大麦籽粒β-葡聚糖含量的全基因组关联分析

doi:10.3724/SP.J.1006.2021.01074

Abstract

Abstract:

β-glucan is an important trait in barley, as its content greatly affects the quality in the applications of malting, feeding, and food. Although the genes associated with β-glucan synthesis have been reported, genetic regulation of β-glucan accumulation in barley grains is still unclear. In this study, genome-wide association study (GWAS) with mixed linear model (MLM) and general linear model (GLM) was performed to analyze the grain β-glucan content of 119 barley germplasms collected from worldwide previously, which were planted at two plots with certain differences in soil and climate conditions. The results showed β-glucan content in barley grains was significantly different in genotypes and the heritability of β-glucan was 73.9% in two environments. There were eight and 40 loci for grain β-glucan content detected by MLM and GLM, respectively. A total of 44 loci were obtained by combining the same loci of the two models. HORVU5Hr1G022710 gene identified in both models and sites was considered as a putative candidate gene significantly associated with β-glucan content. Significantly positive correlation was detected between grain β-glucan content and the number of favorable alleles in both models. In addition, 10 enzymatic genes related to sugar synthesis, transport and decomposition were identified based on gene annotations. These genes may significantly relate to β-glucan synthesis, accumulation and hydrolysis. The results provided a new insight into the genetic regulation of β-glucan accumulation and laid a foundation for the genetic improvement breeding of barley seed β-glucan.

Key words: barley, β-glucan;, genome-wide association study (GWAS), SNP loci, favorable allele

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.

Figures/Tables 10

Fig. 1

Table 1

Fig. 2

Table 2

Table 3

SNP markers significantly associated with β-glucan content in GLM model"

