Journal of Agricultural Science and Technology ›› 2024, Vol. 26 ›› Issue (2): 46-55.DOI: 10.13304/j.nykjdb.2022.0818
• BIOTECHNOLOGY & LIFE SCIENCE • Previous Articles Next Articles
Lihua LI(), Zhengwen SUN, Huifeng KE, Qishen GU, Liqiang WU, Yan ZHANG, Guiyin ZHANG, Xingfen WANG()
Received:
2022-09-25
Accepted:
2022-10-18
Online:
2024-02-15
Published:
2024-02-04
Contact:
Xingfen WANG
李丽花(), 孙正文, 柯会锋, 谷淇深, 吴立强, 张艳, 张桂寅, 王省芬()
通讯作者:
王省芬
作者简介:
李丽花 E-mail:13473229312@163.com;
基金资助:
CLC Number:
Lihua LI, Zhengwen SUN, Huifeng KE, Qishen GU, Liqiang WU, Yan ZHANG, Guiyin ZHANG, Xingfen WANG. Development and Effect Evaluation of KASP Markers for Fiber Strength in Gossypium hirsutum L.[J]. Journal of Agricultural Science and Technology, 2024, 26(2): 46-55.
李丽花, 孙正文, 柯会锋, 谷淇深, 吴立强, 张艳, 张桂寅, 王省芬. 陆地棉纤维强度KASP-SNP标记的开发及效应评价[J]. 中国农业科技导报, 2024, 26(2): 46-55.
标记 Marker | 等位碱基 Allele | 引物名称 Primer name | 序列 Sequence (5’-3’) |
---|---|---|---|
FS-15 | G/T | FS-15-FAM | TTGTTCTTCCAGACACCTTTGAAC |
FS-15-HEX | CTTTGTTCTTCCAGACACCTTTGAAA | ||
FS-15-Reverse | AGCTAAAAAATTGGAGGCTGAGAGGAAT | ||
FS-16 | A/T | FS-15-FAM | AAATTGAGCAAATTCAGGATGGAACCT |
FS-16-HEX | AAATTGAGCAAATTCAGGATGGAACCA | ||
FS-15-Reverse | ACATCAAAACAATCTGCTTGTACTGGCTT | ||
FS-29 | A/G | FS-29-FAM | ACGGAGCTGAAGGATGCAAGTAA |
FS-29-HEX | CGGAGCTGAAGGATGCAAGTAG | ||
FS-29-Reverse | GCAAACTCTCGATTTCAAATCCAAAGGTT |
Table 1 Primer sequences used for KASP assays
标记 Marker | 等位碱基 Allele | 引物名称 Primer name | 序列 Sequence (5’-3’) |
---|---|---|---|
FS-15 | G/T | FS-15-FAM | TTGTTCTTCCAGACACCTTTGAAC |
FS-15-HEX | CTTTGTTCTTCCAGACACCTTTGAAA | ||
FS-15-Reverse | AGCTAAAAAATTGGAGGCTGAGAGGAAT | ||
FS-16 | A/T | FS-15-FAM | AAATTGAGCAAATTCAGGATGGAACCT |
FS-16-HEX | AAATTGAGCAAATTCAGGATGGAACCA | ||
FS-15-Reverse | ACATCAAAACAATCTGCTTGTACTGGCTT | ||
FS-29 | A/G | FS-29-FAM | ACGGAGCTGAAGGATGCAAGTAA |
FS-29-HEX | CGGAGCTGAAGGATGCAAGTAG | ||
FS-29-Reverse | GCAAACTCTCGATTTCAAATCCAAAGGTT |
年份Year | 环境 Environment | 最大值Max/(cN·tex-1) | 最小值Min/ (cN·tex-1) | 平均值Mean/ (cN·tex-1) | 标准差 SD | 偏度 Skew | 峰度 Kurt | 变异系数 CV/% |
---|---|---|---|---|---|---|---|---|
2014 | E1:保定Baoding | 35.80 | 23.30 | 29.38 | 2.51 | 0.11 | -0.045 | 8.54 |
E2:河间Hejian | 34.80 | 24.20 | 29.17 | 2.24 | 0.31 | -0.26 | 7.68 | |
E3:辛集Xinji | 36.30 | 25.20 | 30.80 | 2.21 | 0.068 | -0.004 | 7.18 | |
E4:青县Qing county | 36.80 | 24.80 | 30.08 | 2.16 | 0.16 | 0.066 | 7.18 | |
E5:崖城Yacheng | 36.30 | 23.30 | 28.47 | 2.12 | 0.34 | 0.39 | 7.45 | |
2015 | E6:辛集Xinji | 37.47 | 23.23 | 31.01 | 2.01 | 0.059 | 0.89 | 6.48 |
E7:青县Qing county | 35.51 | 19.91 | 28.39 | 2.34 | 0.044 | 0.29 | 8.24 | |
E8:崖城Yacheng | 31.61 | 22.70 | 25.61 | 1.76 | 0.68 | 0.30 | 6.87 |
Table 2 Phenotypic variation for fiber strength of 376 accessions in 8 environments
