New Arabidopsis recombinant inbred line populations genotyped using SNPWave and their use for mapping flowering-time quantitative trait loci.

The SNPWave marker system, based on SNPs between the reference accessions Colombia-0 and Landsberg erecta (Ler), was used to distinguish a set of 92 Arabidopsis accessions from various parts of the world. In addition, we used these markers to genotype three new recombinant inbred line populations for Arabidopsis, having Ler as a common parent that was crossed with the accessions Antwerp-1, Kashmir-2, and Kondara. The benefit of using multiple populations that contain many similar markers and the fact that all markers are linked to the physical map of Arabidopsis facilitates the quantitative comparison of maps. Flowering-time variation was analyzed in the three recombinant inbred line populations. Per population, four to eight quantitative trait loci (QTL) were detected. The comparison of the QTL positions related to the physical map allowed the estimate of 12 different QTL segregating for flowering time for which Ler has an allele different from one, two, or three of the other accessions.

Analysis of natural allelic variation of Arabidopsis seed germination and seed longevity traits between the accessions Landsberg erecta and Shakdara, using a new recombinant inbred line population.

Quantitative trait loci (QTL) mapping was used to identify loci controlling various aspects of seed longevity during storage and germination. Similar locations for QTLs controlling different traits might be an indication for a common genetic control of such traits. For this analysis we used a new recombinant inbred line population derived from a cross between the accessions Landsberg erecta (Ler) and Shakdara (Sha). A set of 114 F9 recombinant inbred lines was genotyped with 65 polymerase chain reaction-based markers and the phenotypic marker erecta. The traits analyzed were dormancy, speed of germination, seed sugar content, seed germination after a controlled deterioration test, hydrogen peroxide (H2O2) treatment, and on abscisic acid. Furthermore, the effects of heat stress, salt (NaCl) stress, osmotic (mannitol) stress, and natural aging were analyzed. For all traits one or more QTLs were identified, with some QTLs for different traits colocating. The relevance of colocation for mechanisms underlying the various traits is discussed.

Quantitative trait locus analysis of growth-related traits in a new Arabidopsis recombinant inbred population.

Arabidopsis natural variation was used to analyze the genetics of plant growth rate. Screening of 22 accessions revealed a large variation for seed weight, plant dry weight and relative growth rate but not for water content. A positive correlation was observed between seed weight and plant area 10 d after planting, suggesting that seed weight affects plant growth during early phases of development. During later stages of plant growth this correlation was not significant, indicating that other factors determine growth rate during this phase. Quantitative trait locus (QTL) analysis, using 114 (F9 generation) recombinant inbred lines derived from the cross between Landsberg erecta (Ler, from Poland) and Shakdara (Sha, from Tadjikistan), revealed QTLs for seed weight, plant area, dry weight, relative growth rate, chlorophyll fluorescence, flowering time, and flowering-related traits. Growth traits (plant area, dry weight, and relative growth rate) colocated at five genomic regions. At the bottom of chromosome 5, colocation was found of QTLs for leaf area, leaf initiation speed, specific leaf area, and chlorophyll fluorescence but not for dry weight, indicating that this locus might be involved in leaf development. No consistent relation between growth traits and flowering time was observed despite some colocations. Some of the QTLs detected for flowering time overlapped with loci detected in other recombinant inbred line populations, but also new loci were identified. This study shows that Arabidopsis can successfully be used to study the genetic basis of complex traits like plant growth rate.

Characterization of green seed, an enhancer of abi3-1 in Arabidopsis that affects seed longevity.

Seeds are usually stored in physiological conditions in which they gradually lose their viability and vigor depending on storage conditions, storage time, and genotype. Very little is known about the underlying genetics of seed storability and seed deterioration. We analyzed a mutant in Arabidopsis disturbed in seed storability. This mutant was isolated as a grs (green-seeded) mutant in an abi3-1 (abscisic acid 3) mutant background. Genetic and physiological characterization showed that the monogenic grs mutant was not visibly green seeded and mapped on chromosome 4. This enhancer mutation did not affect the ABA sensitivity of seed germination or seed dormancy but was found to affect seed storability and seedling vigor. Seed storability was assessed in a controlled deterioration test, in which the germination capacity of the mutant decreased with the duration of the treatment. The decrease in viability and vigor was confirmed by storing the seeds in two relative humidities (RHs) for a prolonged period. At 60% RH, the mutant lost germinability, but storage at 32% RH showed no decrease of germination although seed vigor decreased. The decrease in viability and vigor could be related to an increase in conductivity, suggesting membrane deterioration. This was not affected by light conditions during imbibition, expected to influence the generation of active oxygen species. During seed maturation, ABI3 regulates several processes: acquiring dormancy and long-term storability and loss of chlorophyll. Our results indicate that GRS is a common regulator in the latter two but not of dormancy/germination.