Simple Interval Mapping Research Articles

Quantitative trait loci for resistance in wheat (Triticum aestivum) to Ustilago tritici

Loose smut [Ustilago tritici (Pers) Rostr.] of wheat (Triticum aestivum L) causes losses in grain yield roughly proportional to the incidence of the disease. Efforts to control this disease utilizing genetic resistance are being made in breeding programmes around the world. DNA markers for genetic resistance would greatly enhance breeding efforts by reducing the substantial time and labour resources necessary to screen for resistant lines using traditional inoculation methods. The objective of this study was to identify DNA markers associated with resistance. Doubled haploid progeny from the four crosses ‘Glenlea’/‘AC Taber’, ‘SC8021V2’/‘AC Karma’, ‘Diamant’/TD12A, and 9340-CP*/‘AC Vista’ were evaluated with individual races of U. tritici and simple sequence repeat markers. Simple interval mapping was performed using MQTL software and single point analysis. ‘Glenlea’, which has complete and broad resistance to all known races of U. tritici in Canada, contributed a QTL for resistance to races T2, T10, T15, T19 and T39 at Xwmc160 on chromosome 5B. ‘Glenlea’ also contributed QTL for resistance to races T2, T9 and T15 at Xgwm302 on chromosome 7B and to races T9, T19 and T39 on chromosome 3A at marker Xwmc559. The chromosome 5B QTL from ‘Glenlea’ coincided with a race T39 resistance locus from ‘AC Karma’. The 7B QTL from ‘Glenlea’ coincided with resistance to race T9 from 9340-CP* and T2, T9 and T27 resistance from TD12A. The QTL on 3A from ‘Glenlea’ was coincidental with T9 resistance from 9340-CP*. When evaluated with race T10, a QTL was identified near Xbarc183 on chromosome 6D from ‘SC8021V2’. A QTL to race T9 from ‘SC8021V2’ within the interval Xcfa2019 to Xgwm344a was identified on 7A. A third QTL from ‘SC8021V2’ was located on 6B at Xbarc223 and Xbarc332b. The chromosome 5B locus together with either the 7A or 7B genetic loci would provide resistance to predominant races of loose smut found on the Canadian prairies.

Family and/or Friends? Gene Mapping at Crossroads

Mapping gene(s) underlying a specific trait offers an opportunity to plant breeders to apply marker assisted selection. All gene mapping approaches except LD mapping use family based segregation populations developed by crossing two or more parents. These family based gene mapping approaches include simple interval mapping, composite interval mapping, multiple interval mapping and Bayesian mapping etc. Each approach has its own advantages and disadvantages based on type of population and underlying statistical model. Unlike family based approaches, LD mapping uses population of unrelated individuals which are like friends belonging to different family backgrounds. Relative pros and cons of family and friends based approaches make them complementary to each other. Family based approaches identify wide chromosomal region underlying the trait of interest with relatively lower markers density, and therefore, have low mapping resolution. Conversely, friends based LD mapping identifies chromosomal region of interest with higher resolution using higher marker density. The integration of family and friends based approaches addresses their respective pros and cons successfully to enhance mapping resolution for more valid application of marker assisted selection.

QTLs influencing IGF-1 levels in a LOU/CxFischer 344 F2 rat population. Tracks towards the metabolic theory of Ageing

ObjectiveSince a reduction of the insulin/IGF-1 signaling cascade extends life span in many species and IGF-1 signaling might partly mediate the effects of caloric restriction (CR), an experimental intervention for increasing longevity, the purpose of the present study was to use quantitative trait loci (QTL) analysis, an unbiased genetic approach, to identify particular regions of the genome influencing plasma IGF-1 levels in an F2 intercross between F344 and LOU/C rats; the latter being an inbred strain of Wistar origin, considered as a model of healthy aging since it resists to age (and diet)-induced obesity. DesignF1 hybrids were obtained by crossbreeding LOU/C with F344 rats, and then F1 were bred inter se to obtain the F2 population, of which 93 males and 94 females were studied. Total plasma IGF-1 levels were determined by radioimmunoassay. A genome scan of the F2 population was made with 100 microsatellite markers) selected for their polymorphism between LOU/C and F344 strains (and by covering evenly the whole genome. ResultsBy simple interval mapping sex-dependent QTLs were found on chromosome 17 in males and on chromosome 18 in females. By multiple interval mapping, additional QTLs were found on chromosomes 1, 4, 5, 6, 12, 15 and 19 in males and on chromosomes 3, 5, 6, 12 and 17 in females. Only the markers D1Rat196 and D12Mgh5 were found in both males and females. The majority of QTLs corresponded to metabolic syndrome (cardiac function: n=45 (30%), obesity/diabetes: n=22 (15%), inflammation: n=19 (13%) and only a limited number to body weight: n=13 (9%), proliferation (n=10 (7%) or ossification: n=7 (5%). Ninety-six candidate genes were located on the different QTLs. A significant proportion of these genes are connected to IGF-1 production and receptor pathways (n=18) or metabolic syndrome (n=11). ConclusionsSubsequent studies are necessary to determine whether the genetic networks underscored are also involved in age-associated obesity, diabetes and inflammation as well as cardiovascular impairments.

