Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety “SSR41” and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1
Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality referenc...
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Frontiers Media S.A.
2021
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oai:doaj.org-article:3311428d928b4c4995b8a5ac72cdd6af2021-11-11T08:40:26ZGenome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety “SSR41” and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS11664-462X10.3389/fpls.2021.743782https://doaj.org/article/3311428d928b4c4995b8a5ac72cdd6af2021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fpls.2021.743782/fullhttps://doaj.org/toc/1664-462XGenome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the “Yugu1” variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, “SSR41”, which is morphologically similar to, and readily cross-pollinates with, “Yugu1”. High-throughput resequencing of “SSR41” identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used “SSR41” and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria.Hui ZhangHui ZhangSha TangJames C. SchnableQiang HeYuanzhu GaoMingzhao LuoGuanqing JiaBaili FengHui ZhiXianmin DiaoFrontiers Media S.A.articleSetaria italicamolecular markerpositional cloningwhite leaf sheathmutantPlant cultureSB1-1110ENFrontiers in Plant Science, Vol 12 (2021) |
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| topic |
Setaria italica molecular marker positional cloning white leaf sheath mutant Plant culture SB1-1110 |
| spellingShingle |
Setaria italica molecular marker positional cloning white leaf sheath mutant Plant culture SB1-1110 Hui Zhang Hui Zhang Sha Tang James C. Schnable Qiang He Yuanzhu Gao Mingzhao Luo Guanqing Jia Baili Feng Hui Zhi Xianmin Diao Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety “SSR41” and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1 |
| description |
Genome-wide DNA polymorphism analysis and molecular marker development are important for forward genetics research and DNA marker-assisted breeding. As an ideal model system for Panicoideae grasses and an important minor crop in East Asia, foxtail millet (Setaria italica) has a high-quality reference genome as well as large mutant libraries based on the “Yugu1” variety. However, there is still a lack of genetic and mutation mapping tools available for forward genetics research on S. italica. Here, we screened another S. italica genotype, “SSR41”, which is morphologically similar to, and readily cross-pollinates with, “Yugu1”. High-throughput resequencing of “SSR41” identified 1,102,064 reliable single nucleotide polymorphisms (SNPs) and 196,782 insertions/deletions (InDels) between the two genotypes, indicating that these two genotypes have high genetic diversity. Of the 8,361 high-quality InDels longer than 20 bp that were developed as molecular markers, 180 were validated with 91.5% accuracy. We used “SSR41” and these developed molecular markers to map the white leaf sheath gene SiWLS1. Further analyses showed that SiWLS1 encodes a chloroplast-localized protein that is involved in the regulation of chloroplast development in bundle sheath cells in the leaf sheath in S. italica and is related to sensitivity to heavy metals. Our study provides the methodology and an important resource for forward genetics research on Setaria. |
| format |
article |
| author |
Hui Zhang Hui Zhang Sha Tang James C. Schnable Qiang He Yuanzhu Gao Mingzhao Luo Guanqing Jia Baili Feng Hui Zhi Xianmin Diao |
| author_facet |
Hui Zhang Hui Zhang Sha Tang James C. Schnable Qiang He Yuanzhu Gao Mingzhao Luo Guanqing Jia Baili Feng Hui Zhi Xianmin Diao |
| author_sort |
Hui Zhang |
| title |
Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety “SSR41” and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1 |
| title_short |
Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety “SSR41” and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1 |
| title_full |
Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety “SSR41” and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1 |
| title_fullStr |
Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety “SSR41” and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1 |
| title_full_unstemmed |
Genome-Wide DNA Polymorphism Analysis and Molecular Marker Development for the Setaria italica Variety “SSR41” and Positional Cloning of the Setaria White Leaf Sheath Gene SiWLS1 |
| title_sort |
genome-wide dna polymorphism analysis and molecular marker development for the setaria italica variety “ssr41” and positional cloning of the setaria white leaf sheath gene siwls1 |
| publisher |
Frontiers Media S.A. |
| publishDate |
2021 |
| url |
https://doaj.org/article/3311428d928b4c4995b8a5ac72cdd6af |
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