scholarly journals QTL detection of yield-related traits of cashew

2012 ◽  
Vol 12 (1) ◽  
pp. 60-66 ◽  
Author(s):  
José Jaime Vasconcelos Cavalcanti ◽  
Francisco Herbeth Costa dos Santos ◽  
Fanuel Pereira da Silva ◽  
Cássia Renata Pinheiro
Keyword(s):  
Quantitative Trait ◽  
Marker Assisted Selection ◽  
Interval Mapping ◽  
Phenotypic Variance ◽  
Qtl Detection ◽  
Total Phenotypic Variance ◽  
Breeding Programs ◽  
Multiple Qtl ◽  
Male Flowers ◽  
Selection Of

The identification of quantitative trait loci (QTL) and marker-assisted selection with a view to breeding programs have aroused great interest, including for cashew improvement. This study identified QTL for yield-related traits: nut weight, male and hermaphrodite flowers. The traits were evaluated in 71 F1 genotypes of the cross CCP 1001 x CP 96. The methods of interval mapping and multiple QTL mapping were applied to identify QTL. Eleven QTL were detected: three for nut weight, four for male flowers and four for hermaphrodite flowers. The QTL accounted for 3.79 to 12.98 % of the total phenotypic variance and had phenotypic effects of -31.81 to 34.25 %. The potential for marker-assisted selection of the QTL hf-2f and hf-3m is great and the phenotypic effects and percentage of phenotypic variation higher than of the others.

scholarly journals Mapping QTL for spike fertility and related traits in two doubled haploid wheat (Triticum aestivum L.) populations

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Nicole Pretini ◽  
Leonardo S. Vanzetti ◽  
Ignacio I. Terrile ◽  
Guillermo Donaire ◽  
Fernanda G. González
Keyword(s):  
Doubled Haploid ◽  
Marker Assisted Selection ◽  
Triticum Aestivum L ◽  
Physiological Model ◽  
Yield Potential ◽  
Breeding Programs ◽  
Per Se ◽  
Genomic Regions ◽  
Fertility Traits ◽  
Selection Of

Abstract Background In breeding programs, the selection of cultivars with the highest yield potential consisted in the selection of the yield per se, which resulted in cultivars with higher grains per spike (GN) and occasionally increased grain weight (GW) (main numerical components of the yield). In this study, quantitative trait loci (QTL) for GW, GN and spike fertility traits related to GN determination were mapped using two doubled haploid (DH) populations (Baguette Premium 11 × BioINTA 2002 and Baguette 19 × BioINTA 2002). Results In total 305 QTL were identified for 14 traits, out of which 12 QTL were identified in more than three environments and explained more than 10% of the phenotypic variation in at least one environment. Eight hotspot regions were detected on chromosomes 1A, 2B, 3A, 5A, 5B, 7A and 7B in which at least two major and stable QTL sheared confidence intervals. QTL on two of these regions (R5A.1 and R5A.2) have previously been described, but the other six regions are novel. Conclusions Based on the pleiotropic analysis within a robust physiological model we conclude that two hotspot genomic regions (R5A.1 and R5A.2) together with the QGW.perg-6B are of high relevance to be used in marker assisted selection in order to improve the spike yield potential. All the QTL identified for the spike related traits are the first step to search for their candidate genes, which will allow their better manipulation in the future.

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

Genetics ◽  
1999 ◽  
Vol 153 (3) ◽  
pp. 1233-1243 ◽  
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.

scholarly journals Short communication: QTL mapping for ear tip-barrenness in maize

2016 ◽  
Vol 14 (3) ◽  
pp. e07SC01 ◽  
Author(s):  
Junqiang Ding ◽  
Jinliang Ma ◽  
Jiafa Chen ◽  
Tangshun Ai ◽  
Zhimin Li ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Genetic Basis ◽  
Mixed Model ◽  
Short Communication ◽  
Genotypic Variation ◽  
Interval Mapping ◽  
Mapping Method ◽  
Additive Effects ◽  
Breeding Programs ◽  
Model Composite