标记编号 MTA No.	标记名称 Marker	染色体 Chr.	位置 Positon	峰值 -lg (P)	表型贡献率 R² (%)	环境 Environment	最佳等位基因 SNP ^a	最小等位基因频率 MAF	候选基因 Putative candidate genes
1	M-3256305	1	20684690	6.55 4.18	21.39 14.56	CHX CX	C/T	0.235	HORVU1Hr1G009320, HORVU1Hr1G009330
2	M-3432526	1	443440212	4.89 4.08	14.79 12.24	CHX CX	A/G	0.050	HORVU1Hr1G061160, HORVU1Hr1G061160
3	M-3259980	2	40851287	4.89	19.40	CX	A/G	0.143	HORVU2Hr1G017350
4	M-5249622	2	41956883	4.10	15.89	CX	C/G	0.286	HORVU2Hr1G017400
5	M-29425925	2	42674382	4.45	17.86	CX	C/T	0.235	HORVU2Hr1G017470
6	M-3259183	2	752978172	4.79 4.18	19.75 16.80	CHX CX	C/T	0.370	HORVU2Hr1G122270, HORVU2Hr1G122280 HORVU2Hr1G122300, HORVU2Hr1G122310 HORVU2Hr1G122320
7	M-3918521	3	27028266	4.42	19.16	CX	A/G	0.168	HORVU3Hr1G012510, HORVU3Hr1G012520 HORVU3Hr1G012530, HORVU3Hr1G012550
8	M-4014347	3	597391541	4.56	13.78	CHX	G/T	0.076	HORVU3Hr1G082030
9	M-3917069	3	601025304	4.23	15.20	CX	C/T	0.067	HORVU3Hr1G082940, HORVU3Hr1G082980
10	M-3262394	3	640508648	5.48	19.22	CX	A/G	0.124	HORVU3Hr1G092890
11	M-3258241	4	594473630	4.56	16.27	CHX	C/G	0.092	HORVU4Hr1G074460, HORVU4Hr1G074470
12	M-3398576	5	103430100	4.55	13.72	CHX	C/T	0.092	HORVU5Hr1G021420, HORVU5Hr1G021430
13	M-3924095	5	116486105	5.68 5.03	20.83 18.82	CHX CX	A/G	0.067	HORVU5Hr1G022710
14	M-4330916	5	554243179	4.58	16.84	CHX	G/T	0.370	HORVU5Hr1G077910, HORVU5Hr1G077920 HORVU5Hr1G077930, HORVU5Hr1G077940
15	M-3257651	5	569528889	4.94	18.77	CHX	A/C	0.092	HORVU5Hr1G083170, HORVU5Hr1G083210 HORVU5Hr1G083240, HORVU5Hr1G083260
16	M-3272118	5	573026756	4.53	13.80	CHX	A/G	0.092	HORVU5Hr1G084630, HORVU5Hr1G084650
17	M-3923379	5	573026822	4.66	14.19	CHX	A/G	0.092	HORVU5Hr1G084630, HORVU5Hr1G084650
18	M-4000027	5	573026822	4.55	13.72	CHX	A/G	0.092	HORVU5Hr1G084630, HORVU5Hr1G084650
19	M-3254699	5	573766812	5.23	15.85	CHX	C/T	0.080	HORVU5Hr1G085020
20	M-5255433	5	596702361	5.60	16.99	CHX	C/G	0.403	HORVU5Hr1G094660, HORVU5Hr1G094670 HORVU5Hr1G094680, HORVU5Hr1G094690 HORVU5Hr1G094700, HORVU5Hr1G094710
21	M-3255521	5	597561678	4.79	16.99	CHX	C/T	0.395	HORVU5Hr1G095040, HORVU5Hr1G095050 HORVU5Hr1G095080, HORVU5Hr1G095090
