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Haplotype analysis of Saltol QTL region in diverse landraces, wild rice and introgression lines of rice (Oryza sativa L.)

Published online by Cambridge University Press:  25 May 2021

K. K. Manohara Open the ORCID record for K. K. Manohara [Opens in a new window] ,
Shaiesh Morajkar ,
Yogini Shanbhag ,
Pratham Phadte  and
Nagendra Kumar Singh
K. K. Manohara*
Affiliation:
Crop Science Section, ICAR-Central Coastal Agricultural Research Institute, Old Goa, 403 402, Goa, India
Shaiesh Morajkar
Affiliation:
Crop Science Section, ICAR-Central Coastal Agricultural Research Institute, Old Goa, 403 402, Goa, India
Yogini Shanbhag
Affiliation:
Crop Science Section, ICAR-Central Coastal Agricultural Research Institute, Old Goa, 403 402, Goa, India
Pratham Phadte
Affiliation:
Crop Science Section, ICAR-Central Coastal Agricultural Research Institute, Old Goa, 403 402, Goa, India
Nagendra Kumar Singh
Affiliation:
ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, 110012, India
*
*Corresponding author. E-mail: manohar.gpb@gmail.com
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Abstract

Salt stress is a major abiotic stress affecting the productivity of rice crop worldwide. This study screened a set of 71 rice genotypes collected from coastal parts of Goa and Karnataka states in India for seedling stage salinity tolerance to identify genotypes alternative to standard salt-tolerant donors Pokkali, FL478, etc. Phenotyping for seedling stage tolerance was carried out under micro plots at an induced salinity of 12 dS/m. For haplotyping, 14 Saltol QTL linked simple sequence repeat (SSR) markers on chromosome 1 were utilized. On the basis of the response to salt stress, 10 genotypes were found tolerant, 16 moderately tolerant, 29 sensitive and 15 as highly sensitive. Among the SSR markers, marker RM10871 was the most polymorphic with a polymorphic information content of 0.90, exhibiting 14 different alleles followed by RM10793 (0.84) and RM3412 (0.80) with 8 and 7 alleles, respectively. These markers also exhibited high values for the effective number of alleles (Ne) and gene diversity (I). The haplotype analysis revealed that the allelic constitution of the Saltol region of 10 tolerant genotypes from our study varied in comparison to the reference tolerant check FL478. Further, the haplotype of three tolerant genotypes, namely, Goa Dhan 2, Panvel 1 and Goa wild rice (GWR) 005 appears to be completely different from the FL478 haplotype indicating tolerance in these genotypes is controlled by genomic region other than Saltol. These three genotypes with probable novel regions for seedling stage salt tolerance can be considered for enhancing salinity tolerance of rice cultivars.

Keywords

coastal salinityGoa & Karnataka coastpolymorphic information contentsimple sequence repeat markerwild rice
Type
Research Article
Information
Plant Genetic Resources , Volume 19 , Issue 4 , August 2021 , pp. 289 - 298
Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of NIAB

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