Research Article Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety “Pusa Basmati 1” Vivek Kumar Singh, 1 Brahma Deo Singh, 2 Amit Kumar, 1 Sadhna Maurya, 3 Subbaiyan Gopala Krishnan, 1 Kunnummal Kurungara Vinod , 4 Madan Pal Singh, 3 Ranjith Kumar Ellur, 1 Prolay Kumar Bhowmick, 1 and Ashok Kumar Singh 1 1 ICAR-Indian Agricultural Research Institute, Division of Genetics, New Delhi 110012, India 2 Banaras Hindu University, School of Biotechnology, Varanasi 221005, Uttar Pradesh, India 3 ICAR-Indian Agricultural Research Institute, Division of Plant Physiology, New Delhi 110012, India 4 Rice Breeding and Genetics Research Centre, ICAR-Indian Agricultural Research Institute, Aduthurai 612 101, India Correspondence should be addressed to Ashok Kumar Singh; aks_gene@yahoo.com Received 29 August 2017; Revised 14 November 2017; Accepted 28 November 2017; Published 11 February 2018 Academic Editor: Gunvant B. Patil Copyright © 2018 Vivek Kumar Singh et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Marker-assisted selection is an unequivocal translational research tool for crop improvement in the genomics era. Pusa Basmati 1 (PB1) is an elite Indian Basmati rice cultivar sensitive to salinity. Here, we report enhanced seedling stage salt tolerance in improved PB1 genotypes developed through marker-assisted transfer of a major QTL, Saltol. A highly salt tolerant line, FL478, was used as the Saltol donor. Parental polymorphism survey using 456 microsatellite (SSR)/QTL-linked markers revealed 14.3% polymorphism between PB1 and FL478. Foreground selection was carried out using three Saltol-linked polymorphic SSR markers RM8094, RM493, and RM10793 and background selection by 62 genome-wide polymorphic SSR markers. In every backcross generation, foreground selection was restricted to the triple heterozygotes of foreground markers, which was followed by phenotypic and background selections. Twenty-four near isogenic lines (NILs), with recurrent parent genome recovery of 96.0–98.4%, were selected after two backcrosses followed by three selfing generations. NILs exhibited agronomic traits similar to those of PB1 and additional improvement in the seedling stage salt tolerance. They are being tested for per se performance under salt-affected locations for release as commercial varieties. These NILs appear promising for enhancing rice production in salinity-affected pockets of Basmati Geographical Indication (GI) areas of India. 1. Introduction Rice plants suffer severe salt injury in both seedling and reproductive stages; the most common damages are attrib- uted to osmotic imbalance, membrane destabilisation, and failure of photosynthetic machinery [1]. The damage due to salt stress is often cumulative as the seedling stage sensitivity leads to poor crop establishment, and reproductive stage sen- sitivity results in reduced yields [2]; the combined effect of damages at both the stages may lead to total crop loss. Never- theless, seedling stage tolerance can sustain crop production in salinity prone areas by promoting good initial establishment leading to healthy vegetative growth that can augment crop yield [3]. There are some saline ecosystem- adapted traditional rice landraces such as Pokkali and Nona Bokra that are known to be salt tolerant. Salt tolerance in rice is manifested through morphological, physiological, and metabolic responses that includes stomatal changes, sodium exclusion, tissue tolerance, apoplastic salt compartmentaliza- tion, salt sequestration into older tissues, and regulation of the antioxidants [2–5]. Apart from the understanding of physiological and metabolic responses to salt stress, quantita- tive trait loci (QTLs) and genes governing salt tolerance have also been reported in rice. These include a major QTL, Saltol Hindawi International Journal of Genomics Volume 2018, Article ID 8319879, 12 pages https://doi.org/10.1155/2018/8319879