Population-specific quantitative trait loci mapping for functional stay-green trait in rice (Oryza sativa L.)

The functional stay-green trait gives leaves a longer duration of greenness and photosynthetic capacity during the grain-filling period. We developed two independent recombinant inbred line populations from the intra- and intersubspecific crosses of Oryza sativa L. subsp. japonica 'Suweon490' (japonica) × O. sativa subsp. japonica 'SNU-SG1' (japonica) and O. sativa subsp. indica 'Andabyeo' (indica) × O. sativa subsp. japonica 'SNU-SG1' (japonica), respectively. The common parental line 'SNU-SG1' was the functional source for the stay-green trait. Quantitative trait locus (QTL) mapping based on simple sequence repeat markers identified a total of six QTLs associated with two stay-green traits across two populations. The two traits were cumulative chlorophyll content (SPAD value) of flag leaf (CSFL) and total cumulative SPAD value of the four upper leaves (TCS). Four QTLs, tcs4, csfl6, csfl9 (or tcs9), and csfl12, located on chromosomes 4, 6, 9, and 12, respectively, were detected simultaneously in both populations. The remaining two QTLs, csfl2 (or tcs2) and tcs5, on chromosomes 2 and 5, respectively, were found to be population specific. Moreover, the functional stay-green trait of 'SNU-SG1' positively correlated with grain yield performance. Two yield QTLs, yld6 and yld9, on chromosomes 6 and 9 found in both populations were positioned at the same locations with the csfl6 and tcs9 QTLs for stay-green traits. Thus, the identified chromosomal regions can be promising targets of marker-assisted introgression of the functional stay-green trait into breeding materials for improvement of rice yield.     

Quantitative trait loci associated with drought tolerance at reproductive stage in rice

Drought is a major constraint to rice (Oryza sativa) yield and its stability in rainfed and poorly irrigated environments. Identifying genomic regions influencing the response of yield and its components to water deficits will aid in our understanding of the genetics of drought tolerance and development of more drought tolerant cultivars. Quantitative trait loci (QTL) for grain yield and its components and other agronomic traits were identified using a subset of 154 doubled haploid lines derived from a cross between two rice cultivars, CT9993-510 to 1-M and IR62266-42 to 6-2. Drought stress treatments were managed by use of a line source sprinkler irrigation system, which provided a linearly decreasing level of irrigation coinciding with the sensitive reproductive growth stages. The research was conducted at the Ubon Rice Research Center, Ubon, Thailand. A total of 77 QTL were identified for grain yield and its components under varying levels of water stress. Out of the total of 77 QTL, the number of QTL per trait were: 7-grain yield (GY); 8-biological yield (BY); 6-harvest index (HI); 5-d to flowering after initiation of irrigation gradient (DFAIG); 10-total spikelet number (TSN); 7-percent spikelet sterility (PSS); 23-panicle number (PN); and 11-plant height (PH). The phenotypic variation explained by individual QTL ranged from 7.5% to 55.7%. Under well-watered conditions, we observed a high genetic association for BY, HI, DFAIG, PSS, TSN, PH, and GY. However, only BY and HI were found to be significantly associated with GY under drought treatments. QTL flanked by markers RG104 to RM231, EMP2_2 to RM127, and G2132 to RZ598 on chromosomes 3, 4, and 8 were associated with GY, HI, DFAIG, BY, PSS, and PN under drought treatments. The aggregate effects of these QTL on chromosomes 3, 4, and 8 resulted in higher grain yield. These QTL will be useful for rainfed rice improvement, and will also contribute to our understanding of the genetic control of GY under drought conditions at the sensitive reproductive stage. Close linkage or pleiotropy may be responsible for the coincidence of QTL detected in this experiment. Digenic interactions between QTL main effects for GY, BY, HI, and PSS were observed under irrigation treatments. Most (but not all) DH lines have the same response in measure of productivity when the intensity of water deficit was increased, but no QTL by irrigation treatment interaction was detected. The identification of genomic regions associated with GY and its components under drought stress will be useful for marker-based approaches to improve GY and its stability for farmers in drought-prone rice environments.     