年份Year | 环境 Environment | 最大值Max/(cN·tex-1) | 最小值Min/ (cN·tex-1) | 平均值Mean/ (cN·tex-1) | 标准差 SD | 偏度 Skew | 峰度 Kurt | 变异系数 CV/% |
---|---|---|---|---|---|---|---|---|
2014 | E1:保定Baoding | 35.80 | 23.30 | 29.38 | 2.51 | 0.11 | -0.045 | 8.54 |
E2:河间Hejian | 34.80 | 24.20 | 29.17 | 2.24 | 0.31 | -0.26 | 7.68 | |
E3:辛集Xinji | 36.30 | 25.20 | 30.80 | 2.21 | 0.068 | -0.004 | 7.18 | |
E4:青县Qing county | 36.80 | 24.80 | 30.08 | 2.16 | 0.16 | 0.066 | 7.18 | |
E5:崖城Yacheng | 36.30 | 23.30 | 28.47 | 2.12 | 0.34 | 0.39 | 7.45 | |
2015 | E6:辛集Xinji | 37.47 | 23.23 | 31.01 | 2.01 | 0.059 | 0.89 | 6.48 |
E7:青县Qing county | 35.51 | 19.91 | 28.39 | 2.34 | 0.044 | 0.29 | 8.24 | |
E8:崖城Yacheng | 31.61 | 22.70 | 25.61 | 1.76 | 0.68 | 0.30 | 6.87 |
Fig. 2 Genotyping results of FS-15 in the population and allelic effects on fiber strengthA: Genotyping results of accessions, each dot represents 1 material,the red and blue represent homozygous, green represents heterozygous, pink represents failed data and black represents the non-template control, respectively; B: Allele effects, * and ** indicate significant difference at P<0.05 and P<0.01 levels, respectively, and NA indicates no significant difference; code of environment is same as Table 2
年份Year | 环境 Environment | FS-15/ (cN·tex-1) | 效应值 Allele effect G<T | 概率值 P-value | FS-16/ (cN·tex-1) | 效应值 Allele effect A<T | 概率值 P-value | FS-29/ (cN·tex-1) | 效应值 Allele effect G<A | 概率值 P-value | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
GG | TT | AA | TT | AA | GG | ||||||||
2014 | E1:保定Baoding | 29.27 | 30.97 | 1.70 | 0.003 9 | 29.26 | 30.80 | 1.54 | 0.008 2 | 29.49 | 28.91 | 0.58 | 0.082 8 |
E2:河间Hejian | 29.06 | 30.32 | 1.26 | 0.017 8 | 29.12 | 30.21 | 1.08 | 0.036 0 | 29.27 | 28.83 | 0.44 | 0.139 7 | |
E3:辛集Xinji | 30.67 | 32.27 | 1.61 | 0.002 0 | 30.74 | 32.11 | 1.36 | 0.006 7 | 30.81 | 30.63 | 0.18 | 0.543 5 | |
E4:青县Qing county | 29.99 | 31.23 | 1.24 | 0.014 4 | 30.00 | 31.15 | 1.15 | 0.021 0 | 30.24 | 29.37 | 0.87 | 0.002 1 | |
E5:崖城Yacheng | 28.29 | 29.98 | 1.69 | 0.000 5 | 28.38 | 29.84 | 1.46 | 0.002 9 | 28.58 | 27.93 | 0.65 | 0.020 9 | |
2015 | E6:辛集Xinji | 30.98 | 31.14 | 0.15 | 0.753 9 | 30.97 | 31.09 | 0.12 | 0.798 9 | 31.03 | 30.92 | 0.11 | 0.693 7 |
E7:青县Qing county | 28.36 | 28.70 | 0.35 | 0.538 9 | 28.34 | 28.68 | 0.34 | 0.527 4 | 28.58 | 27.83 | 0.75 | 0.015 8 | |
E8:崖城Yacheng | 25.54 | 26.44 | 0.90 | 0.031 4 | 25.56 | 26.39 | 0.83 | 0.041 7 | 25.76 | 24.98 | 0.78 | 0.000 7 |
Table 3 Allelic effects of KASP-SNP markers on fiber strength
年份Year | 环境 Environment | FS-15/ (cN·tex-1) | 效应值 Allele effect G<T | 概率值 P-value | FS-16/ (cN·tex-1) | 效应值 Allele effect A<T | 概率值 P-value | FS-29/ (cN·tex-1) | 效应值 Allele effect G<A | 概率值 P-value | |||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
