scholarly journals Detection of Quantitative Trait Loci and Inheritance of Root-knot Nematode Resistance in Sweetpotato

2008 ◽  
Vol 133 (6) ◽  
pp. 844-851 ◽  
Author(s):  
Jim C. Cervantes-Flores ◽  
G. Craig Yencho ◽  
Kenneth V. Pecota ◽  
Bryon Sosinski ◽  
Robert O.M. Mwanga
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Ipomoea Batatas ◽  
The United States ◽  
Genetic Maps ◽  
Aflp Markers ◽  
Root Knot Nematodes ◽  
Egg Masses ◽  
Positive Effects ◽  
Trait Loci

Resistance to root-knot nematodes [Meloidogyne incognita (Kofoid & White) Chitwood] in sweetpotato [Ipomoea batatas (L.) Lam.] was studied in a mapping population consisting of 240 progeny derived from a cross between ‘Beauregard’, the predominant cultivar in the United States, and ‘Tanzania’, an African landrace. Quantitative trait loci (QTL) analyses to locate markers associated with resistance to root-knot nematodes (RKN) were performed using genetic maps based on parental segregation in ‘Beauregard’ and ‘Tanzania’ consisting of 726 and 947 single-dose amplified fragment length polymorphism (AFLP) markers, respectively. RKN resistance in the progeny was highly skewed with most of the progeny exhibiting medium to high levels of resistance. Single-point analysis of variance and interval mapping revealed seven consistently significant QTL in ‘Tanzania’ and two significant QTL in ‘Beauregard’. In ‘Tanzania’, three QTL were associated with reduction in resistance as measured by the number of RKN egg masses and explained ≈20% of the variation. Another four QTL had positive effects on resistance and explained ≈21% of the variation. Other minor QTL explained ≈2% or less of the variation but were not always consistent across geographical locations. In ‘Beauregard’, two QTL had positive effects on RKN resistance and explained ≈6% of the observed variation. Based on molecular and phenotypic data, RKN resistance in sweetpotato is hypothesized to be conferred by several genes, but at least nine AFLP markers (seven from ‘Tanzania’ and two from ‘Beauregard’) are associated with genomic regions that have the biggest effect in the number of egg masses of RKN produced in the root system.

scholarly journals Quantitative Trait Loci Associated with Rotylenchulus reniformis Host Suitability in Soybean

2020 ◽  
Vol 110 (9) ◽  
pp. 1511-1521
Author(s):  
Juliet Wilkes ◽  
Christopher Saski ◽  
Mariola Klepadlo ◽  
Benjamin Fallen ◽  
Paula Agudelo
Keyword(s):  
Quantitative Trait Loci ◽  
Qtl Analysis ◽  
Quantitative Trait ◽  
The United States ◽  
Host Suitability ◽  
Reniform Nematode ◽  
Rotylenchulus Reniformis ◽  
Chromosome 18 ◽  
Nematode Reproduction ◽  
Trait Loci

Reniform nematode (Rotylenchulus reniformis) is a yield-limiting pathogen of soybean (Glycine max) in the southeastern region of the United States. A population of 250 recombinant inbred lines (RIL) (F2:8) developed from a cross between reniform nematode resistant soybean cultivar Forrest and susceptible cultivar Williams 82 was utilized to identify regions associated with host suitability. A genetic linkage map was constructed using single-nucleotide polymorphism markers generated by genotyping-by-sequencing. The phenotype was measured in the RIL population and resistance was characterized using normalized and transformed nematode reproduction indices in an optimal univariate cluster analysis. Quantitative trait loci (QTL) analysis using normalized phenotype scores identified two QTLs on each arm of chromosome 18 (rrn-1 and rrn-2). The same QTL analysis performed with log10(x) transformed phenotype data also identified two QTLs: one on chromosome 18 overlapping the same region in the other analysis (rrn-1), and one on chromosome 11 (rrn-3). While rrn-1 and rrn-3 have been reported associated with reduced reproduction of reniform nematode, this is the first report of the rrn-2 region associated with host suitability to reniform nematode. The resistant parent allele at rrn-2 showed an inverse relationship with the resistance phenotype, correlating with an increase in nematode reproduction or host suitability. Several candidate genes within these regions corresponded with host plant defense systems. Interestingly, a characteristic pathogen resistance gene with a leucine-rich repeat was discovered within rrn-2. These genetic markers can be used by soybean breeders in marker-assisted selection to develop lines with resistance to reniform nematode.