Quantitative trait loci for phyllochron and tillering in rice

Morphogenetic processes in sequentially growing leaves and tiller buds are highly synchronized in rice (Oryza sativa L.). Consequently, the appearance of successive leaves in the main tiller acts as the pacemaker for the whole shoot system development. The time interval between the appearance of successive leaves (days/leaf) in the main tiller is called the phyllochron. The objectives of the investigation reported here were: (1) to identify quantitative trait loci (QTLs) that control rice phyllochron and (2) to understand the roles of phyllochron QTLs as an underlying developmental factor for rice tillering. For this purpose we developed a set of recombinant inbred lines derived from a cross between IR36 (indica) and Genjah Wangkal (tropical japonica). Composite interval mapping detected three phyllochron QTLs located on chromosomes 4, 10 and 11, where the presence of a Genjah Wangkal allele increased phyllochron. The largest QTL (on chromosome 4) was located on the genomic region syntenic to the vicinity of the maize Teopod 2 mutation, while the QTL on chromosome 10 was close to the rice plastochron 1 mutation. These three phyllochron QTLs failed to coincide with major tiller number QTLs. However, one tiller number QTL was associated with small LOD peaks for phyllochron and tiller-bud dormancy that were linked in coupling phase, suggesting that linked small effects of phyllochron and tiller-bud dormancy might result in a multiplicative effect on tiller number.     

Functional mapping of quantitative trait loci associated with rice tillering

Several biologically significant parameters that are related to rice tillering are closely associated with rice grain yield. Although identification of the genes that control rice tillering and therefore influence crop yield would be valuable for rice production management and genetic improvement, these genes remain largely unidentified. In this study, we carried out functional mapping of quantitative trait loci (QTLs) for rice tillering in 129 doubled haploid lines, which were derived from a cross between IR64 and Azucena. We measured the average number of tillers in each plot at seven developmental stages and fit the growth trajectory of rice tillering with the Wang–Lan–Ding mathematical model. Four biologically meaningful parameters in this model––the potential maximum for tiller number (K), the optimum tiller time (t ₀), and the increased rate (r), or the reduced rate (c) at the time of deviation from t ₀––were our defined variables for multi-marker joint analysis under the framework of penalized maximum likelihood, as well as composite interval mapping. We detected a total of 27 QTLs that accounted for 2.49–8.54% of the total phenotypic variance. Nine common QTLs across multi-marker joint analysis and composite interval mapping showed high stability, while one QTL was environment-specific and three were epistatic. We also identified several genomic segments that are associated with multiple traits. Our results describe the genetic basis of rice tiller development, enable further marker-assisted selection in rice cultivar development, and provide useful information for rice production management.     

Quantitative trait loci and molecular markers associated with wheat allelopathy

Wheat (Triticum aestivum L.) has been examined for allelopathic potential against annual ryegrass (Lolium rigidum). The bioassay technique, 'equal-compartment-agar-method', was employed to evaluate seedling allelopathy in a doubled-haploid (DH) population derived from cv Sunco (weakly allelopathic) and cv Tasman (strongly allelopathic). A significant difference in allelopathic activity was found among the DH lines, which inhibited the root length of ryegrass across a range from 23.7 to 88.3%. The phenotypic data showed that wheat allelopathic activity was distributed normally within this DH population and a substantial transgressive segregation for seedling allelopathic activity was also found. Analysis of restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP) and microsatellite (SSRs) markers identified two major QTLs on chromosome 2B associated with wheat allelopathy. The linkage analysis of genetic markers and the QTLs may improve genetic gains for the allelopathic activity through marker-assisted selection in wheat breeding. The development of wheat allelopathic cultivars could reduce the over-reliance of weed control on synthetic herbicides.Communicated by J. Dvorak     

