Crops ›› 2019, Vol. 35 ›› Issue (2): 61-70.doi: 10.16035/j.issn.1001-7283.2019.02.009

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Association Analysis of Root-Related Traits in Common Bean

Lei Wu,Lanfen Wang,Jing Wu,Shumin Wang   

  1. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2018-10-23 Revised:2018-12-26 Online:2019-04-15 Published:2019-04-12
  • Contact: Shumin Wang

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Abstract:

The root development at seeding stage plays an important role in crop growth and development. In this study, nine root-related traits such as taproot length, root dry weight, root volume and root surface area of 324 common bean accessions were examined by phenotyping using the growth bag paper culture system, and 116 polymorphic SSR (simple sequence repeats) markers covering the whole genome were performed by association analysis. Molecular markers and 9 root traits were analyzed by the program of MLM (mixed linear model) in Tassel 2.1 based on population structure and kinship. The results showed that the 324 common bean accessions were rich in phenotypic variation, and the average coefficient of variation (CV) ranged from 10.09% to 37.03%. Genotype analysis showed that 116 polymorphic SSR markers generated 919 allele loci. The range of genetic diversity index was from 0.0051 to 0.9098 with an average of 0.59. The average PIC (polymorphism information content) was 0.54 with range from 0.0051 to 0.9033. The results indicated that these markers had larger genetic diversity among the alleles in common bean accessions. The population structure analysis indicated that 324 common bean varieties were divided into two subgroups, which were consistent with the theory of common beans originated from two gene banks. Association analysis showed that 48 significant marker loci were detected with P<0.01 as a significant condition. Among these loci, ten marker loci were associated with more than two root traits simultaneously, five marker loci were coincident with previous studies, 43 marker loci were verified as new associated loci. The results provide a theoretical basis for further understandings of the genetic mechanism of roots and provide a basis for improvement of root system by molecular-assisted breeding selection in common bean.

Key words: Common bean, Root trait, SSR marker, Association analysis

Table 1

Origins of common bean germplasm resources"

