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Acta Agronomica Sinica ›› 2024, Vol. 50 ›› Issue (10): 2483-2492.doi: 10.3724/SP.J.1006.2024.31084

• CROP GENETICS & BREEDING·GERMPLASM RESOURCES·MOLECULAR GENETICS • Previous Articles     Next Articles

Genome-wide association analysis and candidate genes prediction of β-glucan content in barley grains

LU Zong-Hui1,2(), SI Er-Jing1,2, YE Pei-Yin1,2, WANG Jun-Cheng1,2, YAO Li-Rong1,2, MA Xiao-Le1,2, LI Bao-Chun1,3, WANG Hua-Jun1,2, SHANG Xun-Wu2, MENG Ya-Xiong1,2,*()   

  1. 1State Key Laboratory of Arid Land Crop Science, Gansu Provincial Key Laboratory of Crop Improvement & Germplasm Enhancement, Lanzhou 730070, Gansu, China
    2College of Agriculture, Gansu Agricultural University, Lanzhou 730070, Gansu, China
    3College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, Gansu, China
  • Received:2023-12-28 Accepted:2024-05-21 Online:2024-10-12 Published:2024-07-15
  • Contact: *E-mail: yxmeng1@163.com
  • Supported by:
    China Agriculture Research System of MOF and MARA(Barley, CARS-05-03B-03);China Agriculture Research System of MOF and MARA(CARS-05-03B-03);National Natural Science Foundation of China(31960426);Provincial College Students Innovation and Entrepreneurship Training Program of Gansu Province(S202010733001);Gansu Youth Science and Technology Fund Program(20JR5RA010);Innovation Fund of Gansu Provincial Department of Education(2021A-055);Industry Support Plan of Education Department of Gansu Province(2021CYZC-12)

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Abstract:

A total of 238 barley germplasm resources from various sources were genotyped using a high-throughput SNP chip. The β-glucan content of barley grain was determined for two consecutive years. Genome-wide association analysis was conducted using a general linear model based on the PCA model. The results showed that the β-glucan content of the 238 barley materials ranged from 1.23% to 6.55% and 1.79% to 6.64% for the respective years, exhibiting a normal distribution. In the GWAS analysis, a total of 19 significant SNP markers were detected, located on chromosomes 1H, 2H, 3H, 4H, and 5H. These markers accounted for 7.39% to 10.29% of the observed phenotypic variation. Candidate genes were identified within a 300 kb range upstream and downstream of the SNP sites showing significant associations, and a total of 37 genes were identified. Through a combination of previous studies and BLAST gene annotation, four candidate genes most likely involved in β-glucan synthesis were identified. Notably, within 89 kb upstream of the most significant SNP locus B1_1033963, the candidate gene HORVU.MOREX.R3.1 HG0000140 was detected, which may play a crucial role in the process of beta-glucan synthesis. This study provides theoretical guidance and valuable gene resources for the genetic improvement of β-glucan content in barley.

Key words: barley, β-glucan, genome-wide association analysis, SNP marker

Table S1

Basic information of 238 barley materials"

