浙江农业学报 ›› 2024, Vol. 36 ›› Issue (5): 1055-1066.DOI: 10.3969/j.issn.1004-1524.20230663
李亚东1,2(), 罗小波3, 彭潇1,2, 杨光乾1,2, 金月月1,2, 祖贵东4, 田欢5, 张万萍1,2,*(
)
收稿日期:
2023-05-20
出版日期:
2024-05-25
发布日期:
2024-05-29
作者简介:
李亚东(1994—),男,贵州思南人,硕士研究生,研究方向为萝卜育种。E-mail:1475264389@qq.com
通讯作者:
* 张万萍,E-mail:1226190368@qq.com
基金资助:
LI Yadong1,2(), LUO Xiaobo3, PENG Xiao1,2, YANG Guangqian1,2, JIN Yueyue1,2, ZU Guidong4, TIAN Huan5, ZHANG Wanping1,2,*(
)
Received:
2023-05-20
Online:
2024-05-25
Published:
2024-05-29
摘要:
为了挖掘与萝卜表型性状显著相关的分子标记,对60份萝卜的14个表型数据进行鉴定,筛选出具有多态性的分子标记29个(其中12个SNP标记和17个InDel标记)进行遗传多样性分析,并利用TASSEL5.0软件的广义线性模型(general linear mode, GLM)对萝卜的14个表型数据进行关联分析。研究结果表明,29个分子标记的等位基因(Na)数范围在2~3个,平均为2.14个;主等位基因频率(MAF)为0.53~0.94个,平均为0.68个;每个标记的期望杂合度(He)范围为0.12~0.93,平均为0.63。每个位点的多态性信息含量(PIC)值范围在0.11~0.37,平均为0.32;在12个表型性状中关联到17个显著相关的分子标记位点(其中7个SNP标记和10个InDel标记)(P≤0.01),贡献率在7.24%~23.25%。
中图分类号:
李亚东, 罗小波, 彭潇, 杨光乾, 金月月, 祖贵东, 田欢, 张万萍. 萝卜SNP和InDel分子标记开发及与表型性状关联分析[J]. 浙江农业学报, 2024, 36(5): 1055-1066.
LI Yadong, LUO Xiaobo, PENG Xiao, YANG Guangqian, JIN Yueyue, ZU Guidong, TIAN Huan, ZHANG Wanping. Development of SNP and InDel markers in radish and their association with phenotypic characters[J]. Acta Agriculturae Zhejiangensis, 2024, 36(5): 1055-1066.
序号 No. | 品种 Variety | 序号 No. | 品种 Variety | 序号 No. | 品种 Variety | 序号 No. | 品种 Variety |
---|---|---|---|---|---|---|---|
1 | 彩虹一号 Caihong 1 | 16 | 盛青三号 Shengqing No.3 | 31 | 君川玉洁 Junchunyujie | 46 | 脆宝萝卜 Cuibaoluobo |
2 | 紫美人F1 Zimeiren F1 | 17 | 德高清泉 Degaoqingquan | 32 | 玉娇龙 Yujiaolong | 47 | 德蔬秋玉791 Deshuqiuyu 791 |
3 | 首尔紫脆 Shouerzicui | 18 | 大韩白春 Dahanbaichun | 33 | 珍白玉 Zhenbaiyu | 48 | 青云萝卜 Qingyunluobo |
4 | 笑脸 Xiaolian | 19 | 新西兰短叶13号 Xinxilanduanye 13 | 34 | 金天厚971 Jintianhou 971 | 49 | 冰糖脆里外青 Bingtangcuiliwaiqing |
5 | 手指萝卜 Shouzhiluobo | 20 | WN1 | 35 | 金天厚906 Jintianhou 906 | 50 | 露头青萝卜 Lutouqingluobo |
6 | 京红30 Jinghong 30 | 21 | WN2 | 36 | 金天厚949 Jintianhou 949 | 51 | 渝星翠雪 Yuxingcuixue |
7 | 徐州大红袍萝卜 Xuzhoudahongpaoluobo | 22 | WN3 | 37 | 金天厚112 Jintianhou 112 | 52 | 盛青一号 Shengqing No.1 |
8 | 盛农串心红 Shengnongchuanxinhong | 23 | 慕田红福二号 Mutianhongfu No.2 | 38 | 金天厚948 Jintianhou 948 | 53 | 富莹一号 Fuying No.1 |
9 | 樱桃萝卜萨丁 Yingtaoluobosading | 24 | 地增宝2号 Dizengbao 2 | 39 | 半夏萝卜 Banxialuobo | 54 | 凯撒203 Kaisa 203 |
10 | 红心萝卜 Hongxinluobo | 25 | 日本大根 Ribendagen | 40 | 胭脂白玉 Yanzhibaiyu | 55 | GZ1号 |
11 | 凤梨水果萝卜 Fenglishuiguoluobo | 26 | 春不老 Chunbulao | 41 | 玉露218 Yulu218 | 56 | GZ2号 |
12 | 江南圆白 Yunnanyuanbai | 27 | 金天厚R2008 Jintianhou R2008 | 42 | 春白玉 Chunbaiyu | 57 | GDE |
13 | 扬州圆白 Yangzhouyuanbai | 28 | 地增宝4号 Dizengbao 4 | 43 | 德高秋玉 Degaoqiuyu | 58 | GDL |
14 | 韩国大根 Hanguodagen | 29 | 美龙123 Meilong 123 | 44 | 白玉2号 Baiyu 2 | 59 | YZH |
15 | 中萝1号 Zhongluo 1 | 30 | 上将9号 Shangjiang 9 | 45 | 郫县黑叶春不老 Pixianheiyechunbulao | 60 | XHT |
表1 萝卜材料
Table 1 Materials of radish
序号 No. | 品种 Variety | 序号 No. | 品种 Variety | 序号 No. | 品种 Variety | 序号 No. | 品种 Variety |
---|---|---|---|---|---|---|---|
1 | 彩虹一号 Caihong 1 | 16 | 盛青三号 Shengqing No.3 | 31 | 君川玉洁 Junchunyujie | 46 | 脆宝萝卜 Cuibaoluobo |
2 | 紫美人F1 Zimeiren F1 | 17 | 德高清泉 Degaoqingquan | 32 | 玉娇龙 Yujiaolong | 47 | 德蔬秋玉791 Deshuqiuyu 791 |
3 | 首尔紫脆 Shouerzicui | 18 | 大韩白春 Dahanbaichun | 33 | 珍白玉 Zhenbaiyu | 48 | 青云萝卜 Qingyunluobo |
4 | 笑脸 Xiaolian | 19 | 新西兰短叶13号 Xinxilanduanye 13 | 34 | 金天厚971 Jintianhou 971 | 49 | 冰糖脆里外青 Bingtangcuiliwaiqing |
5 | 手指萝卜 Shouzhiluobo | 20 | WN1 | 35 | 金天厚906 Jintianhou 906 | 50 | 露头青萝卜 Lutouqingluobo |
6 | 京红30 Jinghong 30 | 21 | WN2 | 36 | 金天厚949 Jintianhou 949 | 51 | 渝星翠雪 Yuxingcuixue |
7 | 徐州大红袍萝卜 Xuzhoudahongpaoluobo | 22 | WN3 | 37 | 金天厚112 Jintianhou 112 | 52 | 盛青一号 Shengqing No.1 |
8 | 盛农串心红 Shengnongchuanxinhong | 23 | 慕田红福二号 Mutianhongfu No.2 | 38 | 金天厚948 Jintianhou 948 | 53 | 富莹一号 Fuying No.1 |
9 | 樱桃萝卜萨丁 Yingtaoluobosading | 24 | 地增宝2号 Dizengbao 2 | 39 | 半夏萝卜 Banxialuobo | 54 | 凯撒203 Kaisa 203 |
10 | 红心萝卜 Hongxinluobo | 25 | 日本大根 Ribendagen | 40 | 胭脂白玉 Yanzhibaiyu | 55 | GZ1号 |
