Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence
This study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was develo...
| Main Authors: | , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2020-09-01
|
| Series: | Genes |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2073-4425/11/9/1026 |
| _version_ | 1797554833767530496 |
|---|---|
| author | K. N. S. Usha Kiranmayee C. Tom Hash S. Sivasubramani P. Ramu Bhanu Prakash Amindala Abhishek Rathore P. B. Kavi Kishor Rajeev Gupta Santosh P. Deshpande |
| author_facet | K. N. S. Usha Kiranmayee C. Tom Hash S. Sivasubramani P. Ramu Bhanu Prakash Amindala Abhishek Rathore P. B. Kavi Kishor Rajeev Gupta Santosh P. Deshpande |
| author_sort | K. N. S. Usha Kiranmayee |
| collection | DOAJ |
| description | This study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was developed from an introgression line cross—RSG04008-6 (stay-green) × J2614-11 (moderately senescent). The fine-mapping population with 1894 F<sub>2</sub> was genotyped with eight SSRs and a set of 152 recombinants was identified, advanced to the F<sub>4</sub> generation, field evaluated with three replications over 2 seasons, and genotyped with the GBS approach. A high-resolution linkage map was developed for SBI-10L using 260 genotyping by sequencing—Single Nucleotide Polymorphism (GBS–SNPs). Using the best linear unpredicted means (BLUPs) of the percent green leaf area (%GL) traits and the GBS-based SNPs, we identified seven quantitative trait loci (QTL) clusters and single gene, mostly involved in drought-tolerance, for each QTL cluster, viz., AP2/ERF transcription factor family (<i>Sobic.010G202700</i>), NBS-LRR protein (<i>Sobic.010G205600</i>), ankyrin-repeat protein (<i>Sobic.010G205800</i>), senescence-associated protein (<i>Sobic.010G270300</i>), WD40 (<i>Sobic.010G205900</i>), CPK1 adapter protein (<i>Sobic.010G264400</i>), LEA2 protein (<i>Sobic.010G259200</i>) and an expressed protein (<i>Sobic.010G201100</i>). The target genomic region was thus delimited from 15 Mb to 8 genes co-localized with QTL clusters, and validated using quantitative real-time (qRT)–PCR. |
| first_indexed | 2024-03-10T16:38:38Z |
| format | Article |
| id | doaj.art-4ee2f90b7d27486c8b22ac0230f8ef30 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T16:38:38Z |
| publishDate | 2020-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-4ee2f90b7d27486c8b22ac0230f8ef302023-11-20T12:13:46ZengMDPI AGGenes2073-44252020-09-01119102610.3390/genes11091026Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed SenescenceK. N. S. Usha Kiranmayee0C. Tom Hash1S. Sivasubramani2P. Ramu3Bhanu Prakash Amindala4Abhishek Rathore5P. B. Kavi Kishor6Rajeev Gupta7Santosh P. Deshpande8International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, IndiaInternational Crop Research Institute for the Semi-Arid Tropics, Niamey BP12404, NigerInternational Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, IndiaInternational Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, IndiaInternational Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, IndiaInternational Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, IndiaDepartment of Biotechnology, Vignan’s Foundation for Science, Technology & Research, Vadlamudi, Guntur, Andhra Pradesh 522213, IndiaInternational Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, IndiaInternational Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad 502324, IndiaThis study was conducted to dissect the genetic basis and to explore the candidate genes underlying one of the important genomic regions on an SBI-10 long arm (L), governing the complex stay-green trait contributing to post-flowering drought-tolerance in sorghum. A fine-mapping population was developed from an introgression line cross—RSG04008-6 (stay-green) × J2614-11 (moderately senescent). The fine-mapping population with 1894 F<sub>2</sub> was genotyped with eight SSRs and a set of 152 recombinants was identified, advanced to the F<sub>4</sub> generation, field evaluated with three replications over 2 seasons, and genotyped with the GBS approach. A high-resolution linkage map was developed for SBI-10L using 260 genotyping by sequencing—Single Nucleotide Polymorphism (GBS–SNPs). Using the best linear unpredicted means (BLUPs) of the percent green leaf area (%GL) traits and the GBS-based SNPs, we identified seven quantitative trait loci (QTL) clusters and single gene, mostly involved in drought-tolerance, for each QTL cluster, viz., AP2/ERF transcription factor family (<i>Sobic.010G202700</i>), NBS-LRR protein (<i>Sobic.010G205600</i>), ankyrin-repeat protein (<i>Sobic.010G205800</i>), senescence-associated protein (<i>Sobic.010G270300</i>), WD40 (<i>Sobic.010G205900</i>), CPK1 adapter protein (<i>Sobic.010G264400</i>), LEA2 protein (<i>Sobic.010G259200</i>) and an expressed protein (<i>Sobic.010G201100</i>). The target genomic region was thus delimited from 15 Mb to 8 genes co-localized with QTL clusters, and validated using quantitative real-time (qRT)–PCR.https://www.mdpi.com/2073-4425/11/9/1026sorghum chromosome 10 long arm (SBI-10L), fine-mappingstay-greencandidate genespercent green leaf areadelayed senescence |
| spellingShingle | K. N. S. Usha Kiranmayee C. Tom Hash S. Sivasubramani P. Ramu Bhanu Prakash Amindala Abhishek Rathore P. B. Kavi Kishor Rajeev Gupta Santosh P. Deshpande Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence Genes sorghum chromosome 10 long arm (SBI-10L), fine-mapping stay-green candidate genes percent green leaf area delayed senescence |
| title | Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence |
| title_full | Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence |
| title_fullStr | Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence |
| title_full_unstemmed | Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence |
| title_short | Fine-Mapping of Sorghum Stay-Green QTL on Chromosome10 Revealed Genes Associated with Delayed Senescence |
| title_sort | fine mapping of sorghum stay green qtl on chromosome10 revealed genes associated with delayed senescence |
| topic | sorghum chromosome 10 long arm (SBI-10L), fine-mapping stay-green candidate genes percent green leaf area delayed senescence |
| url | https://www.mdpi.com/2073-4425/11/9/1026 |
| work_keys_str_mv | AT knsushakiranmayee finemappingofsorghumstaygreenqtlonchromosome10revealedgenesassociatedwithdelayedsenescence AT ctomhash finemappingofsorghumstaygreenqtlonchromosome10revealedgenesassociatedwithdelayedsenescence AT ssivasubramani finemappingofsorghumstaygreenqtlonchromosome10revealedgenesassociatedwithdelayedsenescence AT pramu finemappingofsorghumstaygreenqtlonchromosome10revealedgenesassociatedwithdelayedsenescence AT bhanuprakashamindala finemappingofsorghumstaygreenqtlonchromosome10revealedgenesassociatedwithdelayedsenescence AT abhishekrathore finemappingofsorghumstaygreenqtlonchromosome10revealedgenesassociatedwithdelayedsenescence AT pbkavikishor finemappingofsorghumstaygreenqtlonchromosome10revealedgenesassociatedwithdelayedsenescence AT rajeevgupta finemappingofsorghumstaygreenqtlonchromosome10revealedgenesassociatedwithdelayedsenescence AT santoshpdeshpande finemappingofsorghumstaygreenqtlonchromosome10revealedgenesassociatedwithdelayedsenescence |