹^,², 卢坤¹^,², 李加纳¹^,²^,^*()

¹ 西南大学农学与生物科技学院, 重庆 400715
² 西南大学现代农业科学研究院, 重庆 400715

收稿日期:2020-01-12 接受日期:2020-04-15 出版日期:2020-10-12 网络出版日期:2020-04-27
通讯作者: 李加纳
作者简介:荐红举, E-mail: hjjian518@swu.edu.cn;|霍强, E-mail: 354011524@qq.com
基金资助:
国家重点研发计划项目(2018YFD0100504-05);重庆市民生工程主题专项(cstc2016shms-ztzx80020)

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

JIAN Hong-Ju¹^,²(), HUO Qiang¹^,²(), GAO Yu-Min¹^,², LI Yang-Yang¹^,², XIE Ling¹^,², WEI Li-Juan¹^,², LIU Lie-Zhao¹^,², LU Kun¹^,², LI Jia-Na¹^,²^,^*()

¹ College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
² Academy of Agricultural Sciences, Southwest University, Chongqing 400715, China

Received:2020-01-12 Accepted:2020-04-15 Published:2020-10-12 Published online:2020-04-27
Contact: Jia-Na LI
Supported by:
National Key Research and Development Program of China(2018YFD0100504-05);Special Project of Chongqing People’s Livelihood(cstc2016shms-ztzx80020)

摘要/Abstract

摘要：

提高油菜产量是保障国家粮油安全的重要举措。作物“源”“流”“库”理论表明, 充足的光合产物(源)是高产的前提, 而叶绿素是直接参与光合作用的物质, 因此, 选育高叶绿素含量的甘蓝型油菜是提高产量的重要途径。本课题组前期对全球收集的588份优异油菜种质资源进行5X重测序, 获得385,692个高质量SNP标记。利用SPAD-502叶绿素仪于2018—2019连续2年测定苗期完全伸展的叶片叶绿素总量, 结合获得的SNP标记进行全基因组关联分析(genome-wide association study, GWAS), 筛选与叶绿素含量显著关联的SNP位点。结果表明, 2018年鉴定到5个显著关联的SNP位点, 贡献率为5.51%~7.89%, 其中S6_3493805位点贡献率最大; 2019年检测到46个SNP位点, 贡献率为7.29%~10.34%, 其中S13_11413088位点贡献率最大。将显著关联SNP位点上下游各500 kb区间内的基因与参考基因组比对, 初步筛选出2022个油菜基因。将其基因序列在拟南芥基因组内进行BLAST比对, 结合前人已报道的拟南芥同源基因功能, 筛选到23个候选基因, 其中5个属于叶绿素合成途径同源基因。本研究结果为后续油菜叶片叶绿素含量的遗传改良奠定了基础。

关键词: 甘蓝型油菜, 叶绿素含量, 全基因组关联分析, 候选基因

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

荐红举, 霍强, 高玉敏, 李阳阳, 谢玲, 魏丽娟, 刘列钊, 卢坤, 李加纳. 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[J]. 作物学报, 2020, 46(10): 1557-1565.

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.

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链接本文: https://zwxb.chinacrops.org/CN/10.3724/SP.J.1006.2020.04007

https://zwxb.chinacrops.org/CN/Y2020/V46/I10/1557

图/表 8

表1

表2

图1

图2

图3

表3

最佳模型下叶绿素含量显著位点表"

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

表3

表4

叶绿素含量候选基因"

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)

表4

图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

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

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

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