胡萝卜抽薹相关性状全基因组关联分析

doi:10.13560/j.cnki.biotech.bull.1985.2023-1120

摘要/Abstract

摘要：

【目的】胡萝卜受低温及长日照的影响易发生先期抽薹现象，挖掘与胡萝卜抽薹性状相关联的SNP位点及候选基因，有利于胡萝卜耐抽薹新品种的选育。【方法】以240份胡萝卜种质资源为材料，分别在2021年及2022年调查胡萝卜抽薹（抽薹时间、抽薹率、薹高、抽薹速度）性状，基于质控得到的高质量SNP位点进行抽薹相关性状的GWAS分析。【结果】240份胡萝卜种质资源的抽薹性状具有丰富的遗传多样性，对2年的数据进行分析发现各性状表型均有较大的变异，抽薹率的变异系数最大为144.32%、187.89%，抽薹时间的变异系数同比最小为94.89%和74.63%，BLUE值降低了环境所带来的误差，其变异系数最小为22.53%。相关性分析结果表明，2021年抽薹率与2022年的抽薹性状呈显著正相关，与BLUE值为极显著相关，BLUE值除与2021年的抽薹时间无显著相关外，与其它性状均为极显著相关。GWAS分析共检测到与抽薹性状显著相关的344 个SNP 标记位点，其中有20个多效位点，根据注释信息筛选出29个与抽薹相关的候选基因，主要与光周期途径、春化途径和开花整合子有关。【结论】通过GWAS分析获得多个与抽薹性状相关联的SNP位点，并挖掘到相关候选基因。

关键词: 胡萝卜, 种质资源, 抽薹, 全基因组关联分析, SNP标记

Abstract:

【Objective】Carrot plants are prone to early bolting under the influence of low temperature and long sunshine. Exploring SNP loci and candidate genes associated with carrot bolting traits would be beneficial for the breeding of new carrot varieties that are resistant to bolting. 【Method】This study used 240 carrot germplasm resources as materials to investigate the characteristics of carrot bolt（bolt time, bolt rate, bolt height, and bolt speed）in 2021 and 2022, respectively. Through DNA sequencing and SNP variation detection, high-quality SNP loci obtained from quality control were used for genome-wide association study（GWAS）of bolting related traits. 【Result】The bolting traits of 240 carrot germplasm resources demonstrated rich genetic diversity. After analyzing the 2-year data, it was found that there was significant variation in the phenotypes of each trait, with the highest coefficient of variation for bolting rate being 144.32% and 187.89%, and the lowest coefficient of variation for bolting time being 94.89% and 74.63%, respectively. The BLUE value reduced the error caused by the environment, with the lowest coefficient of variation being 22.53%. The correlation analysis results showed that the bolting rate in 2021 was significantly positively correlated with the bolting traits in 2022, and was extremely significantly correlated with the BLUE value. The BLUE value was highly significantly correlated with other traits except for no significant correlation with the bolt time in 2021. Based on the group structure analysis and cluster analysis, the associated groups were divided into four subgroups. Through a 2-year GWAS of the correlation among bolting traits, a total of 344 SNP marker loci were detected that were significantly correlated with bolting traits. Among them, 20 multi-effect loci were significantly correlated with 2 or more bolting traits, and the same loci can be considered as the same SNP. Based on the annotation information, 29 candidate genes related to bolting were screened, of which 14 genes had inhibitory effects on bolting and flowering, and 13 genes that promoted bolting and flowering were mainly related to the photoperiod pathway, vernalization pathway, and flowering integron. The mechanism of action of the other two genes was not yet clear and thus further verification is needed.【Conclusion】Multiple SNP loci associated with bolting traits were obtained by GWAS analysis, and related candidate genes were identified.

Key words: carrot, germplasm resources, bolting, genome-wide association tudy, snp marker

孔小平, 陈利文, 刘思思, 严湘萍. 胡萝卜抽薹相关性状全基因组关联分析[J]. 生物技术通报, 2024, 40(5): 120-130.

KONG Xiao-ping, CHEN Li-wen, LIU Si-si, YAN Xiang-ping. Genome-wide Association Study of Bolting Related Traits in Carrot[J]. Biotechnology Bulletin, 2024, 40(5): 120-130.