Detection and Mapping of QTLs Affecting Contents of Pharmaceutical Alkaloids in Leaf and Root of Catharanthus roseus

Catharanthus roseus leaves and roots hyper-accumulate the terpenoid indole alkaloids, which are required for the economic production of pharmaceutical molecules vindoline (V), catharanthine (C), vinblastine (VB), vincristine (VC), ajmalicine (A) and serpentine (S). For developing marker-assisted selection (MAS) breeding in C. roseus, the objectives of the present study were: (a) To characterize variability and associations between six traits—V (VL), C (CL), VB + VC (VBL) contents of leaves and C (CR), A (AR) and S (SR) contents in roots, in a recombinant inbred line (RIL) population in two environments. (b) To identify and place quantitative trait loci (QTLs) associated with the traits on the map. The population of 191 RILs was found to segregate transgressively for all the six traits. The intra-organ correlations of leaf and root traits were positive and significant. The inter-organ traits were not correlated. All the traits except AR were highly heritable (h2 = 41−79 %). A RIL population genetic map of 179 markers on 8 linkage groups (LGs) covering 1,786.5 cM genetic distance was constructed. The RIL-generated genetic map led to identification of 20 QTLs for 6 traits (5, 4, 1, 4, 2, and 4 QTLs, respectively for CL, VL, VBL, CR, AR, and SR) by the use of single marker regression, simple interval mapping and composite interval mapping approaches. QTLs were detected only on 4 of the 8 LGs. QTL for the same or different traits were mapped in clusters or singularly. The results suggest that a combination of MAS and phenotypic selection offer possibilities of realizing simultaneous improvement in C and V accumulation in leaves and roots of C. roseus.

Roles of Root Aerenchyma Development and Its Associated QTL in Dry Matter Production under Transient Moisture Stress in Rice

Enhanced aerenchyma development in rice under transient drought-to-waterlogged (TD-W) stress promotes root system development by promoting lateral root production. This study analyzed the quantitative trait loci (QTLs) associated with the plasticity in aerenchyma development under TD-W stress. A mapping population of 60 F2 genotypes of chromosome segment substituted lines (CSSL) derived from CSSL47 and Nipponbare crosses were grown in rootboxes and evaluated for shoot and root growth, and aerenchyma development (expressed as root porosity). The TD-W stress was imposed starting with water saturated soil condition at sowing and then to progressive drought from 0 to 21 days after sowing (DAS) prior to exposure to sudden waterlogging for another 17 days (21 to 38 DAS). We performed simple and composite interval mapping to identify QTLs for aerenchyma development. QTL associated with aerenchyma development was mapped on the short-arm of chromosome 12 and designated as qAER-12. The effect of qAER-12 on the plasticity in aerenchyma development under TD-W was significantly associated with the increase in lateral root elongation and branching. This resulted in greater root system development as expressed in total root length and consequently contributed to higher dry matter production. This qAER-12 is probably the first reported QTL associated with aerenchyma development in rice under TD-W and is a useful trait for the improvement of the adaptive capability under fluctuating soil moisture conditions.