Barren tip on corn ear is an important agronomic trait in maize, which is highly associated with grain yield. Understanding the genetic basis of tip-barrenness may help to reduce the ear tip-barrenness in breeding programs. In this study, ear tip-barrenness was evaluated in two environments in a F2:3 population, and it showed significant genotypic variation for ear tip-barrenness in both environments. Using mixed-model composite interval mapping method, three additive effects quantitative trait loci (QTL) for ear tip-barrenness were mapped on chromosomes 2, 3 and 6, respectively. They explained 16.6% of the phenotypic variation, and no significant QTL × Environment interactions and digenic interactions were detected. The results indicated that additive effect was the main genetic basis for ear tip-barrenness in maize. This is the first report of QTL mapped for ear tip-barrenness in maize.

Microsatellite markers linked to QTL for resistance to Mal de Río Cuarto disease in Zea mays L.

2004 ◽  
Vol 142 (3) ◽  
pp. 289-295 ◽  
Author(s):  
M. A. DI RENZO ◽  
N. C. BONAMICO ◽  
D. G. DÍAZ ◽  
M. A. IBAÑEZ ◽  
M. E. FARICELLI ◽  
...  
Keyword(s):  
Zea Mays ◽  
Inbred Line ◽  
Quantitative Trait ◽  
Dominant Gene ◽  
Phenotypic Selection ◽  
Severity Index ◽  
Viral Disease ◽  
Interval Mapping ◽  
Phenotypic Variance ◽  
Ssr Loci

‘Mal de Río Cuarto’ (MRC) disease, caused by a member of the family Reoviridae belonging to the genus Fijivirus, is considered to be the most damaging viral disease of maize (Zea mays L.) in Argentina. Resistance to MRC disease is a quantitative trait with moderate heritability ranging from 0·44 to 0·56. The objective of this study was to identify simple sequence repeats (SSR) loci linked to quantitative trait loci (QTL) contributing to MRC disease resistance. Two hundred and twenty-seven F3 derived-lines from a cross between a susceptible inbred line, Mo17, and a partially resistant inbred line, BLS14, were evaluated across four Río Cuarto environments. A disease severity index (DSI) based on disease grades was calculated and used to rate F3 derived-lines for their resistance to MRC disease. A subset of parental F2 plants belonging to susceptible and resistant F3 derived-lines from field assessments was assayed for 180 SSR primer pairs to map resistance genes. Fifty-six maize SSR were employed for the testing of linkage among DNA markers and the mapping of QTL through composite interval mapping. Resistance to MRC disease was affected by two QTL on chromosomes 1 and 8 which showed overdominance and dominant gene action, respectively. A simultaneous fit with these QTL in the joint analyses explained 36·2% of the phenotypic variance. In spite of the fact that relative efficiency of marker-assisted selection (MAS) in comparison to phenotypic selection was close to 1, the mapped QTL could improve the efficiency of efforts in breeding for resistance to MRC disease.

Comparison of deterministic and stochastic methods of calculating identity-by-descent matrices using multiple markers

2002 ◽  
Vol 2002 ◽  
pp. 56-56
Author(s):  
A.C. Sørensen ◽  
R. Pong-Wong ◽  
J.J. Windig ◽  
J.A. Woolliams
Keyword(s):  
Monte Carlo ◽  
Marker Assisted Selection ◽  
Interval Mapping ◽  
Stochastic Methods ◽  
Qtl Detection ◽  
Identity By Descent ◽  
Deterministic Method ◽  
Practical Applications ◽  
Breeding Schemes ◽  
Computationally Expensive

Identity-by-descent (IBD) matrices are used for a number of practical applications, e.g. QTL-detection, marker assisted selection in breeding schemes (MAS), refining of covariances among relatives, and MAS for maintaining genetic variation. The calculation of IBD matrices can be made using Markov Chain Monte Carlo (MCMC). However, this is a computationally expensive method. Therefore, a simple deterministic method (Det) has been developed (Pong-Wong et al., 2001). The objective of this study is to evaluate this deterministic method relative to MCMC for the precision of the matrices and their performance in interval mapping and MAS.

