Quantitative trait loci for inflorescence development in Arabidopsis thaliana

Variation in inflorescence development patterns is a central factor in the evolutionary ecology of plants. The genetic architectures of 13 traits associated with inflorescence developmental timing, architecture, rosette morphology, and fitness were investigated in Arabidopsis thaliana, a model plant system. There is substantial naturally occurring genetic variation for inflorescence development traits, with broad sense heritabilities computed from 21 Arabidopsis ecotypes ranging from 0.134 to 0.772. Genetic correlations are significant for most (64/78) pairs of traits, suggesting either pleiotropy or tight linkage among loci. Quantitative trait locus (QTL) mapping indicates 47 and 63 QTL for inflorescence developmental traits in Ler x Col and Cvi x Ler recombinant inbred mapping populations, respectively. Several QTL associated with different developmental traits map to the same Arabidopsis chromosomal regions, in agreement with the strong genetic correlations observed. Epistasis among QTL was observed only in the Cvi x Ler population, and only between regions on chromosomes 1 and 5. Examination of the completed Arabidopsis genome sequence in three QTL regions revealed between 375 and 783 genes per region. Previously identified flowering time, inflorescence architecture, floral meristem identity, and hormone signaling genes represent some of the many candidate genes in these regions.     

Genotype-environment interactions at quantitative trait loci affecting inflorescence development in Arabidopsis thaliana

Phenotypic plasticity and genotype-environment interactions (GEI) play a prominent role in plant morphological diversity and in the potential functional capacities of plant life-history traits. The genetic basis of plasticity and GEI, however, is poorly understood in most organisms. In this report, inflorescence development patterns in Arabidopsis thaliana were examined under different, ecologically relevant photoperiod environments for two recombinant inbred mapping populations (Ler x Col and Cvi x Ler) using a combination of quantitative genetics and quantitative trait locus (QTL) mapping. Plasticity and GEI were regularly observed for the majority of 13 inflorescence traits. These observations can be attributable (at least partly) to variable effects of specific QTL. Pooled across traits, 12/44 (27.3%) and 32/62 (51.6%) of QTL exhibited significant QTL x environment interactions in the Ler x Col and Cvi x Ler lines, respectively. These interactions were attributable to changes in magnitude of effect of QTL more often than to changes in rank order (sign) of effect. Multiple QTL x environment interactions (in Cvi x Ler) clustered in two genomic regions on chromosomes 1 and 5, indicating a disproportionate contribution of these regions to the phenotypic patterns observed. High-resolution mapping will be necessary to distinguish between the alternative explanations of pleiotropy and tight linkage among multiple genes.     

Quantitative trait loci for floral morphology in Arabidopsis thaliana

A central question in biology is how genes control the expression of quantitative variation. We used statistical methods to estimate genetic variation in eight Arabidopsis thaliana floral characters (fresh flower mass, petal length, petal width, sepal length, sepal width, long stamen length, short stamen length, and pistil length) in a cosmopolitan sample of 15 ecotypes. In addition, we used genome-wide quantitative trait locus (QTL) mapping to evaluate the genetic basis of variation in these same traits in the Landsberg erecta x Columbia recombinant inbred line population. There was significant genetic variation for all traits in both the sample of naturally occurring ecotypes and in the Ler x Col recombinant inbred line population. In addition, broad-sense genetic correlations among the traits were positive and high. A composite interval mapping (CIM) analysis detected 18 significant QTL affecting at least one floral character. Eleven QTL were associated with several floral traits, supporting either pleiotropy or tight linkage as major determinants of flower morphological integration. We propose several candidate genes that may underlie these QTL on the basis of positional information and functional arguments. Genome-wide QTL mapping is a promising tool for the discovery of candidate genes controlling morphological development, the detection of novel phenotypic effects for known genes, and in generating a more complete understanding of the genetic basis of floral development.     

