Molecular mapping of drought-responsive QTLs during the reproductive stage of rice using a GBS (genotyping-by-sequencing) based SNP linkage map

Abstract

The reproductive stage is the most important critical stage in rice where water is needed for the formation of seeds. Water scarcity in this situation drastically reduces yield which in turn hampers farmers' effort towards agriculture. Traditional landraces do have resistant genes inside them against several abiotic and biotic stresses which can act as valuable donors to produce new gene combinations. A high-density SNP based genetic map was constructed by Genotyping by sequencing (GBS) technique using F7 recombinant inbred line (RIL) population developed from Banglami x Ranjit to identify tightly linked markers associated with QTLs. The total map length was 1306.424 cM which had an average inter-marker distance of 0.281 cM. A total of 42 QTLs were identi ed under both reproductive stage drought stress (RS) and non stress (NS) conditions for sixteen different yield and its component traits which explained a phenotypic variance (PVE) of 1.95-13.36 %. Four QTLs explained a PVE ≥ 10% which denotes they are major QTLs. Analysis of the genes present within the QTL regions revealed the presence of 6 candidate genes which were differentially expressed under stress condition. These genes and QTLs will be helpful for marker-assisted pyramiding to improve drought tolerance in rice.

Genetic mapping identified three hotspot genomic regions and candidate genes controlling heat tolerance-related traits in groundnut

“…A total of 118 main-effect QTLs (31 QTLs for six agronomic traits, 32 QTLs for six phenological traits, and 55 QTLs for physiological traits) were identified; of these, 45 QTLs had major main effects with >10% PVE (13 QTLs for six agronomic traits, 12 QTLs for six phenological traits, and 20 QTL for nine physiological traits). Minor main-effect QTLs have been found in many crops, including groundnut ( Pandey et al., 2020b ), rice ( Roy et al., 2023 ), and maize ( Ribaut et al., 1997 ), for complex traits that are usually controlled by multiple genes. Indeed, the impact of individual locus may be minor, but the cumulative contribution of loci for such complex traits is often significant.…”

Pooled Mapping of Quantitativetrait Loci Associated With Drought Tolerance in Rice (Oryza Sativa L.) at Seedling Stage

“…Since the beginning of this century, over 310 QTLs for drought tolerance have been recognized from rice (Satrio et al, 2021;Huang et al, 2022;Roy et al, 2023). Most of them are mapped based on the performance during the period of reproductive development.…”

“…Drought tolerance refers to a comprehensive and sophisticated trait that exhibits plant response to drought stress. Numerous traits can suggest the drought tolerance of rice, such as biomass (Saikumar et al, 2014), leaf area (Sabar et al, 2019), panicle length (Nie et al, 2015;Prince et al, 2015;Roy et al, 2023), maximum root length (Huang et al, 2022), and fresh shoot weight (Verma et al, 2021). However, different indicator traits of drought tolerance may result in very different QTLs (Verma et al, 2021;Huang et al, 2022).…”

“…Under the control of many quantitative trait loci (QTLs), the mechanism of drought tolerance is sophisticated (Fleury et al, 2010). Considerable research works have been conducted on identification of genes or QTLs related to drought stress of rice (Huang et al, 2022;Roy et al, 2023). It is known that drought stress influences varying developmental phases of rice.…”