Ph.D

Drought is one of the important abiotic stressors that can substantially reduce rice production by 35 - 40 per cent. Water stress will significantly impact the growth and development of rice crops, but drought at the reproductive stage will directly affect the grain yield. In 2018, the State Disaster Management Authority, Kerala declared major rice growing districts including Palakkad and Alappuzha as drought affected. Jyothi is a high-yielding popular rice variety, widely cultivated variety across Kerala. Despite its widespread popularity, it exhibits poor spikelet fertility per cent under water deficit conditions, indicating that it is susceptible to drought.
Considering the negative impact of drought stress on rice production and the losses incurred by farmers, efforts were initiated at the College of Agriculture, Vellanikara to pyramid QTLs (qDTY4.1, qDTY6.1, and qDTY9.1) for yield under drought into the rice variety Jyothi (recurrent parent) from the drought tolerant variety Chuvannamodan (donor parent). The present work was conducted during 2021-2023 with the objective of introgressing the target QTLs of interest into variety Jyothi through marker assisted backcross breeding.
Genomic DNA was isolated from both parents and subjected to PCR amplification for parental polymorphism using a set of 208 microsatellites. Out of which, 85 markers were found to be polymorphic between the parents. Parental varieties were hybridized and resultant F1 hybrids were confirmed using foreground markers (RM518, RM587 and RM566). A total of 27 F1 hybrids showed heterozygous banding pattern for all foreground markers. The F1 hybrids were backcrossed with recurrent parent for the production of the BC1F1 population. Also, F1 hybrids were allowed to selfing for the production of F2 and subsequently F3 generation. Gene annotation and enrichment analysis were done using Simple Sequence Repeat (SSR) markers associated with the target QTLs of interest. It was found that 23 genes were associated with drought tolerance, spikelet fertility and root related traits at three different QTL regions.

Foreground selection in 200 BC1F1 progenies along with the parents was done to identify the plants with the target QTLs. SSR markers RM518, RM587 and RM566 closely linked with qDTY4.1, qDTY6.1 and qDTY9.1, respectively were used as foreground markers. Screening of BC1F1 population revealed that 60 progenies possessed heterozygous alleles for at least one QTL. A total of 27 BC1F1 progenies including 10 with qDTY4.1 + qDTY6.1, 9 with qDTY6.1 + qDTY9.1 and 8 with qDTY9.1 + qDTY4.1 were identified to possess two QTLs pyramided.
Background selection of 27 BC1F1 foreground selected progenies using 76 SSR markers, polymorphic between the parents, revealed the presence of wide variability among these progenies with respect to recurrent parent genome recovery (RPGR). The results of graphical genotyping revealed a maximum RPGR of 57.7 per cent in the BC1F1 progeny 24.165, followed by 56 per cent in progeny 1.2.
Drought tolerance of 15 BC1F1 with two QTL combination along with the parental varieties was characterized under reproductive stage drought stress using thirteen traits as per standard evaluation system (IRRI, 2002), including water mining traits. All the backcrossed progenies exhibited better performance under water deficit condition than the susceptible parent, Jyothi. It was found that progeny 20.118 (qDTY4.1 + qDTY6.1) had a higher number of filled grains (FG) per panicle (41) and spikelet sterility (SS) per cent (49.38 %) compared to Jyothi with 1 FG and 99.29 % SS under drought. The progeny 1.10 (qDTY9.1 + qDTY4.1) possessed higher root length (97 cm), root volume (100 cc), root to shoot ratio (1.70), root dry weight (25.9 g) than Jyothi (82.2 cm, 76 cc, 1.4, 14.64 g). Also, progenies 23.153 (qDTY4.1 + qDTY6.1) and 3.30 (qDTY6.1 + qDTY9.1) exhibited delay of 8 days to show the leaf rolling symptoms than Jyothi with 4.2 days. The BC1F1 progenies positive in foreground selection was backcrossed with the recurrent parent and 87 BC2F1 seeds were harvested.
The resultant BC2F1, BC1F2 and F3 lines with potential drought tolerant QTLs can serve as the base population for enhancing the drought tolerance in Jyothi. Further, genotypic and phenotypic evaluation of the QTL pyramided progeny in subsequent generations will lead to the development of drought tolerant cultivar in the background of popular rice variety Jyothi.