编号
Number		 材料名称
Accessions		 来源
Source		 带壳性
Characteristics		 2021年β-葡聚糖含量
β-glucan content in 2021 (%)		 2021年β-葡聚糖含量
β-glucan content in 2022 (%)
1 ZY5-130R2218 国内 Domestic 皮 Hulled 4.69 4.56
2 27-22VR24W 国外 Foreign 皮 Hulled 4.88 4.74
3 ZY51-浦麦1号 ZY51-Pumai 1 国内 Domestic 皮 Hulled 3.26 3.24
4 法儿菲特 Faerfeite 国内 Domestic 皮 Hulled 3.47 3.45
5 甘啤3号 Ganpi 3 国内 Domestic 皮 Hulled 3.96 3.82
6 黄芒大麦 Huangmang barley 国内 Domestic 皮 Hulled 4.62 4.49
7 北青88 Beiqing 88 国内 Domestic 裸 Hulless 5.18 5.04
8 ZDM04263 国内 Domestic 裸 Hulless 4.32 4.19
9 ZY61-2141V005W 国内 Domestic 皮 Hulled 3.23 3.11
10 0010-18 国外 Foreign 皮 Hulled 5.58 5.43
11 ZY25-K11-DAMA 国内 Domestic 皮 Hulled 4.91 4.77
12 美22 America 22 国外 Foreign 皮 Hulled 4.96 4.82
13 美25 America 25 国外 Foreign 皮 Hulled 5.60 5.46
14 3WNG 国外 Foreign 皮 Hulled 4.99 4.85
15 ZDM04810 国内 Domestic 裸 Hulless 4.66 4.53
16 ZDM08190 国内 Domestic 裸 Hulless 4.38 4.24
17 ZDM01313 国内 Domestic 裸 Hulless 4.09 3.95
18 ZDM06487 国内 Domestic 裸 Hulless 5.43 5.29
19 ZDM05042 国内 Domestic 裸 Hulless 6.36 6.20
20 ZDM07388 国内 Domestic 裸 Hulless 6.38 6.22
21 ZDM08135 国内 Domestic 裸 Hulless 6.31 6.16
22 ZDM03239 国内 Domestic 皮 Hulled 5.87 5.72
23 ZDM08088 国内 Domestic 裸 Hulless 5.48 5.34
24 21099-2316 国外 Foreign 皮 Hulled 4.74 4.60
25 ZDM05475 国内 Domestic 裸 Hulless 4.06 3.92
26 Z122VD24W 国内 Domestic 皮 Hulled 5.00 4.86
27 ZY170-G068270180 国内 Domestic 皮 Hulled 4.14 4.01
28 ZDM08070 国内 Domestic 裸 Hulless 5.19 5.04
29 蒙啤3号 Mengpi 3 国内 Domestic 皮 Hulled 4.86 4.71
30 WDM06805 国外 Foreign 皮 Hulled 4.93 4.80
31 stem 国外 Foreign 皮 Hulled 5.17 5.03
32 WDM00796 国外 Foreign 皮 Hulled 3.03 3.01
33 WDM21804 国外 Foreign 皮 Hulled 5.17 5.03
34 Z220V015W 国内 Domestic 皮 Hulled 4.17 3.51
35 WDM1950 国外 Foreign 皮 Hulled 4.15 3.50
36 ZZNN62660 国内 Domestic 皮 Hulled 3.76 3.16
37 ZDM6550 国内 Domestic 皮 Hulled 3.34 2.80
38 ZDM5188 国内 Domestic 裸 Hulless 4.54 3.84
39 ZDM6170 国内 Domestic 裸 Hulless 3.93 3.31
40 ZDM08664 国内 Domestic 皮 Hulled 5.14 4.35
41 ZDM10027 国内 Domestic 皮 Hulled 3.96 3.34
42 ZYM742 国内 Domestic 皮 Hulled 3.33 2.79
43 ZY164-BONC7-87 国内 Domestic 皮 Hulled 3.22 2.70
44 ZYM0974 国内 Domestic 皮 Hulled 5.07 4.29
45 ZY87-4891 国内 Domestic 皮 Hulled 5.25 4.46
46 ZY45-1451035W 国内 Domestic 皮 Hulled 3.44 2.89
47 WDM0491 国外 Foreign 皮 Hulled 4.92 4.17
48 WDM01953 国外 Foreign 皮 Hulled 4.54 3.84
