A PCR-based marker closely linked to a 2BS QTL conferring wheat yellow spot resistance for marker-assisted breeding

2016 ◽  
Vol 67 (7) ◽  
pp. 719
Author(s):  
Fei Ren ◽  
Jun Ji ◽  
Hui Liu ◽  
Martin J. Barbetti ◽  
Kadambot H. M. Siddique ◽  
...  
Keyword(s):  
Large Scale ◽  
Wheat Chromosome ◽  
Wheat Breeding ◽  
Yellow Spot ◽  
Phenotypic Variance ◽  
Pyrenophora Tritici Repentis ◽  
Trait Locus ◽  
User Friendly ◽  
Suitable Marker ◽  
Major Qtl

Yellow spot (caused by Pyrenophora tritici-repentis) is a major foliar disease in wheat (Triticum aestivum) that has become more serious in recent years, possibly because of climate change. A major quantitative trait locus (QTL) located on the short arm of wheat chromosome 2B explaining 30–40% of the phenotypic variance has been identified as responsible for resistance to Australian yellow spot isolates, which reportedly produce mostly the ToxA effector. The closest marker linked to this QTL was a DArT marker not easy to use in large-scale selections, whereas the closest PCR-based marker available (2.7 cM) was too far away for reliably tagging the locus in wheat breeding. We therefore undertook studies to develop more closely linked and user-friendly markers for this major QTL. Forty-one new markers either synthesised from DArT markers or identified from the GrainGene database were assessed. From these, we developed a new PCR-based marker (Rfsts1), located 0.3 cM away from the major QTL. This is the first suitable marker for marker-assisted selection for yellow spot resistance in Australian wheat-breeding programs.

scholarly journals QTL Mapping and Prediction of Haploid Male Fertility Traits in Maize (Zea mays L.)

Plants ◽  
2020 ◽  
Vol 9 (7) ◽  
pp. 836
Author(s):  
Yanyan Jiao ◽  
Jinlong Li ◽  
Wei Li ◽  
Ming Chen ◽  
Mengran Li ◽  
...  
Keyword(s):  
Male Fertility ◽  
Large Scale ◽  
Chromosome Doubling ◽  
Limiting Factor ◽  
Phenotypic Variance ◽  
Haploid Male ◽  
Haploid Population ◽  
Trait Locus ◽  
Dh Lines ◽  
Major Qtl

Chromosome doubling of maize haploids is a bottleneck in the large-scale application of doubled haploid (DH) technology. Spontaneous chromosome doubling (SCD) of haploid has been taken as an important method in the production of DH lines and low haploid male fertility (HMF) is a main limiting factor for the use of SCD. To study its genetic basis, haploids of 119 DH lines derived from a cross between inbred lines Qi319 and Chang7-2 were used to map the quantitative trait locus (QTL) contributing to HMF. Three traits including anther emergence rate (AER), anther emergence score (AES) and pollen production score (PPS) of the haploid population were evaluated at two locations. The heritability of the three traits ranged from 0.70 to 0.81. The QTL contributing to AER, AES and PPS were identified on the chromosomes 1, 2, 3, 4, 5, 7, 9 and 10. Five major QTL, qAER5-1, qAER5-2, qAES3, qPPS1 and qPPS5, were found and each could explain more than 15% of the phenotypic variance at least in one environment. Two major QTL, qPPS1 and qPPS5, and two minor QTL, qAES2 and qAER3, were repeatedly detected at both locations. To increase the application efficiency of HMF in breeding programs, genomic prediction for the three traits were carried out with ridge regression best linear unbiased prediction (rrBLUP) and rrBLUP adding QTL effects (rrBLUP-QTL). The prediction accuracies of rrBLUP-QTL were significantly higher than that by rrBLUP for three traits (p < 0.001), which indirectly indicates these QTL were effective. The prediction accuracies for PPS were 0.604 (rrBLUP) and 0.703 (rrBLUP-QTL) across both locations, which were higher than that of AER and AES. Overall, this study provides important information to understand the genetic architecture of SCD of maize haploids.

scholarly journals Inferring Linkage Disequilibrium Between a Polymorphic Marker Locus and a Trait Locus in Natural Populations

Genetics ◽  
2000 ◽  
Vol 156 (1) ◽  
pp. 457-467 ◽  
Author(s):  
Z W Luo ◽  
S H Tao ◽  
Z-B Zeng
Keyword(s):  
Linkage Disequilibrium ◽  
Allele Frequency ◽  
Random Mating ◽  
Natural Populations ◽  
Polymorphic Marker ◽  
Marker Locus ◽  
Model Parameters ◽  
Phenotypic Variance ◽  
Wide Range ◽  
Trait Locus

