Improvement of the submergence stress tolerance of local South Sumatran rice through the introgression of the Sub1 gene by using marker-assisted selection

Abstract

Submergence stress due to unpredictable soil flooding is one of the main constraints encountered in rainfed growing areas, especially in Southern Sumatran riparian swamps. The development of submergence-stress-tolerant cultivars through the introgression of Sub1 via marker-assisted backcrossing (MABC) is an ideal solution. This study was carried out during 2020 at Sriwijaya University, Palembang, Indonesia, with the aim to select Sub1-introgressed lines in BC3F1 generations on the basis of MABC and to screen out the SSR markers that were unlinked to the target gene for application in subsequent background selection studies. Results revealed that almost all the backcrossed progenies segregated from the rice parental cultivars ‘FR13A’ and ‘Pegagan’. The backcrossed lines showed significantly improved submergence stress tolerance and recovery rates compared with their parents. Sub1 introgression into the BC3F1 generation was confirmed by the tightly linked Sub1 marker SUB1C173, and marker RM23915 was used for recombinant selection. These markers followed the expected marker segregation ratio in accordance with the Mendelian single gene model. In the parental polymorphism survey, 84 out of 237 SSR markers that were unlinked to the target loci were found to be available for background study. Twenty-seven backcrossed lines were selected on the basis of foreground selection. Seven plants were selected on the basis of the recombinant marker RM23915. Five backcrossed lines were further selected on the basis of submergence stress tolerance and agronomic performance.

Development of Non-Tidal Adaptive Rice Varieties: Molecular Marker Assisted Selection of Bc2f1 Progenies

“…Samples were amplificated in a single 96-well PCR (Biologix) with a total volume of 12.5 μL reactions containing of 0.5 μL template DNA from Inpara 8, Inpago 5, and BC2F1 generations; 0.5 μL the forward and reverse primers; 4.75 μL of MyTaq DNA polymerase (Bioline, BIO); and 6.25 μL of ddH2O. After pre-denaturation at 94°C for 5 min, the amplification was followed a procedure by Adriansyah et al [12] with 34 cycles; each cycle comprised 1 min of denaturation at 94°C, 1 min of annealing at 55°C, 2 min of extension at 72°C, and 2 min of final extension at 72°C. The PCR product was mixed with loading dye gel and separated by electrophoresis on 1% agarose gel in 1x TBA with 100 bp DNA ladder (Promega, USA) to determine the amplicon size.…”

“…A tightly-linked SSR marker, SUB1C173 [17] used for foreground selection (Table 1). The foreground marker used in this study also used by Septiningsih et al [18], Iftekharaddaula et al [13], Mojulat et al [19], and Adriansyah et al [12] to identify Sub1 gene introgressed. In foreground selection, the heterozygous plants were selected, then proceed to background selection.…”

“…The heterozygous plants were selected and subjected to background selection. The SUB1C173 marker is widely used to verify the introgression of Sub1 into various rice cultivars, such as 'Swarna-Sub1' [22], 'Ciherang-Sub1' [17], and 'Pegagan-Sub1' [12].…”

“…Several studies have been widely carried out to obtain high-yielding cultivars as well as adaptive to submerged condition during vegetative phase through the insertion of the Sub1 gene [11], [12]. A study conducted by Iftekharuddaula et al [13], obtained a dual tolerant cultivar by using MABC (Marker-Assisted Backcrossing) method.…”

Development of adaptive rice variety to non-tidal swamp: Growth evaluation of backcrossed progenies (BC1F1) and its parents, Inpago 5 and Inpara 8

“…Chozin et al (2017) suggested to improve rice yield tackled by the genetic and physiological natures. So, increasing of productivity in suboptimal area with adaptive characters and higher production in submergence condition can be initiated by introgressed Sub1 gene in rice cultivar which has good agronomy character (Adriansyah et al 2021). Tiwari et al, (2017) obtained a dual tolerant rice line in submergence and drought conditions, from crosses between Swarna Sub1 x NDR 9830102.…”