scholarly journals Non-parametric interval mapping in half-sib designs: use of midranks to account for ties

2003 ◽  
Vol 81 (3) ◽  
pp. 221-228 ◽  
Author(s):  
P. TILQUIN ◽  
I. VAN KEILEGOM ◽  
W. COPPIETERS ◽  
E. LE BOULENGÉ ◽  
P. V. BARET
Keyword(s):  
Disease Resistance ◽  
Infectious Diseases ◽  
Qtl Analysis ◽  
Statistical Power ◽  
Interval Mapping ◽  
Phenotypic Variance ◽  
Total Phenotypic Variance ◽  
Non Parametric ◽  
Normally Distributed

In QTL analysis of non-normally distributed phenotypes, non-parametric approaches have been proposed as an alternative to the use of parametric tests on mathematically transformed data. The non-parametric interval mapping test uses random ranking to deal with ties. Another approach is to assign to each tied individual the average of the tied ranks (midranks). This approach is implemented and compared to the random ranking approach in terms of statistical power and accuracy of the QTL position. Non-normal phenotypes such as bacteria counts showing high numbers of zeros are simulated (0–80% zeros). We show that, for low proportions of zeros, the power estimates are similar but, for high proportions of zeros, the midrank approach is superior to the random ranking approach. For example, with a QTL accounting for 8% of the total phenotypic variance, a gain from 8% to 11% of power can be obtained. Furthermore, the accuracy of the estimated QTL location is increased when using midranks. Therefore, if non-parametric interval mapping is chosen, the midrank approach should be preferred. This test might be especially relevant for the analysis of disease resistance phenotypes such as those observed when mapping QTLs for resistance to infectious diseases.

Mapping quantitative trait loci for pre-harvest sprouting resistance in white-grained winter wheat line CA 0431

2013 ◽  
Vol 64 (6) ◽  
pp. 573 ◽  
Author(s):  
X. L. Miao ◽  
Y. J. Zhang ◽  
X. C. Xia ◽  
Z. H. He ◽  
Y. Zhang ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Winter Wheat ◽  
Quantitative Trait ◽  
Interval Mapping ◽  
Field Trials ◽  
Economic Losses ◽  
Phenotypic Variance ◽  
Wheat Line ◽  
F2 Population ◽  
Trait Loci

Pre-harvest sprouting (PHS) in wheat severely reduces yield and end-use quality, resulting in substantial economic losses. The Chinese winter wheat line CA 0431, with white grain, showed high PHS resistance for many years. To identify quantitative trait loci (QTLs) of PHS resistance in this line, 220 F2 plants and the corresponding F2 : 3 lines derived from a cross between CA 0431 and the PHS-susceptible cultivar Zhongyou 206 were used for PHS testing and QTL analysis. Field trials were conducted in Beijing during the 2010–11 and 2011–12 cropping seasons, and in Anyang during 2011–12. PHS resistance was evaluated by assessing the sprouting responses of intact spikes. In total, 1444 molecular markers were used to screen the parents, and 31 markers with polymorphisms between the resistant and susceptible bulks were used to genotype the entire F2 population. Broad-sense heritability of sprouting rate was 0.71 across environments. Inclusive composite interval mapping identified four QTLs, QPhs.caas-2BL, QPhs.caas-3AS.1, QPhs.caas-3AS.2, and QPhs.caas-3AL, each explaining 2.8–27.7% of the phenotypic variance across environments. The QTLs QPhs.caas-3AS.1, QPhs.caas-3AS.2, and QPhs.caas-3AL were located at similar positions to QTLs reported previously, whereas QPhs.caas-2BL is likely a new QTL flanked by markers Xbarc1042 and Xmag3319. Line CA 0431 and the identified markers can be used in breeding programs targeting improvement of PHS resistance for white-kernel wheat.