scholarly journals PSV-13 Genetic parameters and quantitative trait loci for heat stress related traits in sheep

2020 ◽  
Vol 98 (Supplement_3) ◽  
pp. 163-164
Author(s):  
Devin R Jacobs ◽  
Claudia E Silvera-Rojas ◽  
Jennifer M Bormann ◽  
Terry A Gipson ◽  
Arthur L Goetsch ◽  
...  
Keyword(s):  
Heat Stress ◽  
Quantitative Trait Loci ◽  
Rectal Temperature ◽  
Quantitative Trait ◽  
Fixed Effects ◽  
Univariate Analysis ◽  
Average Daily Gain ◽  
The United States ◽  
Nucleotide Polymorphisms ◽  
Trait Loci

Abstract Greater selection emphasis has been placed on efficiency than on fitness in livestock populations over the last several decades. Heat stress is a concern in production systems due to the negative effects on production, reproduction, and immunity. The objective of the study was to estimate variance components and identify quantitative trait loci (QTL) for heat stress related traits in sheep. A total of 125 Dorper, Katahdin, and St. Croix ewes originating from four regions of the United States were selected for the experiment. Animals were separated into four trials due to facility limitations. Data were collected for each trial over four consecutive two-week periods in an environmentally controlled facility with targeted heat load index (HLI) for daytime/nighttime of 70/70, 85/77, 90/77, and 95/81. Body weight was collected three times per week and rectal temperature was collected weekly. Black globe temperature and humidity were measured every 15 minutes. Animals were genotyped using the Illumina OvineSNP50 BeadChip. After quality control, 49,396 effective single nucleotide polymorphisms were included in the univariate analysis performed with the BLUPF90 suite of programs. Fixed effects in the models included region of origin, breed, trial, and age as a covariate. Traits analyzed included rectal temperature at 95 HLI (RT95), feed intake at 95 HLI (FI95), and average daily gain for the period for HLI between 90 and 95 (ADG). Heritabilities for RT95, FI95, and ADG were 0.35, 0.10, and 0.10, respectively. Largest effect QTL were identified on chromosomes 23, 9, and 6 for RT95, chromosomes 9, 2, and 20 for FI95, and chromosomes 6, 1, and 5 for ADG. Many of the regions identified have also been associated with weight and carcass traits in other studies, but few had obvious connections to the heat stress related response. In conclusion, results suggest selection could improve heat tolerance in sheep.

scholarly journals Two Independent Quantitative Trait Loci Are Responsible for Novel Resistance to Beet curly top virus in Common Bean Landrace G122

2010 ◽  
Vol 100 (10) ◽  
pp. 972-978 ◽  
Author(s):  
Richard C. Larsen ◽  
Chester J. Kurowski ◽  
Phillip N. Miklas
Keyword(s):  
Quantitative Trait Loci ◽  
Linkage Group ◽  
Common Bean ◽  
Quantitative Trait ◽  
Rapd Marker ◽  
The United States ◽  
Effective Control ◽  
Minor Effect ◽  
Beet Curly Top Virus ◽  
Trait Loci