11 | 凤梨水果萝卜 Fenglishuiguoluobo | 26 | 春不老 Chunbulao | 41 | 玉露218 Yulu218 | 56 | GZ2号 |
12 | 江南圆白 Yunnanyuanbai | 27 | 金天厚R2008 Jintianhou R2008 | 42 | 春白玉 Chunbaiyu | 57 | GDE |
13 | 扬州圆白 Yangzhouyuanbai | 28 | 地增宝4号 Dizengbao 4 | 43 | 德高秋玉 Degaoqiuyu | 58 | GDL |
14 | 韩国大根 Hanguodagen | 29 | 美龙123 Meilong 123 | 44 | 白玉2号 Baiyu 2 | 59 | YZH |
15 | 中萝1号 Zhongluo 1 | 30 | 上将9号 Shangjiang 9 | 45 | 郫县黑叶春不老 Pixianheiyechunbulao | 60 | XHT |
性状 Trait | 赋值 Assignment | |
---|---|---|
叶型 | 1,板叶;2,花叶 | |
Leaf profile | 1, Plate leaf; 2, Flowers and leaves | |
叶形 | 1,卵圆;2,长卵圆;3,倒卵圆;4,长倒卵圆;5,椭圆;6,长椭圆;7,批针 | |
Leaf shape | 1, Oval; 2, Long oval; 3, Inverted oval; 4, Long oblong oval; 5, Ellipse; 6, Long ellipse; 7, Batches of needles | |
叶尖 | 1,锐尖;2,尖;3,圆;4,阔圆 | |
Leaf opex | 1, Sharp point; 2, Tip; 3, Circles; 4, Wide round | |
叶色 | 1,黄绿;2,浅绿;3,绿;4,深绿 | |
Leaf colour | 1, Yellow green; 2, Light green; 3, Green; 4, Dark green | |
叶脉色 | 1,黄绿;2,浅绿;3,绿;4,红;5,浅紫;6,紫 | |
Color of leaf veins | 1, Yellow green; 2, Light green; 3, Green; 4, Red; 5, Light purple; 6, Purple | |
叶面刺毛Leaf seta | 0,无;1,少; 2,中;3,多;0, None; 1, Less; 2, Medium; 3, More | |
叶缘 | 0,无裂刻;1,全缘;2,波状;3,锯齿 | |
Leaf margin | 0, No cracking; 1, Whole margin; 2, Wave-like; 3, Sawtooth | |
叶裂刻 | 1,浅裂;2,深裂;3,全裂 | |
Leaf crack | 1, Lobulated; 2, Deep cleft; 3, Complete cleavage | |
肉质根侧根分布 | 0,无;1,少;2,中;3,多 | |
Lateral root distribution | 0, None; 1, Less; 2, Medium; 3, More | |
肉质根表面光滑度 | 1,光滑;2,中等;3,粗糙 | |
Smoothness of the fleshy | 1, Smooth; 2, Medium; 3, Rough | |
root surface | ||
根形Root form | 1,长圆柱;2,短圆柱;3,长弯号角;4,短弯号角;5,长圆锥;6,短圆锥;7,倒长圆锥;8,倒短圆锥;9,卵圆;10,扁圆;11,近圆;12,梨形;13,纺锤形;14,高圆台;15,矮圆台 | |
1, Long cylinder; 2, Short cylinder; 3, Long horn; 4, Short horn; 5, Long cone; 6, Short cone; 7, Inverted long cone; 8, Inverted short cone; 9, Oval; 10, Oblong; 11, Near round; 12, Pear shaped; 13, Spindle shape; 14, High round table; 15, Low round table | ||
肉质根地上部皮色 | 1,白;2,白绿;3,浅绿;4,绿;5,深绿;6,粉红;7,红;8,浅紫;9,紫 | |
Color of aboveground part | 1, White; 2, White green; 3, Light green; 4, Green; 5, Dark green; 6, Pink; 7, Red; 8, Light purple; 9, Purple | |
of fleshy root | ||
肉质根地下部皮色 | 1,白;2,浅绿;3,绿;4,粉红;5,红;6,紫 | |
Color of underground part | 1, White; 2, Light green; 3, Green; 4, Pink; 5, Red; 6, Purple | |
of fleshy root | ||
肉色 | 1,白;2,浅绿;3,绿;4,深绿;5,粉红;6,红;7,浅紫;8,紫 | |
Color of flesh | 1, White; 2, Light green; 3, Green; 4, Dark green; 5, Pink; 6, Red; 7, Light purple; 8, Purple |
表2 萝卜表型性状及赋值标准
Table 2 Phenotypic characters and evaluation criteria of radish
性状 Trait | 赋值 Assignment | |
---|---|---|
叶型 | 1,板叶;2,花叶 | |
Leaf profile | 1, Plate leaf; 2, Flowers and leaves | |
叶形 | 1,卵圆;2,长卵圆;3,倒卵圆;4,长倒卵圆;5,椭圆;6,长椭圆;7,批针 | |
Leaf shape | 1, Oval; 2, Long oval; 3, Inverted oval; 4, Long oblong oval; 5, Ellipse; 6, Long ellipse; 7, Batches of needles | |
叶尖 | 1,锐尖;2,尖;3,圆;4,阔圆 | |
Leaf opex | 1, Sharp point; 2, Tip; 3, Circles; 4, Wide round | |
叶色 | 1,黄绿;2,浅绿;3,绿;4,深绿 | |
Leaf colour | 1, Yellow green; 2, Light green; 3, Green; 4, Dark green | |
叶脉色 | 1,黄绿;2,浅绿;3,绿;4,红;5,浅紫;6,紫 | |
Color of leaf veins | 1, Yellow green; 2, Light green; 3, Green; 4, Red; 5, Light purple; 6, Purple | |
叶面刺毛Leaf seta | 0,无;1,少; 2,中;3,多;0, None; 1, Less; 2, Medium; 3, More | |
叶缘 | 0,无裂刻;1,全缘;2,波状;3,锯齿 | |
Leaf margin | 0, No cracking; 1, Whole margin; 2, Wave-like; 3, Sawtooth | |
叶裂刻 | 1,浅裂;2,深裂;3,全裂 | |
Leaf crack | 1, Lobulated; 2, Deep cleft; 3, Complete cleavage | |
肉质根侧根分布 | 0,无;1,少;2,中;3,多 | |
Lateral root distribution | 0, None; 1, Less; 2, Medium; 3, More | |
肉质根表面光滑度 | 1,光滑;2,中等;3,粗糙 | |
Smoothness of the fleshy | 1, Smooth; 2, Medium; 3, Rough | |
root surface | ||
根形Root form | 1,长圆柱;2,短圆柱;3,长弯号角;4,短弯号角;5,长圆锥;6,短圆锥;7,倒长圆锥;8,倒短圆锥;9,卵圆;10,扁圆;11,近圆;12,梨形;13,纺锤形;14,高圆台;15,矮圆台 | |
1, Long cylinder; 2, Short cylinder; 3, Long horn; 4, Short horn; 5, Long cone; 6, Short cone; 7, Inverted long cone; 8, Inverted short cone; 9, Oval; 10, Oblong; 11, Near round; 12, Pear shaped; 13, Spindle shape; 14, High round table; 15, Low round table | ||