49 ZDM10060 国内 Domestic 皮 Hulled 2.11 1.87
50 ZDM0404 国内 Domestic 皮 Hulled 2.48 2.23
51 ZDM6470 国内 Domestic 裸 Hulless 2.42 2.19
52 ZDM06415 国内 Domestic 裸 Hulless 2.45 2.20
53 ZYM2510 国内 Domestic 皮 Hulled 2.17 1.93
54 ZY121-9918-3 国内 Domestic 皮 Hulled 1.94 1.80
55 spettam 国外 Foreign 皮 Hulled 2.38 2.15
56 ZDM0004 国内 Domestic 裸 Hulless 2.17 1.93
57 ZDM10038 国内 Domestic 裸 Hulless 2.13 1.90
58 ZY62-86-5093 国内 Domestic 皮 Hulled 2.85 2.59
59 蒙啤1号 Mengpi 1 国内 Domestic 皮 Hulled 2.19 1.97
60 ZDM16414 国内 Domestic 皮 Hulled 3.55 3.26
61 ZDM090075 国内 Domestic 裸 Hulless 3.31 3.29
62 ZDM5160 国内 Domestic 裸 Hulless 2.51 2.26
63 美国26 America 26 国外 Foreign 皮 Hulled 2.18 1.95
64 美8 Mei8 国外 Foreign 皮 Hulled 2.72 2.46
65 ZDM6152 国内 Domestic 裸 Hulless 3.25 2.97
66 ZDM0400 国内 Domestic 裸 Hulless 4.78 4.44
67 ZDM6401 国内 Domestic 裸 Hulless 2.82 2.56
68 乐啤4号 Lepi 4 国内 Domestic 皮 Hulled 2.43 2.19
69 ZDM5199 国内 Domestic 裸 Hulless 2.28 2.03
70 ZDM03645 国内 Domestic 皮 Hulled 2.51 2.26
71 ZDM03835 国内 Domestic 裸 Hulless 2.77 2.51
72 ZDM04094 国内 Domestic 皮 Hulled 2.20 1.96
73 ZDM5453 国内 Domestic 裸 Hulless 2.85 2.59
74 ZDM01837 国内 Domestic 皮 Hulled 3.41 3.39
75 ZDM515 国内 Domestic 裸 Hulless 2.54 2.29
76 美国45 America 45 国外 Foreign 皮 Hulled 3.05 2.79
77 ZDM5192 国内 Domestic 裸 Hulless 3.22 2.95
78 晚熟a907 Wanshu a907 国内 Domestic 皮 Hulled 2.71 2.45
79 ZDM5151 国内 Domestic 裸 Hulless 2.57 2.33
80 20901M061M 国外 Foreign 皮 Hulled 3.08 2.93
81 华中农大 Huazhongnongda 国内 Domestic 皮 Hulled 3.61 3.44
82 12-D3928888 国外 Foreign 裸 Hulless 3.70 3.53
83 08京-118 08Jing-118 国内 Domestic 皮 Hulled 3.48 3.31
84 08京-222 08Jing-222 国内 Domestic 皮 Hulled 4.22 4.03
85 单2 Dan 2 国内 Domestic 皮 Hulled 2.90 2.75
86 08京-329 08Jing-329 国内 Domestic 皮 Hulled 3.54 3.37
87 甘啤5号 Ganpi 5 国内 Domestic 皮 Hulled 3.21 3.05
88 黑龙江123 Heilongjiang 123 国内 Domestic 皮 Hulled 6.55 6.27
89 鄂58288 E 58288 国内 Domestic 皮 Hulled 3.38 3.22
90 08京-P48 08Jing-P48 国内 Domestic 皮 Hulled 3.39 3.23
91 ZYM963 国内 Domestic 皮 Hulled 4.60 4.40
92 2019-DM-0119 国内 Domestic 皮 Hulled 3.28 3.12
93 富士二条 Fuji 2 国外 Foreign 皮 Hulled 3.20 3.04
94 12-03101 国外 Foreign 裸 Hulless 3.33 3.17
95 北青1号 Beiqing 1 国内 Domestic 裸 Hulless 4.70 4.49
96 ZYP4-Z033120555 国内 Domestic 皮 Hulled 3.56 3.39
97 015-宝丹 015-Baodan 国内 Domestic 皮 Hulled 3.40 3.24