统一编号Number 种质Germplasm 来源Origin 统一编号Number 种质Germplasm 来源Origin
F0002119 白小豆 中国甘肃 - 刀豆 中国山东
F0002120 白小豆 中国甘肃 F0000045 洋菜豆 中国山西
F0002275 浅红菜豆 中国甘肃 F0000049 架连豆 中国山西
F0002276 红菜豆 中国甘肃 F0000054 坚豆 中国山西
F0002277 红黑花豆 中国甘肃 F0000058 粘豆 中国山西
F0003342 白菜豆 中国甘肃 F0000089 花菜豆 中国山西
F0004027 褐菜豆 中国甘肃 F0000103 花灰灰豆 中国山西
F0005253 红腰豆 中国甘肃 F0001292 洋菜豆 中国山西
F0005263 四季豆 中国甘肃 F0001295 白眉豆 中国山西
F0005295 文昌四季豆 中国甘肃 F0001318 白菜豆 中国山西
F0001802 白桩桩豆 中国贵州 F0001339 白菜豆 中国山西
F0001809 玉滑豆 中国贵州 F0001342 白粒菜豆 中国山西
F0001823 大红金豆 中国贵州 F0001346 粉红紫皮连豆 中国山西
F0001850 木梳豆 中国贵州 F0001361 红梅豆 中国山西
F0001914 灰褐子 中国贵州 F0001380 小红豆 中国山西
F0002870 白云豆 中国贵州 F0001394 紫红豆 中国山西
F0002972 黑籽鳝豆 中国贵州 F0001416 红菜豆 中国山西
F0002974 黑金豆 中国贵州 F0001428 紫连豆 中国山西
F0003010 笔划豆 中国贵州 F0001434 黄红豆 中国山西
F0003067 白洋豆 中国贵州 F0001445 黄红豆 中国山西
F0003082 硬壳鸡腰豆 中国贵州 F0001459 无丝豆角 中国山西
F0003096 红芸豆 中国贵州 F0001463 到底青 中国山西
F0003274 五花大铁悫豆 中国贵州 F0001474 小灰豆 中国山西
F0003711 白金豆 中国贵州 F0001497 小灰豆 中国山西
F0003740 四季豆 中国贵州 F0001515 洋菜豆 中国山西
F0003757 大红豆 中国贵州 F0001523 灰菜豆 中国山西
F0003758 四季豆 中国贵州 F0001542 黑红豆 中国山西
F0003817 棒豆 中国贵州 F0001567 黑粘菜豆 中国山西
F0003843 四季豆 中国贵州 F0001600 白脸豆 中国山西
F0003970 黑花豆 中国贵州 F0001619 粉花梅豆 中国山西
F0003990 大蛋豆 中国贵州 F0001652 花色豆 中国山西
F0003992 红花豆 中国贵州 F0001663 花刀豆 中国山西
F0003405 秋白芸豆 中国河北 F0001670 梅豆 中国山西
F0003407 红芸豆 中国河北 F0001675 麻雀蛋 中国山西
F0003453 黑芸豆 中国河北 F0001691 花皮连豆 中国山西
F0005300 小黑芸豆 中国河北 F0001704 花金豆 中国山西
F0005620 泰科六号 中国河北 F0002223 洋菜豆 中国山西
F0000195 小白芸豆 中国黑龙江 F0002229 桔黄梅豆 中国山西
F0000199 精米豆 中国黑龙江 F0002240 小杂豆 中国山西
F0000203 精米豆 中国黑龙江 F0002262 秋红豆 中国山西
F0000211 红芸豆 中国黑龙江 F0001089 洋菜豆 中国陕西
F0000217 饭豆 中国黑龙江 F0001090 白芸豆 中国陕西
F0000272 龙70-8014 中国黑龙江 F0001102 洋蔓菜豆 中国陕西
F0000278 干枝密 中国黑龙江 F0001200 花红豆 中国陕西
F0000281 白腰豆 中国黑龙江 F0001244 没茎豆 中国陕西
F0000344 饭豆 中国黑龙江 F0001924 洋小豆 中国陕西
F0000385 花饭豆 中国黑龙江 F0001932 六十日早 中国陕西
F0000398 大马长 中国黑龙江 F0001942 红豆 中国陕西
F0000404 兔子腿 中国黑龙江 F0001972 五月黄 中国陕西
F0000415 花腰豆 中国黑龙江 F0002032 四茬四季豆 中国陕西
F0000528 紫花豆 中国黑龙江 F0002060 雀儿蛋 中国陕西
统一编号Number 种质Germplasm 来源Origin 统一编号Number 种质Germplasm 来源Origin
F0001749 灰小豆 中国黑龙江 F0002069 架四季豆 中国陕西
F0001757 毛毛豆 中国黑龙江 F0002073 画眉豆 中国陕西
F0001760 兔脚 中国黑龙江 F0002080 雀儿蛋 中国陕西