22	M-3254781	5	597650244	4.55	14.12	CHX	G/T	0.387	HORVU5Hr1G095060, HORVU5Hr1G095090 HORVU5Hr1G095100, HORVU5Hr1G095110 HORVU5Hr1G095120
23	M-3264230	5	646301855	4.48	16.04	CX	G/T	0.059	HORVU5Hr1G115310, HORVU5Hr1G115320 HORVU5Hr1G115340
24	M-3265903	6	17194598	4.67	17.25	CHX	C/T	0.303	HORVU6Hr1G009620, HORVU6Hr1G009670 HORVU6Hr1G009690, HORVU6Hr1G009700
25	M-3261129	6	42557400	6.03	21.68	CHX	A/G	0.361	HORVU6Hr1G017720, HORVU6Hr1G017740
26	M-4185933	6	48980591	4.47 4.82	15.96 17.11	CHX CX	A/G	0.051	HORVU6Hr1G018830
27	M-3257746	6	49613603	4.31	15.55	CHX	A/C	0.420	HORVU6Hr1G018930, HORVU6Hr1G018950
28	M-3263056	6	68979147	6.08	18.45	CHX	G/T	0.050	HORVU6Hr1G022070, HORVU6Hr1G022080
29	M-3920842	6	264916265	4.64	16.9	CHX	A/G	0.050	HORVU6Hr1G045550, HORVU6Hr1G045590 HORVU6Hr1G045600
30	M-3257940	6	545380415	4.30	17.26	CHX	A/G	0.353	HORVU6Hr1G081290, HORVU6Hr1G081310
31	M-3662578	7	3735940	6.55 4.68	22.93 17.46	CHX CX	A/G	0.303	HORVU7Hr1G001750, HORVU7Hr1G001760 HORVU7Hr1G001790, HORVU7Hr1G001800
32	M-3262082	7	4764013	5.25 5.12	19.29 18.53	CHX CX	G/T	0.387	HORVU7Hr1G002490, HORVU7Hr1G002500 HORVU7Hr1G002530
33	M-4016281	7	4834039	4.74 4.64	18.97 18.67	CHX CX	A/G	0.336	HORVU7Hr1G002530, HORVU7Hr1G002540 HORVU7Hr1G002550, HORVU7Hr1G002560 HORVU7Hr1G002570
34	M-3256657	7	7391399	4.44	20.21	CX	A/C	0.328	HORVU7Hr1G005200
35	M-6284081	7	21620741	5.41	16.70	CHX	C/T	0.050	HORVU7Hr1G016920
36	M-3911599	7	93157425	4.68	16.66	CHX	A/C	0.050	HORVU7Hr1G038040, HORVU7Hr1G038060 HORVU7Hr1G038070, HORVU7Hr1G038080
37	M-9772928	7	636164939	4.71 4.36	16.73 15.64	CHX CX	C/T	0.076	HORVU7Hr1G112900, HORVU7Hr1G112910 HORVU7Hr1G112920, HORVU7Hr1G112930 HORVU7Hr1G112940, HORVU7Hr1G112950
38	M-4015782	7	636588717	5.84	20.31	CHX	C/T	0.479	HORVU7Hr1G113200, HORVU7Hr1G113210 HORVU7Hr1G113230, HORVU7Hr1G113270 HORVU7Hr1G113290, HORVU7Hr1G113300 HORVU7Hr1G113320
39	M-3258181	7	641059108	5.15	18.14	CHX	A/G	0.437	HORVU7Hr1G115230, HORVU7Hr1G115240 HORVU7Hr1G115250, HORVU7Hr1G115260 HORVU7Hr1G115270, HORVU7Hr1G115280
40	M-5333232	7	641079051	4.65	16.74	CHX	G/T	0.370	HORVU7Hr1G115230, HORVU7Hr1G115240 HORVU7Hr1G115250, HORVU7Hr1G115260 HORVU7Hr1G115270, HORVU7Hr1G115280