Beet curly top virus, often referred to as Curly top virus (CTV), is an important virus disease of common bean in the semiarid regions of the United States, Canada, and Mexico and the only effective control is genetic resistance. Our objective was to determine if dry bean landrace G122, which lacks the Bct gene for resistance to CTV, contains novel resistance to the virus. Two populations, GT-A and GT-B, consisting of 98 F5:7 recombinant inbred lines (RILs) in total were derived from a cross between G122 and the susceptible variety Taylor Horticultural and evaluated for phenotypic response to natural CTV field infection. Genetic analyses revealed random amplified polymorphism DNA (RAPD) markers associated with a major-effect quantitative trait loci (QTL) from G122 which exhibited stable expression across 3 years in both populations. Phenotypic variation explained by the QTL in GT-A (37.6%) was greater than in GT-B (20.4%). RAPD marker Q14.973 was converted to a sequence-characterized amplified region (SCAR) and designated SQ14.973. The SCAR was used to locate the QTL on linkage group 6 of the Phaseolus core map. A survey of 74 common bean cultivars and breeding lines revealed SQ14.973 would be widely useful for marker-assisted selection of the QTL. An additional minor-effect QTL from G122 was detected on linkage group 7. G122 was determined to possess novel resistance to CTV conditioned by at least two genes, one with major the other minor effect.

scholarly journals Evidence for Colinearity among Genetic Linkage Maps in Cucumber

HortScience ◽  
2007 ◽  
Vol 42 (1) ◽  
pp. 20-27 ◽  
Author(s):  
Jack E. Staub ◽  
Zhanyong Sun ◽  
Sang-Min Chung ◽  
Richard L. Lower
Keyword(s):  
Quantitative Trait Loci ◽  
Fragment Length ◽  
Quantitative Trait ◽  
Yield Component ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Length Polymorphisms ◽  
Trait Loci ◽  
Processing Line ◽  
Simple Sequence

Cucumber (Cucumis sativus L. var. sativus; 2n = 2x = 14), has a narrow genetic base (3% to 8% polymorphism). Nevertheless, several genetic maps exist for this species. It is important to know the degree of colinearity among these maps. Thus, the positions of random amplified polymorphic DNAs, sequenced characterized amplified regions, simple sequence repeat, restriction fragment length polymorphisms, and fluorescent amplified fragment length polymorphism markers were compared in four maps. A previously unreported map was constructed in a narrow cross (processing line 2A × Gy8; C. s. var. sativus; ≈7% polymorphism) and compared with the three published maps [two narrow-based (processing type; C. s. var. sativus; 8% to 12% polymorphism) and a broad-based (C. s. var. sativus × C. s. var. hardwickii (R.) Alef. ≈12%)]. Common makers were identified in seven linkage groups, providing evidence for microsynteny. These common markers were used as anchor markers for map position comparisons of yield component quantitative trait loci. The relative order of anchor markers in each of six linkage groups (linkage groups 1, 2, and 4–7) that had two or more anchor markers within each group was colinear, and instances of microsynteny were detected. Commonalities in the position of some yield component quantitative trait loci exist in linkage groups 1 and 4 of the maps examined, and the general synteny among these maps indicates that identification and mapping of additional anchor markers would lead to successful map merging to increase cucumber map saturation for use in cucumber breeding.

scholarly journals Mapping Quantitative Trait Loci onto Chromosome-Scale Pseudomolecules in Flax

2020 ◽  
Vol 3 (2) ◽  
pp. 28 ◽  
Author(s):  
Frank M. You ◽  
Sylvie Cloutier
Keyword(s):  
Quantitative Trait Loci ◽  
Candidate Genes ◽  
Quantitative Trait ◽  
Quantitative Traits ◽  
Snp Markers ◽  
Genetic Maps ◽  
Nucleotide Polymorphisms ◽  
Genome Wide ◽  
Trait Loci ◽  
Genomic Regions

Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits. To date, a total of 313 QTL for 31 quantitative traits have been reported in 14 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, the scaffold sequences, or the pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but the most used ones were simple sequence repeats (SSRs) or single nucleotide polymorphisms (SNPs). To uniquely map the SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules, methods with several scripts and database files were developed to locate PCR- and SNP-based markers onto the same reference, co-locate QTL, and scan genome-wide candidate genes. Using these methods, 195 out of 200 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters; the candidate genes that co-located with these QTL clusters were also predicted. The methods and tools presented in this article facilitate marker re-mapping to a new reference, genome-wide QTL analysis, candidate gene scanning, and breeding applications in flax and other crops.