图/表 10

参考文献 33

[1]	洪丽萍, 黄青云, 张庆美, 等. 胡萝卜育种研究[J]. 亚热带植物科学, 2011, 40(2): 79-82.
	Hong LP, Huang QY, Zhang QM, et al. A review of research on carrot breeding[J]. Subtrop Plant Sci, 2011, 40(2): 79-82.
[2]	却枫, 黄莹, 王枫, 等. 胡萝卜中DcDofD1转录因子的克隆及其对非生物逆境胁迫的响应分析[J]. 植物遗传资源学报, 2015, 16(5): 1073-1079.
	Que F, Huang Y, Wang F, et al. Cloning and expression analysis of a transcription factor, DcDofD1 related to abiotic stress reaction in carrot[J]. J Plant Genet Resour, 2015, 16(5): 1073-1079.
[3]	刘星, 黄建新, 等. 胡萝卜根色及其色素组分的遗传和育种研究进展[J]. 植物遗传资源学报, 2022, 23(5): 1241-1248. doi: 10.13430/j.cnki.jpgr.20220317001
	Liu X, Huang JX, et al. Current advances on inheritance and breeding of carrot root color and its pigment components[J]. J Plant Genet Resour, 2022, 23(5): 1241-1248.
[4]	马振国. 胡萝卜种质资源多样性及耐抽薹鉴定方法研究[D]. 北京: 中国农业科学院, 2015.
	Ma ZG. Genetic diversity of carrot germplasm and method of bolting tolerance identification[D]. Beijing: Chinese Academy of Agricultural Sciences, 2015.
[5]	毛笈华, 庄飞云, 欧承刚, 等. 胡萝卜FLC同源基因对低温及光周期响应[J]. 园艺学报, 2013, 40(12): 2453-2462.
	Mao JH, Zhuang FY, Ou CG, et al. Expression analysis of FLC homologues responding to low temperature and photoperiod in carrot[J]. Acta Hortic Sin, 2013, 40(12): 2453-2462.
[6]	鲍生有. 胡萝卜(Daucus carota L.)先期抽薹遗传模型及QTL研究[D]. 南京: 南京农业大学,20013.
	Bao SY. Genetic model and QTL study on early bolting of carrots(Daucus carota L.)[D]. Nanjing: Nanjing Agricultural University, 20013.
[7]	马娟, 王利锋, 曹言勇, 等. 玉米出籽率全基因组关联分析[J]. 植物遗传资源学报, 2021, 22(2): 448-454. doi: 10.13430/j.cnki.jpgr.20200822001
	Ma J, Wang LF, Cao YY, et al. Genome-wide association studies for kernel ratio in maize[J]. J Plant Genet Resour, 2021, 22(2): 448-454.
[8]	李洪超, 王晓楠, 李紫薇, 等. 工业大麻中全基因组关联分析研究进展[J]. 植物遗传资源学报, 2023, 24(5): 1257-1266.
	Li HC, Wang XN, Li ZW, et al. Advances in genome-wide association study in industrial hemp[J]. J Plant Genet Resour, 2023, 24(5): 1257-1266. doi: 10.13430/j.cnki.jpgr.20230322002
[9]	Li YX, Li CH, et al. Identification of genetic variants associated with maize flowering time using an extremely large multi-genetic background population[J]. Plant J, 2016, 86(5): 391-402.
[10]	Zhang JP, Song QJ, Cregan PB, et al. Genome-wide association study for flowering time, maturity dates and plant height in early maturing soybean(Glycine max)germplasm[J]. BMC Genomics, 2015, 16(1): 217.
[11]	龚振平. 大白菜抗病和晚抽薹性状的GWAS分析及其优异资源发掘[D]. 北京: 中国农业科学院, 2016.
	Gong ZP. Genome wide association study(GWAS)on disease resistance and late bolting and mining excellent germplasms in Brassica rapa L.[D]. Beijing: Chinese Academy of Agricultural Sciences, 2016.
[12]	汪精磊, 邱杨, 程锋, 等. 萝卜全基因组抽薹开花相关基因的鉴定及比较基因组学分析[C]. 中国园艺学会2015年学术年会论文摘要集:《园艺学报》编辑部, 2015, 42(S1):2654.
	Wang JL, Qiu Y, Cheng F, et al. Identification and comparative genomic analysis of genes related to whole genome bolting and flowering in radish[C]. Proceedings of the 2015 Academic Annual Meeting of the Chinese Horticultural Society:Editorial Department of the Journal of Horticulture, 2015, 42(S1): 2654.
[13]	陈贵菊, 靳义荣, 等. 普通小麦根系建成相关性状的全基因组关联分析[J]. 植物遗传资源学报, 2020, 21(4): 975-983. doi: 10.13430/j.cnki.jpgr.20191126002
	Chen GJ, Jin YR, et al. Genome-wide association study of root system architecture related traits in common wheat(Triticum aes-tivum L.)[J]. J Plant Genet Resour, 2020, 21(4): 975-983.
[14]	康从彬. 玉米耐盐基因主效位点挖掘及连锁分子标记的开发[D]. 泰安: 山东农业大学, 2021.
	Kang CB. Mining of major loci of maize salt tolerance genes and development of linked molecular markers[D]. Tai'an: Shandong Agricultural University, 2021.
[15]	Yang N, Lu YL, Yang XH, et al. Genome wide association studies using a new nonparametric model reveal the genetic architecture of 17 agronomic traits in an enlarged maize association panel[J]. PLoS Genet, 2014, 10(9): e1004573.
[16]	高炯浩, 段海洋, 熊雪航. 玉米雄穗相关性状的全基因组关联分析及候选基因筛选[J/OL]. 分子植物育种:1-14. http://kns.cnki.net/kcms/detail/46.1068.s.20221215.1612.006.html.
