Knockdown resistance to heat stress and slow recovery from chill coma are genetically associated in a quantitative trait locus region of chromosome 2 in Drosophila melanogaster

In insects, two ecologically relevant traits of thermal adaptation are knockdown resistance to high temperature (KRHT) and chill-coma recovery (CCR). Chromosome 2 of Drosophila melanogaster was tested for quantitative trait loci (QTL) affecting both CCR and KRHT in backcrosses between homosequential lines that are fixed for the standard (noninverted) sequence of this autosome. These lines were obtained by artificial selection on KRHT and subsequent inbreeding from a stock that was derived from a single wild population. Heat-induced expression of the 70KD heat-shock protein (Hsp70) was also examined for variation between the lines. Composite interval mapping was performed for each trait on each reciprocal backcross, identifying one QTL region in the middle of chromosome 2 for both KRHT and CCR. The largest estimates of additive effects were found in pericentromeric regions of chromosome 2, accounting for 10–14% (CCR) and 10–17% (KRHT) of the phenotypic variance in BC populations. No QTL was found in the region of the heat-shock factor ( hsf ) gene. However, the two parental lines have diverged in the heat-induced Hsp70 expression. Distribution of KRHT QTL on chromosome 2 was similar between this study based on crosses between lines selected from a single wild population and previous work based on crosses between selection lines from different continents. Colocalized QTL showed a trade–off association between CCR and KRHT, which should be the result of either multiple, tightly linked trait-specific genes or a single gene with pleiotropic effects on the traits. We discuss candidate loci contained within the QTL regions.     

Combined expression patterns of QTL-linked candidate genes best predict thermotolerance in Drosophila melanogaster

Knockdown resistance to high temperature (KRHT) is a thermal adaptation trait in Drosophila melanogaster. Here we used quantitative real-time PCR (qRT-PCR) to test for possible associations between KRHT and the expression of candidate genes within quantitative trait loci (QTL) in eight recombinant inbred lines (RIL). hsp60 and hsc70-3 map within an X-linked QTL, while CG10383, catsup, ddc, trap1, and cyp6a13 are linked in a KRHT-QTL on chromosome 2. hsc70-3 expression increased by heat-hardening. Principal Components analysis revealed that catsup, ddc and trap1 were either co-expressed or combined in their expression levels. This composite expression variable (e-PC1) was positively associated to KRHT in non-hardened RIL. In heat-hardened flies, hsp60 was negatively related to hsc70-3 on e-PC2, with effects on KRHT. These results are consistent with the notion that QTL can be shaped by expression variation in combined candidate loci. We found composite variables of gene expression (e-PCs) that best correlated to KRHT. Network effects with other untested linked loci are apparent because, in spite of their associations with KRHT phenotypes, e-PCs were sometimes uncorrelated with their QTL genotype.     

QTL for the thermotolerance effect of heat hardening, knockdown resistance to heat and chill-coma recovery in an intercontinental set of recombinant inbred lines of Drosophila melanogaster

The thermotolerance effect of heat hardening (also called short-term acclimation), knockdown resistance to high temperature (KRHT) with and without heat hardening and chill-coma recovery (CCR) are important phenotypes of thermal adaptation in insects and other organisms. Drosophila melanogaster from Denmark and Australia were previously selected for low and high KRHT, respectively. These flies were crossed to construct recombinant inbred lines (RIL). KRHT was higher in heat-hardened than in nonhardened RIL. We quantify the heat-hardening effect (HHE) as the ratio in KRHT between heat-hardened and nonhardened RIL. Composite interval mapping revealed a more complex genetic architecture for KRHT without heat-hardening than for KRHT in heat-hardened insects. Five quantitative trait loci (QTL) were found for KRHT, but only two of them were significant after heat hardening. KRHT and CCR showed trade-off associations for QTL both in the middle of chromosome 2 and the right arm of chromosome 3, which should be the result of either pleiotropy or linkage. The major QTL on chromosome 2 explained 18% and 27-33% of the phenotypic variance in CCR and KRHT in nonhardened flies, respectively, but its KRHT effects decreased by heat hardening. We discuss candidate loci for each QTL. One HHE-QTL was found in the region of small heat-shock protein genes. However, HHE-QTL explained only a small fraction of the phenotypic variance. Most heat-resistance QTL did not colocalize with CCR-QTL. Large-effect QTL for CCR and KRHT without hardening (basal thermotolerance) were consistent across continents, with apparent transgressive segregation for CCR. HHE (inducible thermotolerance) was not regulated by large-effect QTL.     

