Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage
Abstract Background Salinity is a major abiotic stress seriously hindering crop yield. Development and utilization of tolerant varieties is the most economical way to address soil salinity. Upland cotton is a major fiber crop and pioneer plant on saline soil and thus its genetic architecture underly...
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| Format: | Article |
| Language: | English |
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BMC
2019-09-01
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| Series: | BMC Plant Biology |
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| Online Access: | http://link.springer.com/article/10.1186/s12870-019-1989-2 |
| _version_ | 1819044803344596992 |
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| author | Yanchao Yuan Huixian Xing Wenguan Zeng Jialing Xu Lili Mao Liyuan Wang Wei Feng Jincai Tao Haoran Wang Haijun Zhang Qingkang Wang Guihua Zhang Xianliang Song Xue-Zhen Sun |
| author_facet | Yanchao Yuan Huixian Xing Wenguan Zeng Jialing Xu Lili Mao Liyuan Wang Wei Feng Jincai Tao Haoran Wang Haijun Zhang Qingkang Wang Guihua Zhang Xianliang Song Xue-Zhen Sun |
| author_sort | Yanchao Yuan |
| collection | DOAJ |
| description | Abstract Background Salinity is a major abiotic stress seriously hindering crop yield. Development and utilization of tolerant varieties is the most economical way to address soil salinity. Upland cotton is a major fiber crop and pioneer plant on saline soil and thus its genetic architecture underlying salt tolerance should be extensively explored. Results In this study, genome-wide association analysis and RNA sequencing were employed to detect salt-tolerant qualitative-trait loci (QTLs) and candidate genes in 196 upland cotton genotypes at the germination stage. Using comprehensive evaluation values of salt tolerance in four environments, we identified 33 significant single-nucleotide polymorphisms (SNPs), including 17 and 7 SNPs under at least two and four environments, respectively. The 17 stable SNPs were located within or near 98 candidate genes in 13 QTLs, including 35 genes that were functionally annotated to be involved in salt stress responses. RNA-seq analysis indicated that among the 98 candidate genes, 13 were stably differentially expressed. Furthermore, 12 of the 13 candidate genes were verified by qRT-PCR. RNA-seq analysis detected 6640, 3878, and 6462 differentially expressed genes at three sampling time points, of which 869 were shared. Conclusions These results, including the elite cotton accessions with accurate salt tolerance evaluation, the significant SNP markers, the candidate genes, and the salt-tolerant pathways, could improve our understanding of the molecular regulatory mechanisms under salt stress tolerance and genetic manipulation for cotton improvement. |
| first_indexed | 2024-12-21T10:18:29Z |
| format | Article |
| id | doaj.art-a935d7c400c440daa8ed92eef406044d |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-21T10:18:29Z |
| publishDate | 2019-09-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj.art-a935d7c400c440daa8ed92eef406044d2022-12-21T19:07:31ZengBMCBMC Plant Biology1471-22292019-09-0119111910.1186/s12870-019-1989-2Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stageYanchao Yuan0Huixian Xing1Wenguan Zeng2Jialing Xu3Lili Mao4Liyuan Wang5Wei Feng6Jincai Tao7Haoran Wang8Haijun Zhang9Qingkang Wang10Guihua Zhang11Xianliang Song12Xue-Zhen Sun13State Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityState Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityState Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityState Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityState Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityState Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityState Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityState Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityState Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityState Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityState Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityHeze Academy of Agricultural SciencesState Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityState Key Laboratory of Crop Biology/Agronomy College, Shandong Agricultural UniversityAbstract Background Salinity is a major abiotic stress seriously hindering crop yield. Development and utilization of tolerant varieties is the most economical way to address soil salinity. Upland cotton is a major fiber crop and pioneer plant on saline soil and thus its genetic architecture underlying salt tolerance should be extensively explored. Results In this study, genome-wide association analysis and RNA sequencing were employed to detect salt-tolerant qualitative-trait loci (QTLs) and candidate genes in 196 upland cotton genotypes at the germination stage. Using comprehensive evaluation values of salt tolerance in four environments, we identified 33 significant single-nucleotide polymorphisms (SNPs), including 17 and 7 SNPs under at least two and four environments, respectively. The 17 stable SNPs were located within or near 98 candidate genes in 13 QTLs, including 35 genes that were functionally annotated to be involved in salt stress responses. RNA-seq analysis indicated that among the 98 candidate genes, 13 were stably differentially expressed. Furthermore, 12 of the 13 candidate genes were verified by qRT-PCR. RNA-seq analysis detected 6640, 3878, and 6462 differentially expressed genes at three sampling time points, of which 869 were shared. Conclusions These results, including the elite cotton accessions with accurate salt tolerance evaluation, the significant SNP markers, the candidate genes, and the salt-tolerant pathways, could improve our understanding of the molecular regulatory mechanisms under salt stress tolerance and genetic manipulation for cotton improvement.http://link.springer.com/article/10.1186/s12870-019-1989-2SalinityTranscriptomeGenetic variationGenome-wide association studyGermination stageComprehensive evaluation |
| spellingShingle | Yanchao Yuan Huixian Xing Wenguan Zeng Jialing Xu Lili Mao Liyuan Wang Wei Feng Jincai Tao Haoran Wang Haijun Zhang Qingkang Wang Guihua Zhang Xianliang Song Xue-Zhen Sun Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage BMC Plant Biology Salinity Transcriptome Genetic variation Genome-wide association study Germination stage Comprehensive evaluation |
| title | Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage |
| title_full | Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage |
| title_fullStr | Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage |
| title_full_unstemmed | Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage |
| title_short | Genome-wide association and differential expression analysis of salt tolerance in Gossypium hirsutum L at the germination stage |
| title_sort | genome wide association and differential expression analysis of salt tolerance in gossypium hirsutum l at the germination stage |
| topic | Salinity Transcriptome Genetic variation Genome-wide association study Germination stage Comprehensive evaluation |
| url | http://link.springer.com/article/10.1186/s12870-019-1989-2 |
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