98 80544 国外 Foreign 皮 Hulled 3.58 3.41
99 丹青1号 Danqing 1 国内 Domestic 皮 Hulled 4.10 3.91
100 川农大5号 Chuannongda 5 国内 Domestic 皮 Hulled 3.77 3.60
101 丹青4号 Danqing 4 国内 Domestic 皮 Hulled 3.65 3.48
102 ZYM00957 国内 Domestic 裸 Hulless 4.52 4.31
103 舟麦2号 Zhoumai 2 国内 Domestic 皮 Hulled 3.35 3.19
104 120 国外 Foreign 皮 Hulled 3.43 3.26
105 美国20 America 20 国外 Foreign 皮 Hulled 4.08 3.89
106 美25/1 America 25/1 国外 Foreign 皮 Hulled 4.16 3.97
107 云啤4号 Yunpi 4 国内 Domestic 皮 Hulled 2.85 2.71
108 美15 America 15 国外 Foreign 皮 Hulled 4.74 4.52
109 08京-341 08Jing-341 国内 Domestic 皮 Hulled 3.13 2.97
110 美4/I America 4/I 国外 Foreign 皮 Hulled 2.89 3.41
111 新啤2号 Xinpi 2 国内 Domestic 皮 Hulled 2.72 3.23
112 美国4 America 4 国外 Foreign 皮 Hulled 2.98 3.51
113 嘉士伯1 Carlsberg 1 国外 Foreign 皮 Hulled 1.23 1.79
114 苏啤6号 Supi 6 国内 Domestic 皮 Hulled 3.49 4.10
115 08京-211 08Jing-211 国内 Domestic 皮 Hulled 3.08 3.63
116 莫特44 Mott 44 国外 Foreign 皮 Hulled 2.84 3.35
117 毛大麦 Mao barley 国内 Domestic 皮 Hulled 3.76 4.40
118 龙09026 Long 09026 国内 Domestic 皮 Hulled 1.83 2.22
119 青永4026 Qingyong 4026 国内 Domestic 皮 Hulled 2.56 3.03
120 浙农大2 Zhenongda 2 国内 Domestic 皮 Hulled 3.07 3.61
121 美32/I America 32/I 国外 Foreign 皮 Hulled 2.92 3.45
122 浙农15 Zhenong 15 国内 Domestic 皮 Hulled 2.99 3.52
123 鉴19 Jian 19 国内 Domestic 皮 Hulled 3.09 3.64
124 08京-288 08Jing-288 国内 Domestic 裸 Hulless 3.29 3.86
125 08京-319 08Jing-319 国内 Domestic 裸 Hulless 2.29 2.73
126 青426 Qing426 国内 Domestic 裸 Hulless 2.35 2.79
127 西-2915 Xi-2915 国内 Domestic 皮 Hulled 3.25 3.82
128 美42 America 42 国外 Foreign 皮 Hulled 2.35 2.80
129 美37 America 37 国外 Foreign 皮 Hulled 2.77 3.28
130 08京-306 08Jing-306 国内 Domestic 皮 Hulled 3.11 3.66
131 美国19 America 19 国外 Foreign 皮 Hulled 2.61 3.10
132 驻大麦7号 Zhudamai 7 国内 Domestic 皮 Hulled 1.87 2.26
133 周麦02 Zhoumai 02 国内 Domestic 皮 Hulled 2.02 2.43
134 ZDM01224 国内 Domestic 皮 Hulled 2.49 2.96
135 扬饲麦3号 Yangsimai 3 国内 Domestic 皮 Hulled 2.54 3.02
136 陇啤1号 Longpi 1 国内 Domestic 皮 Hulled 1.98 2.38
137 苏啤3号 Supi 3 国内 Domestic 皮 Hulled 2.28 2.72
138 美5 America 5 国外 Foreign 皮 Hulled 3.00 3.54
139 垦啤麦2号 Kenpimai 2 国内 Domestic 皮 Hulled 2.71 3.22
140 美国14 America 14 国外 Foreign 皮 Hulled 1.88 2.28
141 盐品08-12 Yanpin 08-12 国内 Domestic 皮 Hulled 3.67 4.29
142 ZY49-西-2900 ZY49-Xi-2900 国内 Domestic 皮 Hulled 4.97 5.77