F0002503 白芸豆 中国黑龙江 F0005090 大豆 中国陕西
F0002509 白芸豆 中国黑龙江 F0005096 白豆 中国陕西
F0002521 黑芸豆 中国黑龙江 F0005219 红芸豆 中国陕西
F0002523 黑芸豆 中国黑龙江 F0002584 白四季豆 中国四川
F0002528 花芸豆 中国黑龙江 F0002608 鸡腰子豆 中国四川
F0002535 大马掌 中国黑龙江 F0002612 小猪腰豆 中国四川
F0002537 菜豆 中国黑龙江 F0002620 红腰子豆 中国四川
F0003346 龙饭豆一号 中国黑龙江 F0002623 红田季豆 中国四川
F0004837 黑芸豆 中国黑龙江 F0002624 紫红豆 中国四川
F0004845 黑芸豆 中国黑龙江 F0002628 腰子豆 中国四川
F0004851 黑芸豆 中国黑龙江 F0002673 乌褐豆 中国四川
F0004867 奶花芸豆 中国黑龙江 F0002683 硬壳豆 中国四川
F0004868 奶花芸豆 中国黑龙江 F0002755 小黑四季豆 中国四川
F0004869 奶花芸豆 中国黑龙江 F0002810 黑纹花豆 中国四川
F0004882 奶花芸豆 中国黑龙江 F0002838 四十豆 中国四川
F0004883 奶花芸豆 中国黑龙江 F0002863 奶花 中国四川
F0004886 奶花芸豆 中国黑龙江 F0003673 花四季豆 中国四川
F0004890 奶花芸豆 中国黑龙江 - 圆奶花芸豆X 中国新疆
F0004895 奶花芸豆 中国黑龙江 F0000666 小杂豆 中国云南
F0004899 奶花芸豆 中国黑龙江 F0000698 鸡腰子豆 中国云南
F0004910 奶花芸豆 中国黑龙江 F0000867 菜豆 中国云南
F0004911 奶花芸豆 中国黑龙江 F0000907 荷苞豆 中国云南
F0004923 奶花芸豆 中国黑龙江 F0001006 雀蛋豆 中国云南
F0004926 奶花芸豆 中国黑龙江 F0005027 NV 中国云南
F0005030 龙22-0579 中国黑龙江 F0005031 云丰2号 中国云南
F0005033 品芸2号 中国黑龙江 F0005035 260205 中国云南
F0005034 龙芸豆3号 中国黑龙江 F0005039 260219 中国云南
F0005237 龙芸豆4号 中国黑龙江 F0005361 浪台白菜豆 中国云南
F0005244 龙270267 中国黑龙江 F0005363 哈施菜豆 中国云南
F0005245 龙270270 中国黑龙江 F0005684 四季豆 中国云南
F0005246 龙270280 中国黑龙江 F0005857 02A4 阿根廷
F0005248 龙270705 中国黑龙江 F0005514 GURGUTUBA 巴西
F0005861 龙芸豆7号 中国黑龙江 F0005524 60 dias 巴西
- 圆奶花芸豆H 中国黑龙江 F0005526 Cubano 巴西
F0003554 白刀豆 中国湖北 F0005529 Paraná 1 巴西
F0003567 黄眉豆 中国湖北 F0005534 Paraná 巴西
F0003569 早菜豆 中国湖北 F0005536 BR IPA 10 巴西
F0003575 丛生四季豆 中国湖北 F0005550 Jalo Precoce 巴西
F0003578 灰米米 中国湖北 F0005555 Novo Jalo 巴西
F0003591 乌四季豆 中国湖北 F0005568 EMGOPA 201-Ouro 巴西
F0003624 四月娥 中国湖北 F0005574 Carioca MG 巴西
F0003626 小黑子 中国湖北 F0005575 Tambó 巴西
F0003635 黑豆子 中国湖北 F0005715 不详 巴西
F0003645 四季豆 中国湖北 F0005716 不详 巴西
F0004523 花四季豆 中国湖北 F0005717 不详 巴西
F0004529 白四季豆 中国湖北 F0005718 不详 巴西
F0004538 草白豆 中国湖北 F0005719 不详 巴西
F0004558 花饭豆 中国湖北 F0005721 不详 巴西
F0004562 紫莲豆 中国湖北 F0005875 不详 巴西
统一编号Number 种质Germplasm 来源Origin 统一编号Number 种质Germplasm 来源Origin
F0004564 面豆角 中国湖北 - Manaus No5 巴西
F0004566 圆奶花芸豆 中国湖北 - Manaus No4 巴西
F0004568 紫轱辘坡豆 中国湖北 - Manaus No2 巴西
F0002305 豆 中国湖南 - Manaus No3 巴西
F0000440 精米豆 中国吉林 F0002177 不详 法国
