Combined BSA-Seq and RNA-Seq Reveal Genes Associated with the Visual Stay-Green of Maize (<i>Zea mays</i> L.)
Maize has become one of the most widely grown grains in the world, and the stay-green mutant allows these plants to maintain their green leaves and photosynthetic potential for longer following anthesis than in non-mutated plants. As a result, stay-green plants have a higher production rate than non...
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MDPI AG
2023-12-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/24/17617 |
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| author | Ran Zheng Min Deng Dan Lv Bo Tong Yuqing Liu Hongbing Luo |
| author_facet | Ran Zheng Min Deng Dan Lv Bo Tong Yuqing Liu Hongbing Luo |
| author_sort | Ran Zheng |
| collection | DOAJ |
| description | Maize has become one of the most widely grown grains in the world, and the stay-green mutant allows these plants to maintain their green leaves and photosynthetic potential for longer following anthesis than in non-mutated plants. As a result, stay-green plants have a higher production rate than non-stay-green varieties due to their prolonged grain-filling period. In this study, the candidate genes related to the visual stay-green at the maturation stage of maize were investigated. The F<sub>2</sub> population was derived from the T01 (stay-green) and the Xin3 (non-stay-green) cross. Two bulked segregant analysis pools were constructed. According to the method of combining ED (Euclidean distance), Ridit (relative to an identified distribution unit), SmoothG, and SNP algorithms, a region containing 778 genes on chromosome 9 was recognized as the candidate region associated with the visual stay-green in maize. A total of eight modules were identified using WGCNA (weighted correlation network analysis), of which green, brown, pink, and salmon modules were significantly correlated with visual stay-green. BSA, combined with the annotation function, discovered 7 potential candidate genes, while WGCNA discovered 11 stay-green potential candidate genes. The candidate range was further reduced due through association analysis of BSA-seq and RNA-seq. We identified <i>Zm00001eb378880</i>, <i>Zm00001eb383680,</i> and <i>Zm00001eb384100</i> to be the most likely candidate genes. Our results provide valuable insights into this new germplasm resource with reference to increasing the yield for maize. |
| first_indexed | 2024-03-08T20:41:07Z |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-08T20:41:07Z |
| publishDate | 2023-12-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-b0e7dc89b36d4236ae65a206b1935a552023-12-22T14:15:22ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-12-0124241761710.3390/ijms242417617Combined BSA-Seq and RNA-Seq Reveal Genes Associated with the Visual Stay-Green of Maize (<i>Zea mays</i> L.)Ran Zheng0Min Deng1Dan Lv2Bo Tong3Yuqing Liu4Hongbing Luo5College of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaCollege of Agronomy, Hunan Agricultural University, Changsha 410128, ChinaMaize has become one of the most widely grown grains in the world, and the stay-green mutant allows these plants to maintain their green leaves and photosynthetic potential for longer following anthesis than in non-mutated plants. As a result, stay-green plants have a higher production rate than non-stay-green varieties due to their prolonged grain-filling period. In this study, the candidate genes related to the visual stay-green at the maturation stage of maize were investigated. The F<sub>2</sub> population was derived from the T01 (stay-green) and the Xin3 (non-stay-green) cross. Two bulked segregant analysis pools were constructed. According to the method of combining ED (Euclidean distance), Ridit (relative to an identified distribution unit), SmoothG, and SNP algorithms, a region containing 778 genes on chromosome 9 was recognized as the candidate region associated with the visual stay-green in maize. A total of eight modules were identified using WGCNA (weighted correlation network analysis), of which green, brown, pink, and salmon modules were significantly correlated with visual stay-green. BSA, combined with the annotation function, discovered 7 potential candidate genes, while WGCNA discovered 11 stay-green potential candidate genes. The candidate range was further reduced due through association analysis of BSA-seq and RNA-seq. We identified <i>Zm00001eb378880</i>, <i>Zm00001eb383680,</i> and <i>Zm00001eb384100</i> to be the most likely candidate genes. Our results provide valuable insights into this new germplasm resource with reference to increasing the yield for maize.https://www.mdpi.com/1422-0067/24/24/17617maizevisual stay-greenBSARNA-seqgenes |
| spellingShingle | Ran Zheng Min Deng Dan Lv Bo Tong Yuqing Liu Hongbing Luo Combined BSA-Seq and RNA-Seq Reveal Genes Associated with the Visual Stay-Green of Maize (<i>Zea mays</i> L.) International Journal of Molecular Sciences maize visual stay-green BSA RNA-seq genes |
| title | Combined BSA-Seq and RNA-Seq Reveal Genes Associated with the Visual Stay-Green of Maize (<i>Zea mays</i> L.) |
| title_full | Combined BSA-Seq and RNA-Seq Reveal Genes Associated with the Visual Stay-Green of Maize (<i>Zea mays</i> L.) |
| title_fullStr | Combined BSA-Seq and RNA-Seq Reveal Genes Associated with the Visual Stay-Green of Maize (<i>Zea mays</i> L.) |
| title_full_unstemmed | Combined BSA-Seq and RNA-Seq Reveal Genes Associated with the Visual Stay-Green of Maize (<i>Zea mays</i> L.) |
| title_short | Combined BSA-Seq and RNA-Seq Reveal Genes Associated with the Visual Stay-Green of Maize (<i>Zea mays</i> L.) |
| title_sort | combined bsa seq and rna seq reveal genes associated with the visual stay green of maize i zea mays i l |
| topic | maize visual stay-green BSA RNA-seq genes |
| url | https://www.mdpi.com/1422-0067/24/24/17617 |
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