Quantitative trait locus mapping for seed mineral concentrations in two Arabidopsis thaliana recombinant inbred populations

Biofortification of foods, achieved by increasing the concentrations of minerals such as iron (Fe) and zinc (Zn), is a goal of plant scientists. Understanding genes that influence seed mineral concentration in a model plant such as Arabidopsis could help in the development of nutritionally enhanced crop cultivars. Quantitative trait locus (QTL) mapping for seed concentrations of calcium (Ca), copper (Cu), Fe, potassium (K), magnesium (Mg), manganese (Mn), phosphorus (P), sulfur (S), and Zn was performed using two recombinant inbred line (RIL) populations, Columbia (Col) x Landsberg erecta (Ler) and Cape Verde Islands (Cvi) x Ler, grown on multiple occasions. QTL mapping was also performed using data from silique hulls and the ratio of seed:hull mineral concentration of the Cvi x Ler population. Over 100 QTLs that affected seed mineral concentration were identified. Twenty-nine seed QTLs were found in more than one experiment, and several QTLs were found for both seed and hull mineral traits. A number of candidate genes affecting seed mineral concentration are discussed. These results indicate that A. thaliana is a suitable and convenient model for discovery of genes that affect seed mineral concentration. Some strong QTLs had no obvious candidate genes, offering the possibility of identifying unknown genes that affect mineral uptake and translocation to seeds.     

From plant genomics to breeding practice

New alleles are constantly accumulated during intentional crop selection. The molecular understanding of these alleles has stimulated new genomic approaches to mapping quantitative trait loci (QTL) and haplotype multiplicity of the genes concerned. A limited number of quantitative trait nucleotides responsible for QTL variation have been described, but an acceleration in their rate of discovery is expected with the adoption of linkage disequilibrium and candidate gene strategies for QTL fine mapping and cloning. Additional layers of regulatory variation have been studied that could also contribute to the molecular basis of quantitative genetics of crop traits. Despite this progress, the role of marker-assisted selection in plant breeding will ultimately depend on the genetic model underlying quantitative variation.     

Mapping quantitative trait loci associated with selenate tolerance in Arabidopsis thaliana

Selenium is essential for many organisms, but is toxic at higher levels. To investigate the genetic basis of selenate tolerance in Arabidopsis thaliana, quantitative trait loci (QTL) associated with selenate tolerance in accessions Landsberg erecta and Columbia were mapped using recombinant inbred lines (RILs). The selenate tolerance index (TI(D10) = root growth + 30 microm selenate/root growth control x 100%) was fourfold higher for parental line Col-4 (59%) than for parent Ler-0 (15%). Among the 96 F8 RILs, TI(D10) ranged from 11 to 75% (mean 37%). Using composite interval mapping, three QTL were found on chromosomes 1, 3 and 5, which together explained 24% of variation in TI(D10) and 32% of the phenotypic variation for the difference in root length +/- Se (RL(D10)). Highly significant epistatic interactions between the QTL and markers on chromosome 2 explained additional variation for both traits. Potential candidate genes for Se tolerance in each of the QTL regions are discussed. These results offer insight into the genetic basis of selenate tolerance, and may be useful for identification of selenate-tolerance genes.     

Seasonal and plant-density dependency for quantitative trait loci affecting flowering time in multiple populations of Arabidopsis thaliana

Multiple environmental cues regulate the transition to flowering. In natural environments, plants perceive seasonal progression by changes in day length and growth temperature, and plant density is monitored by changes in the light quality reflected from neighbouring vegetation. To understand the seasonal and plant-density dependence associated with natural allelic variation in flowering time, we conducted a quantitative trait loci (QTL) mapping study in Ler x Cvi, Bay x Sha and Ler x No-0 recombinant inbred line (RIL) populations of Arabidopsis thaliana. Days and total leaf number to bolting were examined under low and high plant density (200 or 1600 plants m(-2)) in autumn-winter and spring seasons. We found between 4 and 10 QTLs associated with seasonal and density variations in each RIL population. For Ler x Cvi and Bay x Sha RIL populations, a major proportion of QTLs showed seasonal and density interaction (up to 63%) and four QTLs were common to all environments (21%). Only three QTLs showed seasonal or density dependency. By aligning the linkage maps onto a common physical map, we detected at least one QTL at chromosome 2 and two QTLs at chromosome 5 that overlap between the three RIL populations, suggesting that these QTLs play a crucial role in the adaptive control of flowering time.     