F0000442 白乌鸦菜豆 中国吉林 F0003363 不详 法国
F0000444 白乌鸦菜豆 中国吉林 F0003382 法引11号 法国
F0000445 白太 中国吉林 F0003386 歌47 法国
F0000446 白太 中国吉林 F0002125 A48 哥伦比亚
F0000448 白芸豆 中国吉林 F0002127 W126 哥伦比亚
F0000452 饭豆 中国吉林 F0002157 BAT896 哥伦比亚
F0000460 白饭豆 中国吉林 F0002166 BAT331 哥伦比亚
F0000470 白饭豆 中国吉林 F0002167 BAT85 哥伦比亚
F0000473 红芸豆 中国吉林 F0002169 BAT336 哥伦比亚
F0000474 菜豆 中国吉林 F0002170 M101 哥伦比亚
F0000475 菜豆 中国吉林 F0002171 A51 哥伦比亚
F0000490 饭豆 中国吉林 F0005767 SER4 哥伦比亚
F0000492 罗唐豆 中国吉林 F0005769 SER6 哥伦比亚
F0000493 乌鸦菜豆 中国吉林 F0005771 SER8 哥伦比亚
F0000494 乌鸦菜豆 中国吉林 F0005798 SER35 哥伦比亚
F0000495 乌鸦菜豆 中国吉林 F0005813 SEN13 哥伦比亚
F0000501 饭大豆 中国吉林 F0005830 SEN32 哥伦比亚
F0000502 饭豆 中国吉林 F0005833 SEC1 哥伦比亚
F0000503 无季豆 中国吉林 F0005841 SEC10 哥伦比亚
F0002477 小白豆 中国吉林 F0005843 SEC14 哥伦比亚
F0002481 扁白豆 中国吉林 F0005849 引红4 哥伦比亚
F0002486 白豆 中国吉林 F0005879 不详 哥伦比亚
F0002489 白饭豆 中国吉林 F0005910 不详 哥伦比亚
F0002492 红芸豆 中国吉林 F0003370 不详 美国
F0002493 红芸豆 中国吉林 - BAT-93 美国
F0002502 奶花芸豆 中国吉林 - PI 633451 美国
- 小红芸豆 中国吉林 F0005919 不详 秘鲁
F0000117 天鹅豆 中国内蒙古 F0005722 不详 墨西哥
F0000120 黄芸豆 中国内蒙古 F0005924 不详 墨西哥
F0000126 挑花枚白连豆 中国内蒙古 F0005093 芸豆 中国内蒙古
F0000143 饭豆 中国内蒙古 F0005877 不详 委内瑞拉
F0000153 小菜豆 中国内蒙古 F0004313 英国红芸豆 英国
F0000154 跃进豆 中国内蒙古 F0004321 ANT49 CIAT
F0001723 紫芸豆 中国内蒙古 F0004322 BRB-130 CIAT
F0001731 粉老来少 中国内蒙古 F0004333 UNS-27342-51 CIAT
F0001744 粉老来少 中国内蒙古 F0004334 LRK32 CIAT
F0002380 羊眼圈 中国内蒙古 F0004339 SEQ1006 CIAT
F0002399 红芸豆 中国内蒙古 F0004341 9249-3 CIAT
F0002400 面豆荚 中国内蒙古 F0004348 FOI10 CIAT
F0002441 大红菜豆 中国内蒙古 F0004349 FOI11 CIAT
F0002462 花菜豆 中国内蒙古 F0004350 MCD2409 CIAT
F0002471 家雀蛋 中国内蒙古 F0004357 DOR483 CIAT
F0003497 架菜豆 中国内蒙古 F0004374 DRK139 CIAT
F0003503 白连豆 中国内蒙古 F0004378 FOT32 CIAT
F0004188 江米豆 中国内蒙古 F0004395 ISB-82-865 CIAT
F0004216 架菜豆 中国内蒙古 F0004396 DRK134 CIAT
F0004227 芸豆 中国内蒙古 F0004398 FOT25 CIAT
统一编号Number 种质Germplasm 来源Origin 统一编号Number 种质Germplasm 来源Origin
F0004268 小芸豆 中国内蒙古 F0004403 DOR476 CIAT
F0004273 矮生红 中国内蒙古 F0004404 DOR482 CIAT
F0004587 紫轱辘坡豆 中国内蒙古 F0004410 VIVA CIAT
F0004592 奶花芸豆 中国内蒙古 F0004413 BAT58 CIAT
F0004594 金豆角 中国内蒙古 F0002152 R-5550 不详
F0005624 改良绿丰 中国山东 F0002153 R5350 不详
F0005629 四季架豆王 中国山东 - 圆奶花芸豆D 不详