肉质根地上部皮色 | 1,白;2,白绿;3,浅绿;4,绿;5,深绿;6,粉红;7,红;8,浅紫;9,紫 | |
Color of aboveground part | 1, White; 2, White green; 3, Light green; 4, Green; 5, Dark green; 6, Pink; 7, Red; 8, Light purple; 9, Purple | |
of fleshy root | ||
肉质根地下部皮色 | 1,白;2,浅绿;3,绿;4,粉红;5,红;6,紫 | |
Color of underground part | 1, White; 2, Light green; 3, Green; 4, Pink; 5, Red; 6, Purple | |
of fleshy root | ||
肉色 | 1,白;2,浅绿;3,绿;4,深绿;5,粉红;6,红;7,浅紫;8,紫 | |
Color of flesh | 1, White; 2, Light green; 3, Green; 4, Dark green; 5, Pink; 6, Red; 7, Light purple; 8, Purple |
引物名称 Primer name | 染色体 Chr | 位置 Position | 注释的基因 Anno_ Gene | 注释的位置 Anno_Pos | 正向引物 Forward primer | 反向引物 Reverse primer | 产物大小 Product size/bp |
---|---|---|---|---|---|---|---|
InDelR1-2 | R1 | 776 114 | Rs001290 | frameshift | TCTGTTTGCCAGTTTCGT | AAACAAGAACAGCCCCAT | 123 |
InDelR1-3 | R1 | 1 313 749 | Rs002390 | nonframeshift | GTTTCCGTCGTCACTTCT | GAAGCCAAATCACAAGTC | 167 |
InDelR2-1 | R2 | 2 594 367 | Rs101280 | intronic | TCCCTGTAAATTCTTGTC | AAGAAACAGTACCGTCAA | 198 |
InDelR2-3 | R2 | 9 755 367 | Rs093700 | upstream | GATGATTCGTGTTTCTTG | GCACTAACGAATTAGGTG | 170 |
InDelR3-1 | R3 | 17 365 594 | Rs128600 | intronic | GGCTCAATGATACCTCCC | GTCAGCCAAGGTACGACC | 169 |
InDelR3-2 | R3 | 22 641 607 | Rs136110 | intergenic | TGCAATAGTGTTGAGGAC | CGTATCCACCACTACATA | 167 |
InDelR4-2 | R4 | 6 629 791 | Rs161140 | intronic | CAAACCCTGAAAACCCAT | CTTGTGGTGCGATGCTAT | 199 |
InDelR5-1 | R5 | 3 652 986 | Rs225420 | intronic | GCTGGTATCCATTCTCCT | TAAAGTGCAAGAAGCGAG | 141 |
InDelR5-2 | R5 | 7 215 633 | Rs231360 | upstream | GAATCATTTACAGCATCA | TGGAACCGATTAAAGTGT | 128 |
InDelR5-3 | R5 | 11 178 127 | Rs237340 | UTR3 | GTTGTGGGACTCTTGTGA | AGAACAAGATCAGATCCATG | 200 |
InDelR6-3 | R6 | 11 171 972 | Rs308290 | nonframeshift | TAAGGGAGACGATGAACC | GCTCTGTTTCCTGCAAAG | 197 |
InDelR7-1 | R7 | 5 269 877 | Rs396800 | UTR3 | GGTTGATGGATGGGAATT | ACTCCCAAGTTCCTTTGC | 176 |
InDelR7-3 | R7 | 15 927 653 | Rs381480 | intergenic | TATGTGATTGATTGGCAT | GAAGATGTGGAAAACGAT | 199 |
InDelR8-1 | R8 | 5 489 898 | Rs416170 | UTR5 | TGGGTTTGTACGTTGTTG | TCTATCAAATCCCTCGTA | 135 |
InDelR8-2 | R8 | 11 419 948 | Rs425900 | intergenic | GCATCCTGACTTGCTCTG | AGGAGGGGAGATGACAAG | 133 |
InDelR9-1 | R9 | 5 051 478 | Rs455320 | intronic | TGTCTTCTTTCGTGTCCT | CTAATGACACCCAGAAAGA | 170 |
InDelR9-2 | R9 | 11 215 705 | Rs463920 | intergenic | TTATAGGGTCTTCTTGAG | ATGTGCCTCAAAATCTGT | 187 |
表3 InDel引物信息
Table 3 InDel primer information
引物名称 Primer name | 染色体 Chr | 位置 Position | 注释的基因 Anno_ Gene | 注释的位置 Anno_Pos | 正向引物 Forward primer | 反向引物 Reverse primer | 产物大小 Product size/bp |
---|---|---|---|---|---|---|---|
InDelR1-2 | R1 | 776 114 | Rs001290 | frameshift | TCTGTTTGCCAGTTTCGT | AAACAAGAACAGCCCCAT | 123 |
InDelR1-3 | R1 | 1 313 749 | Rs002390 | nonframeshift | GTTTCCGTCGTCACTTCT | GAAGCCAAATCACAAGTC | 167 |
InDelR2-1 | R2 | 2 594 367 | Rs101280 | intronic | TCCCTGTAAATTCTTGTC | AAGAAACAGTACCGTCAA | 198 |
InDelR2-3 | R2 | 9 755 367 | Rs093700 | upstream | GATGATTCGTGTTTCTTG | GCACTAACGAATTAGGTG | 170 |
InDelR3-1 | R3 | 17 365 594 | Rs128600 | intronic | GGCTCAATGATACCTCCC | GTCAGCCAAGGTACGACC | 169 |
InDelR3-2 | R3 | 22 641 607 | Rs136110 | intergenic | TGCAATAGTGTTGAGGAC | CGTATCCACCACTACATA | 167 |
InDelR4-2 | R4 | 6 629 791 | Rs161140 | intronic | CAAACCCTGAAAACCCAT | CTTGTGGTGCGATGCTAT | 199 |
InDelR5-1 | R5 | 3 652 986 | Rs225420 | intronic | GCTGGTATCCATTCTCCT | TAAAGTGCAAGAAGCGAG | 141 |
InDelR5-2 | R5 | 7 215 633 | Rs231360 | upstream | GAATCATTTACAGCATCA | TGGAACCGATTAAAGTGT | 128 |
InDelR5-3 | R5 | 11 178 127 | Rs237340 | UTR3 | GTTGTGGGACTCTTGTGA | AGAACAAGATCAGATCCATG | 200 |
InDelR6-3 | R6 | 11 171 972 | Rs308290 | nonframeshift | TAAGGGAGACGATGAACC | GCTCTGTTTCCTGCAAAG | 197 |
InDelR7-1 | R7 | 5 269 877 | Rs396800 | UTR3 | GGTTGATGGATGGGAATT | ACTCCCAAGTTCCTTTGC | 176 |
InDelR7-3 | R7 | 15 927 653 | Rs381480 | intergenic | TATGTGATTGATTGGCAT | GAAGATGTGGAAAACGAT | 199 |
