Genome-wide Association Study of Bolting Related Traits in Carrot

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

Abstract

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

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.

Figures/Tables 10

References 33

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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