Direct and correlated responses to artificial selection for high and low knockdown resistance to high temperature in Drosophila buzzatii

Knockdown resistance to high temperature (KRHT) is a genetically variable trait for thermal adaptation in insects. Selection for KRHT may affect a number of fitness components as well as resistance to several forms of environmental stress. To test for heritable (co)-variation in KRHT, we examined direct and correlated responses to bi-directional selection on this trait in Drosophila buzzatii. Replicated lines were artificially selected for decreased and increased KRHT. After 12 generations of artificial selection, lines diverged significantly for high KRHT only. Starvation resistance increased in two lines that strongly responded to selection for high KRHT, and these two lines also showed relatively longer chill-coma recovery time. Developmental time and body size showed no correlated responses to KRHT-selection. These results suggest that KRHT is a heritable trait that can evolve towards increased thermotolerance with no genetic trade-offs associated to starvation resistance, developmental time and body size.     

Quantitative trait loci (QTL) analysis for rice grain width and fine mapping of an identified QTL allele gw-5 in a recombination hotspot region on chromosome 5

Rice grain width and shape play a crucial role in determining grain quality and yield. The genetic basis of rice grain width was dissected into six additive quantitative trait loci (QTL) and 11 pairs of epistatic QTL using an F(7) recombinant inbred line (RIL) population derived from a single cross between Asominori (japonica) and IR24 (indica). QTL by environment interactions were evaluated in four environments. Chromosome segment substitution lines (CSSLs) harboring the six additive effect QTL were used to evaluate gene action across eight environments. A major, stable QTL, qGW-5, consistently decreased rice grain width in both the Asominori/IR24 RIL and CSSL populations with the genetic background Asominori. By investigating the distorted segregation of phenotypic values of rice grain width and genotypes of molecular markers in BC(4)F(2) and BC(4)F(3) populations, qGW-5 was dissected into a single recessive gene, gw-5, which controlled both grain width and length-width ratio. gw-5 was narrowed down to a 49.7-kb genomic region with high recombination frequencies on chromosome 5 using 6781 BC(4)F(2) individuals and 10 newly developed simple sequence repeat markers. Our results provide a basis for map-based cloning of the gw-5 gene and for marker-aided gene/QTL pyramiding in rice quality breeding.     

High-resolution mapping of quantitative trait loci for sternopleural bristle number in Drosophila melanogaster.

We have mapped quantitative trait loci (QTL) harboring naturally occurring allelic variation for Drosophila bristle number. Lines with high (H) and low (L) sternopleural bristle number were derived by artificial selection from a large base population. Isogenic H and L sublines were extracted from the selection lines, and populations of X and third chromosome H/L recombinant isogenic lines were constructed in the homozygous low line background. The polymorphic cytological locations of roo transposable elements provided a dense molecular marker map with an average intermarker distance of 4.5 cM. Two X chromosome and six chromosome 3 QTL affecting response to selection for sternopleural bristle number and three X chromosome and three chromosome 3 QTL affecting correlated response in abdominal bristle number were detected using a composite interval mapping method. The average effects of bristle number QTL were moderately large, and some had sex-specific effects. Epistasis between QTL affecting sternopleural bristle number was common, and interaction effects were large. Many of the intervals containing bristle number QTL coincided with those mapped in previous studies. However, resolution of bristle number QTL to the level of genetic loci is not trivial, because the genomic regions containing bristle number QTL often did not contain obvious candidate loci, and results of quantitative complementation tests to mutations at candidate loci affecting adult bristle number were ambiguous.     