	Gao JH, Duan HY, Xiong XH, et al. Genome wide association analysis and candidate gene screening of maize tassel related traits[J/OL]. Molecular Plant Breeding: 1-14. http://kns.cnki.net/kcms/detail/46.1068.s.20221215.1612.006.html.
[17]	史大坤, 姚天茏, 刘楠楠, 等. 玉米叶绿素含量的全基因组关联分析[J]. 中国农业科学, 2019, 52(11): 1839-1857. doi: 10.3864/j.issn.0578-1752.2019.11.001
	Shi DK, Yao TL, Liu NN, et al. Genome-wide association study of chlorophyll content in maize[J]. Sci Agric Sin, 2019, 52(11): 1839-1857. doi: 10.3864/j.issn.0578-1752.2019.11.001
[18]	白鼎臣, 赵支飞, 等. 贵州栽培型地方茶树叶片气孔性状全基因组关联分析[J]. 浙江农业学报, 2023, 35(7): 1550-1563. doi: 10.3969/j.issn.1004-1524.20230261
	Bai DC, Zhao ZF, et al. Genome-wide association analysis of stomatal characters of cultivated local tea plants in Guizhou, China[J]. Acta Agric Zhejiangensis, 2023, 35(7): 1550-1563. doi: 10.3969/j.issn.1004-1524.20230261
[19]	Zhou X, Stephens M. Genome-wide efficient mixed-model analysis for association studies[J]. Nat Genet, 2012, 44(7): 821-824. doi: 10.1038/ng.2310 pmid: 22706312
[20]	李敏. 胡萝卜FT基因的克隆及遗传转化体系优化[D]. 北京: 中国农业科学院, 2021.
	Li M. Cloning and genetic transformation system optimization of FT gene in carrot[D]. Beijing: Chinese Academy of Agricultural Sciences, 2021.
[21]	尹淑英. 紫花苜蓿的种子功能性状及SSR分子标记的遗传多样性[D]. 兰州: 兰州大学, 2018.
	Yin SY. Genetic diversity of seed functional traits and SSR markers in alfalfa germplasm resources[D]. Lanzhou: Lanzhou University, 2018.
[22]	谢刘勇. 玉米茎秆强度相关性状全基因组关联分析与重要基因挖掘[D]. 泰安: 山东农业大学, 2021.
	Xie LY. Genome-wide association studies and important gene mining of maize stalk strength related traits[D]. Tai'an: Shandong Agricultural University, 2021.
[23]	王姣梅, 汪磊, 等. 蓖麻种质资源遗传多样性与群体结构的SSR分析[J]. 中国油料作物学报, 2022, 44(1): 87-93. doi: 10.19802/j.issn.1007-9084.2020262
	Wang JM, Wang L, et al. Genetic diversity and population structure analysis of castor bean accessions based on SSR markers[J]. Chin J Oil Crop Sci, 2022, 44(1): 87-93.
[24]	陈坚剑, 张慧, 王婷甄, 等. 甜玉米自交系遗传多样性和群体结构分析[J]. 分子植物育种, 2022, 20(19): 6559-6565.
	Chen JJ, Zhang H, Wang TZ, et al. Genetic diversity and population genetic structure analysis of sweet corn inbred lines[J]. Mol Plant Breed, 2022, 20(19): 6559-6565.
[25]	孙倩, 邹枚伶, 张辰笈, 等. 基于SNP和InDel标记的巴西木薯遗传多样性与群体遗传结构分析[J]. 作物学报, 2021, 47(1): 42-49. doi: 10.3724/SP.J.1006.2021.04067
	Sun Q, Zou ML, Zhang CJ, et al. Genetic diversity and population structure analysis by SNP and InDel markers of cassava in Brazil[J]. Acta Agron Sin, 2021, 47(1): 42-49. doi: 10.3724/SP.J.1006.2021.04067
[26]	Ou CG, Mao JH, Liu LJ, et al. Characterising genes associated with flowering time in carrot(Daucus carota L.) using transcriptome analysis[J]. Plant Biol, 2017, 19(2): 286-297.
[27]	Liu LJ, Ou CG, Chen SM, et al. The response of COL and FT homologues to photoperiodic regulation in carrot(Daucus carota L.)[J]. Sci Rep, 2020, 10: 9984.
[28]	López-González L, Mouriz A, Narro-Diego L, et al. Chromatin-dependent repression of the Arabidopsis floral integrator genes involves plant specific PHD-containing proteins[J]. Plant Cell, 2014, 26(10): 3922-3938.
[29]	Piñeiro M, Gómez-Mena C, Schaffer R, et al. EARLY BOLTING IN SHORT DAYS is related to chromatin remodeling factors and regulates flowering in Arabidopsis by repressing FT[J]. Plant Cell, 2003, 15(7): 1552-1562. pmid: 12837946
[30]	Chen MJ, Ni M. RFI₂, a RING-domain zinc finger protein, negatively regulates CONSTANS expression and photoperiodic flowering[J]. Plant J, 2006, 46(5): 823-833. pmid: 16709197
[31]	Xu YF, Gan ES, Zhou J, et al. Arabidopsis MRG domain proteins bridge two histone modifications to elevate expression of flowering genes[J]. Nucleic Acids Res, 2014, 42(17): 10960-10974.
[32]	Ellis CM, Nagpal P, Young JC, et al. Auxin response factor1 and auxin response factor2 regulate senescence and floral organ abscission in Arabidopsis thaliana[J]. Development, 2005, 132(20): 4563-4574.
[33]	Bu ZY, Yu Y, Li ZP, et al. Regulation of Arabidopsis flowering by the histone mark readers MRG1/2 via interaction with CONSTANS to modulate FT expression[J]. PLoS Genet, 2014, 10(9): e1004617.

