普通菜豆抗菜豆象性状的全基因组关联分析

doi:10.11983/CBB22138

植物学报 ›› 2023, Vol. 58 ›› Issue (1): 77-89.DOI: 10.11983/CBB22138

普通菜豆抗菜豆象性状的全基因组关联分析

李晓明¹, 王兰芬¹, 唐永生², 常玉洁¹, 张菊香², 王述民¹, 武晶¹^,^*()

¹中国农业科学院作物科学研究所, 北京 100081
²曲靖市农业科学院, 曲靖 655000

收稿日期:2022-06-30 接受日期:2022-09-19 出版日期:2023-01-01 发布日期:2023-01-05
通讯作者: *E-mail: wujing@caas.cn
作者简介:^†共同第一作者
基金资助:
国家自然科学基金(32072017);国家食用豆现代农业产业技术体系(CARS-08)

Genome-wide Association Analysis of Resistance to Acanthoscelides obtectus in Common Bean

Xiaoming Li¹, Lanfen Wang¹, Yongsheng Tang², Yujie Chang¹, Juxiang Zhang², Shumin Wang¹, Jing Wu¹^,^*()

¹Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
²Qujing Academy of Agricultural Sciences, Qujing 655000, China

Received:2022-06-30 Accepted:2022-09-19 Online:2023-01-01 Published:2023-01-05
Contact: *E-mail: wujing@caas.cn
About author:^†These authors contributed equally to this paper

摘要/Abstract

摘要：

普通菜豆(Phaseolus vulgaris)具有丰富的营养价值, 菜豆象(Acanthoscelides obtectus)是危害菜豆的主要害虫, 利用抗虫种质资源防治菜豆象是最安全且经济有效的方法。该研究利用改良的室内人工接虫方法, 对625份普通菜豆种质资源进行2次菜豆象抗性重复鉴定, 筛选出2份抗性稳定且种子受害率均在10%以下的高抗种质。利用种子受害率和蛀孔总数的表型数据, 基于3 767 432个SNP标记进行全基因组关联分析, 鉴定出15个与种子受害率相关的显著关联遗传位点, 8个与蛀孔总数相关的显著关联位点, 解释了4.54%-5.56%的表型变异。在候选位点筛选出包括编码蛋白酶抑制剂、凝集素和过氧化物酶等在内的20个与抗虫防御相关的候选基因。

关键词: 普通菜豆, 菜豆象, 全基因组关联分析, 数量性状位点, 抗性基因

Abstract:

Common beans (Phaseolus vulgaris) have rich nutritional value, and Acanthoscelides obtectus are major pests during the storage. It is a safe, economical and effective method to control the damage of A. obtectus by screening the germplasm resources of bruchid resistance. In this study, a total of 625 common bean germplasms were identified for resistance to A. obtectus by using improved indoor artificial inoculation method. Among them, two germplasms showed stable resistance in both two repeated identifications, with the percentage of damaged seeds less than 10%. Genome-wide association analysis was conducted based on 3 767 432 SNP and phenotypic data of the percentage of damaged seeds and the number of perforations from 625 common beans. Fifteen significant QTLs were associated with the percentage of damaged seeds and 8 significant QTLs were associated with the number of perforations, explaining 4.54% to 5.56% of the phenotypic variation. A total of 20 candidate genes were screened from all loci, including the genes encoding protease inhibitors, lectin, peroxidase and so on, which were related to the defense of bruchids.

Key words: common bean, Acanthoscelides obtectus, genome-wide association analysis, quantitative trait locus, resistant genes

李晓明, 王兰芬, 唐永生, 常玉洁, 张菊香, 王述民, 武晶. 普通菜豆抗菜豆象性状的全基因组关联分析. 植物学报, 2023, 58(1): 77-89.

Xiaoming Li, Lanfen Wang, Yongsheng Tang, Yujie Chang, Juxiang Zhang, Shumin Wang, Jing Wu. Genome-wide Association Analysis of Resistance to Acanthoscelides obtectus in Common Bean. Chinese Bulletin of Botany, 2023, 58(1): 77-89.

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图/表 11

参考文献 54

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Gene pool	Outside of China^a		Inside of China^b		All
Gene pool	BL	L	BL	L	All
Andean	33	16	27	206	282
Mesoamerican	64	11	20	248	343
All	97	27	47	454	625

Gene pool	Outside of China^a		Inside of China^b		All
Gene pool	BL	L	BL	L	All
Andean	33	16	27	206	282
Mesoamerican	64	11	20	248	343
All	97	27	47	454	625

Rating scale	PDS (%)	Resistant evaluation
1	≤10	Highly resistance (HR)
3	10<PDS≤35	Resistance (R)
5	35<PDS≤65	Medium resistance (MR)
7	65<PDS≤90	Susceptible (S)
9	>90	Highly susceptible (HS)

Rating scale	PDS (%)	Resistant evaluation
1	≤10	Highly resistance (HR)
3	10<PDS≤35	Resistance (R)
5	35<PDS≤65	Medium resistance (MR)
7	65<PDS≤90	Susceptible (S)
9	>90	Highly susceptible (HS)

Traits	Min	Median	Max	Mean	SD (%)	Kurtosis	Skewness	CV (%)
PDS I (%)	1.00	67.50	100	64.14	25.65	-0.71	-0.45	40.00
NP I	3.00	263.50	1224	294.12	181.20	1.48	0.96	61.61
PDS II (%)	0.00	72.00	100	66.44	27.17	-0.76	-0.62	40.89
NP II	0.00	329.00	1816	376.20	254.91	3.12	1.37	67.76
PDS-BLUE (%)	4.00	70.00	100	65.44	0.23	-0.63	-0.58	35.07
NP-BLUE	0.56	318.00	1126	335.55	174.94	1.56	0.92	52.02