InDelR8-1 | R8 | 5 489 898 | Rs416170 | UTR5 | TGGGTTTGTACGTTGTTG | TCTATCAAATCCCTCGTA | 135 |
InDelR8-2 | R8 | 11 419 948 | Rs425900 | intergenic | GCATCCTGACTTGCTCTG | AGGAGGGGAGATGACAAG | 133 |
InDelR9-1 | R9 | 5 051 478 | Rs455320 | intronic | TGTCTTCTTTCGTGTCCT | CTAATGACACCCAGAAAGA | 170 |
InDelR9-2 | R9 | 11 215 705 | Rs463920 | intergenic | TTATAGGGTCTTCTTGAG | ATGTGCCTCAAAATCTGT | 187 |
引物名称 Primer name | 染色体 Chromo- some | 位置 Position | 注释的基因 Anno_ Gene | 注释的位置 Anno_Pos | 参考序列 Reference sequence | 突变序列 Mutant sequence | 正向引物 Forward primer | 反向引物 Reverse primer | 酶 Enzyme | 产物 大小 Product size/bp |
---|---|---|---|---|---|---|---|---|---|---|
SNP-R1-11 | R1 | 169 238 | Rs000940 | Intergenic | G | A | TTGCTGAAGTGCTGTGAGT | TGCGAATGGAAGATGATG | HinfⅠ | 436 |
SNP-R1-15 | R1 | 183 664 | Rs000900 | Exonic | C | G | CAGGTTTTTGCCCCCA | ATTCCCCGGCCATTG | TaqⅠ | 281 |
SNP-R2-2 | R2 | 954 | Rs104740 | Exonic | T | C | CATGAGATGCGGAGAGAGCA | TGTCAGTCCCACCGTTGAGA | TaqⅠ | 214 |
SNP-R2-9 | R2 | 230 920 | Rs103580 | Downstream | C | G | AGCCTGAACAGAGAAGCCA | CCACCATGATCCCGAATATA | HinfⅠ | 325 |
SNP-R2-10 | R2 | 238 894 | Rs103540 | Exonic | A | T | CAGTGGCGAAGCGAAGA | CCTAACGTGCAAAGGAGGT | HinfⅠ | 263 |
SNP-R3-2 | R3 | 50 058 | Rs105180 | Intergenic | T | C | CTATCCACGAATCCCAC | GTAATCAATGCCTATGTCC | HinfⅠ | 514 |
SNP-R3-3 | R3 | 52 883 | Rs105200 | Exonic | G | A | AGAGGAGTGTTGGATGGAGT | CAGAGCGGCTATGGTGA | HinfⅠ | 459 |
SNP-R3-10 | R3 | 642 112 | Rs105440 | Intergenic | G | A | AAACTCCATCACCATCACA | GCAAAAGGAAAGCACACT | HinfⅠ | 533 |
SNP-R4-1 | R4 | 75 754 | Rs148670 | Splicing | G | C | ATGTCGTCCAAAATACCTCC | AGCACCAGCCATCAAGC | SacⅠ | 417 |
SNP-R5-2 | R5 | 121 387 | Rs219310 | Intergenic | A | G | CTGTCTTGTTTGCTATTACTCG | TATCTCAGCCTCCGTCG | HinfⅠ | 406 |
SNP-R6-5 | R6 | 279 865 | Rs289940 | Intergenic | C | G | TTTAGGATTGGGAGTGAAGAC | AATAACAAAACGGGGAAGG | TaqⅠ | 390 |
SNP-R8-3 | R8 | 113 322 | Rs405880 | Exonic | A | G | TTCAGTCCCTTGTTTAGTCTTC | GGCATGTAACGTGCATCC | BamHⅠ | 472 |
表4 SNP引物信息
Table 4 SNP primer information
引物名称 Primer name | 染色体 Chromo- some | 位置 Position | 注释的基因 Anno_ Gene | 注释的位置 Anno_Pos | 参考序列 Reference sequence | 突变序列 Mutant sequence | 正向引物 Forward primer | 反向引物 Reverse primer | 酶 Enzyme | 产物 大小 Product size/bp |
---|---|---|---|---|---|---|---|---|---|---|
SNP-R1-11 | R1 | 169 238 | Rs000940 | Intergenic | G | A | TTGCTGAAGTGCTGTGAGT | TGCGAATGGAAGATGATG | HinfⅠ | 436 |
SNP-R1-15 | R1 | 183 664 | Rs000900 | Exonic | C | G | CAGGTTTTTGCCCCCA | ATTCCCCGGCCATTG | TaqⅠ | 281 |
SNP-R2-2 | R2 | 954 | Rs104740 | Exonic | T | C | CATGAGATGCGGAGAGAGCA | TGTCAGTCCCACCGTTGAGA | TaqⅠ | 214 |
SNP-R2-9 | R2 | 230 920 | Rs103580 | Downstream | C | G | AGCCTGAACAGAGAAGCCA | CCACCATGATCCCGAATATA | HinfⅠ | 325 |
SNP-R2-10 | R2 | 238 894 | Rs103540 | Exonic | A | T | CAGTGGCGAAGCGAAGA | CCTAACGTGCAAAGGAGGT | HinfⅠ | 263 |
SNP-R3-2 | R3 | 50 058 | Rs105180 | Intergenic | T | C | CTATCCACGAATCCCAC | GTAATCAATGCCTATGTCC | HinfⅠ | 514 |
SNP-R3-3 | R3 | 52 883 | Rs105200 | Exonic | G | A | AGAGGAGTGTTGGATGGAGT | CAGAGCGGCTATGGTGA | HinfⅠ | 459 |
SNP-R3-10 | R3 | 642 112 | Rs105440 | Intergenic | G | A | AAACTCCATCACCATCACA | GCAAAAGGAAAGCACACT | HinfⅠ | 533 |
SNP-R4-1 | R4 | 75 754 | Rs148670 | Splicing | G | C | ATGTCGTCCAAAATACCTCC | AGCACCAGCCATCAAGC | SacⅠ | 417 |
SNP-R5-2 | R5 | 121 387 | Rs219310 | Intergenic | A | G | CTGTCTTGTTTGCTATTACTCG | TATCTCAGCCTCCGTCG | HinfⅠ | 406 |
SNP-R6-5 | R6 | 279 865 | Rs289940 | Intergenic | C | G | TTTAGGATTGGGAGTGAAGAC | AATAACAAAACGGGGAAGG | TaqⅠ | 390 |
SNP-R8-3 | R8 | 113 322 | Rs405880 | Exonic | A | G | TTCAGTCCCTTGTTTAGTCTTC | GGCATGTAACGTGCATCC | BamHⅠ | 472 |
序号 Numerical order | 叶型 Leaf profile | 叶形 Leaf shape | 叶尖 Leaf opex | 叶色 Leaf colour | 叶脉色 Color of leaf veins | 叶面 毛刺 Leaf seta | 肉质根地 上部皮色 Color of aboveground part of fleshy root | 叶缘 Leaf margin | 叶裂刻 Leaf crack | 肉质根侧 根分布 Lateral root distribu- tion | 肉质根表 面光滑度 Smoothness of the fleshy root surface | 根形 Root form | 肉色 Color of flesh | 肉质根地 下部皮色 Color of underground part of fleshy root |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2 | 6 | 3 | 3 | 5 | 2 | 7 | 2 | 2 | 1 | 1 | 9 | 5 | 5 |
