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Genomic Prediction of Kernel Zinc Concentration in Multiple Maize Populations Using Genotyping-by-Sequencing and Repeat Amplification Sequencing Markers

文献类型： 外文期刊

作者： Guo, Rui 1 ; Dhliwayo, Thanda 2 ; Mageto, Edna K. 4 ; Palacios-Rojas, Natalia 2 ; Lee, Michael 4 ; Yu, Diansi 5 ; Ruan 1 ;

作者机构： 1.Shenyang Agr Univ, Coll Agron, Shenyang, Peoples R China

2.Int Maize & Wheat Improvement Ctr CIMMYT, Texcoco, Mexico

3.Shenyang Agr Univ, Coll Biosci & Biotechnol, Shenyang, Peoples R China

4.Iowa State Univ, Dept Agron, Ames, IA USA

5.Shanghai Acad Agr Sci, CIMMYT China Specialty Maize Res Ctr, Shanghai, Peoples R China

6.Shanghai Acad Agr Sci, Crop Breeding & Cultivat Res Inst, Shanghai, Peoples R China

7.Int Maize & Wheat Improvement Ctr CIMMYT, Nairobi, Kenya

关键词： maize; kernel Zn concentration; genomic selection; GBS; rAmpSeq

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.753； 五年影响因子：6.612 ）

ISSN： 1664-462X

年卷期： 2020 年 11 卷

页码：

收录情况： SCI

摘要： Enriching of kernel zinc (Zn) concentration in maize is one of the most effective ways to solve the problem of Zn deficiency in low and middle income countries where maize is the major staple food, and 17% of the global population is affected with Zn deficiency. Genomic selection (GS) has shown to be an effective approach to accelerate genetic gains in plant breeding. In the present study, an association-mapping panel and two maize double-haploid (DH) populations, both genotyped with genotyping-by-sequencing (GBS) and repeat amplification sequencing (rAmpSeq) markers, were used to estimate the genomic prediction accuracy of kernel Zn concentration in maize. Results showed that the prediction accuracy of two DH populations was higher than that of the association mapping population using the same set of markers. The prediction accuracy estimated with the GBS markers was significantly higher than that estimated with the rAmpSeq markers in the same population. The maximum prediction accuracy with minimum standard error was observed when half of the genotypes were included in the training set and 3,000 and 500 markers were used for prediction in the association mapping panel and the DH populations, respectively. Appropriate levels of minor allele frequency and missing rate should be considered and selected to achieve good prediction accuracy and reduce the computation burden by balancing the number of markers and marker quality. Training set development with broad phenotypic variation is possible to improve prediction accuracy. The transferability of the GS models across populations was assessed, the prediction accuracies in a few pairwise populations were above or close to 0.20, which indicates the prediction accuracies across years and populations have to be assessed in a larger breeding dataset with closer relationship between the training and prediction sets in further studies. GS outperformed MAS (marker-assisted-selection) on predicting the kernel Zn concentration in maize, the decision of a breeding strategy to implement GS individually or to implement MAS and GS stepwise for improving kernel Zn concentration in maize requires further research. Results of this study provide valuable information for understanding how to implement GS for improving kernel Zn concentration in maize.

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