
A method of peanut breeding of large pod and high yield based on genomic selection
Min-jie GUO, Li DENG, Jian-li MIAO, Jun-hua YIN, Li REN
CHINESE JOURNAL OF OIL CROP SCIENCES ›› 2024, Vol. 46 ›› Issue (3) : 697-702.
A method of peanut breeding of large pod and high yield based on genomic selection
The batch selection of peanut cross combination study was carried out to provide theoretical guidance for the efficient breeding of new peanut varieties with high yield. Genomic selection analysis of 220 peanut germplasm resources was conducted using phenotypic data of single plant productivity and 100-pod weight at multiple locations for many years and re-sequencing data with depth of 10. Results showed that the phenotypic data were normally distributed, after genome data control, a total of 527 469 high-quality SNP (single nucleotide polymorphism) sites were obtained. The estimated breeding values of single plant productivity and 100-pod weight were calculated by GBLUP (genomic best linear unbiased prediction) model based on phenotypic data. The estimated breeding values were standardized, and the weights of single plant productivity and 100-pod weight were 70% and 30%, respectively, to obtain the comprehensive breeding index of peanut germplasm individuals. There were 190 hybrid combinations of the top 20 materials which showed comprehensive breeding values, and the comprehensive breeding index of any two combinations were calculated. The coefficient of parentage between each two materials was calculated using G matrix based on the genome data. Standardize the comprehensive breeding index of combination and coefficient of parentage, assign 80% and 20% weights respectively to calculate the comprehensive score of the combination. According to the ranking of the comprehensive score of the combination, we could select the parent directly to set hybrid combination. In conclusion, the germplasm materials derived from the combination Kainong30 × Kaixuan016 are suitable for high-yield parents. Genomic selection can efficiently and accurately calculate the ranking among combinations to select the parents and to make cross combinations in batches, improving the breeding efficiency rapidly.
peanut / high yield / phenotype / re-sequencing / genomic selection / hybrid combination {{custom_keyword}} /
Table 1 GBLUP of single plant productivity and 100-pod weight of partial germplasm resources表1 部分种质资源的单株生产力和百果重的GBLUP育种值 |
Cultivar | 单株生产力育种值 GBLUP of single plant productivity | 百果重育种值 GBLUP of 100-pod weight |
---|---|---|
G1 | 1.5546 | 48.9476 |
G2 | -1.8278 | -14.0914 |
G3 | 0.3472 | 69.1758 |
G4 | -0.4957 | -1.4890 |
G5 | 0.3152 | 26.1357 |
G6 | -0.4381 | 5.7234 |
G7 | -1.2601 | -17.8866 |
G8 | 1.0415 | 55.0564 |
G9 | 1.7146 | 39.9853 |
G10 | 1.0923 | -43.2856 |
Table 2 Comprehensive breeding index of top 20 individuals表2 前20名个体综合育种值 |
Cultivar | 单株生产力育种值 GBLUP of single plant productivity | 百果重育种值 GBLUP of 100-pod weight | 综合育种值 Comprehensive breeding index |
---|---|---|---|
G103 | 0.8639 | 3.1718 | 169.5928 |
G130 | 2.8529 | 2.2649 | 168.5229 |
G56 | 1.3225 | 2.1229 | 152.8460 |
G108 | 0.3389 | 2.4902 | 151.7811 |
G100 | 1.3729 | 1.7461 | 145.8683 |
G3 | 0.2858 | 2.1172 | 144.0051 |
G21 | 1.3112 | 1.5930 | 142.3395 |
G38 | 1.2366 | 1.6227 | 142.2953 |
G8 | 0.8573 | 1.6851 | 140.3270 |
G1 | 1.2796 | 1.4981 | 140.2097 |
G80 | 0.9894 | 1.6011 | 139.7902 |
G166 | -0.1630 | 2.0001 | 137.9245 |
G113 | 1.3960 | 1.3148 | 137.5874 |
G170 | 1.0297 | 1.4321 | 136.8081 |
G132 | 1.3874 | 1.2557 | 136.3545 |
G23 | 0.9294 | 1.4442 | 136.2024 |
G70 | 1.5240 | 1.1888 | 136.1911 |
G131 | 0.9505 | 1.4300 | 136.0994 |
G9 | 1.4113 | 1.2238 | 135.9293 |
G112 | 1.4482 | 1.1973 | 135.7183 |
Table 3 Comprehensive breeding index among partial combinations表3 部分组合间的综合育种值 |
ID1 Cultivar | ID2 Cultivar | 组合综合育种值 Comprehensive breeding index of combination |
---|---|---|