Quantitative trait loci associated with seed and seedling traits in Lactuca

Seed and seedling traits related to germination and stand establishment are important in the production of cultivated lettuce (Lactuca sativa L.). Six seed and seedling traits segregating in a L. sativa cv. Salinas x L. serriola recombinant inbred line population consisting of 103 F8 families revealed a total of 17 significant quantitative trait loci (QTL) resulting from three seed production environments. Significant QTL were identified for germination in darkness, germination at 25 and 35°C, median maximum temperature of germination, hypocotyl length at 72 h post-imbibition, and plant (seedling) quality. Some QTL for germination and early seedling growth characteristics were co-located, suggestive of pleiotropic loci regulating these traits. A single QTL (Htg6.1) described 25 and 23% of the total phenotypic variation for high temperature germination in California- and Netherlands-grown populations, respectively, and was significant between 33 and 37°C. Additionally, Htg6.1 showed significant epistatic interactions with other Htg QTL and a consistent effect across all the three seed production environments. L. serriola alleles increased germination at these QTL. The estimate of narrow-sense heritability (h²) of Htg6.1 was 0.84, indicating potential for L. serriola as a source of germination thermotolerance for lettuce introgression programs.     

Quantitative trait loci associated with maximal exercise endurance in mice.

The role of genetics in the determination of maximal exercise endurance is unclear. Six- to nine-week-old F2 mice (n = 99; 60 female, 39 male), derived from an intercross of two inbred strains that had previously been phenotyped as having high maximal exercise endurance (Balb/cJ) and low maximal exercise endurance (DBA/2J), were treadmill tested to estimate exercise endurance. Selective genotyping of the F2 cohort (n = 12 high exercise endurance; n = 12 low exercise endurance) identified a significant quantitative trait locus (QTL) on chromosome X (53.7 cM, DXMit121) in the entire cohort and a suggestive QTL on chromosome 8 (36.1 cM, D8Mit359) in the female mice. Fine mapping with the entire F2 cohort and additional informative markers confirmed and narrowed the QTLs. The chromosome 8 QTL (EE8(F)) is homologous with two suggestive human QTLs and one significant rat QTL previously linked with exercise endurance. No effect of sex (P = 0.33) or body weight (P = 0.79) on exercise endurance was found in the F2 cohort. These data indicate that genetic factors in distinct chromosomal regions may affect maximal exercise endurance in the inbred mouse. Whereas multiple genes are located in the identified QTL that could functionally affect exercise endurance, this study serves as a foundation for further investigations delineating the identity of genetic factors influencing maximum exercise endurance.     

Quantitative trait loci associated with parasitic infection in Scottish blackface sheep

This study aimed to identify quantitative trait loci associated with endoparasitic infection in Scottish Blackface sheep. Data were collected from 789 animals over a 3-year period. All of the animals were continually exposed to a mixed nematode infection by grazing. Faecal samples were collected in August, September and October each year at ca. 16, 20 and 24 weeks of age; Nematodirus spp. eggs were counted separately from the other species of nematodes. Blood samples were collected in October from which immunoglobulin A (IgA) activity was measured and DNA was extracted for genotyping. In total, 139 Microsatellite markers were genotyped across eight chromosomal regions (chromosomes 1, 2, 3, 5, 14, 18, 20 and 21) in the sires and progeny were genotyped for the markers that were polymorphic in their sire. Evidence was found for quantitative trait loci (QTL) on chromosomes 2, 3, 14 and 20. QTL associated with specific IgA activity were identified in chromosomes 3 and 20, in regions close to IFNG (chromosome 3) and the MHC (chromosome 20). QTL associated with Nematodirus FEC were identified on chromosomes 2, 3 and 14. Lastly, QTL associated with non-Nematodirus Strongyle FEC were identified on chromosomes 3 and 20. This study has shown that some aspects of host resistance to gastrointestinal parasites are under strong genetic control, therefore these QTL could be utilised in a marker-assisted selection scheme to increase host resistance to gastrointestinal parasites.     

