Chinese Journal OF Rice Science ›› 2016, Vol. 30 ›› Issue (5): 487-492.DOI: 10.16819/j.1001-7216.2016.6038
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Chuan-deng YI*(), De-rong WANG, Wei JIANG, Wei LI, Xiao-jun CHENG, Ying WANG, Yong ZHOU, Guo-hua LIANG, Ming-hong GU
Received:
2016-03-07
Revised:
2016-04-12
Online:
2016-09-10
Published:
2016-09-10
Contact:
Chuan-deng YI
裔传灯*(), 王德荣, 蒋伟, 李玮, 成晓俊, 王颖, 周勇, 梁国华, 顾铭洪
通讯作者:
裔传灯
基金资助:
CLC Number:
Chuan-deng YI, De-rong WANG, Wei JIANG, Wei LI, Xiao-jun CHENG, Ying WANG, Yong ZHOU, Guo-hua LIANG, Ming-hong GU. Development of Functional Markers and Identification of Haplotypes for Rice Grain Width Gene GS5[J]. Chinese Journal OF Rice Science, 2016, 30(5): 487-492.
裔传灯, 王德荣, 蒋伟, 李玮, 成晓俊, 王颖, 周勇, 梁国华, 顾铭洪. 水稻粒宽基因GS5的功能标记开发和单倍型鉴定[J]. 中国水稻科学, 2016, 30(5): 487-492.
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URL: http://www.ricesci.cn/EN/10.16819/j.1001-7216.2016.6038
标记名称 Marker | 变异位点所在区域a Region of sequence variationa | 基因型 Genotype | 引物序列 Primer sequence | 标记类型 Marker type |
---|---|---|---|---|
GS5-1 | Exon 2(817 bp) | ACC/CTA | F:GCAAGACAAGGAGCAGCACTA | CAPS-DdeⅠ |
R:AGAAGCCGACCCCAACAG | ||||
GS5-2 | Exon 9(3796 bp) | A/C | F:CAGTTCTCGGTACTGCGTCGA | dCAPS-SalⅠ |
R:CACAAACCTCCCAGCAACC |
Table 1 PCR primers based on the GS5 DNA sequence variations of exon 2 and exon 9.
标记名称 Marker | 变异位点所在区域a Region of sequence variationa | 基因型 Genotype | 引物序列 Primer sequence | 标记类型 Marker type |
---|---|---|---|---|
GS5-1 | Exon 2(817 bp) | ACC/CTA | F:GCAAGACAAGGAGCAGCACTA | CAPS-DdeⅠ |
R:AGAAGCCGACCCCAACAG | ||||
GS5-2 | Exon 9(3796 bp) | A/C | F:CAGTTCTCGGTACTGCGTCGA | dCAPS-SalⅠ |
R:CACAAACCTCCCAGCAACC |
Fig. 1. PCR identification and enzyme-digested characterization of specific primers GS5-1(A) and GS5-2(B) for gene GS5 in rice. A, PCR amplification products and their corresponding DdeⅠ-digested ones of primer GS5-1; B, PCR amplification products and their corresponding SalⅠ-digested ones of primer GS5-2. M, DL2000 DNA Marker(TaKaRa). Lanes 1 and 3, Nipponbare; Lanes 2 and 4, Zhenshan 97.
性状 Trait | GS5-1 | GS5-2 | ||||||
---|---|---|---|---|---|---|---|---|
基因型 Genotype | 样本数 Sample number | 平均数± 标准误 Mean±SE | t值 t value | 基因型 Genotype | 样本数 Sample number | 平均数± 标准误 Mean±SE | t值 t value | |
粒长 Grain length/mm | ACC | 170 | 8.03±0.08 | 2.98** | A | 210 | 8.09±0.07 | 2.33* |
CTA | 124 | 8.34±0.07 | C | 83 | 8.33±0.08 | |||
粒宽 Grain width/mm | ACC | 170 | 3.05±0.03 | 2.21* | A | 210 | 3.04±0.03 | 2.01* |
CTA | 124 | 2.97±0.02 | C | 83 | 2.96±0.03 | |||
粒厚 Grain thickness/mm | ACC | 170 | 2.13±0.01 | 1.03 | A | 210 | 2.13±0.01 | 1.68 |
CTA | 124 | 2.11±0.01 | C | 83 | 2.10±0.01 | |||
长宽比 Ratio of length to width | ACC | 170 | 2.70±0.05 | 2.29* | A | 210 | 2.72±0.04 | 2.04* |
CTA | 124 | 2.84±0.04 | C | 83 | 2.85±0.05 | |||
千粒重 1000-grain weight/g | ACC | 170 | 24.71±0.31 | 0.26 | A | 210 | 24.74±0.28 | 0.04 |
CTA | 124 | 24.82±0.30 | C | 83 | 24.75±0.33 |
Table 2 Grain-related traits and their t-tests of different alleles in gene GS5.
