Genetic architecture of Al3+ toxicity tolerance in rice F2:3 populations determined through QTL mapping

Jahan, Nusrat; Javed, Muhammad Arshad; Khan, Anwar; Manan, Fazilah Abd; Tabassum, Bushra

doi:10.1007/s10646-021-02413-6

Cited by 5 publications

(5 citation statements)

References 30 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Among them, we found two QTLs co-located with previously reported SV-related QTLs using the traditional mapping method, suggesting that our GWAS results are pretty reliable ( Table 2 ). For instance, qGR1-1 corresponds to QAlGC1.2 , a QTL for germination capacity under aluminum stress and mapped between markers RM14 and RM243 ( Jahan et al., 2021 ). qFW1-1 shares the same location with qSWW1b , a major QTL for the wet seedling weight ( Zhang et al., 2017 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice

Dai

Shen

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

Highly seed vigor (SV) is essential for rice direct seeding (DS). Understanding the genetic mechanism of SV-related traits could contribute to increasing the efficiency of DS. However, only a few genes responsible for SV have been determined in rice, and the regulatory network of SV remains obscure. In this study, the seed germination rate (GR), seedling shoot length (SL), and shoot fresh weight (FW) related to SV traits were measured, and a genome-wide association study (GWAS) was conducted to detect high-quality loci responsible for SV using a panel of 346 diverse accessions. A total of 51 significant SNPs were identified and arranged into six quantitative trait locus (QTL) regions, including one (qGR1-1), two (qSL1-1, qSL1-2), and three (qFW1-1, qFW4-1, and qFW7-1) QTLs associated with GR, SL, and FW respectively, which were further validated using chromosome segment substitution lines (CSSLs). Integrating gene expression, gene annotation, and haplotype analysis, we found 21 strong candidate genes significantly associated with SV. In addition, the SV-related functions of LOC_Os01g11270 and LOC_Os01g55240 were further verified by corresponding CRISPR/Cas9 gene-edited mutants. Thus, these results provide clues for elucidating the genetic basis of SV control. The candidate genes or QTLs would be helpful for improving DS by molecular marker-assisted selection (MAS) breeding in rice.

show abstract

Section: Discussionmentioning

confidence: 99%

Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice

Dai

Shen

et al. 2022

Front. Plant Sci.

View full text Add to dashboard Cite

show abstract

“…The rice material was F2:3 progenies consisting of 129 (Dufey et al, 2009;Wu et al, 2014) families each derived from the cross between rice variety 'Pokkali' exhibit tolerance against Fe 2+ toxicity as 'Pokkali' retained most of the absorbed Fe 2+ in the roots and stopped or slows the transport of Fe 2+ to leaves and flag leaf (Jahan et al, 2015). 'Pak Basmati' was classified as a relatively sensitive variety against Fe 2+ (Jahan et al, 2021).…”

Section: Plant Materialsmentioning

confidence: 99%

“…Parental line stress optimization was performed at 0, 10mM, 15mM and 20mM of stress levels Fe 2+ toxicity at pH 4.0 to obtain the threshold level for F3 phenotyping. At 20mM germination and growth parameters showed significance response to Fe 2+ toxicity (Jahan et al, 2021). Therefore, 20mM was considered as threshold level for F3 phenotyping.…”

Section: Phenotypic Evaluationmentioning

confidence: 99%

Multiple interval mapping of QTLs and epistasis for iron toxicity tolerance in segregating population of Indica rice

