Identifying Quantitative Trait Loci for Resistance to Sclerotinia Head Rot in Two USDA Sunflower Germplasms

Sclerotinia head rot is a major disease of sunflower in the world, and quantitative trait loci (QTL) mapping could facilitate understanding of the genetic basis of head rot resistance and breeding in sunflower. One hundred twenty-three F2:3 and F2:4 families from a cross between HA 441 and RHA 439 were studied. The mapping population was evaluated for disease resistance in three field experiments in a randomized complete block design with two replicates. Disease incidence (DI) and disease severity (DS) were assessed. A genetic map with 180 target region amplification polymorphism, 32 simple sequence repeats, 11 insertion-deletion, and 2 morphological markers was constructed. Nine DI and seven DS QTL were identified with each QTL explaining 8.4 to 34.5% of phenotypic variance, suggesting the polygenic basis of the resistance to head rot. Five of these QTL were identified in more than one experiment, and each QTL explained more than 12.9% of phenotypic variance. These QTL could be useful in sunflower breeding. Although a positive correlation existed between the two disease indices, most of the respective QTL were located in different chromosomal regions, suggesting a different genetic basis for the two indices.

Download Full-text

Quantitative Trait Loci for Susceptibility to Tapeworm Infection in the Red Flour Beetle

Genetics ◽

10.1093/genetics/165.3.1307 ◽

2003 ◽

Vol 165 (3) ◽

pp. 1307-1315

Author(s):

Daibin Zhong ◽

Aditi Pai ◽

Guiyun Yan

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Genetic Basis ◽

Life Cycles ◽

Red Flour Beetle ◽

Phenotypic Variance ◽

Flour Beetle ◽

Trait Loci ◽

Host Ecology ◽

Tapeworm Infection

Abstract Parasites have profound effects on host ecology and evolution, and the effects of parasites on host ecology are often influenced by the magnitude of host susceptibility to parasites. Many parasites have complex life cycles that require intermediate hosts for their transmission, but little is known about the genetic basis of the intermediate host's susceptibility to these parasites. This study examined the genetic basis of susceptibility to a tapeworm (Hymenolepis diminuta) in the red flour beetle (Tribolium castaneum) that serves as an intermediate host in its transmission. Quantitative trait loci (QTL) mapping experiments were conducted with two independent segregating populations using amplified fragment length polymorphism (AFLP) markers and randomly amplified polymorphic DNA (RAPD) markers. A total of five QTL that significantly affected beetle susceptibility were identified in the two reciprocal crosses. Two common QTL on linkage groups 3 and 6 were identified in both crosses with similar effects on the phenotype, and three QTL were unique to each cross. In one cross, the three main QTL accounted for 29% of the total phenotypic variance and digenic epistasis explained 39% of the variance. In the second cross, the four main QTL explained 62% of the variance and digenic epistasis accounted for only 5% of the variance. The actions of these QTL were either overdominance or underdominance. Our results suggest that the polygenic nature of beetle susceptibility to the parasites and epistasis are important genetic mechanisms for the maintenance of variation within or among beetle strains in susceptibility to tapeworm infection.

Download Full-text

Identification of microsatellite markers linked to quantitative trait loci controlling resistance to Fusarium root rot in field pea

Canadian Journal of Plant Science ◽

10.4141/cjps09176 ◽

2011 ◽

Vol 91 (1) ◽

pp. 199-204 ◽

Cited By ~ 21

Author(s):