143 美18/I America 18/I 国外 Foreign 皮 Hulled 3.84 4.49
144 青0059 Qing 0059 国内 Domestic 裸 Hulless 5.01 5.81
145 黄长尖大麦Huangchangjian barley 国内 Domestic 裸 Hulless 5.17 5.98
146 美1612 America 1612 国外 Foreign 皮 Hulled 4.21 4.90
147 美17 America 17 国外 Foreign 皮 Hulled 3.89 4.55
148 08京-0369-1 08Jing-0369-1 国内 Domestic 皮 Hulled 4.09 4.76
149 斯库那 Schooner 国外 Foreign 皮 Hulled 3.92 4.58
150 美国25 America 25 国外 Foreign 皮 Hulled 3.58 4.19
151 08京-825 08Jing-825 国内 Domestic 皮 Hulled 4.53 5.26
152 西安91-2 Xi’an 91-2 国内 Domestic 皮 Hulled 3.95 4.60
153 苏啤4号 Supi 4 国内 Domestic 皮 Hulled 3.54 4.15
154 美31/I America 31/I 国外 Foreign 皮 Hulled 3.38 3.97
155 美国1 America 1 国外 Foreign 皮 Hulled 4.44 5.16
156 ZDM03581 国内 Domestic 皮 Hulled 3.56 4.16
157 ZDM05863 国内 Domestic 皮 Hulled 3.50 4.10
158 ZDM037S4107 国内 Domestic 皮 Hulled 3.37 3.95
159 ZDM02065 国内 Domestic 皮 Hulled 4.86 5.64
160 ZDM00128 国内 Domestic 皮 Hulled 4.26 4.95
161 ZDM02894 国内 Domestic 皮 Hulled 4.14 4.82
162 ZDM00513 国内 Domestic 皮 Hulled 4.34 5.06
163 ZDM01798 国内 Domestic 皮 Hulled 4.32 5.03
164 ZDM6552 国内 Domestic 皮 Hulled 3.46 4.05
165 ZDM09978 国内 Domestic 皮 Hulled 4.29 5.00
166 ZDM5455 国内 Domestic 皮 Hulled 4.65 5.41
167 ZDM10004 国内 Domestic 皮 Hulled 6.13 6.64
168 ZDM08845 国内 Domestic 裸 Hulless 4.98 5.77
169 ZDM10064 国内 Domestic 皮 Hulled 5.21 6.03
170 Z16 国内 Domestic 皮 Hulled 4.35 5.05
171 ZDM03637 国内 Domestic 皮 Hulled 3.24 3.92
172 ZDM01278 国内 Domestic 皮 Hulled 4.30 5.11
173 ZDM01419 国内 Domestic 皮 Hulled 3.74 4.49
174 ZDM05244 国内 Domestic 皮 Hulled 5.37 6.33
175 ZDM01082 国内 Domestic 皮 Hulled 3.20 3.87
176 ZDM00062 国内 Domestic 皮 Hulled 3.99 4.75
177 ZD2751405 国内 Domestic 皮 Hulled 4.42 5.25
178 ZDM5169 国内 Domestic 皮 Hulled 4.25 5.05
179 ZDM5187 国内 Domestic 裸 Hulless 3.86 4.63
180 ZDM5166 国内 Domestic 裸 Hulless 4.83 5.71
181 ZDM390404 国内 Domestic 皮 Hulled 3.28 3.95
182 ZDM5108 国内 Domestic 皮 Hulled 4.64 5.50
183 ZDM9311 国内 Domestic 皮 Hulled 4.59 4.56
184 ZDM5492 国内 Domestic 皮 Hulled 4.30 5.10
185 ZDM01366 国内 Domestic 皮 Hulled 4.45 5.26
186 ZDM06162 国内 Domestic 皮 Hulled 4.13 4.93
187 苏盐005 Suyan 005 国内 Domestic 皮 Hulled 3.51 4.23
188 ZDM01201 国内 Domestic 皮 Hulled 3.80 4.55
189 ZDM20057W 国内 Domestic 皮 Hulled 4.09 4.86
190 ZY22-83观-30 ZY22-83Guan-30 国内 Domestic 皮 Hulled 4.37 5.17
191 0020-4 国外 Foreign 皮 Hulled 3.04 3.69