Quantitative trait locus for starvation resistance in an intercontinental set of mapping populations of Drosophila melanogaster

Starvation resistance (SR) is an important trait for survival of insects in the wild. We used recombinant inbred lines (RIL) to search for quantitative trait loci (QTL) in crosses between intercontinental inbred lines that were originally selected for heat-knockdown resistance. SR was measured as the time of survival under repeated events of starvation. SR was consistently higher in females than in males. Composite interval mapping identified one QTL region (cytological range 64D - 66E2) on the left arm of chromosome 3 in males, and no QTL was found in females. Many candidate genes that were identified in previous studies of QTL for stress resistance are included within this QTL region. The QTL-allele that decreased SR was found in the line originating from the colder population (Denmark). We discuss our results with regard to multiple candidate genes, non-colocalization with thermotolerance QTL, and possible geographical variation.     

Consistent effects of a major QTL for thermal resistance in field-released Drosophila melanogaster

Molecular genetic markers can be used to identify quantitative trait loci (QTL) for thermal resistance and this has allowed characterization of a major QTL for knockdown resistance to high temperature in Drosophila melanogaster. The QTL showed trade-off associations with cold resistance under laboratory conditions. However, assays of thermal tolerance conducted in the laboratory may not necessarily reflect performance at varying temperatures in the field. Here we tested if lines with different genotypes in this QTL show different thermal performance under high and low temperatures in the field using a release recapture assay. We found that lines carrying the QTL genotype for high thermal tolerance were significantly better at locating resources in the field releases under hot temperatures while the QTL line carrying the contrasting genotype were superior at cold temperatures. Further, we studied copulatory success between the different QTL genotypes at different temperatures. We found higher copulatory success in males of the high tolerance QTL genotype under hot temperature conditions, while there was no difference in females at cold temperatures. The results allow relating components of field fitness at different environmental temperatures with genotypic variation in a QTL for thermal tolerance.     

The genetic architecture of Drosophila sensory bristle number

We have mapped quantitative trait loci (QTL) for Drosophila mechanosensory bristle number in six recombinant isogenic line (RIL) mapping populations, each of which was derived from an isogenic chromosome extracted from a line selected for high or low, sternopleural or abdominal bristle number and an isogenic wild-type chromosome. All RILs were evaluated as male and female F(1) progeny of crosses to both the selected and the wild-type parental chromosomes at three developmental temperatures (18 degrees, 25 degrees, and 28 degrees ). QTL for bristle number were mapped separately for each chromosome, trait, and environment by linkage to roo transposable element marker loci, using composite interval mapping. A total of 53 QTL were detected, of which 33 affected sternopleural bristle number, 31 affected abdominal bristle number, and 11 affected both traits. The effects of most QTL were conditional on sex (27%), temperature (14%), or both sex and temperature (30%). Epistatic interactions between QTL were also common. While many QTL mapped to the same location as candidate bristle development loci, several QTL regions did not encompass obvious candidate genes. These features are germane to evolutionary models for the maintenance of genetic variation for quantitative traits, but complicate efforts to understand the molecular genetic basis of variation for complex traits.     

Quantitative trait loci regulating sugar moiety of acylsugars in tomato

Acylsugars are broad-spectrum insect resistance sugar esters produced at very high levels by some accessions of the wild tomato, Solanum pennellii. Transferring acylsugar production from S. pennellii LA716 to cultivated tomato through traditional breeding developed the benchmark acylsugar breeding line CU071026. The base moiety of acylsugars (sucrose vs. glucose) can vary among S. pennellii accessions. Additionally the accession S. pennellii LA716 produces almost exclusively acylglucoses, but the breeding line CU071026 derived from S. pennellii LA716 produces exclusively acylsucroses. This study uses a BC1F1 and a BC1F2 population derived from the cross CU071026 × (CU071026 × S. pennellii LA716) to identify and confirm the action of three quantitative trait loci (QTL) on chromosomes 3, 4, and 11. The QTL on chromosomes 3 and 11 are both required for acylglucose production, while addition of the chromosome 4 QTL affects the level of acylglucose produced in the presence of the QTL on chromosomes 3 and 11. A three-way interaction between these acylglucose QTL was confirmed with a post hoc ANOVA. Identification of these three QTL provides a blueprint for breeding to shift acylsucrose production to acylglucose production in tomato breeding lines. The implications of these QTL and two additional QTL affecting total acylsugar level in the BC1F2 are discussed.     