Quantitative trait loci mapping of flag-leaf ligule length in rice and alignment with ZmLG1 gene

A doubled haploid (DH) population,which consists of 120 lines dedved from anther culture of a typical Indica and japonica hybrid 'CJ06'/'TN1',was used in this study.Ligule lengths of flag leaf were investigated for quantitative trait loci (QTL) mapping using the DH population.Five QTLs (qLL-2,qLL-4,qLL-6,qLL-10 and qLL-12) controlling the ligule length (LL) were detected on chromosomes 2,4,6,10 and 12,with the variances explained 11.4%,13.6%,27.8%,22.1% and 11.0%,respectively.Using four known genes of ZmGL1,ZmGL2,ZmGL3 and ZmGL4 in maize from the MaizeGDB,their homologs in rice were aligned and integrated into the existing simple sequence repeats linkage map by in silico mapping.A ZmLG1 homolog gene,OsLG1 encoding a squamosa promoter binding protein,was located between the markers RM255 and RM280,which is just identical to the interval of qLL-4 on the long arm of chromosome 4.The results are beneficial to dissection of the ligule molecular mechanism and the study of cereal evolution.     

Quantitative trait loci associated with fatness in a broiler–layer cross

An F₂ population established by crossing a broiler male line and a layer line was used to map quantitative trait loci (QTL) affecting abdominal fat weight, abdominal fat percentage and serum cholesterol and triglyceride concentrations. Two genetic models, the line-cross and the half-sib, were applied in the QTL analysis, both using the regression interval method. Three significant QTL and four suggestive QTL were mapped in the line-cross analysis and four significant and four suggestive QTL were mapped in the half-sib analysis. A total of five QTL were mapped for abdominal fat weight, six for abdominal fat percentage and four for triglyceride concentration in both analyses. New QTL associated with serum triglyceride concentration were mapped on GGA5, GGA23 and GG27. QTL mapped between markers LEI0029 and ADL0371 on GGA3 for abdominal fat percentage and abdominal fat weight and a suggestive QTL on GGA12 for abdominal fat percentage showed significant parent-of-origin effects. Some QTL mapped here match QTL regions mapped in previous studies using different populations, suggesting good candidate regions for fine-mapping and candidate gene searches.     

Quantitative trait loci associated with adaptation to Mediterranean dryland conditions in barley

The objective of the present study was to identify quantitative trait loci (QTL) influencing agronomic performance across rain fed Mediterranean environments in a recombinant inbred line (RIL) population derived from the barley cultivars ER/Apm and Tadmor. The population was tested in four locations (two in Syria and two in Lebanon) during four consecutive years. This allowed the analysis of marker main effects as well as of marker by location and marker by year within location interactions. The analysis demonstrated the significance of crossover interactions in environments with large differences between locations and between years within locations. Alleles from the parent with the higher yield potential, ER/Apm, were associated with improved performance at all markers exhibiting main effects for grain yield. The coincidence of main effect QTL for plant height and yield indicated that average yield was mainly determined by plant height, where Tadmor's taller plants, being susceptible to lodging, yielded less. However, a number of crossover interactions were detected, in particular for yield, where the Tadmor allele improved yield in the locations with more severe drought stress. The marker with the highest number of cross-over interactions for yield and yield component traits mapped close to the flowering gene Ppd-H2 and a candidate gene for drought tolerance HVA1 on chromosome 1H. Effects of these candidate genes and QTL may be involved in adaptation to severe drought as frequently occurring in the driest regions in the Mediterranean countries. Identification of QTL and genes affecting field performance of barley under drought stress is a first step towards the understanding of the genetics behind drought tolerance.     

