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.

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 Mapping Quantitative Trait Loci for 1000-Grain Weight in a Double Haploid Population of Common Wheat

2020 ◽  
Vol 21 (11) ◽  
pp. 3960 ◽  
Author(s):  
Tao Liu ◽  
Lijun Wu ◽  
Xiaolong Gan ◽  
Wenjie Chen ◽  
Baolong Liu ◽  
...  
Keyword(s):  
Quantitative Trait ◽  
Genetic Distances ◽  
Snp Markers ◽  
Grain Weight ◽  
High Yield ◽  
Doubled Haploid Population ◽  
Phenotypic Variance ◽  
Yield Trait ◽  
Haploid Population ◽  
Trait Locus

Thousand-grain weight (TGW) is a very important yield trait of crops. In the present study, we performed quantitative trait locus (QTL) analysis of TGW in a doubled haploid population obtained from a cross between the bread wheat cultivar “Superb” and the breeding line “M321” using the wheat 55-k single-nucleotide polymorphism (SNP) genotyping assay. A genetic map containing 15,001 SNP markers spanning 2209.64 cM was constructed, and 9 QTLs were mapped to chromosomes 1A, 2D, 4B, 4D, 5A, 5D, 6A, and 6D based on analyses conducted in six experimental environments during 2015–2017. The effects of the QTLs qTgw.nwipb-4DS and qTgw.nwipb-6AL were shown to be strong and stable in different environments, explaining 15.31–32.43% and 21.34–29.46% of the observed phenotypic variance, and they were mapped within genetic distances of 2.609 cM and 5.256 cM, respectively. These novel QTLs may be used in marker-assisted selection in wheat high-yield breeding.

scholarly journals Diallelic Analysis of Tropical Maize Germplasm Response to Spontaneous Chromosomal Doubling

Plants ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1224
Author(s):  
Vijay Chaikam ◽  
Manje Gowda ◽  
Leocadio Martinez ◽  
Gregório Alvarado Beltrán ◽  
Xuecai Zhang ◽  
...  
Keyword(s):  
Chromosome Doubling ◽  
Reproductive Organs ◽  
Hybrid Performance ◽  
Maize Breeding ◽  
F1 Hybrid ◽  
Maize Germplasm ◽  
Genetic Components ◽  
Maize Genotypes ◽  
Haploid Male ◽  
Dh Lines

Chromosome doubling is an important step in the production of maize doubled haploid (DH) lines to induce fertility in the male and female reproductive organs of haploid plants. Chromosomal doubling is routinely accomplished by treating haploid seedlings with mitosis-inhibiting chemicals. However, chromosomal doubling involves several labor-intensive steps and toxic chemicals. Spontaneous chromosomal doubling without any chemical treatments occurs at high frequency in haploids from a few maize genotypes. This study focused on elucidating the genetic components of two traits important for using spontaneous doubling in maize-breeding programs, namely, haploid male fertility (HMF) and haploid fertility (HF). In two different sets of diallel crosses, haploids were derived and assessed for HMF and HF in two environments in replicated trials. The results revealed significant genotypic variations for both traits. The general combining ability (GCA) and specific combining (SCA) were significant for both traits. Significant and positive GCA effects of up to 14% and 9% were found for HMF and HF, respectively. No significant reciprocal effects and genotype-by-environment (G×E) interactions were found for HF in both experiments, but HMF showed significant effects for both in one of the experiments. The GCA effects were more important than the SCA effects for HMF and HF across environments, implying that selection could facilitate their improvement. The high correlations between F1-hybrid performance and mid-parent values, as well as that between F1-hybrid performance and GCA effects, also supports the assumption that these traits are controlled by a few genes. SCA effects also played a role, especially when lines with low spontaneous doubling were used as parents. Overall, spontaneous doubling can be introgressed and improved in elite germplasm with selection, and it has the potential to be employed in DH pipelines.

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.

Current State of (Dis)Integration: Public Health and Fusion Centers

2020 ◽  
Vol 17 (2) ◽  
Author(s):  
Cody Minks ◽  
Anke Richter
Keyword(s):  
Public Health ◽  
Law Enforcement ◽  
Information Sharing ◽  
Homeland Security ◽  
Large Scale ◽  
Ad Hoc ◽  
Limiting Factor ◽  
Fusion Centers ◽  
Public Health Emergencies ◽  
Public Health Information

AbstractObjectiveResponding to large-scale public health emergencies relies heavily on planning and collaboration between law enforcement and public health officials. This study examines the current level of information sharing and integration between these domains by measuring the inclusion of public health in the law enforcement functions of fusion centers.MethodsSurvey of all fusion centers, with a 29.9% response rate.ResultsOnly one of the 23 responding fusion centers had true public health inclusion, a decrease from research conducted in 2007. Information sharing is primarily limited to information flowing out of the fusion center, with little public health information coming in. Most of the collaboration is done on a personal, informal, ad-hoc basis. There remains a large misunderstanding of roles, capabilities, and regulations by all parties (fusion centers and public health). The majority of the parties appear to be willing to work together, but there but there is no forward momentum to make these desires a reality. Funding and staffing issues seem to be the limiting factor for integration.ConclusionThese problems need to be urgently addressed to increase public health preparedness and enable a decisive and beneficial response to public health emergencies involving a homeland security response.

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.

Towards A Multi-FPGA Infrared Simulator

2007 ◽  
Vol 4 (4) ◽  
pp. 343-355 ◽  
Author(s):  
Vinay Sriram ◽  
David Kearney
Keyword(s):  
Homeland Security ◽  
Reconfigurable Computing ◽  
High Speed ◽  
High Performance ◽  
Large Scale ◽  
Computation Time ◽  
Ccd Camera ◽  
Hardware Acceleration ◽  
Limiting Factor ◽  
Scene Simulation

High speed infrared (IR) scene simulation is used extensively in defense and homeland security to test sensitivity of IR cameras and accuracy of IR threat detection and tracking algorithms used commonly in IR missile approach warning systems (MAWS). A typical MAWS requires an input scene rate of over 100 scenes/second. Infrared scene simulations typically take 32 minutes to simulate a single IR scene that accounts for effects of atmospheric turbulence, refraction, optical blurring and charge-coupled device (CCD) camera electronic noise on a Pentium 4 (2.8GHz) dual core processor [7]. Thus, in IR scene simulation, the processing power of modern computers is a limiting factor. In this paper we report our research to accelerate IR scene simulation using high performance reconfigurable computing. We constructed a multi Field Programmable Gate Array (FPGA) hardware acceleration platform and accelerated a key computationally intensive IR algorithm over the hardware acceleration platform. We were successful in reducing the computation time of IR scene simulation by over 36%. This research acts as a unique case study for accelerating large scale defense simulations using a high performance multi-FPGA reconfigurable computer.

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