192 ZY9-3-096 国内 Domestic 皮 Hulled 4.99 5.90
193 08京-309 08Jing-309 国内 Domestic 皮 Hulled 4.33 5.14
194 宝鸡 Baoji 国内 Domestic 皮 Hulled 4.05 4.82
195 NFC-Tcccple 国外 Foreign 皮 Hulled 3.17 3.85
196 12-p108 国外 Foreign 皮 Hulled 3.82 4.56
197 黑大麦诱变-1 Heidamaiyoubian-1 国内 Domestic 皮 Hulled 3.63 4.35
198 WDM06690 国外 Foreign 皮 Hulled 4.97 5.88
199 大麦11 Damai 11 国内 Domestic 皮 Hulled 4.07 3.48
200 WDM06933 国外 Foreign 皮 Hulled 3.91 3.34
201 韭岐12号 Jiuqi 12 国内 Domestic 皮 Hulled 3.76 3.20
202 12-PR40-大麦 12-PR40-Damai 国外 Foreign 皮 Hulled 5.00 4.33
203 ZY157-60477071v 国内 Domestic 皮 Hulled 4.62 3.99
204 Z140v015w 国内 Domestic 皮 Hulled 3.85 3.28
205 内0807-36 Nei 0807-36 国内 Domestic 皮 Hulled 2.99 2.50
206 9910-49 国外 Foreign 皮 Hulled 4.82 4.16
207 ZY102-RcsEARCN 国内 Domestic 裸 Hulless 4.03 3.40
208 ZY46-菲特36 ZY46-Feite 36 国内 Domestic 皮 Hulled 4.95 4.28
209 8810-31-3 国外 Foreign 皮 Hulled 4.45 3.83
210 ZYM0031 国内 Domestic 皮 Hulled 3.56 3.01
211 WDM05667 国外 Foreign 皮 Hulled 4.17 3.58
212 ZY95-04R1213 国内 Domestic 皮 Hulled 3.98 3.40
213 2019-DM-0132 国内 Domestic 皮 Hulled 3.57 3.03
214 ZY07-Z0260151R 国内 Domestic 皮 Hulled 4.78 4.13
215 SCARLETT 国外 Foreign 皮 Hulled 3.73 3.19
216 ZY71-Z141V027W 国内 Domestic 皮 Hulled 3.46 3.44
217 ZDM0630 国内 Domestic 皮 Hulled 4.63 3.98
218 TDCADA 国外 Foreign 皮 Hulled 3.79 3.23
219 嘉士伯3 Carlsberg 3 国外 Foreign 皮 Hulled 3.39 2.87
220 ZY56-BYTCT18 国内 Domestic 皮 Hulled 4.11 3.53
221 ZYM0207 国内 Domestic 皮 Hulled 4.36 3.75
222 美3312 America 3312 国外 Foreign 皮 Hulled 4.15 3.56
223 ZY86-B0NT36 国内 Domestic 皮 Hulled 3.40 2.87
224 ZY51-0014-28 国内 Domestic 皮 Hulled 2.85 2.37
225 德13 Germany 13 国外 Foreign 皮 Hulled 2.67 2.22
226 ZY43Y0661V 国内 Domestic 皮 Hulled 2.74 2.28
227 08京-307 08Jing-307 国内 Domestic 皮 Hulled 3.82 3.21
228 MAPDMMA 国外 Foreign 皮 Hulled 2.85 2.37
229 ZY1153-2122V072W 国内 Domestic 皮 Hulled 4.11 3.47
230 ZY716-99263 国内 Domestic 皮 Hulled 4.10 3.45
231 0010-13 国外 Foreign 皮 Hulled 3.66 3.07
232 华6 Hua 6 国内 Domestic 皮 Hulled 4.45 3.76
233 08京-3599 08Jing-3599 国内 Domestic 皮 Hulled 4.55 3.85
234 08京-318 08Jing-318 国内 Domestic 皮 Hulled 3.78 3.18
235 8967-BONCT68 国外 Foreign 皮 Hulled 3.72 3.12
236 Z141V055W 国内 Domestic 皮 Hulled 3.08 3.06
237 12-D320-08京 12-D320-08Jing 国内 Domestic 皮 Hulled 3.88 3.86
238 08京-c69 08Jing-c69 国内 Domestic 裸 Hulless 4.21 4.10

