Marker-Assisted Introgression of Saltol QTL Enhances Seedling Stage Salt Tolerance in the Rice Variety “Pusa Basmati 1”

Abstract

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.

Pyramiding QTLs controlling tolerance against drought, salinity, and submergence in rice through marker assisted breeding

“…At 125 mM, IWP recorded only 26.7% germination, whereas all three BILs recorded more than 66.7%. This clearly indicated that introgression of Saltol loci enabled enhanced tolerance against salinity as reported earlier [20,21]. During vegetative stage stress, IWP recorded the maximum SES score of 9 (extreme susceptibility), whereas BILs exhibited an average SES score of 5.…”

“…Gregorio, Senadhira [46] identified a major QTL Saltol in a salinity tolerant Pokkali responsible for maintaining Na + /K + homeostasis at the seedling stage. Introgression of the Saltol loci from Pokkali or its derivative, FL478, through MABB enabled the development of a salinity-tolerant version of popular rice varieties [20,21]. IWP is one of the popular rice varieties of South India known for its high yield, superior grain quality, and excellent cooking quality.…”

“…Recent advancements in molecular genetics and genotyping led to the identification of major effect quantitative trait loci (QTLs) linked to major abiotic stresses viz., drought tolerance (qDTY 1.1 , qDTY 2.1 , qDTY 3.1 and qDTY 6.1 in Apo [10][11][12] and qDTY 12.1 in Way rarem [13], submergence tolerance Sub1 in FR13A [14], and salinity tolerance Saltol in Pokkali [15]. Deployment of the above QTLs through molecular breeding paved the way for the development and release of a submergencetolerant version of a popular rice variety Swarna [16], submergence-tolerant version of CO 43 [17], drought-tolerant version of IR64, namely DRR Dhan 42, drought-tolerant MR219 [5], drought-tolerant Sabitri [18], salinity-tolerant version of BR28 [19], salinity-tolerant Pusa Basmati 1 [20], and salinity-tolerant Improved White Ponni (IWP) [21] through the marker assisted back cross breeding (MABB) approach. However, very little research has been conducted to develop multiple abiotic stress-tolerant rice genotype(s) by pyramiding QTLs that control tolerance against drought, salinity, and submergence through marker assisted selection (MAS).…”

Identification and Validation a Major QTL from “Sea Rice 86” Seedlings Conferred Salt Tolerance

“…"Saltol" has proven to be an effective salt tolerance region and was successfully applied in breeding. Field experiments proved that "Saltol" significantly improved the salt tolerance of rice at the seedling stage and maintained stable yield under salt stress [28,33]. Thomson et al also found some QTL segments related to salt tolerance at the seedling stage in this chromosome region, and some segments overlapped with SKC1, possibly encoding the same gene (OsHKT1;5) [13].…”

Identification of new QTL for salt tolerance from rice variety Pokkali

“…A cluster of genes in addition to SKC1 was found to be associated with salinity tolerance within the Saltol region (Nutan, Kushwaha, Singla-Pareek, & Pareek, 2017;Walia et al, 2005). Markers closely linked to Saltol were developed and used for improving rice salt tolerance through marker-assisted breeding in many countries (Babu et al, 2017;Linh et al, 2012;Singh et al, 2018). A newly reported QTL qSE3, which was isolated from a Chinese landrace Jiucaiqing by map-based cloning, was found to encode a HAK transporter (OsHAK21) and promote seed germination and seedling establishment under salinity stress in rice (He et al, 2019).…”