G130 | G103 | 169.0578 |
G56 | G103 | 161.2194 |
G108 | G103 | 160.6869 |
G56 | G130 | 160.6844 |
G130 | G108 | 160.1520 |
G103 | G100 | 157.7305 |
G130 | G100 | 157.1956 |
G3 | G103 | 156.7989 |
G3 | G130 | 156.2640 |
G21 | G103 | 155.9661 |
Table 4 Kinship coefficients among partial germplasm resources表4 部分种质资源间的亲缘关系系数 |
Cultivar | Cultivar | 亲缘关系系数 kinship coefficients |
---|---|---|
G109 | G109 | 1.0000 |
G87 | G109 | 0.0054 |
G46 | G109 | 0.0000 |
G23 | G109 | 0.0000 |
G47 | G109 | 0.0000 |
G56 | G109 | 0.4029 |
G169 | G109 | 0.2918 |
G64 | G109 | 0.0000 |
G98 | G109 | 0.2134 |
G71 | G109 | 0.0000 |
Table 5 The top 60 hybrid combinations in terms of comprehensive score表5 组配综合得分排名前60的杂交组合 |
序号 No. | 组合(♀×♂) Combination (♀×♂) | 组合综合育种值标准化 Standardized comprehensive breeding index of combination | 亲缘关系系数标准化 Standardized kinship coefficients | 组配综合得分 Comprehensive score of combination | 序号 No. | 组合(♀×♂) Combination (♀×♂) | 组合综合育种值标准化 Standardized comprehensive breeding index of combination | 亲缘关系系数标准化 Standardized kinship coefficients | 组配综合得分 Comprehensive score of combination |
---|---|---|---|---|---|---|---|---|---|
1 | G130 × G103 | 3.7805 | -0.9688 | 3.2181 | 31 | G112 × G103 | 1.3713 | -0.2001 | 1.1370 |
2 | G130 × G108 | 2.4724 | -1.2451 | 2.2269 | 32 | G9 × G130 | 1.3082 | -0.4481 | 1.1362 |
3 | G130 × G108 | 2.6291 | -0.5762 | 2.2186 | 33 | G23 × G103 | 1.4068 | -0.0297 | 1.1314 |
4 | G130 × G100 | 2.0381 | -0.3559 | 1.7017 | 34 | G130 × G112 | 1.2927 | -0.4724 | 1.1286 |
5 | G56 × G130 | 2.5506 | 1.8192 | 1.6766 | 35 | G170 × G103 | 1.4513 | 0.3512 | 1.0908 |
6 | G3 × G130 | 1.9013 | -0.7194 | 1.6649 | 36 | G131 × G103 | 1.3993 | 0.1893 | 1.0815 |
7 | G108 × G103 | 2.5509 | 2.0757 | 1.6256 | 37 | G166 × G103 | 1.5333 | 0.7762 | 1.0714 |
8 | G103 × G100 | 2.1167 | 0.6990 | 1.5536 | 38 | G80 × G130 | 1.5917 | 1.0516 | 1.0631 |
9 | G38 × G103 | 1.8543 | -0.3422 | 1.5519 | 39 | G56 × G100 | 0.8868 | -0.5322 | 0.8159 |
10 | G21 × G130 | 1.7790 | -0.5031 | 1.5238 | 40 | G56 × G38 | 0.6244 | -1.0736 | 0.7142 |
11 | G38 × G130 | 1.7757 | -0.4143 | 1.5034 | 41 | G56 × G3 | 0.7500 | -0.4690 | 0.6938 |
12 | G80 × G103 | 1.6703 | -0.7874 | 1.4937 | 42 | G56 × G21 | 0.6276 | -0.7604 | 0.6542 |
13 | G8 × G130 | 1.6312 | -0.7546 | 1.4558 | 43 | G38 × G108 | 0.5462 | -0.7768 | 0.5923 |
14 | G130 × G1 | 1.6225 | -0.5612 | 1.4103 | 44 | G8 × G56 | 0.4798 | -0.9442 | 0.5727 |
15 | G8 × G103 | 1.7097 | -0.1595 | 1.3997 | 45 | G108 × G100 | 0.8086 | 0.3840 | 0.5701 |
16 | G3 × G103 | 1.9799 | 0.9723 | 1.3894 | 46 | G56 × G1 | 0.4712 | -0.8239 | 0.5418 |
17 | G21 × G103 | 1.8575 | 0.5234 | 1.3813 | 47 | G80 × G108 | 0.3622 | -1.0917 | 0.5081 |
18 | G103 × G1 | 1.7011 | 0.0943 | 1.3420 | 48 | G56 × G113 | 0.2786 | -1.0661 | 0.4361 |
19 | G131 × G130 | 1.3207 | -1.3264 | 1.3218 | 49 | G21 × G108 | 0.5494 | 0.0773 | 0.4241 |
20 | G166 × G130 | 1.4547 | -0.6422 | 1.2922 | 50 | G3 × G108 | 0.6718 | 0.5931 | 0.4188 |
21 | G113 × G103 | 1.5085 | -0.2005 | 1.2469 | 51 | G108 × G1 | 0.3930 | -0.4010 | 0.3946 |
22 | G130 × G113 | 1.4300 | -0.4721 | 1.2384 | 52 | G56 × G166 | 0.3034 | -0.6606 | 0.3748 |
23 | G170 × G130 | 1.3727 | -0.6675 | 1.2317 | 53 | G56 × G132 | 0.1881 | -1.0613 | 0.3627 |
24 | G56 × G108 | 1.3210 | -0.8448 | 1.2258 | 54 | G56 × G131 | 0.1694 | -1.1276 | 0.3610 |
25 | G23 × G130 | 1.3282 | -0.6890 | 1.2004 | 55 | G70 × G56 | 0.1761 | -1.0600 | 0.3529 |
26 | G132 × G103 | 1.4180 | -0.2039 | 1.1752 | 56 | G9 × G56 | 0.1569 | -1.0395 | 0.3334 |
27 | G70 × G103 | 1.4060 | -0.2066 | 1.1661 | 57 | G56 × G112 | 0.1414 | -1.0665 | 0.3264 |
28 | G132 × G130 | 1.3394 | -0.4697 | 1.1655 | 58 | G113 × G108 | 0.2004 | -0.6541 | 0.2912 |
29 | G70 × G130 | 1.3274 | -0.4758 | 1.1571 | 59 | G56 × G170 | 0.2214 | -0.4546 | 0.2681 |
30 | G9 × G103 | 1.3868 | -0.2053 | 1.1505 | 60 | G56 × G23 | 0.1769 | -0.5486 | 0.2513 |
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