J. Feng ◽

R. Hwang ◽

K. F. Chang ◽

R. L. Conner ◽

S. F. Hwang ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Microsatellite Markers ◽

Quantitative Trait ◽

Root Rot ◽

Field Experiments ◽

Field Pea ◽

Phenotypic Variance ◽

Fusarium Root Rot ◽

Ril Population ◽

Trait Loci

Feng, J., Hwang, R., Chang, K. F., Conner, R. L., Hwang, S. F., Strelkov, S. E., Gossen, B. D., McLaren, D. L. and Xue, A. G. 2011. Identification of microsatellite markers linked to quantitative trait loci controlling resistance to Fusarium root rot in field pea. Can. J. Plant Sci. 91: 199–204. Fusarium root rot, caused by Fusarium solani (Mart.) Sacc. f. sp. pisi (F. R. Jones) W. C. Snyder & H. N. Hans, is the most common root disease of field pea (Pisum sativum L.) in western Canada. In this study, a recombinant inbred line (RIL) population (n=71) of field pea, derived from crosses between a resistant cultivar Carman, and a susceptible cultivar Reward, was evaluated to identify quantitative trait loci (QTL) controlling resistance to Fusarium root rot. The parental genotypes and RILs were evaluated for resistance to root rot following inoculation with F. solani in field experiments during 2007 and 2008. The frequency distribution of disease severities among the RILs was continuous. Transgressive segregation for resistance was observed among the RILs, with five lines more resistant than Carman, but no lines were more susceptible than Reward. To identify DNA markers linked with the resistance, 213 microsatellite markers were screened with genomic DNA from the two parental cultivars. Only 14 markers were polymorphic between the two parents and were used to genotype each of the RILs. Quantitative trait loci analysis based on the mean disease severity data from 2007 and 2008 identified a QTL that explained 39.0% of the phenotypic variance in the RIL population. This QTL is flanked by markers AA416 and AB60 on linkage group VII. The microsatellite markers that are closely linked to this QTL may be useful for marker assisted selection to develop cultivars with superior Fusarium root rot resistance.

Download Full-text

Overdominance and Epistasis Are Important for the Genetic Basis of Heterosis in Brassica rapa

HortScience ◽

10.21273/hortsci.42.5.1207 ◽

2007 ◽

Vol 42 (5) ◽

pp. 1207-1211 ◽

Cited By ~ 9

Author(s):

De-Kun Dong ◽

Jia-Shu Cao ◽

Kai Shi ◽

Le-Cheng Liu

Keyword(s):

Quantitative Trait Loci ◽

Brassica Rapa ◽

Quantitative Trait ◽

Genetic Basis ◽

Phenotypic Variance ◽

Epistasis Analysis ◽

Main Effect ◽

Trait Loci ◽

Component Traits ◽

The Cross

To investigate the genetic basis of heterosis in Brassica rapa, an F2 population was produced from the cross of B. rapa L. subsp. chinensis (L.) Hanelt and B. rapa L. subsp. rapifera Metzg. Trait performances of the F1 hybrid showed evident mid parent heterosis, which varied from 18.55% to 101.62% for the 11 traits investigated. A total of 23 main effect quantitative trait loci (QTLs) were detected for biomass and its component traits, which could explain 4.38% to 47.80% of the phenotypic variance, respectively. Sixty-five percent of these QTLs showed obvious overdominance. Epistasis analysis detected 444 two-locus interactions for the 11 traits at the threshold of P < 0.005. Some of them remained significant when more stringent threshold were set. These results suggested that overdominance and epistasis might play an important role as the genetic basis of heterosis in B. rapa.

Download Full-text

Quantitative Trait Loci Analysis of Resistance to Sclerotinia sclerotiorum in Sunflower

Phytopathology ◽

10.1094/phyto-95-0834 ◽

2005 ◽

Vol 95 (7) ◽

pp. 834-839 ◽

Cited By ~ 24

Author(s):

S. Rönicke ◽

V. Hahn ◽

A. Vogler ◽

W. Friedt

Keyword(s):