Mapping and Isolation of Quantitative Trait Loci Controlling Plant Height and Heading Date in Rice

Quantitative trait loci (QTL) were identified for heading date and plant height in rice ( Oryza sativa L.) using a recombinant inbred line population consisting of 241 lines. Totally 4 QTLs for heading date and 4 QTLs for plant height were detected in three years. The QTL with large effects located in the interval C1023-R1440 on chromosome 7 was simultaneously detected in three years for both traits. In order to distinguished the interval whether contained one QTL with pleiotropy effect or two close linked QTLs, a recombinant line RIL50, whose genetic background was high similar to Zhenshan 97 except the regions covered the major QTL from Minghui 63, was selected to cross with Zhenshan 97. A BC1F2 population from the cross, which could be regarded as near isogenic lines (NIL) with the targeted QTL (QTL-NIL), was used to collect heading date and plant height data. The frequency distribution of the two traits in the BC1F2 population was bimodal, and their segregation ratios were in accordance with the expected Mendelian inheritance ratios. Normally, the short plants flowered early in the population, the high plants with late heading date, but the relationships between the plant height and the heading date of 6 plants conflicted with the case. The above results clearly demonstrated that QTL could be treated as single Mendelian factor. Moreover, there are two close linked genes controlling the heading date and the plant height on chromosome 7, respectively.     

Identification of quantitative trait loci influencing traits related to energy balance in selection and inbred lines of mice.

Energy balance is a complex trait with relevance to the study of human obesity and maintenance energy requirements of livestock. The objective of this study was to identify, using unique mouse models, quantitative trait loci (QTL) influencing traits that contribute to variation in energy balance. Two F2 resource populations were created from lines of mice differing in heat loss measured by direct calorimetry as an indicator of energy expenditure. The HB F2 resource population originated from a cross between a noninbred line selected for high heat loss and an inbred line with low heat loss. Evidence for significant QTL influencing heat loss was found on chromosomes 1, 2, 3, and 7. Significant QTL influencing body weight and percentage gonadal fat, brown fat, liver, and heart were also identified. The LH F2 resource population originated from noninbred lines of mice that had undergone divergent selection for heat loss. Chromosomes 1 and 3 were evaluated. The QTL for heat loss identified on chromosome 1 in the HB population was confirmed in the LH population, although the effect was smaller. The presence of a QTL influencing 6-wk weight was also confirmed. Suggestive evidence for additional QTL influencing heat loss, percentage subcutaneous fat, and percentage heart was found for chromosome 1.     

Quantitative trait loci affecting body weight and fatness from a mouse line selected for extreme high growth.

Quantitative trait loci (QTL) influencing body weight were mapped by linkage analysis in crosses between a high body weight selected line (DU6) and a control line (DUKs). The two mouse lines differ in body weight by 106% and in abdominal fat weight by 100% at 42 days. They were generated from the same base population and maintained as outbred colonies. Determination of line-specific allele frequencies at microsatellite markers spanning the genome indicated significant changes between the lines on 15 autosomes and the X chromosome. To confirm these effects, a QTL analysis was performed using structured F2 pedigrees derived from crosses of a single male from DU6 with a female from DUKs. QTL significant at the genome-wide level were mapped for body weight on chromosome 11; for abdominal fat weight on chromosomes 4, 11, and 13; for abdominal fat percentage on chromosomes 3 and 4; and for the weights of liver on chromosomes 4 and 11, of kidney on chromosomes 2 and 9, and of spleen on chromosome 11. The strong effect on body weight of the QTL on chromosome 11 was confirmed in three independent pedigrees. The effect was additive and independent of sex, accounting for 21-35% of the phenotypic variance of body weight within the corresponding F2 populations. The test for multiple QTL on chromosome 11 with combined data from all pedigrees indicated the segregation of two loci separated by 36 cM influencing body weight.     