Quantitative trait loci affecting delta13C and response to differential water availibility in Arabidopsis thaliana

Phenotypic plasticity is an important response mechanism of plants to environmental heterogeneity. Here, we explored the genetic basis of plastic responses of Arabidopsis thaliana to water deficit by experimentally mapping quantitative trait loci (QTL) in two recombinant inbred populations (Cvi x Ler and Ler x Col). We detected genetic variation and significant genotype-by-environment interactions for many traits related to water use. We also mapped 26 QTL, including six for carbon isotope composition (delta13C). Negative genetic correlations between fruit length and fruit production as well as between flowering time and branch production were corroborated by QTL colocalization, suggesting these correlations are due to pleiotropy or physical linkage. Water-limited plants were more apically dominant with greater root:shoot ratios and higher delta13C (higher water-use efficiency) when compared to well-watered plants. Many of the QTL effects for these traits interacted significantly with the irrigation treatment, suggesting that the observed phenotypic plasticity is genetically based. We specifically searched for epistatic (QTL-QTL) interactions using a two-dimensional genome scan, which allowed us to detect epistasis regardless of additive genetic effects. We found several significant QTL-QTL interactions including three that exhibited environmental dependence. These results provide preliminary evidence for proposed genetic mechanisms underlying phenotypic plasticity.     

Quantitative trait loci controlling light and hormone response in two accessions of Arabidopsis thaliana

We have mapped quantitative trait loci (QTL) responsible for natural variation in light and hormone response between the Cape Verde Islands (Cvi) and Landsberg erecta (Ler) accessions of Arabidopsis thaliana using recombinant inbred lines (RILs). Hypocotyl length was measured in four light environments: white, blue, red, and far-red light and in the dark. In addition, white light plus gibberellin (GA) and dark plus the brassinosteroid biosynthesis inhibitor brassinazole (BRZ) were used to detect hormone effects. Twelve QTL were identified that map to loci not previously known to affect light response, as well as loci where candidate genes have been identified from known mutations. Some QTL act in all environments while others show genotype-by-environment interaction. A global threshold was established to identify a significant epistatic interaction between two loci that have few main effects of their own. LIGHT1, a major QTL, has been confirmed in a near isogenic line (NIL) and maps to a new locus with effects in all light environments. The erecta mutation can explain the effect of the HYP2 QTL in the blue, BRZ, and dark environments, but not in far-red. LIGHT2, also confirmed in an NIL, has effects in white and red light and shows interaction with GA. The phenotype and map position of LIGHT2 suggest the photoreceptor PHYB as a candidate gene. Natural variation in light and hormone response thus defines both new genes and known genes that control light response in wild accessions.     

Mapping salinity tolerance during Arabidopsis thaliana germination and seedling growth

To characterize and dissect genetic variation for salinity tolerance, we assessed variation in salinity tolerance during germination and seedling growth for a worldwide sample of Arabidopsis thaliana accessions. By combining QTL mapping, association mapping and expression data, we identified genomic regions involved in salinity response. Among the worldwide sample, we found germination ability within a moderately saline environment (150 mM NaCl) varied considerable, from >90% among the most tolerant lines to complete inability to germinate among the most susceptible. Our results also demonstrated wide variation in salinity tolerance within A. thaliana RIL populations and identified multiple genomic regions that contribute to this variation. These regions contain known candidate genes, but at least four of the regions contain loci not yet associated with salinity tolerance response phenotypes. Our observations suggest A. thaliana natural variation may be an underutilized resource for investigating salinity stress response.     

Quantitative trait loci analysis of growth response to varying nitrogen sources in <Emphasis Type="Italic">Arabidopsis thaliana</Emphasis>

Nitrogen absorption and assimilation is variable among plants as a result of two factors: the source of nitrogen available and the genetic variation among species within the resulting nitrogen pathways. Several genes involved in nitrogen cycling have been identified, yet little is known about the genes that control quantitative responses to different nitrogen sources. With quantitative trait loci (QTL) mapping in Arabidopsis thaliana recombinant inbred lines (Columbia x Landsberg erecta) we have identified chromosomal regions controlling aerial mass, root mass, and root length when plants are grown in nitrate, ammonium, ammonium nitrate, or low nitrogen treatments. A total of 16 QTL ( P < 0.01) were identified among the nitrogen treatments. Most of the QTL were specific to a single treatment. The percentage additive genetic effects of significant QTL were as high as 17%. Five significant QTL corresponded to the locations of candidate genes associated with nitrogen assimilation, while a few QTL corresponded with candidate genes in the developmental pathways. Most QTL were not shared across treatments, suggesting that there is no optimal genotype for all nitrogen sources.     