Quantitative trait loci associated with chemical composition of the chicken carcass

Major objectives of the poultry industry are to increase meat production and to reduce carcass fatness, mainly abdominal fat. Information on growth performance and carcass composition are important for the selection of leaner meat chickens. To enhance our understanding of the genetic architecture underlying the chemical composition of chicken carcasses, an F₂ population developed from a broiler × layer cross was used to map quantitative trait loci (QTL) affecting protein, fat, water and ash contents in chicken carcasses. Two genetic models were applied in the QTL analysis: the line‐cross and the half‐sib models, both using the regression interval mapping method. Six significant and five suggestive QTL were mapped in the line‐cross analysis, and four significant and six suggestive QTL were mapped in the half‐sib analysis. A total of eleven QTL were mapped for fat (ether extract), five for protein, four for ash and one for water contents in the carcass using both analyses. No study to date has reported QTL for carcass chemical composition in chickens. Some QTL mapped here for carcass fat content match, as expected, QTL regions previously associated with abdominal fat in the same or in different populations, and novel QTL for protein, ash and water contents in the carcass are presented here. The results described here also reinforce the need for fine mapping and to perform multi‐trait analyses to better understand the genetic architecture of these traits.     

Quantitative trait loci in Drosophila

Phenotypic variation for quantitative traits results from the simultaneous segregation of alleles at multiple quantitative trait loci. Understanding the genetic architecture of quantitative traits begins with mapping quantitative trait loci to broad genomic regions and ends with the molecular definition of quantitative trait loci alleles. This has been accomplished for some quantitative trait loci in Drosophila. Drosophila quantitative trait loci have sex-, environment- and genotype-specific effects, and are often associated with molecular polymorphisms in non-coding regions of candidate genes. These observations offer valuable lessons to those seeking to understand quantitative traits in other organisms, including humans.     

Quantitative trait loci for component physiological traits determining salt tolerance in rice

Rice (Oryza sativa) is sensitive to salinity, which affects one-fifth of irrigated land worldwide. Reducing sodium and chloride uptake into rice while maintaining potassium uptake are characteristics that would aid growth under saline conditions. We describe genetic determinants of the net quantity of ions transported to the shoot, clearly distinguishing between quantitative trait loci (QTL) for the quantity of ions in a shoot and for those that affect the concentration of an ion in the shoot. The latter coincide with QTL for vegetative growth (vigor) and their interpretation is therefore ambiguous. We distinguished those QTL that are independent of vigor and thus directly indicate quantitative variation in the underlying mechanisms of ion uptake. These QTL independently govern sodium uptake, potassium uptake, and sodium:potassium selectivity. The QTL for sodium and potassium uptake are on different linkage groups (chromosomes). This is consistent with the independent inheritance of sodium and potassium uptake in the mapping population and with the mechanistically different uptake pathways for sodium and potassium in rice under saline conditions (apoplastic leakage and membrane transport, respectively). We report the chromosomal location of ion transport and selectivity traits that are compatible with agronomic needs and we indicate markers to assist selection in a breeding program. Based upon knowledge of the underlying mechanisms of ion uptake in rice, we argue that QTL for sodium transport are likely to act through the control of root development, whereas QTL for potassium uptake are likely to act through the structure or regulation of membrane-sited transport components.     

Quantitative trait loci with parent-of-origin effects in chicken

We investigated potential effects of parent-of-origin specific quantitative trait loci (QTL) in chicken. Two divergent egg-layer lines differing in egg quality were reciprocally crossed to produce 305 F2 hens. Searching the genome using models with uni-parental expression, we identified four genome-wide significant QTL with parent-of-origin effects and three highly suggestive QTL affecting age at first egg, egg weight, number of eggs, body weight, feed intake, and egg white quality. None of these QTL had been detected previously using Mendelian models. Two genome-wide significant and one highly suggestive QTL show exclusive paternal expression while the others show exclusive maternal expression. Each of the parent-of-origin specific QTL explained 3-5 % of the total phenotypic variance, with the effects ranging from 0.18 to 0.4 phenotypic SD in the F2. Using simulations and further detailed analyses, it was shown that departure from fixation in the founder lines, grand-maternal effects (i.e. mitochondrial or W-linked) and Z-linked QTL were unlikely to give rise to any spurious parent-of-origin effects. The present results suggest that QTL with parent-of-origin specific expression are a plausible explanation for some reciprocal effects in poultry and deserve more attention. An intriguing hypothesis is whether these effects could be the result of genomic imprinting, which is often assumed to be unique to eutherian mammals.     