scholarly journals Inferences regarding the numbers and locations of QTLs under multiple-QTL models using interval mapping and composite interval mapping

2003 ◽  
Vol 82 (2) ◽  
pp. 139-149 ◽  
Author(s):  
THEODORE W. CORNFORTH ◽  
ANTHONY D. LONG
Keyword(s):  
Simulation Study ◽  
Quantitative Trait ◽  
Composite Interval Mapping ◽  
Genetic Architecture ◽  
Interval Mapping ◽  
Summary Statistics ◽  
Precise Estimation ◽  
Multiple Qtl ◽  
Complex Architectures ◽  
Erroneous Inferences

This paper examines the properties of likelihood maps generated by interval mapping (IM) and composite interval mapping (CIM), two widely used methods for detecting quantitative trait loci (QTLs). We evaluate the usefulness of interpretations of entire maps, rather than only evaluating summary statistics that consider isolated features of maps. A simulation study was performed in which traits with varying genetic architectures, including 20–40 QTLs per chromosome, were examined with both IM and CIM under different marker densities and sample sizes. IM was found to be an unreliable tool for precise estimation of the number and locations of individual QTLs, although it has greater power for simply detecting the presence of QTLs than CIM. The ability of CIM to resolve the correct number of QTLs and to estimate their locations correctly is good if there are three or fewer QTLs per 100 centiMorgans, but can lead to erroneous inferences for more complex architectures. When the underlying genetic architecture of a trait consists of several QTLs with randomly distributed effects and locations likelihood profiles were often indicative of a few underlying genes of large effect. Studies that have detected more than a few QTLs per chromosome should be interpreted with caution.

scholarly journals Selection of powdery mildew resistant and susceptible grapevine genotypes with molecular markers

2007 ◽  
pp. 100-104
Author(s):  
Stella Molnár ◽  
Zsuzsanna Galbács ◽  
Gábor Halász ◽  
Sarolta Hoffmann ◽  
Anikó Veres ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Powdery Mildew ◽  
Marker Assisted Selection ◽  
Powdery Mildew Resistance ◽  
Resistance Breeding ◽  
Breeding Programs ◽  
Pcr Rflp ◽  
Muscadinia Rotundifolia ◽  
Selection Of ◽  
Grape Breeding

Incorporation of competitive quality and resistance against the most important fungal diseases (powdery and downy mildew) in a cultivar is one of the most important aims of grapevine breeding. In the 20th century, the most advanced results in grapevine resistance breeding were achieved by French researchers. They used resistant cultivars in more than 30% of their growing areas. In these varieties, North American wild Vitisspecies were the resistance gene sources. The discovery of immunity-like resistance of Muscadinia rotundifolia opened new perspectives in resistance breeding. M. rotundifolia harbours a dominant powdery mildew gene, providing resistance in highquality cultivars after back-crosses with V. vinifera varieties. M. rotundifolia has been involved in the Hungarian grape breeding programs since 1996, thanks to a French-Hungarian variety exchange. In addition to traditional selection methods, application of MAS (Marker Assisted Selection) based on various types ofmolecular markers, can provide additional tools for these efforts. Run1 locus, responsible for powdery mildew resistance, was identified in Muscadinia rotundifolia. Molecular markers closely linked to this locus are very significant in screening progenies deriving from M. rotundifolia and V. vinifera crosses, making possible the discrimination between resistant and susceptible genotypes at DNA level. In our analyses BC5 progeny of {(M. rotundifola×V. vinifera) BC4}×Cardinal (V. vinifera) tested for powdery symptoms were analysed with PCR-RFLP (GLP1- 12P1P3) and microsatellite markers (VMC4f3.1, VMC8g9). Our results proved the applicability of the linked markers and reliability of marker assisted selection.

Sign in / Sign up

Export Citation Format

Share Document