Abstract Three approaches are proposed in this study for detecting or estimating linkage disequilibrium between a polymorphic marker locus and a locus affecting quantitative genetic variation using the sample from random mating populations. It is shown that the disequilibrium over a wide range of circumstances may be detected with a power of 80% by using phenotypic records and marker genotypes of a few hundred individuals. Comparison of ANOVA and regression methods in this article to the transmission disequilibrium test (TDT) shows that, given the genetic variance explained by the trait locus, the power of TDT depends on the trait allele frequency, whereas the power of ANOVA and regression analyses is relatively independent from the allelic frequency. The TDT method is more powerful when the trait allele frequency is low, but much less powerful when it is high. The likelihood analysis provides reliable estimation of the model parameters when the QTL variance is at least 10% of the phenotypic variance and the sample size of a few hundred is used. Potential use of these estimates in mapping the trait locus is also discussed.

scholarly journals Linkage mapping identifies a non-synonymous mutation in FLOWERING LOCUS T (FT-B1) increasing spikelet number per spike

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jonathan Brassac ◽  
Quddoos H. Muqaddasi ◽  
Jörg Plieske ◽  
Martin W. Ganal ◽  
Marion S. Röder
Keyword(s):  
Flowering Time ◽  
Aspartic Acid ◽  
Synonymous Substitution ◽  
Minor Effect ◽  
Phenotypic Variance ◽  
Spikelet Number ◽  
Wheat Varieties ◽  
Trait Locus ◽  
A Minor ◽  
Spikelet Number Per Spike

AbstractTotal spikelet number per spike (TSN) is a major component of spike architecture in wheat (Triticumaestivum L.). A major and consistent quantitative trait locus (QTL) was discovered for TSN in a doubled haploid spring wheat population grown in the field over 4 years. The QTL on chromosome 7B explained up to 20.5% of phenotypic variance. In its physical interval (7B: 6.37–21.67 Mb), the gene FLOWERINGLOCUST (FT-B1) emerged as candidate for the observed effect. In one of the parental lines, FT-B1 carried a non-synonymous substitution on position 19 of the coding sequence. This mutation modifying an aspartic acid (D) into a histidine (H) occurred in a highly conserved position. The mutation was observed with a frequency of ca. 68% in a set of 135 hexaploid wheat varieties and landraces, while it was not found in other plant species. FT-B1 only showed a minor effect on heading and flowering time (FT) which were dominated by a major QTL on chromosome 5A caused by segregation of the vernalization gene VRN-A1. Individuals carrying the FT-B1 allele with amino acid histidine had, on average, a higher number of spikelets (15.1) than individuals with the aspartic acid allele (14.3) independent of their VRN-A1 allele. We show that the effect of TSN is not mainly related to flowering time; however, the duration of pre-anthesis phases may play a major role.

scholarly journals Genetic architecture underlying the expression of eight α-amylase trypsin inhibitors

2021 ◽  
Author(s):  
Khaoula EL Hassouni ◽  
Malte Sielaff ◽  
Valentina Curella ◽  
Manjusha Neerukonda ◽  
Willmar Leiser ◽  
...  
Keyword(s):  
Genetic Architecture ◽  
Intestinal Inflammation ◽  
Wheat Breeding ◽  
Trypsin Inhibitors ◽  
Potential Candidate ◽  
Lipid Transfer ◽  
Wheat Cultivars ◽  
Genome Wide ◽  
Close Physical Proximity ◽  
Major Qtl

Abstract Key message Wheat cultivars largely differ in the content and composition of ATI proteins, but heritability was quite low for six out of eight ATIs. The genetic architecture of ATI proteins is built up of few major and numerous small effect QTL. Abstract Amylase trypsin inhibitors (ATIs) are important allergens in baker’s asthma and suspected triggers of non-celiac wheat sensitivity (NCWS) inducing intestinal and extra-intestinal inflammation. As studies on the expression and genetic architecture of ATI proteins in wheat are lacking, we evaluated 149 European old and modern bread wheat cultivars grown at three different field locations for their content of eight ATI proteins. Large differences in the content and composition of ATIs in the different cultivars were identified ranging from 3.76 pmol for ATI CM2 to 80.4 pmol for ATI 0.19, with up to 2.5-fold variation in CM-type and up to sixfold variation in mono/dimeric ATIs. Generally, heritability estimates were low except for ATI 0.28 and ATI CM2. ATI protein content showed a low correlation with quality traits commonly analyzed in wheat breeding. Similarly, no trends were found regarding ATI content in wheat cultivars originating from numerous countries and decades of breeding history. Genome-wide association mapping revealed a complex genetic architecture built of many small, few medium and two major quantitative trait loci (QTL). The major QTL were located on chromosomes 3B for ATI 0.19-like and 6B for ATI 0.28, explaining 70.6 and 68.7% of the genotypic variance, respectively. Within close physical proximity to the medium and major QTL, we identified eight potential candidate genes on the wheat reference genome encoding structurally related lipid transfer proteins. Consequently, selection and breeding of wheat cultivars with low ATI protein amounts appear difficult requiring other strategies to reduce ATI content in wheat products.