Table 3

Fig. 3

Fig. 4

Fig. 5

Supporting Information Table S1:

Information for 119 barley cultivated accessions, the grain β-glucan content (%) in CHX and CX, data are means of three replicates. The number of favorable alleles in two models."

品种名	类型	β-葡聚糖含量（%） β-glucan content (%)			最佳等位基因个数 Number of favorable alleles
品种名	类型	长兴（CHX）	慈溪（CX）	均值	MLM	GLM
X1	西藏野生、半野生	2.86%	3.23%	3.04%	4	5
X5	西藏野生、半野生	2.39%	2.92%	2.65%	4	6
X10	西藏野生、半野生	2.69%	3.53%	3.11%	5	20
X15	西藏野生、半野生	3.46%	4.33%	3.90%	5	21
X20	西藏野生、半野生	3.39%	4.38%	3.89%	5	19
X25	西藏野生、半野生	3.26%	2.95%	3.11%	0	10
X30	西藏野生、半野生	3.94%	3.44%	3.69%	5	11
X36	西藏野生、半野生	2.42%	2.75%	2.59%	4	3
X40	西藏野生、半野生	3.16%	3.93%	3.54%	4	23
X45	西藏野生、半野生	3.08%	2.98%	3.03%	4	3
X51	西藏野生、半野生	3.84%	3.80%	3.82%	4	18
X55	西藏野生、半野生	3.86%	4.21%	4.03%	4	30
X60	西藏野生、半野生	3.62%	3.68%	3.65%	4	22
X65	西藏野生、半野生	3.22%	3.30%	3.26%	4	22
X70	西藏野生、半野生	3.14%	3.81%	3.48%	5	17
X76	西藏野生、半野生	3.91%	3.92%	3.92%	4	23
X80	西藏野生、半野生	3.24%	2.75%	3.00%	4	3
X85	西藏野生、半野生	3.04%	3.08%	3.06%	4	17
X90	西藏野生、半野生	3.21%	3.64%	3.43%	4	15
X95	西藏野生、半野生	3.58%	4.05%	3.81%	4	23
X100	西藏野生、半野生	2.83%	3.71%	3.27%	4	27
X104	西藏野生、半野生	3.18%	3.48%	3.33%	4	19
X110	西藏野生、半野生	3.21%	3.51%	3.36%	6	18
X116	西藏野生、半野生	2.91%	3.48%	3.19%	4	15
X120	西藏野生、半野生	2.30%	2.28%	2.29%	2	5
X124	西藏野生、半野生	3.71%	4.54%	4.13%	4	25
X130	西藏野生、半野生	3.30%	3.71%	3.50%	4	21
X135	西藏野生、半野生	2.59%	1.98%	2.29%	2	5
X140	西藏野生、半野生	2.07%	2.76%	2.42%	4	3
X145	西藏野生、半野生	3.78%	4.20%	3.99%	4	23
X150	西藏野生、半野生	2.87%	3.51%	3.19%	4	17
X155	西藏野生、半野生	3.11%	3.31%	3.21%	5	18
X159	西藏野生、半野生	4.75%	5.35%	5.05%	6	30
X165	西藏野生、半野生	3.16%	3.76%	3.46%	5	17
X170	西藏野生、半野生	2.34%	2.99%	2.66%	4	3
X180	西藏野生、半野生	2.81%	2.58%	2.69%	3	7
X185	西藏野生、半野生	2.66%	3.90%	3.28%	4	14
X189	西藏野生、半野生	2.47%	2.80%	2.64%	4	6
X54	西藏野生、半野生	3.18%	3.91%	3.55%	4	20
X82	西藏野生、半野生	3.48%	4.05%	3.76%	4	21
X32	西藏野生、半野生	3.73%	4.11%	3.92%	5	23
X127	西藏野生、半野生	2.88%	3.54%	3.21%	4	15
X173	西藏野生、半野生	4.72%	4.80%	4.76%	4	21
X8	西藏野生、半野生	3.11%	3.05%	3.08%	4	5
处麦1号	国内栽培品种	3.54%	3.11%	3.33%	4	8
仙居早78	国内栽培品种	2.76%	3.35%	3.05%	3	4
浙皮1号	国内栽培品种	2.27%	2.87%	2.57%	3	8
白茎二棱	国内栽培品种	2.82%	3.48%	3.15%	4	15
新登蒙古麦	国内栽培品种	3.01%	3.60%	3.31%	2	7
农大3号	国内栽培品种	2.51%	2.91%	2.71%	3	3
农大5号	国内栽培品种	3.10%	3.61%	3.36%	4	10
早熟3号	国内栽培品种	3.05%	3.47%	3.26%	4	9
舟麦1号	国内栽培品种	1.95%	2.33%	2.14%	3	4
奉矮2号	国内栽培品种	2.14%	2.94%	2.54%	3	4