GG | TT | AA | TT | AA | GG | ||||||||
2014 | E1:保定Baoding | 29.27 | 30.97 | 1.70 | 0.003 9 | 29.26 | 30.80 | 1.54 | 0.008 2 | 29.49 | 28.91 | 0.58 | 0.082 8 |
E2:河间Hejian | 29.06 | 30.32 | 1.26 | 0.017 8 | 29.12 | 30.21 | 1.08 | 0.036 0 | 29.27 | 28.83 | 0.44 | 0.139 7 | |
E3:辛集Xinji | 30.67 | 32.27 | 1.61 | 0.002 0 | 30.74 | 32.11 | 1.36 | 0.006 7 | 30.81 | 30.63 | 0.18 | 0.543 5 | |
E4:青县Qing county | 29.99 | 31.23 | 1.24 | 0.014 4 | 30.00 | 31.15 | 1.15 | 0.021 0 | 30.24 | 29.37 | 0.87 | 0.002 1 | |
E5:崖城Yacheng | 28.29 | 29.98 | 1.69 | 0.000 5 | 28.38 | 29.84 | 1.46 | 0.002 9 | 28.58 | 27.93 | 0.65 | 0.020 9 | |
2015 | E6:辛集Xinji | 30.98 | 31.14 | 0.15 | 0.753 9 | 30.97 | 31.09 | 0.12 | 0.798 9 | 31.03 | 30.92 | 0.11 | 0.693 7 |
E7:青县Qing county | 28.36 | 28.70 | 0.35 | 0.538 9 | 28.34 | 28.68 | 0.34 | 0.527 4 | 28.58 | 27.83 | 0.75 | 0.015 8 | |
E8:崖城Yacheng | 25.54 | 26.44 | 0.90 | 0.031 4 | 25.56 | 26.39 | 0.83 | 0.041 7 | 25.76 | 24.98 | 0.78 | 0.000 7 |
Fig. 3 Genotyping results of FS-16 in the population and allelic effects on fiber strengthA: Genotyping results of accessions, each dot represents 1 material,the red and blue represent homozygous, green represents heterozygous, pink represents failed data and black represents the non-template control, respectively; B: Allele effects, * and ** indicate significant difference at P<0.05 and P<0.01 levels, respectively, and NA indicates no significant difference; code of environment is same as Table 2
Fig. 4 Genotyping results of FS-29 in the population and allelic effects on fiber strengthA: Genotyping results of accessions, each dot represents 1 material,the red and blue represent homozygous, green represents heterozygous, pink represents failed data and black represents the non-template control, respectively; B: Allele effects, * and ** indicate significant difference at P<0.05 and P<0.01 levels, respectively, and NA indicates no significant difference; code of environment is same as Table 2
基因 Gene | 标记 Marker | 等位基因(样本数) Allele (number) | 平均值Average/ (cN·tex-1) | 等位效应 Allele effect | 选择率(样本数) Selection rate/%(number) | 概率值 P value |
---|---|---|---|---|---|---|
Gh_A07G1766(G/T) | FS-15 | G(315) T(19) | 29.12 30.21 | 1.09 | 50.5(159) 63.2(12) | 0.006 9 |
Gh_A07G1765 (A/T) | FS-16 | A(336) T(20) | 29.15 30.10 | 0.95 | 51.8(174) 60.0(12) | 0.016 0 |
Gh_D11G1931 (A/G) | FS-29 | A(294) G(70) | 29.35 28.77 | 0.57 | 56.1(165) 40.0(28) | 0.010 5 |
Table 4 Allelic effects of 3 markers in the population of 376 accessions
基因 Gene | 标记 Marker | 等位基因(样本数) Allele (number) | 平均值Average/ (cN·tex-1) | 等位效应 Allele effect | 选择率(样本数) Selection rate/%(number) | 概率值 P value |
---|---|---|---|---|---|---|