性状Trait	最小值Min	最大值Max	均值Mean	标准偏差SD	变异系数CV%	广义遗传率H²
2021抽薹时间2021 Bolting time/d	0	165	57.73	54.78	94.89	19.47
2022抽薹时间2022 Bolting time/d	0	129	55.65	41.53	74.63	19.47
2021抽薹率2021 Bolting rate/%	0	56.67	6.24	11.72	187.89	95.04
2022抽薹率2022 Bolting rate/%	0	97.5	13.75	19.83	144.22
2021薹高2021 Bolt height/cm	0	140.63	45.24	46.85	103.55	94.86
2022薹高2022 Bolt height/cm	0	148.5	65.32	50.58	77.43	94.86
2021抽薹速度2021 Bolting speed/（cm·d^-1）	0	1.80	0.47	0.52	110.50	96.91
2022抽薹速度2022 Bolting speed/（cm·d^-1）	0	2.01	0.81	0.66	81.78	96.91
BLUE	26	148.50	90.01	20.28	22.53	100

性状Trait	最小值Min	最大值Max	均值Mean	标准偏差SD	变异系数CV%	广义遗传率H²
2021抽薹时间2021 Bolting time/d	0	165	57.73	54.78	94.89	19.47
2022抽薹时间2022 Bolting time/d	0	129	55.65	41.53	74.63	19.47
2021抽薹率2021 Bolting rate/%	0	56.67	6.24	11.72	187.89	95.04
2022抽薹率2022 Bolting rate/%	0	97.5	13.75	19.83	144.22
2021薹高2021 Bolt height/cm	0	140.63	45.24	46.85	103.55	94.86
2022薹高2022 Bolt height/cm	0	148.5	65.32	50.58	77.43	94.86
2021抽薹速度2021 Bolting speed/（cm·d^-1）	0	1.80	0.47	0.52	110.50	96.91
2022抽薹速度2022 Bolting speed/（cm·d^-1）	0	2.01	0.81	0.66	81.78	96.91
BLUE	26	148.50	90.01	20.28	22.53	100