Microcomputer Simulations of Presidential Elections

1983 ◽  
Vol 38 ◽  
pp. 20-20
Author(s):  
Robert S. Ross
Keyword(s):  
Social Sciences ◽  
Large Scale ◽  
Role Playing ◽  
Science Students ◽  
Instructional Programs ◽  
Santa Barbara ◽  
Large Scale Systems ◽  
The Social ◽  
User Friendly ◽  
Machine Interaction

Simulations have been an important adjunct to instructional programs for some time. These have ranged from games, or role playing exercises, such as SIMSOC or Internation Simulation, to student-machine interaction, such as the inter-school simulation run out of University of California, Santa Barbara in the early 70's, to the all machine activities found in some of the early SETUPS. Having social science students use the mainframe computer, however, always posed problems: it definitely was not user-friendly and most instructors had little if any training or interest in the use of large scale systems.The wide-spread use of the micro computer is not only revolutionizing areas traditionally relying upon the computer, but is going to have an impact on the social sciences as well.

scholarly journals Genetic variation in recombination rate in the pig

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Martin Johnsson ◽  
Andrew Whalen ◽  
Roger Ros-Freixedes ◽  
Gregor Gorjanc ◽  
Ching-Yi Chen ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Recombination Rate ◽  
Large Scale ◽  
Genome Wide Association Study ◽  
Genetic Material ◽  
A Genome ◽  
Pig Genome ◽  
Genetic Length ◽  
Trait Locus ◽  
Genomic Regions

Abstract Background Meiotic recombination results in the exchange of genetic material between homologous chromosomes. Recombination rate varies between different parts of the genome, between individuals, and is influenced by genetics. In this paper, we assessed the genetic variation in recombination rate along the genome and between individuals in the pig using multilocus iterative peeling on 150,000 individuals across nine genotyped pedigrees. We used these data to estimate the heritability of recombination and perform a genome-wide association study of recombination in the pig. Results Our results confirmed known features of the recombination landscape of the pig genome, including differences in genetic length of chromosomes and marked sex differences. The recombination landscape was repeatable between lines, but at the same time, there were differences in average autosome-wide recombination rate between lines. The heritability of autosome-wide recombination rate was low but not zero (on average 0.07 for females and 0.05 for males). We found six genomic regions that are associated with recombination rate, among which five harbour known candidate genes involved in recombination: RNF212, SHOC1, SYCP2, MSH4 and HFM1. Conclusions Our results on the variation in recombination rate in the pig genome agree with those reported for other vertebrates, with a low but nonzero heritability, and the identification of a major quantitative trait locus for recombination rate that is homologous to that detected in several other species. This work also highlights the utility of using large-scale livestock data to understand biological processes.

scholarly journals Genetic Mechanisms Underlying Apimaysin and Maysin Synthesis and Corn Earworm Antibiosis in Maize (Zea mays L.)

Genetics ◽  
1998 ◽  
Vol 149 (4) ◽  
pp. 1997-2006
Author(s):  
E A Lee ◽  
P F Byrne ◽  
M D McMullen ◽  
M E Snook ◽  
B R Wiseman ◽  
...  
Keyword(s):  
Helicoverpa Zea ◽  
Larval Growth ◽  
Corn Earworm ◽  
Phenotypic Variance ◽  
Significant Qtls ◽  
F2 Population ◽  
Genetic Mechanisms ◽  
Trait Locus ◽  
Maize Silks ◽  
Related Compounds

Abstract C-glycosyl flavones in maize silks confer resistance (i.e., antibiosis) to corn earworm (Helicoverpa zea [Boddie]) larvae and are distinguished by their B-ring substitutions, with maysin and apimaysin being the di- and monohydroxy B-ring forms, respectively. Herein, we examine the genetic mechanisms underlying the synthesis of maysin and apimaysin and the corresponding effects on corn earworm larval growth. Using an F2 population, we found a quantitative trait locus (QTL), rem1, which accounted for 55.3% of the phenotypic variance for maysin, and a QTL, pr1, which explained 64.7% of the phenotypic variance for apimaysin. The maysin QTL did not affect apimaysin synthesis, and the apimaysin QTL did not affect maysin synthesis, suggesting that the synthesis of these closely related compounds occurs independently. The two QTLs, rem1 and pr1, were involved in a significant epistatic interaction for total flavones, suggesting that a ceiling exists governing the total possible amount of C-glycosyl flavone. The maysin and apimaysin QTLs were significant QTLs for corn earworm antibiosis, accounting for 14.1% (rem1) and 14.7% (pr1) of the phenotypic variation. An additional QTL, represented by umc85 on the short arm of chromosome 6, affected antibiosis (R2 = 15.2%), but did not affect the synthesis of the C-glycosyl flavones.

