GENETICS OF DROUGHT ADAPTATION IN<i>ARABIDOPSIS THALIANA</i>II. QTL ANALYSIS OF A NEW MAPPING POPULATION, KAS-1 × TSU-1

McKay, John; Richards, James H.; Nemali, Krishna; Sen, Sáunak; Mitchell-Olds, Thomas; Boles, Sandra B.; Stahl, Eli A.; Wayne, Tierney; Juenger, Thomas E.

doi:10.1111/j.1558-5646.2008.00474.x

Cited by 116 publications

(140 citation statements)

References 90 publications

(129 reference statements)

Supporting

Mentioning

132

Contrasting

Order By: Relevance

“…Quantitative trait locus (QTL) mapping and global gene expression analyses are useful methods to assess the genetic basis of traits involved in drought adaptation (McKay et al, 2008;Hall et al, 2010;Juenger et al, 2010;Des Marais et al, 2012;Schmalenbach et al, 2014;El-Soda et al, 2015). In particular, the genomic perturbation of experimental crosses utilizes recombination to break up linkage disequilibrium and allows causal inference of how variation at a given locus leads to phenotypic variation.…”

Section: Introductionmentioning

confidence: 99%

Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana

et al. 2015

Self Cite

View full text Add to dashboard Cite

Soil water availability represents one of the most important selective agents for plants in nature and the single greatest abiotic determinant of agricultural productivity, yet the genetic bases of drought acclimation responses remain poorly understood. Here, we developed a systems-genetic approach to characterize quantitative trait loci (QTLs), physiological traits and genes that affect responses to soil moisture deficit in the TSUxKAS mapping population of Arabidopsis thaliana. To determine the effects of candidate genes underlying QTLs, we analyzed gene expression as a covariate within the QTL model in an effort to mechanistically link markers, RNA expression, and the phenotype. This strategy produced ranked lists of candidate genes for several drought-associated traits, including water use efficiency, growth, abscisic acid concentration (ABA), and proline concentration. As a proof of concept, we recovered known causal loci for several QTLs. For other traits, including ABA, we identified novel loci not previously associated with drought. Furthermore, we documented natural variation at two key steps in proline metabolism and demonstrated that the mitochondrial genome differentially affects genomic QTLs to influence proline accumulation. These findings demonstrate that linking genome, transcriptome, and phenotype data holds great promise to extend the utility of genetic mapping, even when QTL effects are modest or complex.

show abstract

Section: Introductionmentioning

confidence: 99%

Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana

et al. 2015

Self Cite

View full text Add to dashboard Cite

show abstract

“…The timing and duration of water limitation, as well as other environmental variables, all influence drought-adaptation strategies used by plants. Thus, we may expect substantial natural variation of these traits within a widely distributed species, such as Arabidopsis (7)(8)(9)(10), with many of these differences related to the local conditions to which a particular accession has adapted (11)(12)(13). Several studies have identified quantative trait loci (QTL) controlling differences in metabolite content (14)(15)(16)(17)(18), but such studies have yet to be extended to drought-induced metabolic changes, such as proline accumulation.…”

mentioning

confidence: 99%

Intron-mediated alternative splicing of Arabidopsis P5CS1 and its association with natural variation in proline and climate adaptation