性状 Trait	21抽薹时间 21 Bolting time	21抽薹率 21 Bolting rate	21薹高 21 Bolt height	21抽薹速度 21 Bolting speed	22抽薹时间 22 Bolting time	22抽薹率 22 Bolting rate	22薹高 22 Bolt height	22抽薹速度 22 Bolting speed	BLUE
21抽薹时间 21 Bolting time	1
21抽薹率 21 Bolting rate	.359**	1
21薹高 21 Bolt height	.711**	.587**	1
21抽薹速度 21 Bolting speed	.629**	.629**	.989**	1
22抽薹时间 22 Bolting time	0.052	.276*	.242*	.268*	1
22抽薹率 22 Bolting rate	0.124	.235*	0.161	0.174	.357**	1
22薹高 22 Bolt height	0.11	.288*	.326**	.358**	.838**	.580**	1
22抽薹速度 22 Bolting speed	0.117	.261*	.310**	.340**	.752**	.655**	.983**	1
BLUE	0.175	.432**	.651**	.704**	.311**	.462**	.707**	.745**	1

性状 Trait	21抽薹时间 21 Bolting time	21抽薹率 21 Bolting rate	21薹高 21 Bolt height	21抽薹速度 21 Bolting speed	22抽薹时间 22 Bolting time	22抽薹率 22 Bolting rate	22薹高 22 Bolt height	22抽薹速度 22 Bolting speed	BLUE
21抽薹时间 21 Bolting time	1
21抽薹率 21 Bolting rate	.359**	1
21薹高 21 Bolt height	.711**	.587**	1
21抽薹速度 21 Bolting speed	.629**	.629**	.989**	1
22抽薹时间 22 Bolting time	0.052	.276*	.242*	.268*	1
22抽薹率 22 Bolting rate	0.124	.235*	0.161	0.174	.357**	1
22薹高 22 Bolt height	0.11	.288*	.326**	.358**	.838**	.580**	1
22抽薹速度 22 Bolting speed	0.117	.261*	.310**	.340**	.752**	.655**	.983**	1
BLUE	0.175	.432**	.651**	.704**	.311**	.462**	.707**	.745**	1

性状 Trait	染色体 Chromosome	位置 Position	P-value
21BH与21BS	NC_030385.1	247837	5.062605543
21BH与21BS			5.181618171
21BH与21BR	NC_030387.1	25943860	7.130938393
21BH与21BR	NC_030387.1	25943860	5.003944095
21BH与21BS	NC_030384.1	29157915	5.963621455
21BH与21BS	NC_030384.1	29157915	5.720245476
21BH与21BR与21BS	NC_030387.1	25945005	5.352303062
			7.088379728
			5.108446375
BLUE与21BH与21BS	NC_030389.1	24736160	5.106787027
			5.557113408
			5.461533219
BLUE与22BH与22BS	NC_030381.1	33254067	6.324538791
			5.49099208
			5.222840507
22BH与22BS与22BT	NC_030381.1	14821077	6.593913937
			6.227883017
			6.232284515
22BH与22BT	NC_030388.1	11132733	5.378648581
	NC_030388.1	11132733	6.444345564
	NC_030388.1	11137259	5.371916716
	NC_030388.1	11137259	5.150990441
	NC_030388.1	11137567	6.154995778
	NC_030388.1	11137567	5.457724322
	NC_030388.1	11138809	5.441207818
	NC_030388.1	11138809	5.942054091
	NC_030388.1	11138870	6.319788809
	NC_030388.1	11138870	5.838568206
	NC_030388.1	11140265	5.265788906
	NC_030388.1	11140265	5.356182472
	NC_030388.1	11140360	5.709912163
	NC_030388.1	11140360	5.090512864
22BH与22BS	NC_030389.1	13789203	5.401099457
	NC_030389.1	13789203	5.039460825
	NC_030387.1	16775792	5.520533385
	NC_030387.1	16775792	5.067802628
	NC_030389.1	20543833	5.662274653
	NC_030389.1	20543833	5.049698785
	NC_030389.1	29589257	5.819082274
	NC_030389.1	29589257	5.128142531
	NC_030381.1	51260915	5.693448241
	NC_030381.1	51260915	5.339222243
22BR与22BS	NC_030387.1	16759553	5.061021806
	NC_030387.1	16759553	5.137172756