Quantitative Trait Loci ◽

Sclerotinia Sclerotiorum ◽

Quantitative Trait ◽

Interval Mapping ◽

Lesion Length ◽

Phenotypic Variance ◽

Linkage Groups ◽

Mapping Procedure ◽

Trait Loci ◽

Head Rot

A quantitative trait loci (QTL) analysis of resistance to Sclerotinia sclerotiorum was carried out with 283 sunflower (Helianthus annuus) F2:3 families derived from a cross between a resistant (SWS-B-04) and a highly susceptible sunflower inbred line. For that purpose, a genetic map based on 195 amplified fragment length polymorphism and 20 simple sequence repeat markers was constructed. The map has a size of 2,273.5 centimorgans and comprises 17 linkage groups, 12 of which could be associated to already defined linkage groups. The heads of sunflower F3 families were artificially inoculated by using sclerotinia mycelium in three field environments. The lesion length was measured in centimeters 1 week postinoculation and head rot was scored according to a 1-to-8 head rot scale 2 weeks postinoculation. Using the composite interval mapping procedure, three QTL for lesion length and two QTL for head rot could be identified. These QTL explain 10.6 to 17.1% of the total phenotypic variance.

Download Full-text

Quantitative Trait Loci Mapping for Adult-Plant Resistance to Powdery Mildew in Chinese Wheat Cultivar Bainong 64

Phytopathology ◽

10.1094/phyto-99-10-1121 ◽

2009 ◽

Vol 99 (10) ◽

pp. 1121-1126 ◽

Cited By ~ 22

Author(s):

Caixia Lan ◽

Shanshan Liang ◽

Zhulin Wang ◽

Jun Yan ◽

Yong Zhang ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Powdery Mildew ◽

Plant Resistance ◽

Quantitative Trait ◽

Adult Plant Resistance ◽

Natural Infection ◽

Block Design ◽

Adult Plant ◽

Phenotypic Variance ◽

Trait Loci

Adult-plant resistance (APR) is an effective means of controlling powdery mildew in wheat. In the present study, 406 simple-sequence repeat markers were used to map quantitative trait loci (QTLs) for APR to powdery mildew in a doubled-haploid (DH) population of 181 lines derived from the cross Bainong 64 × Jingshuang 16. The DH lines were planted in a randomized complete block design with three replicates in Beijing and Anyang during the 2005–06 and 2007–08 cropping seasons. Artificial inoculations were carried out in Beijing using the highly virulent Blumeria graminis f. sp. tritici isolate E20. Disease severities on penultimate leaves were scored twice in Beijing whereas, at Anyang, maximum disease severities (MDS) were recorded following natural infection. Broad-sense heritabilities of MDS and areas under the disease progress curve were 0.89 and 0.77, respectively, based on the mean values averaged across environments. Composite interval mapping detected four QTLs for APR to powdery mildew on chromosomes 1A, 4DL, 6BS, and 7A; these were designated QPm.caas-1A, QPm.caas-4DL, QPm.caas-6BS, and QPm.caas-7A, respectively, and explained 6.3 to 22.7% of the phenotypic variance. QTLs QPm.caas-4DL and QPm.caas-6BS were stable across environments with high genetic effects on powdery mildew response, accounting for 15.2 to 22.7% and 9.0 to 13.2% of the phenotypic variance, respectively. These results should be useful for the future improvement of powdery mildew resistance in wheat.

Download Full-text

The Genetic Basis of the Interspecific Differences in Wing Size in Nasonia (Hymenoptera; Pteromalidae): Major Quantitative Trait Loci and Epistasis

Genetics ◽

10.1093/genetics/161.2.673 ◽

2002 ◽

Vol 161 (2) ◽

pp. 673-684

Author(s):

J Gadau ◽

R E Page ◽

J H Werren

Keyword(s):