Kesari

Lasky

Villamor

et al. 2012

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

125

140

View full text Add to dashboard Cite

Drought-induced proline accumulation is widely observed in plants but its regulation and adaptive value are not as well understood. Proline accumulation of the Arabidopsis accession Shakdara (Sha) was threefold less than that of Landsberg erecta (Ler) and quantitative trait loci mapping identified a reduced function allele of the proline synthesis enzyme Δ 1 -pyrroline-5-carboxylate synthetase1 (P5CS1) as a basis for the lower proline of Sha. Sha P5CS1 had additional TA repeats in intron 2 and a G-to-T transversion in intron 3 that were sufficient to promote alternative splicing and production of a nonfunctional transcript lacking exon 3 (exon 3-skip P5CS1). In Sha, and additional accessions with the same intron polymorphisms, the nonfunctional exon 3-skip P5CS1 splice variant constituted as much as half of the total P5CS1 transcript. In a larger panel of Arabidopsis accessions, low water potential-induced proline accumulation varied by 10-fold and variable production of exon 3-skip P5CS1 among accessions was an important, but not the sole, factor underlying variation in proline accumulation. Population genetic analyses suggest that P5CS1 may have evolved under positive selection, and more extensive correlation of exon 3-skip P5CS1 production than proline abundance with climate conditions of natural accessions also suggest a role of P5CS1 in local adaptation to the environment. These data identify a unique source of alternative splicing in plants, demonstrate a role of exon 3-skip P5CS1 in natural variation of proline metabolism, and suggest an association of P5CS1 and its alternative splicing with environmental adaptation.amino acid metabolism | drought adaptation | stress gene expression | osmoprotectant | compatible solute P roline acts as an osmoprotectant and cryoprotectant in organisms as diverse as bacteria, plants, and insects (1, 2). Many plants accumulate proline in response to low water potential (ψ w ) and dehydration caused by drought or freezing. The mechanisms by which proline may promote drought resistance include osmoprotectant functions, as well as newly emerging functions of proline metabolism in NADP/NADPH balance and transfer or storage of energy and reducing potential (1-3). However, the overall importance of proline in drought adaptation is not as firmly established. In Arabidopsis thaliana, transcriptional up-regulation of Δ 1 -pyrroline-5-carboxylate synthetase1 (P5CS1) is essential for low ψ w -induced proline accumulation, and proline accumulation of p5cs1 mutants is only 15-20% of the wild-type level (4-6). Additional regulation of proline metabolism is likely but not understood. The timing and duration of water limitation, as well as other environmental variables, all influence drought-adaptation strategies used by plants. Thus, we may expect substantial natural variation of these traits within a widely distributed species, such as Arabidopsis (7-10), with many of these differences related to the local conditions to which a particular accession has adapted (11-13). Several studies ha...

show abstract

“…

Studies in A. thaliana reported a genomic region responsible for drought avoidance co-130 mapping with a region contributing to a constitutively lowered Tr and simultaneously 131 leading to an enhanced TE (Masle et al 2005;McKay et al 2008). Following these 132 examples, our current hypothesis is that only critical portions of the large DT-QTL, 133 linked to specific mechanisms, matter for the terminal drought tolerance of pearl millet 134 and these needs to be accurately mapped to enhance the precision of marker assisted 135 introgression.

…”

mentioning

confidence: 99%

Water saving traits co-map with a major terminal drought tolerance quantitative trait locus in pearl millet [Pennisetum glaucum (L.) R. Br.]

et al. 2012

View full text Add to dashboard Cite

Studies in A. thaliana reported a genomic region responsible for drought avoidance co-130 mapping with a region contributing to a constitutively lowered Tr and simultaneously 131 leading to an enhanced TE (Masle et al. 2005;McKay et al. 2008). Following these 132 examples, our current hypothesis is that only critical portions of the large DT-QTL, 133 linked to specific mechanisms, matter for the terminal drought tolerance of pearl millet 134 and these needs to be accurately mapped to enhance the precision of marker assisted 135 introgression. In addition, Tr is only one component of plant water use, which likely 136

show abstract

GENETICS OF DROUGHT ADAPTATION INARABIDOPSIS THALIANAII. QTL ANALYSIS OF A NEW MAPPING POPULATION, KAS-1 × TSU-1

Cited by 116 publications

References 90 publications

Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana

Exploiting Differential Gene Expression and Epistasis to Discover Candidate Genes for Drought-Associated QTLs in Arabidopsis thaliana

Intron-mediated alternative splicing of Arabidopsis P5CS1 and its association with natural variation in proline and climate adaptation

Water saving traits co-map with a major terminal drought tolerance quantitative trait locus in pearl millet [Pennisetum glaucum (L.) R. Br.]

Contact Info

Product

Resources

About