Mapping quantitative trait loci conferring resistance to rice black-streaked virus in maize (Zea mays L.)

Maize rough dwarf disease (MRDD) is one of the most serious virus diseases of maize worldwide, and it causes great reduction of maize production. In China, the pathogen was shown to be rice black-streaked virus (RBSDV). Currently, MRDD has spread broadly and leads to significant loss in China. However, there has been little research devoted to this disease. Our aims were to identify the markers and loci underlying resistance to this virus disease. In this study, segregation populations were constructed from two maize elite lines '90110', which is highly resistant to MRDD and 'Ye478', which is highly susceptible to MRDD. The F(2) and BC(1) populations were used for bulk sergeant analysis (BSA) to identify resistance-related markers. One hundred and twenty F(7:9) RILs were used for quantitative trait loci (QTL) mapping through the experiment of multiple environments over 3 years. Natural occurrence and artificial inoculation were both used and combined to determine the phenotype of plants. Five QTL, qMRD2, qMRD6, qMRD7, qMRD8 and qMRD10 were measured in the experiments. The qMRD8 on chromosome 8 was proved to be one major QTL conferring resistance to RBSDV disease in almost all traits and environments, which explained 12.0-28.9 % of the phenotypic variance for disease severity in this present study.     

Fatness QTL on chicken chromosome 5 and interaction with sex

Quantitative trait loci (QTL) affecting fatness in male chickens were previously identified on chromosome 5 (GGA5) in a three-generation design derived from two experimental chicken lines divergently selected for abdominal fat weight. A new design, established from the same pure lines, produced 407 F2 progenies (males and females) from 4 F1-sire families. Body weight and abdominal fat were measured on the F₂ at 9 wk of age. In each sire family, selective genotyping was carried out for 48 extreme individuals for abdominal fat using seven microsatellite markers from GGA5. QTL analyses confirmed the presence of QTL for fatness on GGA5 and identified a QTL by sex interaction. By crossing one F1 sire heterozygous at the QTL with lean line dams, three recombinant backcross 1 (BC1) males were produced and their QTL genotypes were assessed in backcross 2 (BC2) progenies. These results confirmed the QTL by sex interaction identified in the F2 generation and they allow mapping of the female QTL to less than 8 Mb at the distal part of the GGA5. They also indicate that fat QTL alleles were segregating in both fat and lean lines.     

QTL mapping and molecular marker analysis for the resistance of rice to ozone

The resistance of rice to ozone (O3) is a quantitative trait controlled by nuclear genes. The identification of quantitative trait loci (QTL) and analysis of molecular markers of O3 resistance is important for increasing the resistance of rice to O3 stress. QTL associated with the O3 resistance of rice were mapped on chromosomes 1, 7 and 11 using 164 recombinant inbred (RI) lines from a cross between 'Milyang 23' and 'Gihobyeo'. The quantitative trait loci were tightly linked to the markers RG109, C507 and RG1094 and were detected in each of three replications. The association between these markers and O3 resistance in 26 rice cultivars and doubled haploid (DH) populations was analysed. The markers permit the screening of rice germplasm for O3 resistance and the introduction of resistance into elite lines in breeding programs.     

Candidate defense genes as predictors of quantitative blast resistance in rice

Although quantitative trait loci (QTL) underpin many desirable agronomic traits, their incorporation into crop plants through marker-assisted selection is limited by the low predictive value of markers on phenotypic performance. Here we used candidate defense response (DR) genes to dissect quantitative resistance in rice using recombinant inbred (RI) and advanced backcross (BC) populations derived from a blast-resistant cultivar, Sanhuangzhan 2 (SHZ-2). Based on DNA profiles of DR genes, RI lines were clustered into two groups corresponding to level of resistance. Five DR genes, encoding putative oxalate oxidase, dehydrin, PR-1, chitinase, and 14-3-3 protein, accounted for 30.0, 23.0, 15.8, 6.7, and 5.5% of diseased leaf area (DLA) variation, respectively. Together, they accounted for 60.3% of the DLA variation and co-localized with resistance QTL identified by interval mapping. Average phenotypic contributions of oxalate oxidase, dehydrin, PR-1, chitinase, and 14-3-3 protein in BC lines were 26.1, 19.0, 18.0, 11.5, and 10.6%, respectively, across environments. Advanced BC lines with four to five effective DR genes showed enhanced resistance under high disease pressure in field tests. Our results demonstrate that the use of natural variation in a few candidate genes can solve a long-standing problem in rice production and has the potential to address other problems involving complex traits.     