2 | 2 | 6 | 2 | 4 | 5 | 1 | 7 | 2 | 2 | 0 | 2 | 7 | 6 | 5 |
3 | 2 | 6 | 3 | 4 | 5 | 1 | 7 | 2 | 2 | 0 | 2 | 13 | 6 | 5 |
4 | 2 | 6 | 4 | 3 | 1 | 1 | 7 | 2 | 2 | 0 | 2 | 11 | 5 | 1 |
5 | 2 | 6 | 4 | 3 | 4 | 1 | 7 | 2 | 3 | 0 | 1 | 1 | 1 | 5 |
6 | 1 | 7 | 1 | 3 | 4 | 2 | 7 | 1 | 1 | 0 | 1 | 3 | 1 | 5 |
7 | 2 | 6 | 1 | 4 | 4 | 1 | 7 | 3 | 3 | 3 | 1 | 13 | 1 | 5 |
8 | 1 | 5 | 3 | 4 | 2 | 2 | 4 | 0 | 1 | 1 | 2 | 7 | 5 | 4 |
9 | 2 | 6 | 4 | 4 | 4 | 2 | 7 | 2 | 2 | 0 | 1 | 2 | 1 | 5 |
10 | 2 | 6 | 2 | 3 | 4 | 0 | 7 | 2 | 2 | 1 | 1 | 5 | 6 | 5 |
11 | 2 | 6 | 2 | 4 | 6 | 1 | 9 | 3 | 3 | 2 | 2 | 7 | 7 | 6 |
12 | 1 | 6 | 2 | 4 | 3 | 3 | 1 | 2 | 2 | 0 | 1 | 10 | 1 | 1 |
13 | 2 | 6 | 1 | 3 | 2 | 0 | 1 | 3 | 3 | 1 | 1 | 9 | 1 | 1 |
14 | 2 | 6 | 3 | 4 | 3 | 3 | 3 | 2 | 2 | 2 | 2 | 1 | 1 | 1 |
15 | 2 | 6 | 2 | 4 | 3 | 2 | 1 | 3 | 2 | 3 | 1 | 13 | 1 | 1 |
16 | 2 | 6 | 2 | 3 | 3 | 1 | 4 | 1 | 3 | 0 | 2 | 2 | 3 | 2 |
17 | 2 | 6 | 4 | 4 | 3 | 1 | 5 | 2 | 2 | 1 | 1 | 13 | 3 | 2 |
18 | 2 | 6 | 4 | 4 | 2 | 1 | 3 | 2 | 2 | 2 | 1 | 1 | 1 | 1 |
19 | 1 | 3 | 4 | 4 | 2 | 0 | 1 | 1 | 0 | 3 | 1 | 3 | 1 | 1 |
20 | 1 | 6 | 2 | 3 | 5 | 2 | 9 | 3 | 3 | 3 | 1 | 3 | 1 | 1 |
21 | 2 | 6 | 2 | 3 | 6 | 1 | 9 | 2 | 3 | 3 | 1 | 1 | 1 | 6 |
22 | 2 | 4 | 2 | 2 | 2 | 1 | 1 | 1 | 2 | 2 | 2 | 3 | 1 | 1 |
23 | 1 | 6 | 4 | 4 | 4 | 2 | 7 | 2 | 0 | 2 | 1 | 5 | 1 | 5 |
24 | 2 | 6 | 1 | 4 | 2 | 3 | 3 | 3 | 3 | 2 | 1 | 3 | 1 | 1 |
25 | 2 | 6 | 3 | 3 | 3 | 1 | 2 | 2 | 2 | 2 | 2 | 7 | 6 | 4 |
26 | 2 | 6 | 4 | 4 | 3 | 1 | 4 | 2 | 2 | 1 | 1 | 9 | 2 | 1 |
27 | 1 | 4 | 3 | 1 | 2 | 1 | 1 | 2 | 1 | 1 | 1 | 9 | 1 | 1 |
28 | 2 | 6 | 3 | 4 | 2 | 3 | 1 | 2 | 2 | 2 | 2 | 7 | 1 | 1 |
29 | 2 | 6 | 2 | 4 | 3 | 2 | 1 | 2 | 2 | 2 | 1 | 13 | 1 | 1 |
30 | 2 | 6 | 1 | 4 | 2 | 2 | 1 | 3 | 3 | 2 | 1 | 1 | 1 | 1 |
31 | 1 | 4 | 2 | 4 | 4 | 0 | 7 | 2 | 1 | 3 | 1 | 13 | 1 | 4 |
32 | 2 | 6 | 4 | 4 | 2 | 1 | 2 | 2 | 2 | 3 | 1 | 13 | 1 | 1 |
33 | 2 | 6 | 1 | 4 | 2 | 0 | 1 | 3 | 3 | 3 | 1 | 1 | 1 | 1 |
34 | 1 | 6 | 4 | 4 | 2 | 1 | 4 | 2 | 0 | 1 | 1 | 9 | 1 | 1 |
35 | 2 | 6 | 4 | 4 | 3 | 2 | 1 | 2 | 2 | 2 | 1 | 3 | 1 | 1 |
36 | 2 | 6 | 4 | 4 | 2 | 1 | 1 | 2 | 3 | 1 | 1 | 13 | 1 | 1 |
37 | 2 | 6 | 4 | 4 | 2 | 1 | 1 | 2 | 3 | 2 | 1 | 13 | 1 | 1 |
38 | 2 | 6 | 2 | 4 | 2 | 1 | 1 | 3 | 3 | 2 | 1 | 7 | 1 | 1 |
39 | 1 | 6 | 2 | 3 | 4 | 2 | 7 | 2 | 0 | 2 | 1 | 7 | 1 | 4 |
40 | 2 | 6 | 2 | 3 | 2 | 0 | 1 | 3 | 3 | 1 | 1 | 11 | 1 | 1 |
41 | 2 | 6 | 4 | 4 | 3 | 3 | 1 | 1 | 2 | 2 | 1 | 5 | 1 | 1 |
42 | 2 | 6 | 2 | 4 | 3 | 3 | 1 | 2 | 2 | 3 | 1 | 7 | 1 | 1 |
43 | 2 | 6 | 2 | 4 | 2 | 1 | 1 | 3 | 3 | 3 | 1 | 13 | 1 | 1 |
44 | 2 | 6 | 4 | 4 | 3 | 1 | 1 | 2 | 2 | 2 | 1 | 3 | 1 | 1 |
45 | 1 | 4 | 1 | 3 | 3 | 1 | 1 | 3 | 1 | 2 | 2 | 13 | 1 | 1 |
46 | 2 | 6 | 2 | 4 | 2 | 2 | 5 | 3 | 3 | 3 | 1 | 13 | 1 | 1 |
47 | 2 | 6 | 2 | 4 | 2 | 2 | 1 | 3 | 3 | 2 | 1 | 3 | 1 | 1 |
48 | 2 | 6 | 2 | 3 | 2 | 1 | 4 | 2 | 2 | 1 | 1 | 13 | 3 | 1 |
49 | 2 | 6 | 2 | 4 | 3 | 1 | 5 | 3 | 3 | 1 | 1 | 13 | 2 | 1 |
50 | 2 | 6 | 2 | 4 | 2 | 2 | 1 | 3 | 3 | 3 | 1 | 13 | 1 | 1 |
51 | 2 | 6 | 4 | 3 | 3 | 2 | 2 | 1 | 2 | 2 | 1 | 2 | 1 | 1 |
52 | 2 | 6 | 4 | 4 | 3 | 3 | 1 | 2 | 2 | 1 | 2 | 13 | 1 | 1 |
53 | 1 | 4 | 4 | 4 | 3 | 2 | 1 | 2 | 0 | 2 | 2 | 13 | 1 | 1 |
54 | 1 | 6 | 2 | 4 | 2 | 1 | 1 | 3 | 0 | 2 | 1 | 13 | 1 | 1 |
55 | 1 | 6 | 2 | 4 | 2 | 2 | 2 | 3 | 0 | 1 | 1 | 13 | 1 | 1 |
56 | 2 | 6 | 2 | 3 | 4 | 2 | 7 | 1 | 2 | 1 | 1 | 5 | 7 | 1 |
57 | 1 | 6 | 3 | 3 | 2 | 2 | 1 | 3 | 1 | 1 | 1 | 11 | 1 | 1 |
58 | 1 | 6 | 2 | 4 | 2 | 2 | 1 | 2 | 1 | 1 | 1 | 11 | 1 | 1 |
59 | 1 | 4 | 2 | 3 | 4 | 2 | 7 | 3 | 0 | 1 | 1 | 10 | 1 | 5 |
60 | 1 | 4 | 4 | 3 | 4 | 3 | 7 | 2 | 0 | 1 | 1 | 5 | 4 | 1 |
表5 萝卜表型数据
Table 5 Phenotypic data of radish
