scholarly journals QTL Mapping and Candidate Gene Identification of Swollen Root Formation in Turnip

2021 ◽  
Vol 22 (2) ◽  
pp. 653
Author(s):  
Yudi Wu ◽  
Shifan Zhang ◽  
Hui Zhang ◽  
Fei Li ◽  
Guoliang Li ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Candidate Gene ◽  
Brassica Rapa ◽  
Quantitative Trait ◽  
Root Formation ◽  
Root Diameter ◽  
Root Weight ◽  
Parental Allele ◽  
Root Crops ◽  
Phenotypic Variations

The swollen root is an important agronomic trait and is a determinant of yield for turnips, which are cultivated as both vegetables and fodder. However, the genetic mechanism of swollen root formation is poorly understood. In this study, we analyzed the F2 and BC1P2 populations derived from a cross between “10601” (European turnip with swollen root, Brassica rapa ssp. rapifera, AA, 2n = 2× = 20) and “10603” (Chinese cabbage with normal root, Brassica rapa ssp. pekinensis, AA, 2n = 2× = 20), and suggested that the swollen root is a quantitative trait. Two major quantitative trait loci (QTLs), FR1.1 (Fleshy root 1.1) and FR7.1 (Fleshy root 7.1), were identified by QTL-seq analysis and further confirmed by QTL mapping in F2 and BC1P2 populations. The QTL FR1.1 with a likelihood of odd (LOD) of 7.01 explained 17.2% of the total phenotypic variations for root diameter and the QTL FR7.1 explained 23.0% (LOD = 9.38) and 31.0% (LOD = 13.27) of the total phenotypic variations in root diameter and root weight, respectively. After a recombinant screening, the major QTL FR7.1 was further narrowed down to a 220 kb region containing 47 putative genes. A candidate gene, Bra003652, which is a homolog of AT1G78240 that plays an essential role in cell adhesion and disorganized tumor-like formation in Arabidopsis thaliana, was identified in this region. In addition, expression and parental allele analysis supported that Bra003652 was a possible candidate gene of QTL FR7.1 for swollen root formation in turnip. Our research may provide new insight into the molecular mechanism of swollen root formation in root crops.

Quantitative Trait Loci Mapping and Candidate Gene Identification for Seed Glucosinolates in Brassica rapa L.

Crop Science ◽  
2016 ◽  
Vol 56 (3) ◽  
pp. 942-956 ◽  
Author(s):  
Arvind H. Hirani ◽  
Jianfeng Geng ◽  
Jiefu Zhang ◽  
Carla D. Zelmer ◽  
Peter B. E. McVetty ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Gene ◽  
Brassica Rapa ◽  
Quantitative Trait ◽  
Gene Identification ◽  
Quantitative Trait Loci Mapping ◽  
Candidate Gene Identification ◽  
Trait Loci ◽  
Seed Glucosinolates

scholarly journals On the Differences Between Maximum Likelihood and Regression Interval Mapping in the Analysis of Quantitative Trait Loci

Genetics ◽  
2000 ◽  
Vol 156 (2) ◽  
pp. 855-865 ◽  
Author(s):  
Chen-Hung Kao
Keyword(s):  
Quantitative Trait Loci ◽  
Maximum Likelihood ◽  
Qtl Mapping ◽  
Quantitative Trait ◽  
Mean Squared Error ◽  
Interval Mapping ◽  
Size Difference ◽  
Ratio Test ◽  
Trait Loci ◽  
Variance Explained

AbstractThe differences between maximum-likelihood (ML) and regression (REG) interval mapping in the analysis of quantitative trait loci (QTL) are investigated analytically and numerically by simulation. The analytical investigation is based on the comparison of the solution sets of the ML and REG methods in the estimation of QTL parameters. Their differences are found to relate to the similarity between the conditional posterior and conditional probabilities of QTL genotypes and depend on several factors, such as the proportion of variance explained by QTL, relative QTL position in an interval, interval size, difference between the sizes of QTL, epistasis, and linkage between QTL. The differences in mean squared error (MSE) of the estimates, likelihood-ratio test (LRT) statistics in testing parameters, and power of QTL detection between the two methods become larger as (1) the proportion of variance explained by QTL becomes higher, (2) the QTL locations are positioned toward the middle of intervals, (3) the QTL are located in wider marker intervals, (4) epistasis between QTL is stronger, (5) the difference between QTL effects becomes larger, and (6) the positions of QTL get closer in QTL mapping. The REG method is biased in the estimation of the proportion of variance explained by QTL, and it may have a serious problem in detecting closely linked QTL when compared to the ML method. In general, the differences between the two methods may be minor, but can be significant when QTL interact or are closely linked. The ML method tends to be more powerful and to give estimates with smaller MSEs and larger LRT statistics. This implies that ML interval mapping can be more accurate, precise, and powerful than REG interval mapping. The REG method is faster in computation, especially when the number of QTL considered in the model is large. Recognizing the factors affecting the differences between REG and ML interval mapping can help an efficient strategy, using both methods in QTL mapping to be outlined.