抗南方水稻黑条矮缩病水稻光温敏核不育系的筛选和鉴定

对东乡野生稻(Oryza rufipogon Griff.)3个生态群落株系及协青早B//协青早B/东乡野生稻的BC1F6株系进行了南方水稻黑条矮缩病抗性鉴定,筛选出抗性较好的种质资源。利用筛选到的协青早B//协青早B/东乡野生稻抗性株系,与光温敏核不育系C47S杂交转育,鉴定筛选到6份抗性较好的光温敏核不育系,为选育抗南方水稻黑条矮缩病的两系杂交稻组合奠定了材料基础;同时研究发现,来源于东乡野生稻的对南方水稻黑条矮缩病的抗性可能由数量性状基因控制。     

Genetic dissection of the resistance to Rice stripe virus present in the indica rice cultivar 'IR24'

Rice stripe disease, caused by Rice stripe virus (RSV) and transmitted by the small brown planthopper (Laodelphax striatellus Fallen), is one of the most serious viral diseases of rice in temperate East Asian production regions. Prior quantitative trait loci (QTL) mapping has established that Oryza sativa L. subsp. indica 'IR24' carries positive alleles at the three loci qSTV3, qSTV7, and qSTV11-i. Here, we report an advanced backcross analysis based on three selected chromosome segment substitution lines (CSSLs), each predicted to carry one of these three QTL. Three sets of BC(4)F(2:3) populations were bred from a cross between the critical CSSL and its recurrent parent Oryza sativa L. subsp. japonica 'Asominori'. Both qSTV3 and qSTV11-i were detected in their respective population, but qSTV7 was not. An allelic analysis based on a known carrier of the major RSV resistance gene Stvb-i, which is located on chromosome 11, showed that qSTV11-i was not allelic with Stvb-i. A large mapping population was used to delimit the location of qSTV11-i to a 73.6-kb region. The de novo markers developed for this purpose will be useful as marker-assisted selection tools in efforts to introduce qSTV11-i into breeding programmes aiming to improve the level of RSV resistance.     

Mapping spot blotch resistance genes in four barley populations

Bipolaris sorokiniana (teleomorph: Cochliobolus sativus) is the fungal pathogen responsible for spot blotch in barley (Hordeum vulgare L.) and occurs worldwide in warmer, humid growing conditions. Current Australian barley varieties are largely susceptible to this disease and attempts are being made to introduce sources of resistance from North America. In this study we have compared chromosomal locations of spot blotch resistance reactions in four North American two-rowed barley lines; the North Dakota lines ND11231-12 and ND11231-11 and the Canadian lines TR251 and WPG8412-9-2-1. Diversity arrays technology-based PCR, expressed sequence tag and SSR markers have been mapped across four populations derived from crosses between susceptible parental lines and these four resistant parents to determine the location of resistance loci. Quantitative trait loci (QTL) conferring resistance to spot blotch in adult plants (APR) were detected on chromosomes 3HS and 7HS. In contrast, seedling resistance (SLR) was controlled solely by a locus on chromosome 7HS. The phenotypic variance explained by the APR QTL on 3HS was between 16 and 25% and the phenotypic variance explained by the 7HS APR QTL was between 8 and 42% across the four populations. The SLR QTL on 7HS explained between 52 and 64% of the phenotypic variance. An examination of the pedigrees of these resistance sources supports the common identity of resistance in these lines and indicates that only a limited number of major resistance loci are available in current two-rowed germplasm.