Quantitative Trait Loci ◽

Qtl Analysis ◽

Quantitative Trait ◽

Wing Length ◽

Size Difference ◽

Phenotypic Variance ◽

Wing Size ◽

Epistatic Interactions ◽

Trait Loci ◽

Wing Width

Abstract There is a 2.5-fold difference in male wing size between two haplodiploid insect species, Nasonia vitripennis and N. giraulti. The haploidy of males facilitated a full genomic screen for quantitative trait loci (QTL) affecting wing size and the detection of epistatic interactions. A QTL analysis of the interspecific wing-size difference revealed QTL with major effects and epistatic interactions among loci affecting the trait. We analyzed 178 hybrid males and initially found two major QTL for wing length, one for wing width, three for a normalized wing-size variable, and five for wing seta density. One QTL for wing width explains 38.1% of the phenotypic variance, and the same QTL explains 22% of the phenotypic variance in normalized wing size. This corresponds to a region previously introgressed from N. giraulti into N. vitripennis that accounts for 44% of the normalized wing-size difference between the species. Significant epistatic interactions were also found that affect wing size and density of setae on the wing. Screening for pairwise epistatic interactions between loci on different linkage groups revealed four additional loci for wing length and four loci for normalized wing size that were not detected in the original QTL analysis. We propose that the evolution of smaller wings in N. vitripennis males is primarily the result of major mutations at few genomic regions and involves epistatic interactions among some loci.

Download Full-text

Quantitative Trait Loci Affecting Differences in Floral Morphology Between Two Species of Monkeyflower (Mimulus)

Genetics ◽

10.1093/genetics/149.1.367 ◽

1998 ◽

Vol 149 (1) ◽

pp. 367-382 ◽

Cited By ~ 11

Author(s):

H D Bradshaw ◽

Kevin G Otto ◽

Barbara E Frewen ◽

John K McKay ◽

Douglas W Schemske

Keyword(s):

Quantitative Trait Loci ◽

Reproductive Isolation ◽

Quantitative Trait ◽

Floral Morphology ◽

Cumulative Effect ◽

Sympatric Species ◽

Accurate Estimate ◽

Phenotypic Variance ◽

Trait Loci ◽

Morphological Differences

Abstract Conspicuous differences in floral morphology are partly responsible for reproductive isolation between two sympatric species of monkeyflower because of their effect on visitation of the flowers by different pollinators. Mimulus lewisii flowers are visited primarily by bumblebees, whereas M. cardinalis flowers are visited mostly by hummingbirds. The genetic control of 12 morphological differences between the flowers of M. lewisii and M. cardinalis was explored in a large linkage mapping population of F2 plants (n = 465) to provide an accurate estimate of the number and magnitude of effect of quantitative trait loci (QTLs) governing each character. Between one and six QTLs were identified for each trait. Most (9/12) traits appear to be controlled in part by at least one major QTL explaining ≥25% of the total phenotypic variance. This implies that either single genes of individually large effect or linked clusters of genes with a large cumulative effect can play a role in the evolution of reproductive isolation and speciation.

Download Full-text

Quantitative Trait Loci Affecting Survival and Fertility-Related Traits in Caenorhabditis elegans Show Genotype-Environment Interactions, Pleiotropy and Epistasis

Genetics ◽

10.1093/genetics/153.3.1233 ◽

1999 ◽

Vol 153 (3) ◽

pp. 1233-1243 ◽

Cited By ~ 6

Author(s):

David R Shook ◽

Thomas E Johnson

Keyword(s):

Caenorhabditis Elegans ◽

Quantitative Trait Loci ◽

Population Growth ◽

Quantitative Trait ◽

Age Of Onset ◽

Inbred Strains ◽

Interval Mapping ◽

Phenotypic Variance ◽

Epistatic Interactions ◽

Trait Loci

Abstract We have identified, using composite interval mapping, quantitative trait loci (QTL) affecting a variety of life history traits (LHTs) in the nematode Caenorhabditis elegans. Using recombinant inbred strains assayed on the surface of agar plates, we found QTL for survival, early fertility, age of onset of sexual maturity, and population growth rate. There was no overall correlation between survival on solid media and previous measures of survival in liquid media. Of the four survival QTL found in these two environments, two have genotype-environment interactions (GEIs). Epistatic interactions between markers were detected for four traits. A multiple regression approach was used to determine which single markers and epistatic interactions best explained the phenotypic variance for each trait. The amount of phenotypic variance accounted for by genetic effects ranged from 13% (for internal hatching) to 46% (for population growth). Epistatic effects accounted for 9–11% of the phenotypic variance for three traits. Two regions containing QTL that affected more than one fertility-related trait were found. This study serves as an example of the power of QTL mapping for dissecting the genetic architecture of a suite of LHTs and indicates the potential importance of environment and GEIs in the evolution of this architecture.