普通菜豆抗菜豆象性状的全基因组关联分析

Genome-wide Association Analysis of Resistance to Acanthoscelides obtectus in Common Bean

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Accession No.	Origin	100 seeds weight (g)	Repeat I		Repeat II
Accession No.	Origin	100 seeds weight (g)	PDS (%)	NP	PDS (%)	NP
Longyundou7	China-Heilongjiang	17.29	4	21	4	11
I2K03033	USA	17.34	10	30	6	24

Traits	Min	Median	Max	Mean	SD (%)	Kurtosis	Skewness	CV (%)
SW I (g)	10.80	34.21	80.40	34.95	12.93	-0.57	0.36	37.00
SW II (g)	7.08	31.62	70.23	33.18	12.35	-0.44	0.42	37.22
SL I (mm)	6.30	12.20	17.80	12.30	2.51	-1.01	0.05	20.40
SL II (mm)	6.25	13.89	15.25	14.94	3.02	-0.93	-0.06	20.19
SWI I (mm)	4.20	7.10	15.60	7.11	1.13	9.79	1.59	15.91
SWI II (mm)	4.88	8.70	13.50	8.66	1.40	-0.25	0.19	16.20
SH I (mm)	3.80	5.50	8.50	5.62	0.85	0.71	0.91	15.03
SH II (mm)	3.70	5.40	8.80	5.49	0.82	0.58	0.74	14.90

Traits	Locus	Peak SNP marker	Chromosome	Position (bp)	p-value	R² (%)
PDS	Loc_1	Pv01_43986475	Pv01	43986475	1E-07	5.24
	Loc_2	Pv01_49901915	Pv01	49901915	8.15E-07	4.54
	Loc_3	Pv03_1235524	Pv03	1235524	2.25E-07	4.97
	Loc_4	Pv03_6664019	Pv03	6664019	4.46E-07	4.74
	Loc_5	Pv03_11569042	Pv03	11569042	2.19E-07	4.98
	Loc_6	Pv03_37792879	Pv03	37792879	5.51E-07	4.67
	Loc_7	Pv05_522813	Pv05	522813	3.89E-07	4.79
	Loc_8	Pv05_5075510	Pv05	5075510	3.54E-07	4.82
	Loc_9	Pv05_22022919	Pv05	22022919	3.89E-08	5.56
	Loc_10	Pv06_19260606	Pv06	19260606	7.22E-07	4.58
	Loc_11	Pv07_386049	Pv07	386049	6.01E-07	4.64
	Loc_12	Pv08_13992928	Pv08	13992928	6.42E-07	4.62
	Loc_13	Pv08_43139505	Pv08	43139505	5.06E-07	4.70
	Loc_14	Pv10_9574825	Pv10	9574825	2.3E-07	4.96
	Loc_15	Pv11_11777960	Pv11	11777960	2.62E-07	4.92
NP	Loc_16	Pv02_36436725	Pv02	36436725	5.26E-07	4.74
	Loc_17	Pv03_23935240	Pv03	23935240	5.31E-07	4.74
	Loc_18	Pv04_9609212	Pv04	9609212	2.01E-07	5.07
	Loc_19	Pv04_10133957	Pv04	10133957	5.13E-07	4.75
	Loc_20	Pv04_44834996	Pv04	44834996	7.56E-07	4.62
	Loc_21	Pv10_8170537	Pv10	8170537	6.45E-07	4.68
	Loc_22	Pv11_13013375	Pv11	13013375	2.37E-07	5.01
	Loc_23	Pv11_19511385	Pv11	19511385	7.45E-07	4.63

Traits	Gene	Chromosome	Locus	Gene annotation or coding protein
PDS	Phvul.001G239200	Pv01	Loc_2	Concanavalin A-like lectin family protein
	Phvul.003G014200	Pv03	Loc_3	Hydroxyproline-rich glycoprotein family protein
	Phvul.003G169100	Pv03	Loc_6	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein
	Phvul.005G005800	Pv05	Loc_7	WRKY DNA-binding protein 2
	Phvul.005G046000	Pv05	Loc_8	Peroxidase superfamily protein
	Phvul.006G073200	Pv06	Loc_10	Hydroxyproline-rich glycoprotein family protein
	Phvul.008G113100	Pv08	Loc_12	Kunitz family trypsin and protease inhibitor protein
	Phvul.008G113900	Pv08		Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein
	Phvul.010G057000	Pv10	Loc_14	S-locus lectin protein kinase family protein
	Phvul.010G057100	Pv10		S-locus lectin protein kinase family protein
	Phvul.010G057300	Pv10		S-locus lectin protein kinase family protein
	Phvul.010G057500	Pv10		S-locus lectin protein kinase family protein
	Phvul.010G057900	Pv10		WRKY DNA-binding protein 70
NP	Phvul.002G205700	Pv02	Loc_16	Defensin-like (DEFL) family protein
	Phvul.002G205900	Pv02		Defensin-like (DEFL) family protein
	Phvul.003G099300	Pv03	Loc_17	S-locus lectin protein kinase family protein
	Phvul.004G067300	Pv04	Loc_18	Sterol
	Phvul.004G068800	Pv04	Loc_19	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin superfamily protein
	Phvul.011G108700	Pv11	Loc_22	S-locus lectin protein kinase family protein
	Phvul.011G119200	Pv11	Loc_23	Concanavalin A-like lectin protein kinase family protein

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