Table 1

Statistical analysis of β-glucan content in 238 barley materials"

年份
Year		 最大值 Max. (%) 最小值
Min. (%)		 平均值±标准差
Average ± SD
(%)		 峰度
Kurtosis		 偏度
Skewness		 变异系数
Coefficient of variation (%)		 相关系数
Correlation coefficient
2021 2022
2021 6.55 1.23 3.77±0.98 -0.17 0.18 0.26
2022 6.64 1.79 3.81±1.08 -0.52 0.29 0.28 0.88**
BLUP 6.24 1.66 3.79±0.93 -0.34 0.21 0.24 0.97** 0.97**

Fig. 1

Distribution frequency of β-glucan content of the examined 238 barley accessions in different years A: Year of 2021; B: Year of 2022; C: BLUP for combined two years."

Fig. 2

Marker density map of genome-wide association study"

Table 2

Basic statistics of the SNP markers in GWAS"

染色体
Chr.		 标记数目
Number of markers		 物理长度
Physical distance (Mb)		 标记密度
Density of marker (Mb)
1H 16,547 588.39 28.12
2H 25,489 767.60 33.21
3H 23,484 699.60 33.57
4H 13,428 646.74 20.76
5H 23,189 670.01 34.61
6H 17,819 583.31 30.55
7H 22,090 656.94 33.63

Fig. 3

Population linkage disequilibrium (LD) of 238 barley accessions"

Fig. 4

Frequency plot of relatives (A) and Kinship heatmap (B) of 238 barley materials"

Fig. 5

Analysis of population structure in 238 barley materials A: Trend of estimated K in population structure analysis; B: Population structure analysis diagram of the tested material."

Table 3

Basic statistical information of population structure analysis"

亚群
Subpopulation		 国内来源数量
Quantity of domestic origin		 国外来源数量
Quantity of foreign
origin		 皮大麦数量
Quantity of hulled
barley		 裸大麦数量
Quantity of hulless
barley		 合计
Total
Pop 1 44 17 51 10 61
Pop 2 51 22 66 7 66
Pop 3 52 15 50 17 37
Pop 4 30 7 29 8 74

Fig. 6

Quantile-quantile (QQ) plots resulting from GWAS results using five methods for β-glucan contents in two years A: Year of 2021; B: Year of 2022; C: BLUP for combined two years. Green spot: Q model; Purple spot: K model; Red spot: PCA model; Yellow spot: Q+K model; Black spot: PCA+K model."

Fig. 7

Manhattan plots of β-glucan contents in the optimal model for two years Purple spot: year of 2021; Blue spot: year of 2022; Yellow spot: BLUP for combined two years; Pink spot: significant SNPs."

Table 4

Summary of significant SNPs for β-glucan contents by using the optimal model"

年份
Year		 标记名称
Marker name		 染色体
Chr.		 位置
Position (bp)		 显著性域值
-log10 (P-value)		 贡献率
R2 (%)
2021 B1_1033963 1 1033963 6.40 0.10293
B2_34865369 2 34865369 4.95 0.07825
B3_598264349 3 598264349 4.81 0.07585
B1_2999129 1 2999129 4.71 0.08901
B4_645231560 4 645231560 4.70 0.07517
B4_533351773 5 533351773 4.69 0.07385
B5_516850066 5 516850066 4.66 0.08696
2022 B3_606349426 3 606349426 6.00 0.09726
B3_604763368 3 604763368 5.92 0.09585
B3_606693235 3 606693235 5.47 0.08803
B3_599121973 3 599121973 5.44 0.08763
B3_601166248 3 601166248 5.41 0.10127
B3_607095876 3 607095876 5.27 0.08493
B3_606643867 3 606643867 5.20 0.09745
B3_604951103 3 604951103 4.95 0.09301
B3_608060734 3 608060734 4.78 0.09097
B3_598505264 3 598505264 4.71 0.07504

Table 5

Candidate genes information of significantly associated SNPs with β-glucan content by GWAS"

