Genetic mapping of physiological traits associated with terminal stage drought tolerance in rice

Abstract

Background: Drought during reproductive stage is among the main abiotic stresses responsible for drastic reduction of grain yield in rainfed rice. The genetic mechanism of reproductive stage drought tolerance is very complex. Many physiological and morphological traits are associated with this stress tolerance. Robust molecular markers are required for detection and incorporation of these correlated physiological traits into different superior genetic backgrounds. Identification of gene(s)/QTLs controlling reproductive stage drought tolerance and its deployment in rainfed rice improvement programs are very important. Results: QTLs linked to physiological traits under reproductive stage drought tolerance were detected by using 190 F 7 recombinant inbred lines (RIL) mapping population of CR 143-2-2 and Krishnahamsa. Wide variations were observed in the estimates of ten physiological traits studied under the drought stress. The RIL population was genotyped using the bulk-segregant analysis (BSA) approach. A total of 77 SSR polymorphic markers were obtained from the parental polymorphisms survey of 401 tested primers. QTL analysis using inclusive composite interval mapping detected a total of three QTLs for the physiological traits namely relative chlorophyll content (qRCC1.1), chlorophyll a (qCHLa1.1), and proline content (qPRO3.1) in the studied RIL population. The QTL, qPRO3.1 is found to be a novel one showing LOD value of 13.93 and phenotypic variance (PVE) of 78.19%. The QTL was located within the marker interval of RM22-RM517 on chromosome 3. Another novel QTL, qRCC1.1 was mapped on chromosome 1 at a distance of 142.8 cM and found to control relative chlorophyll content during terminal drought stress. A third novel QTL was detected in the population that controlled chlorophyll a content (qCHLa1.1) under the terminal stress period. The QTL was located on chromosome 1 at a distance of 81.8 cM and showed 64.5% phenotypic variation. Conclusions: The three novel QTLs, qRCC1.1, qCHLa1.1 and qPRO3.1 controlling relative chlorophyll content, chlorophyll a and proline content, respectively were identified in the mapping population derived from CR 143-2-2 and Krishnahamsa. These 3 QTLs will be useful for enhancement of terminal drought stress tolerance through marker-assisted breeding approach in rice.

Association of molecular markers with physio-biochemical traits related to seed vigour in rice

“…Association mapping based on the linkage disequilibrium, enables researchers to identify QTLs with a higher resolution by targeting multiple alleles at individual loci, by exploiting recombination available in natural variation and by identifying association between marker and phenotype of larger number of traits (Anandan et al 2016;Pradhan et al 2016;Pandit et al 2017) and has been successfully utilized dissecting several complex trait in rice (Pradhan et al 2019(Pradhan et al , 2020. Genome mapping using SSR markers are widely employed to assess genetic diversity and genetic structure in rice and several other crops as they are hyper variable, co-dominant, robust, multi-allelic in nature, chromosome specific and greatly facilitated linkage map construction (Anandan et al 2016;Barik et al 2019Barik et al , 2020. For association mapping, the genetic diversity and structure of the population need to be studied for detecting marker-trait association which could be useful for trait enhancement in molecular breeding programs.…”

An overview of genome-wide association mapping studies in Poaceae species (model crops: wheat and rice)

“…Morgan and his student Alfred Sturtevant, published the rst genetic map, depicting the location of six sex-linked genes on the chromosome of a fruit y. In plants, genetic mapping serves as the foundation for the identi cation of genomic regions underlying important plant traits such as disease resistance, salt, and drought tolerance/resistance, yield and quality characteristics (Sharlach et Barik et al, 2020). These are complex traits controlled by polygenes or minor genes and hold great economical and agricultural importance in the era of climate change, malnutrition and food security.…”

Exploration of traditional rice (Oryza sativa L.) land races: Scope for the future sustainable food production

“…Hence, these landraces would be used as donors for the development of short duration and lodging resistance respectively in rice improvement programme. Barik et al (2020) [6] stated that stress tolerance is associated with many physiological and morphological traits. For the detection of physiological traits, robust molecular markers are needed.…”