宜山大麦	国内栽培品种	1.99%	2.30%	2.15%	3	3
海安大麦	国内栽培品种	3.45%	3.76%	3.60%	4	8
早矮白	国内栽培品种	3.17%	3.09%	3.13%	3	9
余杭糯大麦	国内栽培品种	2.57%	2.43%	2.50%	1	7
崇穗刺毛大麦	国内栽培品种	2.36%	2.58%	2.47%	1	4
义乌二棱	国内栽培品种	2.54%	2.76%	2.65%	3	4
浙农12	国内栽培品种	3.32%	3.43%	3.37%	5	16
牛古特	国内栽培品种	3.19%	3.41%	3.30%	3	8
盐66	国内栽培品种	2.59%	2.97%	2.78%	3	6
岗2	国内栽培品种	2.80%	2.52%	2.66%	2	4
光芒二棱	国内栽培品种	2.99%	3.75%	3.37%	3	18
海紫2号	国内栽培品种	2.45%	2.90%	2.68%	1	6
衢州裸麦	国内栽培品种	3.40%	3.05%	3.23%	1	6
御岛裸	国内栽培品种	3.00%	3.21%	3.11%	1	5
大罗锤	国内栽培品种	3.11%	2.90%	3.01%	2	8
天台白四棱	国内栽培品种	2.94%	2.73%	2.84%	2	8
安吉芒毛大麦	国内栽培品种	2.81%	2.81%	2.81%	2	7
黄青裸	国内栽培品种	3.96%	3.72%	3.84%	5	19
六棱黑麦稞	国内栽培品种	3.05%	3.02%	3.03%	3	6
香川裸1号	国内栽培品种	3.39%	3.20%	3.30%	0	7
嵊县江颈四棱大麦	国内栽培品种	3.06%	3.82%	3.44%	2	4
如皋早六棱	国内栽培品种	2.82%	2.75%	2.79%	1	8
农大2号	国内栽培品种	3.53%	2.85%	3.19%	3	5
甬87-031	国内栽培品种	2.61%	2.12%	2.37%	3	6
秀87-8	国内栽培品种	2.30%	2.55%	2.43%	3	4
早熟7号	国内栽培品种	2.57%	2.54%	2.55%	3	4
无芒六棱	国内栽培品种	3.13%	2.86%	3.00%	1	6
春风皮大麦	国内栽培品种	3.27%	4.08%	3.68%	5	21
肚里黄	国内栽培品种	2.76%	3.31%	3.03%	4	24
丰产二棱	国内栽培品种	3.04%	3.37%	3.20%	3	9
玉环洋大麦	国内栽培品种	3.13%	3.29%	3.21%	1	7
永加仰天冲	国内栽培品种	2.84%	3.07%	2.96%	2	7
秀87-6	国内栽培品种	2.80%	2.69%	2.74%	2	3
浙农14	国内栽培品种	3.24%	3.84%	3.54%	3	19
矮脚二棱	国内栽培品种	3.23%	3.04%	3.13%	2	5
岗33	国内栽培品种	3.09%	3.64%	3.37%	2	15
戈贝纳	国内栽培品种	2.93%	3.09%	3.01%	3	14
浙农白壳	国内栽培品种	2.66%	2.61%	2.63%	4	11
矮早3	国内栽培品种	2.74%	2.71%	2.72%	3	3
红光二棱	国内栽培品种	2.95%	3.65%	3.30%	2	7
奉矮二棱	国内栽培品种	2.95%	3.28%	3.12%	2	3
中熟1号	国内栽培品种	2.59%	4.13%	3.36%	4	8
浙皮2号	国内栽培品种	3.02%	3.73%	3.37%	3	6
不知梅雨	国内栽培品种	2.75%	3.67%	3.21%	3	16
沪麦1号	国内栽培品种	3.41%	3.66%	3.53%	5	16
Gairdner	国外栽培品种	2.71%	3.46%	3.08%	3	16
Metcalfe	国外栽培品种	3.19%	3.04%	3.11%	4	17
harington	国外栽培品种	3.33%	4.35%	3.84%	2	8
triumph	国外栽培品种	1.66%	2.88%	2.27%	4	13
boluke	国外栽培品种	2.72%	2.87%	2.80%	4	14
Franklin	国外栽培品种	3.25%	4.13%	3.69%	2	12
Yerong	国外栽培品种	2.67%	4.10%	3.38%	5	25
morex	国外栽培品种	3.83%	3.91%	3.87%	3	20
Vlamingh	国外栽培品种	3.22%	3.86%	3.54%	4	12
Golden Promise	国外栽培品种	2.33%	2.70%	2.51%	4	12
藏青320	国内栽培品种	5.48%	6.49%	5.98%	7	24
haruna nijo	国外栽培品种	2.40%	2.72%	2.56%	3	9
ZU9	国内栽培品种	3.10%	3.46%	3.28%	2	7
花30	国内栽培品种	3.28%	3.71%	3.50%	3	7
单二	国内栽培品种	3.09%	3.19%	3.14%	2	8
Tadmor	国外栽培品种	2.80%	4.11%	3.45%	4	20
Mikamogold	国外栽培品种	2.53%	3.20%	2.86%	3	5
日本二条2号	国外栽培品种	2.08%	2.86%	2.47%	3	7
拉一把	国内栽培品种	3.48%	4.26%	3.87%	3	8
Ticn	国外栽培品种	3.76%	4.98%	4.37%	6	27