Quantitative trait loci mapping associated with plant regeneration ability from seed derived calli in rice (Oryza sativa L.)

Quantitative trait loci (QTLs), which are associated with the ability of plant regeneration from seed derived calli, were detected using a recombinant inbred (RI) population from a cross between 'Milyang 23 (toingil)' and 'Gihobyeo (japonica)' in rice (Oryza sativa L.). A tongil type cultivar, 'Milyang 23', has a lower frequency of callus induction and plant regeneration than those of japonica 'Gihobyeo'. Transgressive segregations were observed for the callus induction rate and plant regeneration ability from seed derived calli of the RI population. An interval mapping analysis was used to identify the QTL controlling the plant regeneration ability. Two QTLs for the callus induction rate were detected on chromosomes 1 and 2, explaining the 10.9% total phenotypic variation. Four QTLs that are associated with the plant regeneration ability were located on chromosomes 2, 3, and 11, accounting for 25.7% of the total phenotypic variation.     

Mapping quantitative trait loci associated with arsenic accumulation in rice (Oryza sativa)

The quantitative trait loci (QTLs) associated with arsenic (As) accumulation in rice were mapped using a doubled haploid population established by anther culture of F1 plants from a cross between a Japonica cultivar CJ06 and an Indica cultivar TN1 (Oryza sativa). Four QTLs for arsenic (As) concentrations were detected in the map. At the seedling stage, one QTL was mapped on chromosome 2 for As concentrations in shoots with 24.4% phenotypic variance and one QTL for As concentrations in roots was detected on chromosome 3. At maturity, two QTLs for As concentrations in grains were found on chromosomes 6 and 8, with 26.3 and 35.2% phenotypic variance, respectively. No common loci were detected among these three traits. Interestingly, the QTL on chromosome 8 was found to be colocated for As concentrations in grain at maturity and shoot phosphorus (P) concentrations at seedling stage. These results provide an insight into the genetic basis of As uptake and accumulation in rice, and will be useful in identifying genes associated with As accumulation.     

Quantitative trait loci associated with leaf and neck blast resistance in recombinant inbred line population of rice (Oryza sativa).

Blast is an economically important disease of rice. To map genes controlling blast resistance, recombinant inbred lines (RIL) were developed from Khao Dawk Mali 105, an aromatic, blast-susceptible cultivar and the blast resistance donor, CT 9993-5-10-M (CT). A linkage map encompassing 2112 cM was constructed from 141 RILs using 90 restriction fragment length polymorphisms (RFLPs) and 31 simple sequence repeats (SSR). Virulent isolates of blast fungus were identified by screening differential host sets against 87 single-spore isolates collected from the north and northeast of Thailand. Fifteen virulent blast isolates were selected for leaf blast screening. Neck blast was evaluated both under natural conditions and controlled inoculations. Quantitative trait loci (QTLs) for broad resistance spectrum (BRS) to leaf blast were located on chromosomes 7 and 9. In particular, the QTL(ch9) was mapped near the Pi5(t) locus. The QTL(ch7) was located close to a previously mapped partial resistance QTL. Both loci showed significant allelic interaction. Genotypes having CT alleles at both QTL(ch7) and QTL(ch9) were the most resistant. Two neck-blast QTLs were mapped on chromosomes 5 and 6. The inconsistent map locations between the leaf and neck blast QTLs indicate the complexity of fixing both leaf and neck blast resistance. The coincidence of BRS and field resistance QTLs on chromosome 7 supports the idea that BRS may reflect the broad resistance spectrum to leaf blast in rice. These findings laid the foundation for the development of a marker-assisted scheme for improving Khoa Dawk Mali 105 and the majority of aromatic Thai rice varieties that are susceptible to blast.