性状 Trait | GS5-1 | GS5-2 | ||||||
---|---|---|---|---|---|---|---|---|
基因型 Genotype | 样本数 Sample number | 平均数± 标准误 Mean±SE | t值 t value | 基因型 Genotype | 样本数 Sample number | 平均数± 标准误 Mean±SE | t值 t value | |
粒长 Grain length/mm | ACC | 170 | 8.03±0.08 | 2.98** | A | 210 | 8.09±0.07 | 2.33* |
CTA | 124 | 8.34±0.07 | C | 83 | 8.33±0.08 | |||
粒宽 Grain width/mm | ACC | 170 | 3.05±0.03 | 2.21* | A | 210 | 3.04±0.03 | 2.01* |
CTA | 124 | 2.97±0.02 | C | 83 | 2.96±0.03 | |||
粒厚 Grain thickness/mm | ACC | 170 | 2.13±0.01 | 1.03 | A | 210 | 2.13±0.01 | 1.68 |
CTA | 124 | 2.11±0.01 | C | 83 | 2.10±0.01 | |||
长宽比 Ratio of length to width | ACC | 170 | 2.70±0.05 | 2.29* | A | 210 | 2.72±0.04 | 2.04* |
CTA | 124 | 2.84±0.04 | C | 83 | 2.85±0.05 | |||
千粒重 1000-grain weight/g | ACC | 170 | 24.71±0.31 | 0.26 | A | 210 | 24.74±0.28 | 0.04 |
CTA | 124 | 24.82±0.30 | C | 83 | 24.75±0.33 |
籽粒性状与变异来源 Grain trait and source of variation | 籼亚种 indica | 粳亚种 japonica | ||||
---|---|---|---|---|---|---|
自由度 df | 平方和 Mean square | F值 F value | 自由度 df | 平方和 Mean square | F值 F value | |
粒长Grain length | ||||||
单倍型间Among haplotypes | 3 | 0.929 | 1.272 | 3 | 2.482 | 3.493* |
单倍型内Within haplotypes | 154 | 0.730 | 132 | 0.711 | ||
粒宽 Grain width | ||||||
单倍型间Among haplotypes | 3 | 0.568 | 6.131** | 3 | 0.377 | 3.940** |
单倍型内Within haplotypes | 154 | 0.093 | 132 | 0.096 | ||
粒厚 Grain thickness | ||||||
单倍型间Among haplotypes | 3 | 0.129 | 7.354** | 3 | 0.038 | 1.305 |
单倍型内Within haplotypes | 154 | 0.018 | 132 | 0.029 | ||
长宽比 Ratio of length to width | ||||||
单倍型间 Among haplotypes | 3 | 1.424 | 5.145** | 3 | 0.973 | 5.141** |
单倍型内 Within haplotypes | 154 | 0.277 | 132 | 0.189 | ||
千粒重 1000-grain weight | ||||||
单倍型间Among haplotypes | 3 | 31.593 | 2.470 | 3 | 4.165 | 0.279 |
单倍型内Within haplotypes | 154 | 12.788 | 132 | 14.953 |
Table 3 Analysis of variances (ANOVA) of different haplotypes in gene GS5.
