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Research paper | Open Access

Haplotype variation and KASP markers for SiPSY1 – A key gene controlling yellow kernel pigmentation in foxtail millet

Rongjun Zuoa,d,1, Yanyan Zhanga,1, Yanbing Yangb,1, Chunfang Wanga,d, Hui Zhia, Linlin Zhanga, Sha Tanga, Yanan Guanb, Shunguo Lic, Ruhong Chengc, Zhonglin Shangd, Guanqing Jiaa( ), Xianmin Diaoa,c,d( )
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
Institute of Millet Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang 050035, Hebei, China
College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, Hebei, China

1 These authors contributed equally to this work.

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Abstract

Carotenoid biosynthesis and accumulation are important in determining nutritional and commercial value of crop products. Yellow pigmentation of mature kernels caused by carotenoids is considered a vital quality trait in foxtail millet, an ancient and widely cultivated cereal crop across the world. Genomic regions associated with yellow pigment content (YPC), lutein and zeaxanthin in foxtail millet grains were identified by genome-wide association analysis (GWAS), and SiPSY1 (Phytoene synthase 1 which regulates formation of the 40-carbon backbone of carotenoids) was confirmed as the main contributor to all three components by knockout and overexpression analysis. SiPSY1 was expressed in seedlings, leaves, panicles, and mature seeds, and was subcellularly localized to chloroplasts. Transcription of SiPSY1 in 15 DAP immature grains was responsible for YPC in mature seeds. Selection of SiPSY1 combined with increased YPC in mature grains during domestication of foxtail millet was confirmed. Haplotype analysis suggested that expression level of SiPSY1 could be a selection target for future breeding programs, and a KASP marker was developed for selection of favorable SiPSY1 alleles in breeding. The results of this work will benefit nutritional and commercial improvement of foxtail millet varieties, as well as other cereal crops.

Keywords

CarotenoidsMarker assisted selectionLuteinZeaxanthinSetaria italica

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The Crop Journal
Volume 11 Issue 6,
December 2023
Pages 1902-1911
DOI: 10.1016/j.cj.2023.09.008
Cite this article:
Zuo R, Zhang Y, Yang Y, et al. Haplotype variation and KASP markers for SiPSY1 – A key gene controlling yellow kernel pigmentation in foxtail millet. The Crop Journal, 2023, 11(6): 1902-1911. https://doi.org/10.1016/j.cj.2023.09.008

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Received: 03 April 2023
Revised: 25 September 2023
Accepted: 26 September 2023
Published: 26 October 2023
© 2023 Crop Science Society of China and Institute of Crop Science, CAAS.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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