Association mapping of morphological traits in wild and captive zebra finches: reliable within,but not between populations

Identifying causal genetic variants underlying heritable phenotypic variation is a long‐standing goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole‐genome linkage mapping. We here follow up on these studies with the aim to narrow down on the quantitative trait variants (QTN) in one wild and three captive populations. First, we performed an association study using 672 single nucleotide polymorphisms (SNPs) within candidate genes located in the previously identified QTL regions in a sample of 939 wild‐caught zebra finches. Then, we validated the most promising SNP–phenotype associations (n = 25 SNPs) in 5228 birds from four populations. Genotype–phenotype associations were generally weak in the wild population, where linkage disequilibrium (LD) spans only short genomic distances. In contrast, in captive populations, where LD blocks are large, apparent SNP effects on morphological traits (i.e. associations) were highly repeatable with independent data from the same population. Most of those SNPs also showed significant associations with the same trait in other captive populations, but the direction and magnitude of these effects varied among populations. This suggests that the tested SNPs are not the causal QTN but rather physically linked to them, and that LD between SNPs and causal variants differs between populations due to founder effects. While the identification of QTN remains challenging in nonmodel organisms, we illustrate that it is indeed possible to confirm the location and magnitude of QTL in a population with stable linkage between markers and causal variants.     

Population structure and its effect on haplotype diversity and linkage disequilibrium surrounding the xa5 locus of rice (Oryza sativa L.)

To assess the usefulness of linkage disequilibrium mapping in an autogamous, domesticated species, we have characterized linkage disequilibrium in the candidate region for xa5, a recessive gene conferring race-specific resistance to bacterial blight in rice. This trait and locus have good mapping information, a tractable phenotype, and available sequence data, but no cloned gene. We sampled 13 short segments from the 70-kb candidate region in 114 accessions of Oryza sativa. Five additional segments were sequenced from the adjacent 45-kb region in resistant accessions to estimate the distance at which linkage disequilibrium decays. The data show significant linkage disequilibrium between sites 100 kb apart. The presence of the xa5 resistant reaction in two ecotypes and in accessions with different haplotypes in the candidate region may indicate multiple origins or genetic heterogeneity for resistance. In addition, genetic differentiation between ecotypes emphasizes the need for controlling for population structure in the design of linkage disequilibrium studies in rice.     

Quantitative trait loci for the circadian clock in Neurospora crassa

Neurospora crassa has been a model organism for the study of circadian clocks for the past four decades. Among natural accessions of Neurospora crassa, there is significant variation in clock phenotypes. In an attempt to investigate natural allelic variants contributing to quantitative variation, we used a quantitative trait loci mapping approach to analyze three independent mapping populations whose progenitors were collected from geographically isolated locations. Two circadian clock phenotypes, free-running period and entrained phase, were evaluated in the 188 F(1) progeny of each mapping population. To identify the clock QTL, we applied two QTL mapping analyses: composite interval mapping (CIM) and Bayesian multiple QTL analysis (BMQ). When controlling false positive rates < or =0.05, BMQ appears to be the more sensitive of the two approaches. BMQ confirmed most of the QTL from CIM (18 QTL) and identified 23 additional QTL. While 13 QTL colocalize with previously identified clock genes, we identified 30 QTL that were not linked with any previously characterized clock genes. These are candidate regions where clock genes may be located and are expected to lead to new insights in clock regulation.     

Evidence for nucleolus organizer regions as the units of regulation in nucleolar dominance in Arabidopsis thaliana interecotype hybrids

Nucleolar dominance describes the silencing of one parent's ribosomal RNA (rRNA) genes in a genetic hybrid. In Arabidopsis thaliana, rRNA genes are clustered in two nucleolus organizer regions, NOR2 and NOR4. In F(8) recombinant inbreds (RI) of the A. thaliana ecotypes Ler and Cvi, lines that display strong nucleolar dominance inherited a specific combination of NORs, Cvi NOR4 and Ler NOR2. These lines express almost all rRNA from Cvi NOR4. The reciprocal NOR genotype, Ler NOR4/Cvi NOR2, allowed for expression of rRNA genes from both NORs. Collectively, these data reveal that neither Cvi rRNA genes nor NOR4 are always dominant. Furthermore, strong nucleolar dominance does not occur in every RI line inheriting Cvi NOR4 and Ler NOR2, indicating stochastic effects or the involvement of other genes segregating in the RI mapping population. A partial explanation is provided by an unlinked locus, identified by QTL analysis, that displays an epistatic interaction with the NORs and affects the relative expression of NOR4 vs. NOR2. Collectively, the data indicate that nucleolar dominance is a complex trait in which NORs, rather than individual rRNA genes, are the likely units of regulation.     