Cold Sweetening in Diploid Potato: Mapping Quantitative Trait Loci and Candidate Genes

Genetics ◽  
2002 ◽  
Vol 162 (3) ◽  
pp. 1423-1434
Author(s):  
Cristina M Menéndez ◽  
Enrique Ritter ◽  
Ralf Schäfer-Pregl ◽  
Birgit Walkemeier ◽  
Alexandra Kalde ◽  
...  
Keyword(s):  
Candidate Gene ◽  
Cold Storage ◽  
Quantitative Trait ◽  
Metabolic Pathways ◽  
Sugar Content ◽  
Candidate Gene Approach ◽  
Diploid Potato ◽  
Glucose Content ◽  
Gene Markers ◽  
Cold Sweetening

Abstract A candidate gene approach has been used as a first step to identify the molecular basis of quantitative trait variation in potato. Sugar content of tubers upon cold storage was the model trait chosen because the metabolic pathways involved in starch and sugar metabolism are well known and many of the genes have been cloned. Tubers of two F1 populations of diploid potato grown in six environments were evaluated for sugar content after cold storage. The populations were genotyped with RFLP, AFLP, and candidate gene markers. QTL analysis revealed that QTL for glucose, fructose, and sucrose content were located on all potato chromosomes. Most QTL for glucose content mapped to the same positions as QTL for fructose content. QTL explaining >10% of the variability for reducing sugars were located on linkage groups I, III, VII, VIII, IX, and XI. QTL consistent across populations and/or environments were identified. QTL were linked to genes encoding invertase, sucrose synthase 3, sucrose phosphate synthase, ADP-glucose pyrophosphorylase, sucrose transporter 1, and a putative sucrose sensor. The results suggest that allelic variants of enzymes operating in carbohydrate metabolic pathways contribute to the genetic variation in cold sweetening.

scholarly journals A study on the mapping of quantitative trait loci in advanced populations derived from two inbred lines

2009 ◽  
Vol 91 (2) ◽  
pp. 85-99 ◽  
Author(s):  
CHEN-HUNG KAO ◽  
MIAO-HUI ZENG
Keyword(s):  
Qtl Mapping ◽  
Quantitative Trait ◽  
Recombinant Inbred ◽  
Genome Structure ◽  
Recombination Rates ◽  
First Order ◽  
Biological Studies ◽  
Markovian Property ◽  
Inbred Populations ◽  
Markovian Assumption

SummaryIn genetic and biological studies, the F2 population is one of the most popular and commonly used experimental populations mainly because it can be readily produced and its genome structure possesses several niceties that allow for productive investigation. These niceties include the equivalence between the proportion of recombinants and recombination rates, the capability of providing a complete set of three genotypes for every locus and an analytically attractive first-order Markovian property. Recently, there has been growing interest in using the progeny populations from F2 (advanced populations) because their genomes can be managed to meet specific purposes or can be used to enhance investigative studies. These advanced populations include recombinant inbred populations, advanced intercrossed populations, intermated recombinant inbred populations and immortalized F2 populations. Due to an increased number of meiosis cycles, the genomes of these advanced populations no longer possess the Markovian property and are relatively more complicated and different from the F2 genomes. Although issues related to quantitative trait locus (QTL) mapping using advanced populations have been well documented, still these advanced populations are often investigated in a manner similar to the way F2 populations are studied using a first-order Markovian assumption. Therefore, more efforts are needed to address the complexities of these advanced populations in more details. In this article, we attempt to tackle these issues by first modifying current methods developed under this Markovian assumption to propose an ad hoc method (the Markovian method) and explore its possible problems. We then consider the specific genome structures present in the advanced populations without invoking this assumption to propose a more adequate method (the non-Markovian method) for QTL mapping. Further, some QTL mapping properties related to the confounding problems that result from ignoring epistasis and to mapping closely linked QTL are derived and investigated across the different populations. Simulations show that the non-Markovian method outperforms the Markovian method, especially in the advanced populations subject to selfing. The results presented here may give some clues to the use of advanced populations for more powerful and precise QTL mapping.

scholarly journals Consequences of Recombination Rate Variation on Quantitative Trait Locus Mapping Studies: Simulations Based on the Drosophila melanogaster Genome

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 581-588
Author(s):  
Mohamed A F Noor ◽  
Aimee L Cunningham ◽  
John C Larkin
Keyword(s):  
Quantitative Trait Locus ◽  
Drosophila Melanogaster ◽  
Qtl Mapping ◽  
Quantitative Trait ◽  
Recombination Rate ◽  
Genome Project ◽  
Gene Density ◽  
Rate Variation ◽  
Trait Locus ◽  
Recombination Rate Variation