基因名称
Gene name		 物理位置
Physical position		 功能注释
Functional annotation		 拟南芥
同源基因
Homologs in
A. thaliana
HORVU.MOREX.r3.1HG0000140 1H: 412,991-413,576 Glycosyltransferase AT2G41451
HORVU.MOREX.r3.1HG0000130 1H: 382,118-382,803 Paired amphipathic helix protein Sin3 AT1G70060
HORVU.MOREX.r3.1HG0000340 1H: 1,145,563-1,145,771 Acyltransferase AT1G54570
HORVU.MOREX.r3.1HG0001330 1H: 2,970,580-2,971,665 B1 hordein AT3G43540
HORVU.MOREX.r3.2HG0109660 2H: 30,469,069-30,469,472 Trichohyalin AT3G05670
HORVU.MOREX.r3.3HG0298540 3H: 534,080,554-534,082,933 Patellin 3 (PATL) AT4G09160
HORVU.MOREX.r3.3HG0298680 3H: 534,489,522-534,489,915 MYB related protein 308 AT4G05100
HORVU.MOREX.r3.3HG0298750 3H: 534,621,020-534,621,316 Magnesium transporter NIPA6 AT4G38730
HORVU.MOREX.r3.3HG0298790 3H: 534,696,482-534,697,957 Amidophosphoribosyltransferase AT2G16570
HORVU.MOREX.r3.3HG0298800 3H: 534,793,758-534,793,847 3-phosphoinositide-dependent protein kinase 1 AT5G04510
HORVU.MOREX.r3.3HG0299050 3H: 535,318,842-535,321,314 NRT1/PTR Family protein 5.10 AT1G72120
HORVU.MOREX.r3.3HG0299450 3H: 537,115,765-537,116,154 COV 2 protein AT3G29280
HORVU.MOREX.r3.3HG0299460 3H: 537,117,259-537,117,645 Polypyrimidine tract-binding protein homolog 3 AT1G43190
HORVU.MOREX.r3.3HG0300150 3H: 539,838,362-539,839,599 Transcription repressor OFP8 AT4G01985
HORVU.MOREX.r3.3HG0300160 3H: 539,853,495-539,854,163 Transcription repressor OFP13 AT3G58260
HORVU.MOREX.r3.3HG0300190 3H: 540,007,965-540,008,102 GL2 interacting repressor 1 AT5G06270
HORVU.MOREX.r3.3HG0300270 3H: 540,247,069-540,249,781 Subtilisin protease SBT3 AT5G05190
HORVU.MOREX.r3.3HG0300580 3H: 541,231,281-541,231,844 Endo 1,3-β-glucosidase 14 AT2G27500
HORVU.MOREX.r3.3HG0300590 3H: 541,262,653-541,263,099 Ferredoxin R-B1 AT1G10960
HORVU.MOREX.r3.3HG0300620 3H: 541,342,991-541,344,203 Internalin I AT5G51960
HORVU.MOREX.r3.3HG0300630 3H: 541,447,541-541,448,331 Protein suppressor of gene silencing 3 AT5G13500
HORVU.MOREX.r3.3HG0300640 3H: 541,561,354-541,562,251 Acidic endochitinase AT5G24090
HORVU.MOREX.r3.3HG0300650 3H: 541,566,655-541,567,548 Acidic endochitinase AT1G43580
HORVU.MOREX.r3.3HG0300720 3H: 541,841,548-541,842,602 Transcription factor LG2 AT5G10030
HORVU.MOREX.r3.3HG0300770 3H: 542,034,834-542,035,256 BZIP transcription factor ABI5 AT2G36270
HORVU.MOREX.r3.4HG0418520 4H: 609,355,974-609,357,530 Ethylene insensitive 2 AT3G49830
HORVU.MOREX.r3.4HG0418530 4H: 609,367,794-609,368,764 Chaperone protein (ClpB2) AT5G15450
HORVU.MOREX.r3.4HG0418540 4H: 609,385,039-609,385,806 Trichome birefringence 19 AT5G38710
HORVU.MOREX.r3.4HG0418560 4H: 609,395,655-609,396,232 Cis-prenyltransferase 4 AT5G58770
HORVU.MOREX.r3.4HG0418580 4H: 609,459,155-609,459,421 FT5 protein AT1G10330
HORVU.MOREX.r3.5HG0486400 5H: 459,622,075-459,623,326 Unknow protein AT3G23450
HORVU.MOREX.r3.5HG0486420 5H: 459,736,645-459,738,185 Acyl carrier protein desaturase 4 AT5G16230
HORVU.MOREX.r3.5HG0486440 5H: 459,850,945-459,856,351 Heat stress transcription factor B1 AT1G46264
HORVU.MOREX.r3.5HG0489430 5H: 473,610,764-473,612,139 Heavy metal associated isoprenylated plant protein 41 AT3G55840
HORVU.MOREX.r3.5HG0489440 5H: 473,638,330-473,638,935 Subtilisin protease (SBT5.3) AT1G04445
HORVU.MOREX.r3.5HG0489470 5H: 473,682,610-473,683,288 Zinc transporter 2 AT5G65450
HORVU.MOREX.r3.5HG0489530 5H: 473,846,912-473,850,714 Pentatricopeptide repeat containing protein AT3G24000
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