Download Full-text

Meta-Analysis of Quantitative Trait Loci Associated with Seedling-Stage Salt Tolerance in Rice (Oryza sativa L.)

Plants ◽

10.3390/plants8020033 ◽

2019 ◽

Vol 8 (2) ◽

pp. 33 ◽

Cited By ~ 6

Author(s):

Md. Islam ◽

John Ontoy ◽

Prasanta Subudhi

Keyword(s):

Quantitative Trait Loci ◽

Salt Tolerance ◽

Candidate Genes ◽

Quantitative Trait ◽

Oryza Sativa L ◽

Meta Analysis ◽

Seedling Stage ◽

Phenotypic Variance ◽

A Genome ◽

Trait Loci

Soil and water salinity is one of the major abiotic stresses that reduce growth and productivity in major food crops including rice. The lack of congruence of salt tolerance quantitative trait loci (QTLs) in multiple genetic backgrounds and multiple environments is a major hindrance for undertaking marker-assisted selection (MAS). A genome-wide meta-analysis of QTLs controlling seedling-stage salt tolerance was conducted in rice using QTL information from 12 studies. Using a consensus map, 11 meta-QTLs for three traits with smaller confidence intervals were localized on chromosomes 1 and 2. The phenotypic variance of 3 meta-QTLs was ≥20%. Based on phenotyping of 56 diverse genotypes and breeding lines, six salt-tolerant genotypes (Bharathy, I Kung Ban 4-2 Mutant, Langmanbi, Fatehpur 3, CT-329, and IARI 5823) were identified. The perusal of the meta-QTL regions revealed several candidate genes associated with salt-tolerance attributes. The lack of association between meta-QTL linked markers and the level of salt tolerance could be due to the low resolution of meta-QTL regions and the genetic complexity of salt tolerance. The meta-QTLs identified in this study will be useful not only for MAS and pyramiding, but will also accelerate the fine mapping and cloning of candidate genes associated with salt-tolerance mechanisms in rice.

Download Full-text

Detection of Quantitative Trait Loci (QTL) Associated with the Fruit Morphology of Tomato

Genes ◽

10.3390/genes11101117 ◽

2020 ◽

Vol 11 (10) ◽

pp. 1117

Author(s):

Pragya Adhikari ◽

James McNellie ◽

Dilip R. Panthee

Keyword(s):

Quantitative Trait Loci ◽

Quantitative Trait ◽

Recombinant Inbred Lines ◽

Tomato Fruit ◽

Snp Array ◽

Fruit Shape ◽

Phenotypic Variance ◽

Fruit Morphology ◽

Trait Loci ◽

Shape And Size

Tomato (Solanum lycopersicum L.) is the second most-consumed vegetable in the world. The market value and culinary purpose of tomato are often determined by fruit size and shape, which makes the genetic improvement of these traits a priority for tomato breeders. The main objective of the study was to detect quantitative trait loci (QTL) associated with the tomato fruit shape and size. The use of elite breeding materials in the genetic mapping studies will facilitate the detection of genetic loci of direct relevance to breeders. We performed QTL analysis in an intra-specific population of tomato developed from a cross between two elite breeding lines NC 30P × NC-22L-1(2008) consisting of 110 recombinant inbred lines (RIL). The precision software Tomato Analyzer (TA) was used to measure fruit morphology attributes associated with fruit shape and size traits. The RIL population was genotyped with the SolCAP 7720 SNP array. We identified novel QTL controlling elongated fruit shape on chromosome 10, explaining up to 24% of the phenotypic variance. This information will be useful in improving tomato fruit morphology traits.

Download Full-text