Quantitative Trait Loci Affecting Oil Content, Oil Composition, and Other Agronomically Important Traits in Oat

Groat oil content and composition are important determinants of oat (Avena sativa L.) quality. We investigated these traits in a population of 146 recombinant inbred lines from a cross between ‘Dal’ (high oil) and ‘Exeter’ (low oil). A linkage map consisting of 475 Diversity Arrays Technology (DArT) markers spanning 1271.8 cM across 40 linkage groups was constructed. Quantitative trait locus (QTL) analysis for groat oil content and composition was conducted using grain samples grown at Aberdeen, ID, in 1997. Quantitative trait locus analysis for multiple agronomic traits was also conducted using data collected from hill plots and field plots in Ottawa, ON, in 2010. Using simple and composite interval mapping methods, QTLs for oil content, palmitic acid (16:0), stearic acid (18:0), oleic acid (18:1), linoleic acid (18:2), and linolenic acid (18:3) were identified. Two of the loci associated with oil content were associated with all of the fatty acids examined in this study, and most oil‐related QTL showed similar patterns of effect on the fatty acid profile. These results suggest the presence of pleiotropic effects on oil‐related traits through influences at specific nodes of the oil synthesis pathway. In addition, 12 QTL‐associated markers (likely representing nine unique regions) were associated with plant height, heading date, lodging, and protein content.

Quantitative trait loci (QTL) analysis of flag leaf senescence in wheat (Triticum aestivum L.) with microsatellite DNA markers under water-stressed condition

The objective of this study was to detect quantitative trait loci (QTL) associated with drought tolerance in wheat genotypes by simple sequence repeat (SSR) markers and to provide valuable information for marker assisted selection. SSR markers linked to flag leaf senescence (FLS) was identified in two DNA pools, which were established using F 2 mapping population, resulting from a cross between a drought sensitive genotype 'Variant-11' and drought tolerant genotype 'Veery'. Parents were screened initially with 34 SSR primer pairs. The linkage map was constructed with the six linked markers into one linkage group covering 82.7 cm. QTL detection with analysis of variance showed that all of the six markers were significantly associated with drought tolerance in this population. Single marker regression (SMR) analysis revealed that R-square percentage ranged from 39.3% ( Xgwm339 ) and 12.3% ( Xgwm577 ). Simple interval mapping (SIM) located a QTL for leaf flag senescence, between markers interval Xgwm566 and Xgwm339 , while composite interval mapping (CIM) indicated a QTL location between the interval marker Xgwm296 and Xgwm566 . The SSR markers can be used for the detection of QTLs quantitative trait loci linked with flag leaf senescence as indicator for drought tolerance. Key words : Flag leaf senescence, Triticum aestivum L., SSR markers, simple interval mapping (SIM), composite interval mapping (CIM), quantitative trait loci (QTL).

Effect of small mapping population sizes on reliability of quantitative trait locus (QTL) mapping

A limitation of quantitative trait loci (QTL) mapping is that accuracy of determining QTL position and effects are largely determined by population size. Despite the importance of this concept, known as the effect there has generally been a lack of understanding by molecular geneticists and breeders. One possible explanation for this may be that this concept has been explored by using computer simulations and that these findings may not be clearly understood. In this study, we demonstrated the effect of population size on the accuracy of determining QTL positions and effects in a simple and concise manner. Simulated data was generated for extremely large mapping populations (n = 1000) and smaller mapping populations (n = 94 or n = 190) were obtained by random sampling. Populations were defined to segregate for either three or five QTLs with heritabilities of h 2 = 0.75 or h 2 = 0.50. When small populations were used, errors were detected in determining QTL positions, and in some cases, QTLs were not detected (that is, false negatives) especially when h 2 = 0.50. More importantly, R2 values were overestimated or underestimated. Composite interval mapping was more reliable for detecting QTLs compared to simple interval mapping. These findings have important implications for QTLs which are selected in breeding programs via marker-assisted selection. Key words : Quantitative trait loci (QTL) mapping, Beavis effect, population size, confidence intervals, marker-assisted selection.

Characterization of variation and quantitative trait loci related to terpenoid indole alkaloid yield in a recombinant inbred line mapping population of Catharanthus roseus