Gh_A07G1766(G/T) | FS-15 | G(315) T(19) | 29.12 30.21 | 1.09 | 50.5(159) 63.2(12) | 0.006 9 |
Gh_A07G1765 (A/T) | FS-16 | A(336) T(20) | 29.15 30.10 | 0.95 | 51.8(174) 60.0(12) | 0.016 0 |
Gh_D11G1931 (A/G) | FS-29 | A(294) G(70) | 29.35 28.77 | 0.57 | 56.1(165) 40.0(28) | 0.010 5 |
标记Marker | Hap1 | Hap2 | Hap3 | Hap4 |
---|---|---|---|---|
FS-15(G/T) | G | G | T | T |
FS-16(A/T) | A | A | T | T |
FS-29(A/G) | A | G | A | G |
Table 5 Haplotype combination
标记Marker | Hap1 | Hap2 | Hap3 | Hap4 |
---|---|---|---|---|
FS-15(G/T) | G | G | T | T |
FS-16(A/T) | A | A | T | T |
FS-29(A/G) | A | G | A | G |
Fig. 5 Effects of different haplotype combination on fiber strength based on 3 KASP markersA: Frequency of four mainly haplotype combination in 376 accessions; B: Effect of different haplotype combianation on fiber strength, different lowercase letters represent Duncan’s multiple comparison at P<0.05 level
单倍型组合(样本数) Haplotype combination (number) | 纤维强度 Fiber strength/(cN·tex-1) | 选择率(样本数) Selection rate /% (number) | 概率值 P value |
---|---|---|---|
Hap1(242) | 29.30±1.54 b | 55.9(133) | 1.62×10-4 |
Hap2(54) | 28.53±1.65 c | 38.9(21) | |
Hap3(11) | 30.56±1.73 a | 72.7(8) | |
Hap4(7) | 30.42±2.79 ab | 57.1(4) |
Table 6 Effect of different haplotypes combination on accessions with high fiber strength
单倍型组合(样本数) Haplotype combination (number) | 纤维强度 Fiber strength/(cN·tex-1) | 选择率(样本数) Selection rate /% (number) | 概率值 P value |
---|---|---|---|
Hap1(242) | 29.30±1.54 b | 55.9(133) | 1.62×10-4 |
Hap2(54) | 28.53±1.65 c | 38.9(21) | |
Hap3(11) | 30.56±1.73 a | 72.7(8) | |
Hap4(7) | 30.42±2.79 ab | 57.1(4) |
单倍型组合(样本数) Haplotype combination (number) | 纤维长度 FL/mm | 概率值 P value | 铃重 BW/g | 概率值 P-value | 籽指 SI/g | 概率值 P-value | 衣指 LI/g | 概率值 P value |
---|---|---|---|---|---|---|---|---|
Hap1(242) | 29.18±0.99 b | 5.45×10-7 | 6.1±0.48 ab | 0.028 | 11.1±0.83 ab | 0.016 | 7.26±0.27 ab | 0.021 |
Hap2(54) | 28.37±1.14 c | 5.93±0.43 b | 10.91±0.90 b | 7.08±0.67 b | ||||
Hap3(11) | 29.71±0.90 a | 6.29±0.42 a | 11.59±1.04 a | 7.74±1.01 a | ||||
Hap4(7) | 29.3±1.30 ab | 5.92±0.34 b | 11.63±0.92 a | 7.09±0.41 b |
Table 7 Effects ofdifferent haplotype combinationon other traits
单倍型组合(样本数) Haplotype combination (number) | 纤维长度 FL/mm | 概率值 P value | 铃重 BW/g | 概率值 P-value | 籽指 SI/g | 概率值 P-value | 衣指 LI/g | 概率值 P value |
---|---|---|---|---|---|---|---|---|
Hap1(242) | 29.18±0.99 b | 5.45×10-7 | 6.1±0.48 ab | 0.028 | 11.1±0.83 ab | 0.016 | 7.26±0.27 ab | 0.021 |
Hap2(54) | 28.37±1.14 c | 5.93±0.43 b | 10.91±0.90 b | 7.08±0.67 b | ||||
Hap3(11) | 29.71±0.90 a | 6.29±0.42 a | 11.59±1.04 a | 7.74±1.01 a | ||||
Hap4(7) | 29.3±1.30 ab | 5.92±0.34 b | 11.63±0.92 a | 7.09±0.41 b |
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