Nucleotide diversity and linkage disequilibrium in cold-hardiness- and wood quality-related candidate genes in Douglas fir

Nuclear sequence variation and linkage disequilibrium (LD) were studied in 15 cold-hardiness- and 3 wood quality-related candidate genes in Douglas fir [Pseudotsuga menziesii (Mirb.) Franco]. This set of genes was selected on the basis of its function in other plants and collocation with cold-hardiness-related quantitative trait loci (QTL). The single-nucleotide polymorphism (SNP) discovery panel represented 24 different trees from six regions in Washington and Oregon plus parents of a segregating population used in the QTL study. The frequency of SNPs was one SNP per 46 bp across coding and noncoding regions on average. Haplotype and nucleotide diversities were also moderately high with H(d) = 0.827 +/- 0.043 and pi = 0.00655 +/- 0.00082 on average, respectively. The nonsynonymous (replacement) nucleotide substitutions were almost five times less frequent than synonymous ones and substitutions in noncoding regions. LD decayed relatively slowly but steadily within genes. Haploblock analysis was used to define haplotype tag SNPs (htSNPs). These data will help to select SNPs for association mapping, which is already in progress.     

Natural variation in Arabidopsis thaliana revealed a genetic network controlling germination under salt stress

Plant responses to environmental stresses are polygenic and complex traits. In this study quantitative genetics using natural variation in Arabidopsis thaliana was used to investigate the genetic architecture of plant responses to salt stress. Eighty seven A. thaliana accessions were screened and showed a large variation for root development and seed germination under 125 and 200 mM NaCl, respectively. Twenty two quantitative trait loci for these traits have been detected by phenotyping two recombinants inbred line populations, Sha x Col and Sha x Ler. Four QTLs controlling germination under salt were detected in the Sha x Col population. Interestingly, only one allelic combination at these four QTLs inhibits germination under salt stress, implying strong epistatic interactions between them. In this interacting context, we confirmed the effect of one QTL by phenotyping selected heterozygous inbred families. We also showed that this QTL is involved in the control of germination under other stress conditions such as KCl, mannitol, cold, glucose and ABA. Our data highlights the presence of a genetic network which consists of four interacting QTLs and controls germination under limiting environmental conditions.     

人类复杂遗传疾病QTL分析方法的理论探讨

利用连锁不平衡理论,人类遗传学家已能把影响人类疾病的质量基因定位在小至1cM区域内,有些基因已被克隆出来。罗泽伟等进一步发展统计分析方法检测及估算分子标记与QTL之间的连锁不平衡系数,从而提出了人类复杂遗传病高解析度基因定位的理论策略。以此为基础,进一步探讨了供试群体在双亲基因频率存在差异时检测QTL和检测QTL互作的方法,给出了有关的理论结果。     

Analysis of natural allelic variation at seed dormancy loci of Arabidopsis thaliana

Arabidopsis accessions differ largely in their seed dormancy behavior. To understand the genetic basis of this intraspecific variation we analyzed two accessions: the laboratory strain Landsberg erecta (Ler) with low dormancy and the strong-dormancy accession Cape Verde Islands (Cvi). We used a quantitative trait loci (QTL) mapping approach to identify loci affecting the after-ripening requirement measured as the number of days of seed dry storage required to reach 50% germination. Thus, seven QTL were identified and named delay of germination (DOG) 1-7. To confirm and characterize these loci, we developed 12 near-isogenic lines carrying single and double Cvi introgression fragments in a Ler genetic background. The analysis of these lines for germination in water confirmed four QTL (DOG1, DOG2, DOG3, and DOG6) as showing large additive effects in Ler background. In addition, it was found that DOG1 and DOG3 genetically interact, the strong dormancy determined by DOG1-Cvi alleles depending on DOG3-Ler alleles. These genotypes were further characterized for seed dormancy/germination behavior in five other test conditions, including seed coat removal, gibberellins, and an abscisic acid biosynthesis inhibitor. The role of the Ler/Cvi allelic variation in affecting dormancy is discussed in the context of current knowledge of Arabidopsis germination.