Improved Catharanthus roseus cultivars are required for high yields of vinblastine, vindoline and catharanthine and/or serpentine and ajmalicine, the pharmaceutical terpenoid indole alkaloids. An approach to derive them is to map QTL for terpenoid indole alkaloids yields, identify DNA markers tightly linked to the QTL and apply marker assisted selection. Towards the end, 197 recombinant inbred lines from a cross were grown over two seasons to characterize variability for seven biomass and 23 terpenoid indole alkaloids content-traits and yield-traits. The recombinant inbred lines were genotyped for 178 DNA markers which formed a framework genetic map of eight linkage groups (LG), spanning 1786.5 cM, with 10.0 cM average intermarker distance. Estimates of correlations between traits allowed selection of seven relatively more important traits for terpenoid indole alkaloids yields. QTL analysis was performed on them using single marker (regression) analysis, simple interval mapping and composite interval mapping procedures. A total of 20 QTL were detected on five of eight LG, 10 for five traits on LG1, five for four traits on LG2, three for one trait on LG3 and one each for different traits on LG three and four. QTL for the same or different traits were found clustered on three LG. Co-location of two QTL for biomass traits was in accord of correlation between them. The QTL were validated for use in marker assisted selection by the recombinant inbred line which transgressively expressed 16 traits contributory to the yield vinblastine, vindoline and catharanthine from leaves and roots that possessed favourable alleles of 13 relevant QTL.

Construction of a genetic linkage map with SSR, AFLP and morphological markers to locate QTLs controlling pathotype-specific powdery mildew resistance in diploid roses

Disease resistance is a sought-after trait in plant breeding programmes. One strategy to make resistance more durable is to increase the number of resistance genes, thereby increasing the number of pathotypes withstood. One of the most important diseases on roses is powdery mildew (PM) (Podosphaera pannosa). Recent studies show that pathotypes of PM and different types of resistances in roses exist. The results of this study aim to contribute to PM resistance in roses by the development of pathotype-specific markers on a genetic map. A diploid rose population (90 genotypes) derived from a cross between Rosa wichurana and Rosa ‘Yesterday’ was used to construct a genetic linkage map encompassing 20 AFLP primer combinations, 43 SSR, and 2 morphological markers. By applying the F1 pseudo test cross population strategy, two parental linkage maps were constructed (parent ‘Yesterday’ 536 cM; parent R. wichurana 526 cM). Both parental maps consisted of seven linkage groups with an average length of 70 cM (Kosambi) corresponding to the seven haploid rose chromosomes. These new maps were used to identify QTLs controlling disease resistance. The offspring population was screened for resistance to two PM pathotypes, R–E and R–P. QTLs for controlling pathotype-specific disease resistance were mapped by applying Kruskal–Wallis rank-sum tests and simple interval mapping. With two pathotypes analysed, nine QTL loci were detected on linkage groups 2, 3, 5 and 6, explaining 15–73% of the phenotypic variance for pathotype-specific disease response. The genetic maps developed here will be useful for future rose breeding, pathotype-specific resistance research and development of a consensus map for roses.

Identification and Validation of Quantitative Trait Loci for Agronomic Traits in Advanced Backcross Breeding Lines Derived from Oryza rufipogon × Oryza sativa Cultivar MR219

A backcross breeding strategy was used to identify quantitative trait loci (QTLs) associated with 14 traits in a BC2F2 population derived from a cross between MR219, an indica rice cultivar and an accession of Oryza rufipogon (IRGC 105491). A total of 261 lines were genotyped with 96 microsatellite markers and evaluated for plant morphology, yield components and growth period. The genetic linkage map generated for this population with an average interval size of 16.2 cM, spanning 1,553.4 cM (Kosambi) of the rice genome. Thirty-eight QTLs were identified with composite interval mapping (CIM), whereas simple interval mapping (SIM) resulted in 47 QTLs (LOD >3.0). The O. rufipogon allele was favourable for 59% of QTLs detected through CIM. Of 261 BC2F2 families, 26 advanced backcross breeding lines (BC2F5) were used for QTL validation. These lines were selected on the basis of the yield traits potentiality in BC2F3 and BC2F4 generations. The field trial was conducted at three different locations in Malaysia using randomized complete block design with three replications. Trait based marker analysis was done for QTL determination. Twenty-five QTLs were detected in BC2F5 generation whereas 29 QTLs were detected in BC2F2 generation of the same population. Two QTLs (qPL-1 and qSPL-7) were not considered for validation due to their low R 2 values and two QTLs (qPSS-3-2 and qGW-3-2) were not detected in the BC2F5 population. Fifteen QTLs showed the beneficial effect to enhance the trait value of the breeding lines. QTL validation aided to select the promising lines for further utilization.