Jahan

JAVED

Khan

et al. 2022

Not Bot Horti Agrobo

View full text Add to dashboard Cite

The global average temperature has increased by approximately 0.5 °C, over a last few decades and is projected to continue to increase. Environmental stress factors such as, elevated temperature, salinity, toxic elements (Fe, Al, Cd, Cr, Pb, Zn and As), drought and rising CO2 affect plant growth and make a growing threat to agriculture. Rice is a primary food crop in the world and the establishment of rice crop in acidic soil and in marginal soil is a major goal for the improvement of rice production to fulfill the food security. Among environmental stresses, Fe2+ toxicity is one of the main stresses in limiting the cereal crops production. Tolerant rice genotypes that can tolerate the high concentration of Fe2+ toxicity are the potential source genes for rice tolerance improvement in Fe2+ toxicity. In this research work, the genetic basis of seed germination traits and growth traits was investigated in rice using (multiple interval mapping) MIM. Many rice genotypes serve as source of tolerant against toxic metal ion like Fe2+, could be an important factor in controlling the sever effect of Fe2+ toxicity on germination and seedling growth traits. The F3 progenies of cross between Fe2+ toxicity tolerant cultivar ‘Pokkali’ and susceptible cultivar ‘Pak basmati’ were test against the optimized level of Fe2+ toxicity at germination, to determine the mode of inheritance to Fe2+ toxicity tolerance. Wide range of continues variation was found in F3 progenies. Among the 49 quantitative germination trait and 23 growth trait loci (QTLs) on chromosomes 1, 2, 4, 6, 8 and 9 linked with tolerance to Fe2+ toxicity was mapped. Additionally, 21 QTLs for germination traits and 9 QTLs for growth traits were classified as major QTLs using MIM. For germination and growth traits, notable epistasis between the chromosome 1, 2, 4, 6 and 11 was detected across germination and growth traits. Our results suggest that the tolerance mechanisms at germination and seedling phases could differ for Fe2+ toxicity. QTLs detected in this study for germination and seedling growth could be a source of new alleles for development of tolerance rice to Fe2+ toxicity varieties and transformation, gene cloning and gene editing in the future

show abstract

“…Quantitative trait locus (QTL) mapping is an effective method to identify aluminum tolerance genes (Bian et al 2013). Many quantitative trait loci (QTLs) associated with Al 3+ toxicity have been detected in a variety of crops, including wheat (Farokhzadeh et al 2020), soybean (Li et al 2021) and rice (Jahan et al 2021). Consequently, QTL mapping generates a number of candidate genes due to the small population used and the low density of the genetic map (Mackay et al 2009).…”

Section: Introductionmentioning

confidence: 99%

Combining transcriptomics and metabolomics to identify key response genes for aluminum toxicity in the root system of Brassica napus L. seedlings

Shi

et al. 2023

Preprint

View full text Add to dashboard Cite

Aluminum (Al) toxicity has become one of the important abiotic stress factorsin areas with acid soil, which hinders the absorption of water and nutrients by roots, and consequently retards the growth of crops. A deeper understanding of the stress response mechanism of Brassica napus may allow us to identify the tolerance gene(s) and use this information in breeding resistant crop varieties. In this study, a population of 138 recombinant inbred lines (RILs) was subjected to aluminum stress, and QTL (quantitative trait locus) mapping was used to preliminarily locate quantitative trait loci related to aluminum stress. Root tissues from seedlings of aluminum-resistant (R) lines and aluminum-sensitive (S) lines from the RIL population were harvested for transcriptome sequencing and metabolome determination. By combining the data on quantitative trait genes (QTGs), differentially expressed genes (DEGs), and differentially accumulated metabolites (DAMs), key candidate genes related to aluminum tolerance in rapeseed were determined. The results showed that there were 3186 QTGs in the RIL population, 14,232 DEGs and 457 DAMs in the comparison between R and S lines. Lastly, 138 hub genes were selected to have a strong positive or negative correlation with 30 important metabolites (|R|≥0.95). These genes were mainly involved in the metabolism of lipids, carbohydrates, and secondary metabolites in response to Al toxicity stress. In summary, this study provides an effective method for screening key genes by combining QTLs, transcriptome sequencing, and metabolomic analysis, but also lists key genes for exploring the molecular mechanism of Al tolerance in rapeseed seedling roots.

show abstract

Genetic architecture of Al3+ toxicity tolerance in rice F2:3 populations determined through QTL mapping

Cited by 5 publications

References 30 publications

Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice

Genome-wide association study reveals novel QTLs and candidate genes for seed vigor in rice

Multiple interval mapping of QTLs and epistasis for iron toxicity tolerance in segregating population of Indica rice

Combining transcriptomics and metabolomics to identify key response genes for aluminum toxicity in the root system of Brassica napus L. seedlings

Contact Info

Product

Resources

About