Uncovering genome wide novel allelic variants for eating and cooking quality in a popular Indian rice cultivar, Samba Mahsuri
Samba Mahsuri (SM) is an Indian elite rice cultivar preferred by farmers and consumers primarily due to its superior ‘eating and cooking qualities’ (ECQs), and ‘grain size and shape’ (GSS) traits. However, SM is found to be relatively stress susceptible and the link between grain quality and stress...
| Main Authors: | , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Elsevier
2019-05-01
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| Series: | Current Plant Biology |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2214662819300507 |
| _version_ | 1818583767359422464 |
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| author | V.B. Reddy Lachagari Reddaiah Bodanapu Navajeet Chakravartty Sivarama Prasad Lekkala Krishna Lalam Boney Kuriakose Lakshminarayana R. Vemireddy Dinesh Velayutham George Thomas Saurabh Gupta Arjula R. Reddy |
| author_facet | V.B. Reddy Lachagari Reddaiah Bodanapu Navajeet Chakravartty Sivarama Prasad Lekkala Krishna Lalam Boney Kuriakose Lakshminarayana R. Vemireddy Dinesh Velayutham George Thomas Saurabh Gupta Arjula R. Reddy |
| author_sort | V.B. Reddy Lachagari |
| collection | DOAJ |
| description | Samba Mahsuri (SM) is an Indian elite rice cultivar preferred by farmers and consumers primarily due to its superior ‘eating and cooking qualities’ (ECQs), and ‘grain size and shape’ (GSS) traits. However, SM is found to be relatively stress susceptible and the link between grain quality and stress response remained unknown. We have investigated the genetic basis of the underlying mechanism of these traits in SM through whole genome sequencing and comparative genome analysis with IRGSP v1.0 as the reference genome. SNPs/INDELs analysis of 946 known QTLs related to ECQs, GSS and ‘stress tolerance and resistance’ (STR) reveal unique variants associated with insoluble starch biosynthesis and hydrolysis. Besides, variants in genes (22) associated with different stress signal transduction pathways as well as others involved in the formation of GSS have been identified. Comparative analysis with rice SNP-Seek database uncovered 861 SNPs with a unique third allele in SM rice in which 24 SNPs are missense. In addition, comparison with EnsemblPlants v40 rice variants uncovered 37,218 novel SNPs/INDELs in the SM genome. Of those, 1,767 SNPs are of missense type spanning across 1,283 genes. Specifically, 8 novel stop-gain variants were found in protein kinase-2 precursors, disease-related protein-2, WRKY37 TF, bHLH094, bHLH, NB-ARC, and two leucine-rich repeats domain-containing protein. Combined effects of these variants may possibly have relevance to the biotic and abiotic stress response of SM rice. Our study uncovered many allelic variants in candidate genes that serve as a resource for deploying them in breeding strategies to improve ECQs, GSS and stress tolerance. Keywords: Samba Mahsuri, ECQs, GSS, STR, SNPs/INDELs, Variants annotation, Whole genome sequencing |
| first_indexed | 2024-12-16T08:10:31Z |
| format | Article |
| id | doaj.art-e46b6544a52e46439f80dcdc0eb3267f |
| institution | Directory Open Access Journal |
| issn | 2214-6628 |
| language | English |
| last_indexed | 2024-12-16T08:10:31Z |
| publishDate | 2019-05-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Current Plant Biology |
| spelling | doaj.art-e46b6544a52e46439f80dcdc0eb3267f2022-12-21T22:38:21ZengElsevierCurrent Plant Biology2214-66282019-05-0118Uncovering genome wide novel allelic variants for eating and cooking quality in a popular Indian rice cultivar, Samba MahsuriV.B. Reddy Lachagari0Reddaiah Bodanapu1Navajeet Chakravartty2Sivarama Prasad Lekkala3Krishna Lalam4Boney Kuriakose5Lakshminarayana R. Vemireddy6Dinesh Velayutham7George Thomas8Saurabh Gupta9Arjula R. Reddy10AgriGenome Labs Pvt. Ltd., BTIC, MN iHub, Genome Valley, Hyderabad, 500 078, India; Corresponding author at: AgriGenome Labs Pvt. Ltd., G5, BTIC, MN iHub, Genome Valley, Shamirpet, Hyderabad, Telangana State, 500 078, India.AgriGenome Labs Pvt. Ltd., BTIC, MN iHub, Genome Valley, Hyderabad, 500 