A QTL on Chromosome 10 Modulates Cone Photoreceptor Number in the Mouse Retina

This investigation examines the genetic sources of marked variation in cone photoreceptor number among inbred lines of mice, identifying candidate genes that may control the proliferation, differentiation, or survival of this neuronal population. Cone photoreceptor populations were counted in C57BL/6J (B6/J) and A/J strains, and 26 recombinant inbred (RI) strains derived from them. Eyes from RI strains were also collected for microarray analysis. Quantitative trait locus (QTL) analysis was carried out by simple and composite interval mapping and validated using a consomic line. Candidate genes were evaluated based on genetic variance between the parental strains and analysis of gene expression. Expression data, deposited in GeneNetwork (www.GeneNetwork.org), were used to generate a coexpression network of established cone photoreceptor genes as a reference standard. B6/J has 70% more cone photoreceptors than A/J. A significant QTL was mapped to chromosome 10 (Chr 10) and confirmed using B6.A<10> mice. Of 19 positional candidate genes, one-the myeloblastosis oncogene (Myb)-stood out. Myb has a potentially damaging missense mutation, high retinal expression, and a known role in cell proliferation. The ectonucleotide pyrophosphatase/phosphodiesterase 1 gene (Enpp1) was a second strong candidate, with an expression pattern that covaried with cone photoreceptors and that was differentially expressed between the parental strains. Enpp1 and several other candidate genes covaried with multiple genes within the cone photoreceptor gene network. The mouse retina shows marked variation in cone photoreceptor number, some of which must be controlled by polymorphisms in a gene or genes on Chr 10.

Mapping quantitative trait loci for egg production traits in an F2 intercross of Oh-Shamo and White Leghorn chickens

We performed quantitative trait locus (QTL) analyses for egg production traits, including age at first egg (AFE) and egg production rates (EPR) measured every 4 weeks from 22 to 62 weeks of hen age, in a population of 421 F(2) hens derived from an intercross between the Oh-Shamo (Japanese Large Game) and White Leghorn breeds of chickens. Simple interval mapping revealed a main-effect QTL for AFE on chromosome 1 and four main-effect QTL for EPR on chromosomes 1 and 11 (three on chromosome 1 and one on chromosome 11) at the genome-wide 5% levels. Among the three EPR QTL on chromosome 1, two were identified at the early stage of egg laying (26-34 weeks of hen age) and the remaining one was discovered at the late stage (54-58 weeks). The alleles at the two EPR QTL derived from the Oh-Shamo breed unexpectedly increased the trait values, irrespective of the Oh-Shamo being inferior to the White Leghorn in the trait. This suggests that the Oh-Shamo, one of the indigenous Japanese breeds, is an untapped resource that is important for further improvement of current elite commercial laying chickens. In addition, six epistatic QTL were identified on chromosomes 2, 4, 7, 8, 17 and 19, where none of the above main-effect QTL were located. This is the first example of detection of epistatic QTL affecting egg production traits. The main and epistatic QTL identified accounted for 4-8% of the phenotypic variance. The total contribution of all QTL detected for each trait to the phenotypic and genetic variances ranged from 4.1% to 16.9% and from 11.5% to 58.5%, respectively.

Increased Glucocorticoid Receptor Expression and Activity Mediate the LPS Resistance of SPRET/EI Mice

SPRET/Ei mice are extremely resistant to acute LPS-induced lethal inflammation when compared with C57BL/6. We found that in vivo SPRET/Ei mice exhibit strongly reduced expression levels of cytokines and chemokines. To investigate the role of the potent anti-inflammatory glucocorticoid receptor (GR) in the SPRET/Ei phenotype, mice were treated with the GR antagonist RU486 or bilateral adrenalectomy. Under such conditions, both C57BL/6 and SPRET/Ei mice were strongly sensitized to LPS, and the differences in LPS response between SPRET/Ei and C57BL/6 mice were completely gone. These results underscore the central role of GR in the LPS hyporesponsiveness of SPRET/Ei mice. Compared with C57BL/6, SPRET/Ei mice were found to express higher GR levels, which were reflected in increased GR transactivation. Using a backcross mapping strategy, we demonstrate that the high GR transcription levels are linked to the Nr3c1 (GR) locus on chromosome 18 itself. Unexpectedly, SPRET/Ei mice exhibit a basal overactivation of the hypothalamic-pituitary-adrenal axis, namely strongly increased corticosterone levels, ACTH levels, and adrenocortical size. As a consequence of the excess of circulating glucocorticoids (GCs), levels of hepatic gluconeogenic enzymes are increased, and insulin secretion from pancreatic β-cells is impaired, both of which result in hyperglycemia and glucose intolerance in SPRET/Ei mice. We conclude that SPRET/Ei mice are unique as they display an unusual combination of elevated GR expression and increased endogenous GC levels. Hence, these mice provide a new and powerful tool for the study of GR- and GC-mediated mechanisms, including immune repressive functions, neuroendocrine regulation, insulin secretion, and carbohydrate metabolism.