序号 Numerical order | 叶型 Leaf profile | 叶形 Leaf shape | 叶尖 Leaf opex | 叶色 Leaf colour | 叶脉色 Color of leaf veins | 叶面 毛刺 Leaf seta | 肉质根地 上部皮色 Color of aboveground part of fleshy root | 叶缘 Leaf margin | 叶裂刻 Leaf crack | 肉质根侧 根分布 Lateral root distribu- tion | 肉质根表 面光滑度 Smoothness of the fleshy root surface | 根形 Root form | 肉色 Color of flesh | 肉质根地 下部皮色 Color of underground part of fleshy root |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2 | 6 | 3 | 3 | 5 | 2 | 7 | 2 | 2 | 1 | 1 | 9 | 5 | 5 |
2 | 2 | 6 | 2 | 4 | 5 | 1 | 7 | 2 | 2 | 0 | 2 | 7 | 6 | 5 |
3 | 2 | 6 | 3 | 4 | 5 | 1 | 7 | 2 | 2 | 0 | 2 | 13 | 6 | 5 |
4 | 2 | 6 | 4 | 3 | 1 | 1 | 7 | 2 | 2 | 0 | 2 | 11 | 5 | 1 |
5 | 2 | 6 | 4 | 3 | 4 | 1 | 7 | 2 | 3 | 0 | 1 | 1 | 1 | 5 |
6 | 1 | 7 | 1 | 3 | 4 | 2 | 7 | 1 | 1 | 0 | 1 | 3 | 1 | 5 |
7 | 2 | 6 | 1 | 4 | 4 | 1 | 7 | 3 | 3 | 3 | 1 | 13 | 1 | 5 |
8 | 1 | 5 | 3 | 4 | 2 | 2 | 4 | 0 | 1 | 1 | 2 | 7 | 5 | 4 |
9 | 2 | 6 | 4 | 4 | 4 | 2 | 7 | 2 | 2 | 0 | 1 | 2 | 1 | 5 |
10 | 2 | 6 | 2 | 3 | 4 | 0 | 7 | 2 | 2 | 1 | 1 | 5 | 6 | 5 |
11 | 2 | 6 | 2 | 4 | 6 | 1 | 9 | 3 | 3 | 2 | 2 | 7 | 7 | 6 |
12 | 1 | 6 | 2 | 4 | 3 | 3 | 1 | 2 | 2 | 0 | 1 | 10 | 1 | 1 |
13 | 2 | 6 | 1 | 3 | 2 | 0 | 1 | 3 | 3 | 1 | 1 | 9 | 1 | 1 |
14 | 2 | 6 | 3 | 4 | 3 | 3 | 3 | 2 | 2 | 2 | 2 | 1 | 1 | 1 |
15 | 2 | 6 | 2 | 4 | 3 | 2 | 1 | 3 | 2 | 3 | 1 | 13 | 1 | 1 |
16 | 2 | 6 | 2 | 3 | 3 | 1 | 4 | 1 | 3 | 0 | 2 | 2 | 3 | 2 |
17 | 2 | 6 | 4 | 4 | 3 | 1 | 5 | 2 | 2 | 1 | 1 | 13 | 3 | 2 |
18 | 2 | 6 | 4 | 4 | 2 | 1 | 3 | 2 | 2 | 2 | 1 | 1 | 1 | 1 |
19 | 1 | 3 | 4 | 4 | 2 | 0 | 1 | 1 | 0 | 3 | 1 | 3 | 1 | 1 |
20 | 1 | 6 | 2 | 3 | 5 | 2 | 9 | 3 | 3 | 3 | 1 | 3 | 1 | 1 |
21 | 2 | 6 | 2 | 3 | 6 | 1 | 9 | 2 | 3 | 3 | 1 | 1 | 1 | 6 |
22 | 2 | 4 | 2 | 2 | 2 | 1 | 1 | 1 | 2 | 2 | 2 | 3 | 1 | 1 |
23 | 1 | 6 | 4 | 4 | 4 | 2 | 7 | 2 | 0 | 2 | 1 | 5 | 1 | 5 |
24 | 2 | 6 | 1 | 4 | 2 | 3 | 3 | 3 | 3 | 2 | 1 | 3 | 1 | 1 |
25 | 2 | 6 | 3 | 3 | 3 | 1 | 2 | 2 | 2 | 2 | 2 | 7 | 6 | 4 |
26 | 2 | 6 | 4 | 4 | 3 | 1 | 4 | 2 | 2 | 1 | 1 | 9 | 2 | 1 |
27 | 1 | 4 | 3 | 1 | 2 | 1 | 1 | 2 | 1 | 1 | 1 | 9 | 1 | 1 |
28 | 2 | 6 | 3 | 4 | 2 | 3 | 1 | 2 | 2 | 2 | 2 | 7 | 1 | 1 |
29 | 2 | 6 | 2 | 4 | 3 | 2 | 1 | 2 | 2 | 2 | 1 | 13 | 1 | 1 |
30 | 2 | 6 | 1 | 4 | 2 | 2 | 1 | 3 | 3 | 2 | 1 | 1 | 1 | 1 |
31 | 1 | 4 | 2 | 4 | 4 | 0 | 7 | 2 | 1 | 3 | 1 | 13 | 1 | 4 |
32 | 2 | 6 | 4 | 4 | 2 | 1 | 2 | 2 | 2 | 3 | 1 | 13 | 1 | 1 |
33 | 2 | 6 | 1 | 4 | 2 | 0 | 1 | 3 | 3 | 3 | 1 | 1 | 1 | 1 |
34 | 1 | 6 | 4 | 4 | 2 | 1 | 4 | 2 | 0 | 1 | 1 | 9 | 1 | 1 |
35 | 2 | 6 | 4 | 4 | 3 | 2 | 1 | 2 | 2 | 2 | 1 | 3 | 1 | 1 |
36 | 2 | 6 | 4 | 4 | 2 | 1 | 1 | 2 | 3 | 1 | 1 | 13 | 1 | 1 |
37 | 2 | 6 | 4 | 4 | 2 | 1 | 1 | 2 | 3 | 2 | 1 | 13 | 1 | 1 |
38 | 2 | 6 | 2 | 4 | 2 | 1 | 1 | 3 | 3 | 2 | 1 | 7 | 1 | 1 |
39 | 1 | 6 | 2 | 3 | 4 | 2 | 7 | 2 | 0 | 2 | 1 | 7 | 1 | 4 |
40 | 2 | 6 | 2 | 3 | 2 | 0 | 1 | 3 | 3 | 1 | 1 | 11 | 1 | 1 |
41 | 2 | 6 | 4 | 4 | 3 | 3 | 1 | 1 | 2 | 2 | 1 | 5 | 1 | 1 |
42 | 2 | 6 | 2 | 4 | 3 | 3 | 1 | 2 | 2 | 3 | 1 | 7 | 1 | 1 |
43 | 2 | 6 | 2 | 4 | 2 | 1 | 1 | 3 | 3 | 3 | 1 | 13 | 1 | 1 |
44 | 2 | 6 | 4 | 4 | 3 | 1 | 1 | 2 | 2 | 2 | 1 | 3 | 1 | 1 |
45 | 1 | 4 | 1 | 3 | 3 | 1 | 1 | 3 | 1 | 2 | 2 | 13 | 1 | 1 |
46 | 2 | 6 | 2 | 4 | 2 | 2 | 5 | 3 | 3 | 3 | 1 | 13 | 1 | 1 |
47 | 2 | 6 | 2 | 4 | 2 | 2 | 1 | 3 | 3 | 2 | 1 | 3 | 1 | 1 |
48 | 2 | 6 | 2 | 3 | 2 | 1 | 4 | 2 | 2 | 1 | 1 | 13 | 3 | 1 |
49 | 2 | 6 | 2 | 4 | 3 | 1 | 5 | 3 | 3 | 1 | 1 | 13 | 2 | 1 |
50 | 2 | 6 | 2 | 4 | 2 | 2 | 1 | 3 | 3 | 3 | 1 | 13 | 1 | 1 |
51 | 2 | 6 | 4 | 3 | 3 | 2 | 2 | 1 | 2 | 2 | 1 | 2 | 1 | 1 |
52 | 2 | 6 | 4 | 4 | 3 | 3 | 1 | 2 | 2 | 1 | 2 | 13 | 1 | 1 |
53 | 1 | 4 | 4 | 4 | 3 | 2 | 1 | 2 | 0 | 2 | 2 | 13 | 1 | 1 |
54 | 1 | 6 | 2 | 4 | 2 | 1 | 1 | 3 | 0 | 2 | 1 | 13 | 1 | 1 |
55 | 1 | 6 | 2 | 4 | 2 | 2 | 2 | 3 | 0 | 1 | 1 | 13 | 1 | 1 |
56 | 2 | 6 | 2 | 3 | 4 | 2 | 7 | 1 | 2 | 1 | 1 | 5 | 7 | 1 |
57 | 1 | 6 | 3 | 3 | 2 | 2 | 1 | 3 | 1 | 1 | 1 | 11 | 1 | 1 |
58 | 1 | 6 | 2 | 4 | 2 | 2 | 1 | 2 | 1 | 1 | 1 | 11 | 1 | 1 |
59 | 1 | 4 | 2 | 3 | 4 | 2 | 7 | 3 | 0 | 1 | 1 | 10 | 1 | 5 |