078, IndiaAgriGenome Labs Pvt. Ltd., BTIC, MN iHub, Genome Valley, Hyderabad, 500 078, IndiaAgriGenome Labs Pvt. Ltd., BTIC, MN iHub, Genome Valley, Hyderabad, 500 078, IndiaAgriGenome Labs Pvt. Ltd., BTIC, MN iHub, Genome Valley, Hyderabad, 500 078, IndiaAgriGenome Labs Pvt. Ltd., SmartCity Kochi, Infopark Road, Kakkanad, 682 042, IndiaDepartment of Genetics and Plant Breeding, S.V. Agricultural College, Acharya NG Ranga Agricultural University, Tirupati, 517 502, IndiaAgriGenome Labs Pvt. Ltd., SmartCity Kochi, Infopark Road, Kakkanad, 682 042, IndiaAgriGenome Labs Pvt. Ltd., SmartCity Kochi, Infopark Road, Kakkanad, 682 042, IndiaAgriGenome Labs Pvt. Ltd., BTIC, MN iHub, Genome Valley, Hyderabad, 500 078, India; Corresponding author at: AgriGenome Labs Pvt. Ltd., G5, BTIC, MN iHub, Genome Valley, Shamirpet, Hyderabad, Telangana State, 500 078, India.Department of Plant Sciences, University of Hyderabad, Gachibowli, Hyderabad, 500 046, IndiaSamba Mahsuri (SM) is an Indian elite rice cultivar preferred by farmers and consumers primarily due to its superior ‘eating and cooking qualities’ (ECQs), and ‘grain size and shape’ (GSS) traits. However, SM is found to be relatively stress susceptible and the link between grain quality and stress response remained unknown. We have investigated the genetic basis of the underlying mechanism of these traits in SM through whole genome sequencing and comparative genome analysis with IRGSP v1.0 as the reference genome. SNPs/INDELs analysis of 946 known QTLs related to ECQs, GSS and ‘stress tolerance and resistance’ (STR) reveal unique variants associated with insoluble starch biosynthesis and hydrolysis. Besides, variants in genes (22) associated with different stress signal transduction pathways as well as others involved in the formation of GSS have been identified. Comparative analysis with rice SNP-Seek database uncovered 861 SNPs with a unique third allele in SM rice in which 24 SNPs are missense. In addition, comparison with EnsemblPlants v40 rice variants uncovered 37,218 novel SNPs/INDELs in the SM genome. Of those, 1,767 SNPs are of missense type spanning across 1,283 genes. Specifically, 8 novel stop-gain variants were found in protein kinase-2 precursors, disease-related protein-2, WRKY37 TF, bHLH094, bHLH, NB-ARC, and two leucine-rich repeats domain-containing protein. Combined effects of these variants may possibly have relevance to the biotic and abiotic stress response of SM rice. Our study uncovered many allelic variants in candidate genes that serve as a resource for deploying them in breeding strategies to improve ECQs, GSS and stress tolerance. Keywords: Samba Mahsuri, ECQs, GSS, STR, SNPs/INDELs, Variants annotation, Whole genome sequencinghttp://www.sciencedirect.com/science/article/pii/S2214662819300507 |
| spellingShingle | V.B. Reddy Lachagari Reddaiah Bodanapu Navajeet Chakravartty Sivarama Prasad Lekkala Krishna Lalam Boney Kuriakose Lakshminarayana R. Vemireddy Dinesh Velayutham George Thomas Saurabh Gupta Arjula R. Reddy Uncovering genome wide novel allelic variants for eating and cooking quality in a popular Indian rice cultivar, Samba Mahsuri Current Plant Biology |
| title | Uncovering genome wide novel allelic variants for eating and cooking quality in a popular Indian rice cultivar, Samba Mahsuri |
| title_full | Uncovering genome wide novel allelic variants for eating and cooking quality in a popular Indian rice cultivar, Samba Mahsuri |
| title_fullStr | Uncovering genome wide novel allelic variants for eating and cooking quality in a popular Indian rice cultivar, Samba Mahsuri |
| title_full_unstemmed | Uncovering genome wide novel allelic variants for eating and cooking quality in a popular Indian rice cultivar, Samba Mahsuri |
| title_short | Uncovering genome wide novel allelic variants for eating and cooking quality in a popular Indian rice cultivar, Samba Mahsuri |
| title_sort | uncovering genome wide novel allelic variants for eating and cooking quality in a popular indian rice cultivar samba mahsuri |
| url | http://www.sciencedirect.com/science/article/pii/S2214662819300507 |
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