Genetic linkage maps of two interspecific grape crosses (Vitis spp.) used to localize quantitative trait loci for downy mildew resistance

Two populations (Pop) segregating quantitatively for resistance to downy mildew (DM), caused by Plasmopara viticola, were used to construct genetic maps and to carry out quantitative trait locus (QTL) analysis. Pop1 comprised of 174 F1 individuals from a cross of ‘Moscato Bianco’, a susceptible Vitis vinifera cultivar, and a resistant individual of Vitis riparia. Pop2 consisted of 94 progeny from a cross of two interspecific hybrids, ‘VRH3082 1-42’ and ‘SK77 5/3’, with resistance traits inherited from Vitis rotundifolia and Vitis amurensis, respectively. Resistance of progeny was measured in field and greenhouse conditions by visual evaluation of disease symptoms on leaves. Linkage maps of 1037.2 and 651 cM were built essentially with simple sequence repeat markers and were enriched with gene-derived single-strand conformational polymorphism and single-nucleotide polymorphism markers. Simple interval mapping and Kruskall–Wallis analysis detected a stable QTL involved in field resistance to DM on linkage group (LG) 7 of the Pop1 integrated map co-localized with a putative Caffeoyl-CoA O-methyltransferase-derived marker. Additional QTLs were detected on LGs 8, 12 and 17. We were able to identify genetic factors correlated with resistance to P. viticola with lower statistical significance on LGs 1, 6 and 7 of the Pop2 map. Finally, no common QTLs were found between the two crosses analyzed. A search of the grapevine genome sequence revealed either homologues to non-host-, host- or defense-signalling genes within the QTL intervals. These positional candidate genes may provide new information about chromosomal regions hosting phenotypic loci.

Efficiency of selective genotyping for genetic analysis of complex traits and potential applications in crop improvement

Selective genotyping of individuals from the two tails of the phenotypic distribution of a population provides a cost efficient alternative to analysis of the entire population for genetic mapping. Past applications of this approach have been confounded by the small size of entire and tail populations, and insufficient marker density, which result in a high probability of false positives in the detection of quantitative trait loci (QTL). We studied the effect of these factors on the power of QTL detection by simulation of mapping experiments using population sizes of up to 3,000 individuals and tail population sizes of various proportions, and marker densities up to one marker per centiMorgan using complex genetic models including QTL linkage and epistasis. The results indicate that QTL mapping based on selective genotyping is more powerful than simple interval mapping but less powerful than inclusive composite interval mapping. Selective genotyping can be used, along with pooled DNA analysis, to replace genotyping the entire population, for mapping QTL with relatively small effects, as well as linked and interacting QTL. Using diverse germplasm including all available genetics and breeding materials, it is theoretically possible to develop an “all-in-one plate” approach where one 384-well plate could be designed to map almost all agronomic traits of importance in a crop species. Selective genotyping can also be used for genomewide association mapping where it can be integrated with selective phenotyping approaches. We also propose a breeding-to-genetics approach, which starts with identification of extreme phenotypes from segregating populations generated from multiple parental lines and is followed by rapid discovery of individual genes and combinations of gene effects together with simultaneous manipulation in breeding programs.