60 | 1 | 4 | 4 | 3 | 4 | 3 | 7 | 2 | 0 | 1 | 1 | 5 | 4 | 1 |
标记类型 Marker type | R01 | R02 | R03 | R04 | R05 | R06 | R07 | R08 | R09 | 总数 Total |
---|---|---|---|---|---|---|---|---|---|---|
SNP | 40 434 | 42 072 | 31 672 | 37 651 | 63 913 | 66 979 | 23 305 | 26 566 | 34 087 | 366 679 |
InDel | 10 038 | 11 486 | 8 394 | 10 551 | 17 136 | 17 689 | 6 416 | 6 827 | 9 436 | 97 973 |
表6 两个材料间SNP和InDel数量统计
Table 6 Statistics of the number of SNPS and InDels between the two materials
标记类型 Marker type | R01 | R02 | R03 | R04 | R05 | R06 | R07 | R08 | R09 | 总数 Total |
---|---|---|---|---|---|---|---|---|---|---|
SNP | 40 434 | 42 072 | 31 672 | 37 651 | 63 913 | 66 979 | 23 305 | 26 566 | 34 087 | 366 679 |
InDel | 10 038 | 11 486 | 8 394 | 10 551 | 17 136 | 17 689 | 6 416 | 6 827 | 9 436 | 97 973 |
引物名称 Primer name | MAF | Na | He | PIC | 引物名称 Primer name | MAF | Na | He | PIC |
---|---|---|---|---|---|---|---|---|---|
InDelR1-2 | 0.68 | 2 | 0.63 | 0.34 | InDelR9-1 | 0.63 | 2 | 0.73 | 0.36 |
InDelR1-3 | 0.65 | 2 | 0.70 | 0.35 | InDelR9-2 | 0.67 | 2 | 0.67 | 0.35 |
InDelR2-1 | 0.68 | 2 | 0.63 | 0.34 | SNP-R1-11 | 0.58 | 2 | 0.83 | 0.37 |
InDelR2-3 | 0.58 | 2 | 0.85 | 0.37 | SNP-R1-15 | 0.65 | 2 | 0.70 | 0.35 |
InDelR3-1 | 0.94 | 2 | 0.12 | 0.10 | SNP-R2-2 | 0.80 | 2 | 0.40 | 0.27 |
InDelR3-2 | 0.68 | 3 | 0.62 | 0.34 | SNP-R2-9 | 0.88 | 2 | 0.25 | 0.19 |
InDelR4-2 | 0.62 | 3 | 0.73 | 0.36 | SNP-R2-10 | 0.62 | 2 | 0.77 | 0.36 |
InDelR5-1 | 0.54 | 3 | 0.88 | 0.37 | SNP-R3-2 | 0.53 | 2 | 0.93 | 0.37 |
InDelR5-2 | 0.63 | 2 | 0.75 | 0.36 | SNP-R3-3 | 0.87 | 2 | 0.27 | 0.20 |
InDelR5-3 | 0.65 | 2 | 0.70 | 0.35 | SNP-R3-10 | 0.88 | 2 | 0.25 | 0.19 |
InDelR6-3 | 0.73 | 2 | 0.55 | 0.32 | SNP-R4-1 | 0.75 | 2 | 0.50 | 0.30 |
InDelR7-1 | 0.67 | 2 | 0.67 | 0.35 | SNP-R5-2 | 0.58 | 2 | 0.83 | 0.37 |
InDelR7-3 | 0.63 | 2 | 0.73 | 0.36 | SNP-R6-5 | 0.69 | 3 | 0.48 | 0.34 |
InDelR8-1 | 0.67 | 2 | 0.67 | 0.35 | SNP-R8-3 | 0.67 | 2 | 0.67 | 0.35 |
InDelR8-2 | 0.68 | 2 | 0.63 | 0.34 |
表7 SNP和InDel多态性引物多样性分析
Table 7 SNP and InDel polymorphism primers diversity analysis
引物名称 Primer name | MAF | Na | He | PIC | 引物名称 Primer name | MAF | Na | He | PIC |
---|---|---|---|---|---|---|---|---|---|
InDelR1-2 | 0.68 | 2 | 0.63 | 0.34 | InDelR9-1 | 0.63 | 2 | 0.73 | 0.36 |
InDelR1-3 | 0.65 | 2 | 0.70 | 0.35 | InDelR9-2 | 0.67 | 2 | 0.67 | 0.35 |
InDelR2-1 | 0.68 | 2 | 0.63 | 0.34 | SNP-R1-11 | 0.58 | 2 | 0.83 | 0.37 |
InDelR2-3 | 0.58 | 2 | 0.85 | 0.37 | SNP-R1-15 | 0.65 | 2 | 0.70 | 0.35 |
InDelR3-1 | 0.94 | 2 | 0.12 | 0.10 | SNP-R2-2 | 0.80 | 2 | 0.40 | 0.27 |
InDelR3-2 | 0.68 | 3 | 0.62 | 0.34 | SNP-R2-9 | 0.88 | 2 | 0.25 | 0.19 |
InDelR4-2 | 0.62 | 3 | 0.73 | 0.36 | SNP-R2-10 | 0.62 | 2 | 0.77 | 0.36 |
InDelR5-1 | 0.54 | 3 | 0.88 | 0.37 | SNP-R3-2 | 0.53 | 2 | 0.93 | 0.37 |
InDelR5-2 | 0.63 | 2 | 0.75 | 0.36 | SNP-R3-3 | 0.87 | 2 | 0.27 | 0.20 |
InDelR5-3 | 0.65 | 2 | 0.70 | 0.35 | SNP-R3-10 | 0.88 | 2 | 0.25 | 0.19 |
InDelR6-3 | 0.73 | 2 | 0.55 | 0.32 | SNP-R4-1 | 0.75 | 2 | 0.50 | 0.30 |
InDelR7-1 | 0.67 | 2 | 0.67 | 0.35 | SNP-R5-2 | 0.58 | 2 | 0.83 | 0.37 |
InDelR7-3 | 0.63 | 2 | 0.73 | 0.36 | SNP-R6-5 | 0.69 | 3 | 0.48 | 0.34 |
InDelR8-1 | 0.67 | 2 | 0.67 | 0.35 | SNP-R8-3 | 0.67 | 2 | 0.67 | 0.35 |
InDelR8-2 | 0.68 | 2 | 0.63 | 0.34 |
性状 Trait | 标记名称 Marker | 染色体 Chr | GLM | 性状 Trait | 标记名称 Marker | 染色体 Chr | GLM | ||
---|---|---|---|---|---|---|---|---|---|
P值 P value | 贡献率 Contribution rate/% | P值 P value | 贡献率 Contribution rate/% | ||||||
叶脉色 | InDelR6-3 | R06 | 0.000 2 | 15.60 | 肉质根表面光滑度 | InDelR7-1 | R07 | 0.001 1 | 11.78 |
Color of leaf veins | InDelR7-1 | R07 | 0.000 3 | 15.20 | Smoothness of the | InDelR8-2 | R08 | 0.000 4 | 14.32 |
InDelR8-2 | R08 | 0.000 2 | 15.44 | fleshy root surface | SNPR3-10 | R03 | 0.004 2 | 8.86 | |
SNPR3-3 | R03 | 0.006 6 | 7.96 | 根形Root form | SNPR4-1 | R04 | 0.008 0 | 7.55 | |
SNPR4-1 | R04 | 0.001 9 | 10.55 | SNPR6-5 | R06 | 0.008 0 | 7.55 | ||
SNPR6-5 | R06 | 0.001 9 | 10.55 | 肉色 | InDelR6-3 | R06 | 0.000 3 | 14.70 | |