籽粒性状与变异来源 Grain trait and source of variation | 籼亚种 indica | 粳亚种 japonica | ||||
---|---|---|---|---|---|---|
自由度 df | 平方和 Mean square | F值 F value | 自由度 df | 平方和 Mean square | F值 F value | |
粒长Grain length | ||||||
单倍型间Among haplotypes | 3 | 0.929 | 1.272 | 3 | 2.482 | 3.493* |
单倍型内Within haplotypes | 154 | 0.730 | 132 | 0.711 | ||
粒宽 Grain width | ||||||
单倍型间Among haplotypes | 3 | 0.568 | 6.131** | 3 | 0.377 | 3.940** |
单倍型内Within haplotypes | 154 | 0.093 | 132 | 0.096 | ||
粒厚 Grain thickness | ||||||
单倍型间Among haplotypes | 3 | 0.129 | 7.354** | 3 | 0.038 | 1.305 |
单倍型内Within haplotypes | 154 | 0.018 | 132 | 0.029 | ||
长宽比 Ratio of length to width | ||||||
单倍型间 Among haplotypes | 3 | 1.424 | 5.145** | 3 | 0.973 | 5.141** |
单倍型内 Within haplotypes | 154 | 0.277 | 132 | 0.189 | ||
千粒重 1000-grain weight | ||||||
单倍型间Among haplotypes | 3 | 31.593 | 2.470 | 3 | 4.165 | 0.279 |
单倍型内Within haplotypes | 154 | 12.788 | 132 | 14.953 |
单倍型 Haplotype | GS5-1 | GS5-2 | 样品数 Number | 粒长 Grain length /mm | 粒宽 Grain width /mm | 粒厚 Grain thickness/mm | 长宽比 Ratio of length to width | 千粒重 1000-grain weight/g |
---|---|---|---|---|---|---|---|---|
籼亚种 indica | ||||||||
Hap1 | ACC | A | 57 | 8.61±0.14 | 2.74±0.04 b | 2.00±0.02 b | 3.20±0.08 a | 23.07±0.52 |
Hap2 | ACC | C | 8 | 8.13±0.23 | 3.01±0.11 a | 2.10±0.03 ab | 2.75±0.18 b | 23.60±0.41 |
Hap3 | CTA | A | 34 | 8.36±0.13 | 2.99±0.05 a | 2.13±0.02 a | 2.84±0.08 b | 24.76±0.67 |
Hap4 | CTA | C | 59 | 8.38±0.10 | 2.93±0.04 a | 2.09±0.01 a | 2.89±0.06 b | 24.65±0.41 |
粳亚种 japonica | ||||||||
Hap1 | ACC | A | 102 | 7.70±0.08 b | 3.23±0.03 a | 2.20±0.02 | 2.41±0.04 b | 25.68±0.40 |
Hap2 | ACC | C | 3 | 8.28±0.51 a | 3.03±0.27 b | 2.15±0.08 | 2.77±0.28 a | 25.51±2.22 |
Hap3 | CTA | A | 18 | 8.19±0.22 a | 3.01±0.04 b | 2.12±0.03 | 2.73±0.09 a | 24.80±0.85 |
Hap4 | CTA | C | 13 | 8.28±0.18 a | 3.03±0.09 b | 2.14±0.03 | 2.77±0.14 a | 25.76±0.76 |
Table 4 Analysis of the difference of grain-related traits based on different haplotypes in gene GS5.
单倍型 Haplotype | GS5-1 | GS5-2 | 样品数 Number | 粒长 Grain length /mm | 粒宽 Grain width /mm | 粒厚 Grain thickness/mm | 长宽比 Ratio of length to width | 千粒重 1000-grain weight/g |
---|---|---|---|---|---|---|---|---|
籼亚种 indica | ||||||||
Hap1 | ACC | A | 57 | 8.61±0.14 | 2.74±0.04 b | 2.00±0.02 b | 3.20±0.08 a | 23.07±0.52 |
Hap2 | ACC | C | 8 | 8.13±0.23 | 3.01±0.11 a | 2.10±0.03 ab | 2.75±0.18 b | 23.60±0.41 |
Hap3 | CTA | A | 34 | 8.36±0.13 | 2.99±0.05 a | 2.13±0.02 a | 2.84±0.08 b | 24.76±0.67 |
Hap4 | CTA | C | 59 | 8.38±0.10 | 2.93±0.04 a | 2.09±0.01 a | 2.89±0.06 b | 24.65±0.41 |
粳亚种 japonica | ||||||||
Hap1 | ACC | A | 102 | 7.70±0.08 b | 3.23±0.03 a | 2.20±0.02 | 2.41±0.04 b | 25.68±0.40 |
Hap2 | ACC | C | 3 | 8.28±0.51 a | 3.03±0.27 b | 2.15±0.08 | 2.77±0.28 a | 25.51±2.22 |
Hap3 | CTA | A | 18 | 8.19±0.22 a | 3.01±0.04 b | 2.12±0.03 | 2.73±0.09 a | 24.80±0.85 |
Hap4 | CTA | C | 13 | 8.28±0.18 a | 3.03±0.09 b | 2.14±0.03 | 2.77±0.14 a | 25.76±0.76 |
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