scholarly journals fastER: a user-friendly tool for ultrafast and robust cell segmentation in large-scale microscopy

2017 ◽  
Vol 33 (13) ◽  
pp. 2020-2028 ◽  
Author(s):  
Oliver Hilsenbeck ◽  
Michael Schwarzfischer ◽  
Dirk Loeffler ◽  
Sotiris Dimopoulos ◽  
Simon Hastreiter ◽  
...  
Keyword(s):  
Large Scale ◽  
Cell Segmentation ◽  
User Friendly

Rapid identification of a stripe rust resistance gene YrXK in Chinese wheat line Xike01015 using specific locus amplified fragment (SLAF) sequencing

Plant Disease ◽  
2021 ◽  
Author(s):  
Cai Sun ◽  
Yike Liu ◽  
Qiang Li ◽  
Baotong Wang ◽  
Shuhui Chen ◽  
...  
Keyword(s):  
Stripe Rust ◽  
Puccinia Striiformis ◽  
Gene Annotation ◽  
Dominant Gene ◽  
Rapid Identification ◽  
Wheat Breeding ◽  
Stripe Rust Resistance ◽  
Phenotypic Variance ◽  
F2 Population ◽  
Chinese Wheat

Wheat stripe rust, an airborne fungal disease and caused by Puccinia striiformis Westend. f. sp. tritici (Pst), is one of the most devastating diseases on wheat. It is the most effective and economical measure for the diseases control to identify high-level resistance genes and apply in wheat breeding. Chinese wheat cultivar Xike01015 presents high levels of all stage resistance (ASR) to the current predominant Pst race CYR33. In this study, a single dominant gene, designated as YrXk, was identified in Xike01015 conferring resistance to CYR33 with genetic analysis of F2 and BC1 population from cross of Mingxian169 (susceptible) and Xike01015. The specific length amplified fragment sequencing (SLAF-seq) strategy was used to construct linkage map in the F2 population. QTL analysis mapped YrXk to a 12.4 Mb segment on chromosome1BS, explaining over 86.96% phenotypic variance. Gene annotation in the QTL region identified three differential expressed candidate genes , TraesCS1B02G168600.1, TraesCS1B02G170200.1, and TraesCS1B02G172400.1. The qRT-PCR results displayed that TraesCS1B02G170200.1 and TraesCS1B02G168600.1 significantly up-regulated and down-regulated, respectively, and TraesCS1B02G170200.1 slightly up-regulated after changed with CYR33 in the seedling stage, which indicating these genes may function in wheat resistance to stripe rust. The results of this study can be used in wheat breeding for improving resistance to stripe rust.

scholarly journals Relationship between Yield Components and Partial Resistance to Lecanicillium fungicola in the Button Mushroom, Agaricus bisporus, Assessed by Quantitative Trait Locus Mapping

2012 ◽  
Vol 78 (7) ◽  
pp. 2435-2442 ◽  
Author(s):  
Marie Foulongne-Oriol ◽  
Anne Rodier ◽  
Jean-Michel Savoie
Keyword(s):  
Quantitative Trait ◽  
Wild Strain ◽  
Genomic Region ◽  
Yield Component ◽  
Phenotypic Variance ◽  
Button Mushroom ◽  
Content Type ◽  
Dry Bubble ◽  
Trait Locus ◽  
Genomic Regions

ABSTRACTDry bubble, caused byLecanicillium fungicola, is one of the most detrimental diseases affecting button mushroom cultivation. In a previous study, we demonstrated that breeding for resistance to this pathogen is quite challenging due to its quantitative inheritance. A second-generation hybrid progeny derived from an intervarietal cross between a wild strain and a commercial cultivar was characterized forL. fungicolaresistance under artificial inoculation in three independent experiments. Analysis of quantitative trait loci (QTL) was used to determine the locations, numbers, and effects of genomic regions associated with dry-bubble resistance. Four traits related to resistance were analyzed. Two to four QTL were detected per trait, depending on the experiment. Two genomic regions, on linkage group X (LGX) and LGVIII, were consistently detected in the three experiments. The genomic region on LGX was detected for three of the four variables studied. The total phenotypic variance accounted for by all QTL ranged from 19.3% to 42.1% over all traits in all experiments. For most of the QTL, the favorable allele for resistance came from the wild parent, but for some QTL, the allele that contributed to a higher level of resistance was carried by the cultivar. Comparative mapping with QTL for yield-related traits revealed five colocations between resistance and yield component loci, suggesting that the resistance results from both genetic factors and fitness expression. The consequences for mushroom breeding programs are discussed.

Sign in / Sign up

Export Citation Format

Share Document