Abstract We examine the effect of variation in gene density per centimorgan on quantitative trait locus (QTL) mapping studies using data from the Drosophila melanogaster genome project and documented regional rates of recombination. There is tremendous variation in gene density per centimorgan across this genome, and we observe that this variation can cause systematic biases in QTL mapping studies. Specifically, in our simulated mapping experiments of 50 equal-effect QTL distributed randomly across the physical genome, very strong QTL are consistently detected near the centromeres of the two major autosomes, and few or no QTL are often detected on the X chromosome. This pattern persisted with varying heritability, marker density, QTL effect sizes, and transgressive segregation. Our results are consistent with empirical data collected from QTL mapping studies of this species and its close relatives, and they explain the “small X-effect” that has been documented in genetic studies of sexual isolation in the D. melanogaster group. Because of the biases resulting from recombination rate variation, results of QTL mapping studies should be taken as hypotheses to be tested by additional genetic methods, particularly in species for which detailed genetic and physical genome maps are not available.

scholarly journals Nitrogen Application and Leaf Harvesting Improves Yield and Nutritional Quality of Beetroot

2017 ◽  
Vol 27 (3) ◽  
pp. 337-343 ◽  
Author(s):  
Salfina S. Mampa ◽  
Martin M. Maboko ◽  
Puffy Soundy ◽  
Dharini Sivakumar
Keyword(s):  
Block Design ◽  
Root Diameter ◽  
Total Protein Content ◽  
Root Weight ◽  
Nitrogen Application ◽  
Root Yield ◽  
N Application ◽  
Leaf Yield ◽  
Leaf Harvest

Beetroot (Beta vulgaris), commonly known as table beet, is used as a staple in the diet of many people through the consumption of the entire plant, leaf, and the root. The objective of this study was to assess the effects of nitrogen (N) application and leaf harvest percentage on the yield and quality of roots and leaves of beetroot. The treatment design was a randomized complete block design with five levels of N (0, 60, 90, 120, and 150 kg·ha−1) combined with three leaf harvest percentages (0, 30, and 50) and replicated three times. The first leaf harvest was initiated 35 days after transplanting (DAT) by removing the outer matured leaves and the second harvest occurred 80 DAT by removing all the leaves. The results showed increases in leaf and root yield with an increase in N application. Nitrogen application at 90 and 120 kg·ha−1 increased fresh leaf weight, leaf number, and fresh and dry root weight, including root diameter and length with the exception of leaf area which was significantly higher at 120 kg·ha−1 N. Magnesium and iron leaf content, and N root content were significantly improved by the application of 120 kg·ha−1 N. Leaf harvest percentage did not have a significant effect on leaf yield or leaf and root mineral content. However, dry root weight was significantly reduced by the 50% leaf harvest. Leaf harvest at 30% or 50% increased total protein content of the roots of beetroot, whereas an increase in N application decreased concentration of total proteins. Results demonstrate that leaf and root yield, as well as magnesium, zinc, and iron leaf content, increased with the application of 120 kg·ha−1 N, whereas 30% leaf harvest did not negatively affect root yield.

scholarly journals Novel Quantitative Trait Loci for Grain Cadmium Content Identified in Hard White Spring Wheat

2021 ◽  
Vol 12 ◽  
Author(s):  
Ling Qiao ◽  
Justin Wheeler ◽  
Rui Wang ◽  
Kyle Isham ◽  
Natalie Klassen ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Gene ◽  
Spring Wheat ◽  
Quantitative Trait ◽  
Field Trials ◽  
Cadmium Content ◽  
Wheat Population ◽  
Trait Loci ◽  
Multiple Field ◽  
First Time

Cadmium (Cd) is a heavy metal that can cause a variety of adverse effects on human health, including cancer. Wheat comprises approximately 20% of the human diet worldwide; therefore, reducing the concentrations of Cd in wheat grain will have significant impacts on the intake of Cd in food products. The tests for measuring the Cd content in grain are costly, and the content is affected significantly by soil pH. To facilitate breeding for low Cd content, this study sought to identify quantitative trait loci (QTL) and associated molecular markers that can be used in molecular breeding. One spring wheat population of 181 doubled haploid lines (DHLs), which was derived from a cross between two hard white spring wheat cultivars “UI Platinum” (UIP) and “LCS Star” (LCS), was assessed for the Cd content in grain in multiple field trials in Southeast Idaho, United States. Three major QTL regions, namely, QCd.uia2-5B, QCd.uia2-7B, and QCd.uia2-7D, were identified on chromosomes 5B, 7B, and 7D, respectively. All genes in these three QTL regions were identified from the NCBI database. However, three genes related to the uptake and transport of Cd were used in the candidate gene analysis. The sequences of TraesCS5B02G388000 (TaHMA3) in the QCd.uia2-5B region and TraesCS7B02G320900 (TaHMA2) and TraesCS7B02G322900 (TaMSRMK3) in the QCd.uia2-7B region were compared between UIP and LCS. TaHMA2 on 7B is proposed for the first time as a candidate gene for grain Cd content in wheat. A KASP marker associated with this gene was developed and it will be further validated in near-isogenic lines via a gene-editing system in future studies.

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