肉质根地上部皮色 | InDelR4-2 | R04 | 0.003 6 | 9.19 | Color of flesh | InDelR7-1 | R07 | 0.000 1 | 19.20 |
Color of aboveground | InDelR6-3 | R06 | 0.000 9 | 12.34 | InDelR8-2 | R08 | 0.000 0 | 23.25 | |
part of fleshy root | InDelR7-1 | R07 | 0.000 8 | 12.60 | SNPR2-10 | R02 | 0.000 3 | 15.13 | |
InDelR8-2 | R08 | 0.001 9 | 10.63 | SNPR2-2 | R02 | 0.000 2 | 15.27 | ||
SNPR2-10 | R02 | 0.002 9 | 9.66 | SNPR3-10 | R03 | 0.000 9 | 12.32 | ||
SNPR2-2 | R02 | 0.000 8 | 12.43 | SNPR3-3 | R03 | 0.008 9 | 7.33 | ||
SNPR4-1 | R04 | 0.000 1 | 17.94 | 肉质根地下部皮色 | InDelR4-2 | R04 | 0.002 0 | 10.43 | |
SNPR6-5 | R06 | 0.000 1 | 17.94 | Color of underground | InDelR5-3 | R05 | 0.006 8 | 7.89 | |
part of fleshy root | |||||||||
叶缘Leaf margin | InDelR5-1 | R05 | 0.003 5 | 9.30 | InDelR7-1 | R07 | 0.000 4 | 14.03 | |
SNPR1-15 | R01 | 0.005 9 | 8.16 | InDelR8-2 | R08 | 0.000 8 | 12.59 | ||
肉质根侧根分布 | InDelR6-3 | R06 | 0.009 3 | 7.24 | SNPR3-3 | R03 | 0.000 9 | 12.14 | |
Lateral root | InDelR7-3 | R07 | 0.002 3 | 10.19 | SNPR4-1 | R04 | 0.000 0 | 19.26 | |
distribution | InDelR9-1 | R09 | 0.002 3 | 10.19 | SNPR6-5 | R06 | 0.000 0 | 19.26 | |
SNPR1-15 | R01 | 0.006 6 | 7.93 | 叶形Leaf shape | InDelR5-2 | R05 | 0.004 1 | 8.94 | |
SNPR2-10 | R02 | 0.000 4 | 14.20 | InDelR5-3 | R05 | 0.006 9 | 7.84 | ||
SNPR2-2 | R02 | 0.009 1 | 7.29 | 叶色Leaf colour | InDelR7-3 | R07 | 0.001 3 | 11.38 | |
叶裂刻Leaf crack | InDelR2-1 | R02 | 0.005 8 | 8.23 | InDelR9-1 | R09 | 0.001 3 | 11.38 | |
叶面毛刺Leaf seta | InDelR4-2 | R04 | 0.006 8 | 7.87 |
表8 萝卜表型性状与分子标记显著关联位点
Table 8 Phenotypic traits of radish and significant associated sites with molecular markers
性状 Trait | 标记名称 Marker | 染色体 Chr | GLM | 性状 Trait | 标记名称 Marker | 染色体 Chr | GLM | ||
---|---|---|---|---|---|---|---|---|---|
P值 P value | 贡献率 Contribution rate/% | P值 P value | 贡献率 Contribution rate/% | ||||||
叶脉色 | InDelR6-3 | R06 | 0.000 2 | 15.60 | 肉质根表面光滑度 | InDelR7-1 | R07 | 0.001 1 | 11.78 |
Color of leaf veins | InDelR7-1 | R07 | 0.000 3 | 15.20 | Smoothness of the | InDelR8-2 | R08 | 0.000 4 | 14.32 |
InDelR8-2 | R08 | 0.000 2 | 15.44 | fleshy root surface | SNPR3-10 | R03 | 0.004 2 | 8.86 | |
SNPR3-3 | R03 | 0.006 6 | 7.96 | 根形Root form | SNPR4-1 | R04 | 0.008 0 | 7.55 | |
SNPR4-1 | R04 | 0.001 9 | 10.55 | SNPR6-5 | R06 | 0.008 0 | 7.55 | ||
SNPR6-5 | R06 | 0.001 9 | 10.55 | 肉色 | InDelR6-3 | R06 | 0.000 3 | 14.70 | |
肉质根地上部皮色 | InDelR4-2 | R04 | 0.003 6 | 9.19 | Color of flesh | InDelR7-1 | R07 | 0.000 1 | 19.20 |
Color of aboveground | InDelR6-3 | R06 | 0.000 9 | 12.34 | InDelR8-2 | R08 | 0.000 0 | 23.25 | |
part of fleshy root | InDelR7-1 | R07 | 0.000 8 | 12.60 | SNPR2-10 | R02 | 0.000 3 | 15.13 | |
InDelR8-2 | R08 | 0.001 9 | 10.63 | SNPR2-2 | R02 | 0.000 2 | 15.27 | ||
SNPR2-10 | R02 | 0.002 9 | 9.66 | SNPR3-10 | R03 | 0.000 9 | 12.32 | ||
SNPR2-2 | R02 | 0.000 8 | 12.43 | SNPR3-3 | R03 | 0.008 9 | 7.33 | ||
SNPR4-1 | R04 | 0.000 1 | 17.94 | 肉质根地下部皮色 | InDelR4-2 | R04 | 0.002 0 | 10.43 | |
SNPR6-5 | R06 | 0.000 1 | 17.94 | Color of underground | InDelR5-3 | R05 | 0.006 8 | 7.89 | |
part of fleshy root | |||||||||
叶缘Leaf margin | InDelR5-1 | R05 | 0.003 5 | 9.30 | InDelR7-1 | R07 | 0.000 4 | 14.03 | |
SNPR1-15 | R01 | 0.005 9 | 8.16 | InDelR8-2 | R08 | 0.000 8 | 12.59 | ||
肉质根侧根分布 | InDelR6-3 | R06 | 0.009 3 | 7.24 | SNPR3-3 | R03 | 0.000 9 | 12.14 | |
Lateral root | InDelR7-3 | R07 | 0.002 3 | 10.19 | SNPR4-1 | R04 | 0.000 0 | 19.26 | |
distribution | InDelR9-1 | R09 | 0.002 3 | 10.19 | SNPR6-5 | R06 | 0.000 0 | 19.26 | |
SNPR1-15 | R01 | 0.006 6 | 7.93 | 叶形Leaf shape | InDelR5-2 | R05 | 0.004 1 | 8.94 | |
SNPR2-10 | R02 | 0.000 4 | 14.20 | InDelR5-3 | R05 | 0.006 9 | 7.84 | ||
SNPR2-2 | R02 | 0.009 1 | 7.29 | 叶色Leaf colour | InDelR7-3 | R07 | 0.001 3 | 11.38 | |
叶裂刻Leaf crack | InDelR2-1 | R02 | 0.005 8 | 8.23 | InDelR9-1 | R09 | 0.001 3 | 11.38 | |
叶面毛刺Leaf seta | InDelR4-2 | R04 | 0.006 8 | 7.87 |
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