Table 2

Statistical analysis of root-trait of common bean at seedling stage"

性状Trait 平均值Mean 最小值Min. 最大值Max. 标准差Standard deviation 变异系数Coefficient of variation (%)
主根长Taproot length (cm) 20.49 12.80 28.45 2.85 13.92
根干重Root dry weight (mg) 29.56 10.00 75.00 10.94 37.03
侧根数Lateral root number 12.05 5.40 22.80 3.18 26.38
总根长Total root length (cm) 204.93 68.93 476.26 67.36 32.87
根表面积Root surface area (cm2) 35.69 11.44 74.49 11.31 31.69
平均根直径Average root diameter (mm) 0.56 0.26 0.77 0.06 10.09
根体积Root volume (cm3) 0.50 0.15 1.04 0.16 33.08
侧根总长Lateral root length (cm) 184.44 55.29 452.41 65.48 35.50
比根长Special root length (mg/cm) 14.71 0.07 0.45 0.04 28.96

Fig.1

Frequency distribution of root-trait of common bean at seedling stage"

Table 3

Correlation of root traits"

性状
Trait		 主根长
Taproot
length		 根干重
Root dry
weight		 侧根数
Lateral root
number		 总根长
Total root
length		 根表面积
Root surface
area		 平均根直径
Average root
diameter		 根体积
Root
volume		 侧根总长
Lateral root
length		 比根长
Special root
length
主根长
Taproot length		 -1
根干重
Root dry weight		 -0.50** 1
侧根数
Lateral root number		 -0.49** 0.60** -1
总根长
Total root length		 -0.67** 0.68** -0.75** -1
根表面积
Root surface area		 -0.66** 0.79** -0.76** -0.96** -1
平均根直径
Average root diameter		 -0.08 0.27** -0.06 -0.22** -0.05 -1
根体积
Root volume		 -0.60** 0.83** -0.70** -0.83** -0.96** -0.32** 1
侧根总长
Lateral root length		 -0.65** 0.68** -0.75** -1.00** -0.96** -0.22** 0.83** -1
比根长
Special root length		 -0.07 0.54** -0.05 -0.21** -0.03 -0.62** 0.16** -0.21** 1

Fig.2

K and ΔK of population structure analysis based on SSR marker for 324 common bean accessions"

Table 4

Association analysis results based on MLM model"

性状Trait 标记位点
Locus		 P值
P-value		 表型贡献率
R2 (%)
根干重Root dry weight CBS206 6.30×10-6 6.96
CBS419 2.20×10-4 3.36
CBS110 5.67×10-4 3.83
P7S53 9.70×10-4 1.97
P7S191 0.0012 2.93
CBS139 0.0013 2.85
CBS261 0.0014 1.86
CBS208 0.0050 2.24
CBS345 0.0050 2.36
CBS307 0.0075 1.44
侧根数Lateral root number CBS28 0.0034 3.85
总根长Total root length CBS408 8.50×10-5 6.38
CBS22 0.0033 4.63
CBS250 0.0037 5.31
根表面积Root surface area CBS408 5.70×10-6 6.14
P7S53 0.0055 2.17
CBS162 0.0090 4.46
性状Trait 标记位点
Locus		 P值
P-value		 表型贡献率
R2 (%)
平均根直径Average root diameter CBS261 9.35×10-7 6.24
CBS179 1.59×10-6 6.37
CBS43 2.18×10-6 6.33
CBS296 6.58×10-6 7.54
CBS51 7.00×10-6 8.07
CBS216 1.74×10-5 6.15
P11S130 6.62×10-5 7.38
CBS56 1.13×10-4 5.97
CBS28 2.37×10-4 5.18
CBS343 3.55×10-4 5.86
CBS82 5.18×10-4 9.55
CBS126 8.54×10-4 3.86
CBS211 0.0026 3.73
CBS229 0.0028 3.58
CBS349 0.0030 4.27
CBS381 0.0032 6.46
CBS286 0.0050 4.11
P11S186 0.0062 2.43
CBS248 0.0078 3.73
根体积Root volume CBS408 9.74×10-6 5.17
CBS381 4.25×10-4 5.20
P7S53 0.0020 2.28
CBS162 0.0054 4.24
侧根总长Lateral root length CBS408 6.39×10-5 6.56
CBS22 0.0028 4.77
CBS250 0.0043 5.30
比根长Special root length CBS206 1.13×10-10 16.09
CBS419 2.23×10-7 7.35
CBS162 1.04×10-6 9.20
CBS149 1.37×10-4 6.07
CBS323 0.0019 4.81

Table 5

Comparison of the results of associated SSR loci with reported QTLs"

标记位点
SSR marker		 本研究性状
Traits of this study		 关联性状及QTL
Correlation traits and linked QTL
CBS56 平均根直径 比根长（LPSRL_AdvF.1）[27]
CBS208 根干重 比根长（HPSRL_AdvGH1.1）[27]
CBS211 平均根直径 比根长（HPSRL_AdvGH1.1）[27]
CBS286 平均根直径 比根长（LPSRL_AdvGH.2）[27]
P11S186
 平均根直径
 根干重（Rdw11.2）[11]、
总根长（HPAdv_LF.3）[27]
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