Supporting Information Table S1:

Supporting Information Table S2:

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变异源 Source of variation	III型平方和 SS	自由度 DF	均方 MS	F值 F-value	R² (%)
基因型 Genotype	235.00	118	1.98	104.14^***	76.46
环境 Environment	25.13	1	25.13	1325.35^***	8.18
环境×基因型 Genotype × Environment	38.12	118	0.32	16.90^***	12.40
误差 Residual error	9.10	476	0.02		2.96
总计 Total	307.35	713

候选基因 putative candidate genes	EMB	ROO1	LEA	INF2	NOD	CAR5	CAR15	ETI	LEM	LOD	PAL	EPI	RAC	ROO2	SEN
HORVU5Hr1G022710 Transcriptionfactor MYB21	NE	NE	NE	NE	NE	NE	NE	-1.198	-0.620	0.577	-0.946	NE	NE	-1.276	NE
HORVU4Hr1G074470 glycerol-3-phosphate acyltransferase 6	-0.690	-2.088	0.131	-2.060	-1.756	-1.369	NE	-0.377	0.721	0.259	0.431	0.777	-0.592	-0.584	-0.113
HORVU5Hr1G077910 beta glucosidase 11	0.018	0.164	1.380	-1.873	1.112	0.606	0.333	0.806	1.673	1.571	1.610	1.011	0.785	-0.463	1.427
HORVU5Hr1G077920 beta glucosidase 11	1.373	1.652	1.819	-0.679	-0.062	0.186	1.491	0.999	2.055	1.603	1.876	1.222	0.986	2.120	2.165
HORVU5Hr1G095080 Beta-glucosidase C	2.261	1.731	1.810	1.414	2.109	2.429	0.990	2.076	2.297	1.813	2.492	1.634	2.012	2.182	0.133
HORVU5Hr1G095060 Beta-glucosidase C	1.879	1.156	0.797	1.198	0.361	1.308	0.900	0.953	0.989	0.575	1.200	0.335	0.933	1.632	-0.812
HORVU5Hr1G095100 Glycosyl hydrolase family protein	1.028	0.609	0.663	0.441	0.786	1.262	0.413	1.321	0.962	1.338	0.862	1.207	0.842	1.372	0.045
HORVU6Hr1G009620 Mannan endo-1,4-beta-mannosidase 7	-1.591	-1.721	-0.460	-0.635	0.073	0.179	-0.111	-1.140	0.204	0.442	0.436	-1.040	-0.066	NE	NE
HORVU6Hr1G009690 Glucan endo-1,3-beta-glucosidase 3	0.853	0.537	0.355	-0.265	1.207	-0.004	-0.756	0.771	0.631	1.149	0.756	0.632	0.089	0.310	-0.400
HORVU7Hr1G112930 GDP-L-fucose synthase 1	1.177	1.076	1.125	0.666	1.276	1.161	0.870	0.976	1.049	1.119	1.229	1.034	1.156	1.385	1.036
HORVU7Hr1G112940 GDP-L-fucose synthase 1	-1.267	-1.196	-0.819	-0.847	-0.896	-0.769	-0.460	-0.685	-0.376	-0.395	-0.486	-0.131	-0.529	-1.393	-0.911
NE：无表达 NE : No expression

Genome-wide association study of β-glucan content in barley grains

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标记编号 MTA No.	标记名称 Marker	染色体 Chr.	位置 Position	峰值 -log₁₀(P)	表型贡献率 R² (%)	环境 Environment	最佳等位基因^a SNP ^a	最小等位基因频率 MAF	候选基因 Putative candidated genes
1	M-4172115	2	753357365	3.50	16.98	CHX	A/G	0.14	HORVU2Hr1G122510, HORVU2Hr1G122540, HORVU2Hr1G122560, HORVU2Hr1G122570, HORVU2Hr1G122580
2	M-3262394	3	640508648	3.16	13.50	CX	A/G	0.12	HORVU3Hr1G092890
3	M-3432496	4	629360418	3.07	13.55	CHX	C/T	0.14	HORVU4Hr1G084590
4	M-3924095	5	116486105	3.28 3.22	14.20 14.40	CX CHX	A/G	0.07	HORVU5Hr1G022710
5	M-3263056	6	68979147	3.88	13.65	CHX	G/T	0.05	HORVU6Hr1G022070, HORVU6Hr1G022080
6	M-4792001	6	350443314	3.19	15.62	CHX	C/G	0.11	HORVU6Hr1G055090
7	M-3911599	7	93157425	3.29	14.13	CHX	A/C	0.05	HORVU7Hr1G038040, HORVU7Hr1G038060, HORVU7Hr1G038070, HORVU7Hr1G038080
8	M-3665085	7	199549260	3.44	14.79	CHX	A/G	0.17	HORVU7Hr1G052390, HORVU7Hr1G052400

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