Mapping candidate QTLs related to plant persistency in red clover

Red clover (Trifolium pratense L.) is a diploid (2n = 14), self-incompatible legume that is widely cultivated as a forage legume in cold geographical regions. Because it is a short-lived perennial species, improvement of plant persistency is the most important objective for red clover breeding. To develop a marker-assisted selection (MAS) approach for red clover, we identified candidate QTLs related to plant persistency. Two full-sib mapping populations, 272 × WF1680 and HR × R130, were used for QTL identification. Resistance to Sclerotinia trifoliorum and Fusarium species, as well as to winter hardiness, was investigated in the laboratory and in field experiments in Moscow region (Russia), and Sapporo (Japan). With the genotype data derived from microsatellite and other DNA markers, candidate QTLs were identified by simple interval mapping (SIM), Kruskal–Wallis analysis (KW analysis) and genotype matrix mapping (GMM). A total of 10 and 23 candidate QTL regions for plant persistency were identified in the 272 × WF1680 and the HR × R130 mapping populations, respectively. The QTLs identified by multiple mapping approaches were mapped on linkage group (LG) 3 and LG6. The significant QTL interactions identified by GMM explained the higher phenotypic variation than single effect QTLs. Identification of haplotypes having positive effect QTLs in each parent were first demonstrated in this study for pseudo-testcross mapping populations in plant species using experimental data.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-009-1253-5) contains supplementary material, which is available to authorized users.

A new semi-dwarfing gene identified by molecular mapping of quantitative trait loci in barley

Semi-dwarfing genes have been widely used in spring barley (Hordeum vulgare L.) breeding programs in many parts of the world, but the success in developing barley cultivars with semi-dwarfing genes has been limited in North America. Exploiting new semi-dwarfing genes may help in solving this dilemma. A recombinant inbred line population was developed by crossing ZAU 7, a semi-dwarf cultivar from China, to ND16092, a tall breeding line from North Dakota. To identify quantitative trait loci (QTL) controlling plant height, a linkage map comprised of 111 molecular markers was constructed. Simple interval mapping was performed for each of the eight environments. A consistent QTL for plant height was found on chromosome 7HL. This QTL is not associated with maturity and rachis internode length. We suggest the provisional name Qph-7H for this QTL. Qph-7H from ZAU 7 reduced plant height to about 3/4 of normal; thus, Qph-7H is considered a semi-dwarfing gene. Other QTLs for plant height were found, but their expression was variable across the eight environments tested.

Identification and analysis of QTLs controlling cold tolerance at the reproductive stage and validation of effective QTLs in cold-tolerant genotypes of rice (Oryza sativa L.)

Low temperature or cold stress is one of the major constraints of rice production and productivity in temperate rice-growing countries and high-altitude areas in the tropics. Even though low temperature affects the rice plant in all stages of growth, the percent seed set is damaged severely by cold and this reduces the yield potential of cultivars significantly. In this study, a new source of cold-tolerant line, IR66160-121-4-4-2, was used as a donor parent with a cold-sensitive cultivar, Geumobyeo, to produce 153 F(8) recombinant inbred lines (RILs) for quantitative trait locus (QTL) analysis. QTL analysis with 175 polymorphic simple sequence repeat (SSR) markers and composite interval mapping identified three main-effect QTLs (qPSST-3, qPSST-7, and qPSST-9) on chromosomes 3, 7, and 9. The SSR markers RM569, RM1377, and RM24545 were linked to the identified QTLs for cold tolerance with respect to percent seed set using cold-water (18-19 degrees C) irrigation in the field and controlled air temperature (17 degrees C) in the greenhouse. The total phenotypic variation for cold tolerance contributed by the three QTLs was 27.4%. RILs with high percent seed set under cold stress were validated with linked DNA markers and by haplotype analysis that revealed the contribution of progenitor genomes from the tropical japonica cultivar Jimbrug (Javanica) and temperate japonica cultivar Shen-Nung89-366. Three QTLs contributed by the cold-tolerant parent were identified which showed additive effect on percent seed set under cold treatment. This study demonstrated the utility of a new phenotyping method as well as the identification of SSR markers associated with QTLs for selection of cold-tolerant genotypes to improve temperate rice production.

Identification of major and minor genes associated with heading date in an indica × indica cross of rice (Oryza Sativa L.)

In this study, quantitative trait loci (QTLs) controlling rice heading date were detected in a F2:3 population derived from a cross between an indica rice variety, Tarom Mahalli, with early heading date, and an indica variety, Khazar, with late heading date. SSR linkage map was constructed using 74 polymorphic markers and 192 F2 individuals and covered a total of 1231.50 cM of rice genome. QTL mapping of heading date was performed by simple and composite interval mapping. Three major genes (hd1, hd4 and hd9) were identified on chromosomes 1, 4 and 9 and two minor genes (hd2a and hd2b) were mapped on chromosome 2. Major genes explained over 60% of total phenotypic variation and had negative additive effects for decreasing heading date. These results will be useful in marker-assisted breeding to improve rice genotype with early heading date.