Analysis of Natural Allelic Variation of Arabidopsis Seed Germination and Seed Longevity Traits between the Accessions Landsberg <i>erecta</i> and Shakdara, Using a New Recombinant Inbred Line Population

108

Soil salinity limits agricultural production and is a major obstacle for feeding the growing world population. We used natural genetic variation in salt tolerance among different Arabidopsis accessions to map a major quantitative trait locus (QTL) for salt tolerance and abscisic acid (ABA) sensitivity during seed germination and early seedling growth. A recombinant inbred population derived from Landsberg erecta (L er ; salt and ABA sensitive) × Shakdara (Sha; salt and ABA resistant) was used for QTL mapping. High-resolution mapping and cloning of this QTL, Response to ABA and Salt 1 (RAS1 ), revealed that it is an ABA- and salt stress-inducible gene and encodes a previously undescribed plant-specific protein. A premature stop codon results in a truncated RAS1 protein in Sha. Reducing the expression of RAS1 by transfer-DNA insertion in Col or RNA interference in L er leads to decreased salt and ABA sensitivity, whereas overexpression of the L er allele but not the Sha allele causes increased salt and ABA sensitivity. Our results suggest that RAS1 functions as a negative regulator of salt tolerance during seed germination and early seedling growth by enhancing ABA sensitivity and that its loss of function contributes to the increased salt tolerance of Sha.

mentioning

confidence: 99%

RAS1, a quantitative trait locus for salt tolerance and ABA sensitivity in Arabidopsis

Ren

Zheng

Chinnusamy

et al. 2010

108

“…Arabidopsis accessions and the Ler × Sha RIL population (19) were obtained from the Arabidopsis Biological Resource Center. Details of low ψ w treatment and QTL mapping can be found in SI Materials and Methods.…”

Section: Methodsmentioning

confidence: 99%

“…S1A). To find the causal genetic polymorphisms, we scored an existing Ler × Sha recombinant inbred line (RIL) population (19) for proline content at low ψ w (−0.7 MPa and −1.2 MPa) and identified major QTL on chromosomes 2 and 5 (Fig. 1B, and Tables S1 and S2).…”

Section: Large Effect Qtl Controls Differential Proline Accumulationmentioning

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

126

140

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...

“…QTLs for the speed of germination may be important for germination in general and may not be affected by any kind of stress (7,8). QTLs for the speed of germination collocated with those of ABA sensitivity and salt tolerance (9). The molecular identification of the genes responsible for these QTLs provides not only new insights into seed biology, but also understanding of their adaptability in natural variation (10).…”

mentioning

confidence: 99%

Molecular identification of a major quantitative trait locus, qLTG3–1 , controlling low-temperature germinability in rice

Fujino¹,

Sekiguchi²,

Matsuda³

et al. 2008

276

273

Tolerance to abiotic stress is an important agronomic trait in crops and is controlled by many genes, which are called quantitative trait loci (QTLs). Identification of these QTLs will contribute not only to the understanding of plant biology but also for plant breeding, to achieve stable crop production around the world. Previously, we mapped three QTLs controlling low-temperature tolerance at the germination stage (called low-temperature germinability). To understand the molecular basis of one of these QTLs, qLTG3-1 (quantitative trait locus for low-temperature germinability on chromosome 3), map-based cloning was performed, and this QTL was shown to be encoded by a protein of unknown function. The QTL qLTG3-1 is strongly expressed in the embryo during seed germination. Before and during seed germination, specific localization of beta-glucuronidase staining in the tissues covering the embryo, which involved the epiblast covering the coleoptile and the aleurone layer of the seed coat, was observed. Expression of qLTG3-1 was tightly associated with vacuolation of the tissues covering the embryo. This may cause tissue weakening, resulting in reduction of the mechanical resistance to the growth potential of the coleoptile. These phenomena are quite similar to the model system of seed germination presented by dicot plants, suggesting that this model may be conserved in both dicot and monocot plants.natural variation ͉ QTLs ͉ seed germination T he control of seed dormancy and germination is important for the adaptability of plants, and germination under favorable environmental conditions is needed for their survival. Seed dormancy and germination is a complex trait influenced by many genes and environmental conditions (1). In addition, the plant hormones gibberellin and abscisic acid (ABA) play important roles in the expression of seed dormancy and germination (2, 3).Strong seedling vigor under low temperatures is an important objective of rice breeding programs in direct-seeding cultivation methods in temperate rice-growing areas, at high altitudes in tropical and subtropical areas, and in areas with a cold irrigation water supply where low temperature induces retardation of early seedling growth. Germinability (germination rate) and early seedling growth are major components of seedling vigor. A wide range of phenotypic variation of low-temperature germinability was found in rice cultivars. Quantitative trait loci (QTL) analysis for low temperature germinability revealed that many genes control this trait (4-6). However, the molecular functions of the genes for these QTLs have not been identified.A QTL mapping approach is effective to detect genes controlling traits involved in seed germination. Under several kinds of stress, such as temperature, NaCl, and osmotic pressure, germination is delayed or inhibited. QTLs for the speed of germination may be important for germination in general and may not be affected by any kind of stress (7,8). QTLs for the speed of germination collocated with those of ABA sensitivity a...