Integrating BSA-Seq with RNA-Seq Reveals a Novel Fasciated Ear5 Mutant in Maize
Increasing grain yield is required to meet the rapidly expanding demands for food, feed, and fuel. Inflorescence meristems are central to plant growth and development. However, the question concerning whether inflorescence development can be regulated to improve grain yield remains unclear. Here, we...
| Main Authors: | , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-01-01
|
| Series: | International Journal of Molecular Sciences |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1422-0067/24/2/1182 |
| _version_ | 1797441475609362432 |
|---|---|
| author | Pengshuai Yan Weihua Li Enxiang Zhou Ye Xing Bing Li Jing Liu Zhanhui Zhang Dong Ding Zhiyuan Fu Huiling Xie Jihua Tang |
| author_facet | Pengshuai Yan Weihua Li Enxiang Zhou Ye Xing Bing Li Jing Liu Zhanhui Zhang Dong Ding Zhiyuan Fu Huiling Xie Jihua Tang |
| author_sort | Pengshuai Yan |
| collection | DOAJ |
| description | Increasing grain yield is required to meet the rapidly expanding demands for food, feed, and fuel. Inflorescence meristems are central to plant growth and development. However, the question concerning whether inflorescence development can be regulated to improve grain yield remains unclear. Here, we describe a naturally occurring single recessive mutation called <i>fea5</i> that can increase grain yield in maize. Using bulk segregant analysis sequencing (BSA-seq), the candidate region was initially mapped to a large region on chromosome 4 (4.68 Mb–11.26 Mb). Transcriptome sequencing (RNA-seq) revealed a total of 1246 differentially expressed genes (DEGs), of which 835 were up-regulated and 411 were down-regulated. Further analysis revealed the enrichment of DEGs in phytohormone signal transduction. Consistently, phytohormone profiling indicated that auxin (IAA), jasmonic acid (JA), ethylene (ETH), and cytokinin (CK) levels increased significantly, whereas the gibberellin (GA) level decreased significantly in <i>fea5</i>. By integrating BSA-seq with RNA-seq, we identified <i>Zm00001d048841</i> as the most likely candidate gene. Our results provide valuable insight into this new germplasm resource and the molecular mechanism underlying fasciated ears that produce a higher kernel row number in maize. |
| first_indexed | 2024-03-09T12:24:42Z |
| format | Article |
| id | doaj.art-4f856937870749c0bdf1e2a7d96578fd |
| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-09T12:24:42Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | International Journal of Molecular Sciences |
| spelling | doaj.art-4f856937870749c0bdf1e2a7d96578fd2023-11-30T22:36:36ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-01-01242118210.3390/ijms24021182Integrating BSA-Seq with RNA-Seq Reveals a Novel Fasciated Ear5 Mutant in MaizePengshuai Yan0Weihua Li1Enxiang Zhou2Ye Xing3Bing Li4Jing Liu5Zhanhui Zhang6Dong Ding7Zhiyuan Fu8Huiling Xie9Jihua Tang10National Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, ChinaNational Key Laboratory of Wheat and Maize Crop Science, College of Agronomy, Henan Agricultural University, Zhengzhou 450002, ChinaIncreasing grain yield is required to meet the rapidly expanding demands for food, feed, and fuel. Inflorescence meristems are central to plant growth and development. However, the question concerning whether inflorescence development can be regulated to improve grain yield remains unclear. Here, we describe a naturally occurring single recessive mutation called <i>fea5</i> that can increase grain yield in maize. Using bulk segregant analysis sequencing (BSA-seq), the candidate region was initially mapped to a large region on chromosome 4 (4.68 Mb–11.26 Mb). Transcriptome sequencing (RNA-seq) revealed a total of 1246 differentially expressed genes (DEGs), of which 835 were up-regulated and 411 were down-regulated. Further analysis revealed the enrichment of DEGs in phytohormone signal transduction. Consistently, phytohormone profiling indicated that auxin (IAA), jasmonic acid (JA), ethylene (ETH), and cytokinin (CK) levels increased significantly, whereas the gibberellin (GA) level decreased significantly in <i>fea5</i>. By integrating BSA-seq with RNA-seq, we identified <i>Zm00001d048841</i> as the most likely candidate gene. Our results provide valuable insight into this new germplasm resource and the molecular mechanism underlying fasciated ears that produce a higher kernel row number in maize.https://www.mdpi.com/1422-0067/24/2/1182maizefasciated earphytohormoneBSA-seqRNA-seq |
| spellingShingle | Pengshuai Yan Weihua Li Enxiang Zhou Ye Xing Bing Li Jing Liu Zhanhui Zhang Dong Ding Zhiyuan Fu Huiling Xie Jihua Tang Integrating BSA-Seq with RNA-Seq Reveals a Novel Fasciated Ear5 Mutant in Maize International Journal of Molecular Sciences maize fasciated ear phytohormone BSA-seq RNA-seq |
| title | Integrating BSA-Seq with RNA-Seq Reveals a Novel Fasciated Ear5 Mutant in Maize |
| title_full | Integrating BSA-Seq with RNA-Seq Reveals a Novel Fasciated Ear5 Mutant in Maize |
| title_fullStr | Integrating BSA-Seq with RNA-Seq Reveals a Novel Fasciated Ear5 Mutant in Maize |
| title_full_unstemmed | Integrating BSA-Seq with RNA-Seq Reveals a Novel Fasciated Ear5 Mutant in Maize |
| title_short | Integrating BSA-Seq with RNA-Seq Reveals a Novel Fasciated Ear5 Mutant in Maize |
| title_sort | integrating bsa seq with rna seq reveals a novel fasciated ear5 mutant in maize |
| topic | maize fasciated ear phytohormone BSA-seq RNA-seq |
| url | https://www.mdpi.com/1422-0067/24/2/1182 |
| work_keys_str_mv | AT pengshuaiyan integratingbsaseqwithrnaseqrevealsanovelfasciatedear5mutantinmaize AT weihuali integratingbsaseqwithrnaseqrevealsanovelfasciatedear5mutantinmaize AT enxiangzhou integratingbsaseqwithrnaseqrevealsanovelfasciatedear5mutantinmaize AT yexing integratingbsaseqwithrnaseqrevealsanovelfasciatedear5mutantinmaize AT bingli integratingbsaseqwithrnaseqrevealsanovelfasciatedear5mutantinmaize AT jingliu integratingbsaseqwithrnaseqrevealsanovelfasciatedear5mutantinmaize AT zhanhuizhang integratingbsaseqwithrnaseqrevealsanovelfasciatedear5mutantinmaize AT dongding integratingbsaseqwithrnaseqrevealsanovelfasciatedear5mutantinmaize AT zhiyuanfu integratingbsaseqwithrnaseqrevealsanovelfasciatedear5mutantinmaize AT huilingxie integratingbsaseqwithrnaseqrevealsanovelfasciatedear5mutantinmaize AT jihuatang integratingbsaseqwithrnaseqrevealsanovelfasciatedear5mutantinmaize |