scholarly journals Identification of Quantitative Trait Loci Determining Vegetative Growth Traits in Coffea canephor

2011 ◽  
Vol 27 (3) ◽  
Author(s):  
Priyono Priyono ◽  
Ucu Sumirat ◽  
Crouzillat Crouzillat
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Vegetative Growth ◽  
Growth Traits ◽  
Coffea Canephora ◽  
Tree Canopy ◽  
Genetic Maps ◽  
Phenotypic Trait ◽  
Trait Loci ◽  
Vegetative Traits

Recently the use of molecular markers has been successfully applied for some crops. For coffee, new opportunities have been opened since Nestlé R&D Centre in collaboration with ICCRI completed the first genetic map of Coffea canephora. This study was aimed both to evaluate the phenotypic trait and also to identify the quantitative trait loci (QTLs) controlling the vegetative growth in Robusta coffee. Present study used three C. canephora populations and six genetic maps developed based on these populations using simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) markers. A total of 17 different quantitative data were used for the detection of QTLs on each of three populations. Present result showed that most of these traits were not heritable. The nine vegetative traits have been identified and distributed over seven different linkage groups. Due to some QTLs determining one given trait were overlapping on the same linkage group and were coming from the same favourable parent, a total of 19 QTLs detected for vegetative traits might finally be considered as only 12 QTLs involved. However, only two of them were shared for different traits. One involved for the number/length of primary branches and width of the canopy while the other for length of internodes and width of canopy. These two QTLs might determine the size of the tree canopy in this species. Key words: Coffea canephora, heridity, quantitative trait loci (QTLs), vegetative growth.

scholarly journals Multiple quantitative trait loci contribute tolerance to bacterial canker incited by Pseudomonas syringae pv. actinidiae in kiwifruit (Actinidia chinensis)

2019 ◽  
Author(s):  
Jibran Tahir ◽  
Stephen Hoyte ◽  
Heather Bassett ◽  
Cyril Brendolise ◽  
Abhishek Chatterjee ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Pseudomonas Syringae ◽  
Quantitative Trait ◽  
Genetic Maps ◽  
Phenotypic Variance ◽  
Minor Qtls ◽  
Economic Threat ◽  
Trait Loci ◽  
Basal Defense ◽  
Rna Biomarkers

AbstractPseudomonas syringae pv. actinidiae (Psa) Biovar 3, a virulent, canker-inducing pathogen is an economic threat to the kiwifruit (Actinidia spp.) industry worldwide. The commercially grown diploid (2x) A. chinensis var. chinensis is more susceptible to Psa than tetraploid and hexaploid kiwifruit. However information on the genetic loci modulating Psa resistance in kiwifruit is not available. Here we report mapping of quantitative trait loci (QTLs) regulating tolerance to Psa in a diploid kiwifruit population, derived from a cross between an elite Psa-susceptible ‘Hort16A’ and a tolerant male breeding parent P1. Using high-density genetic maps and intensive phenotyping, we identified a single QTL for Psa tolerance on Linkage Group (LG) 27 of ‘Hort16A’ revealing 16-19% phenotypic variance and candidate alleles for susceptibility and tolerance at this loci. In addition, six minor QTLs were identified in P1 on distinct LGs, exerting 4-9% variance. Complete tolerance in the F1 population is attained by additive effects from ‘Hort16A’ and P1 QTLs providing evidence that divergent genetic pathways fend-off virulent Psa strain. Two different bioassays further identified new QTLs for tissue-specific responses to Psa. Transcriptome analysis of Psa-tolerant and susceptible genotypes in field revealed hallmarks of basal defense and provided candidate RNA-biomarkers for screening Psa tolerance.

scholarly journals Mapping Quantitative Trait Loci onto Chromosome-scale Pseudomolecules in Flax

2019 ◽  
Author(s):  
Frank M. You ◽  
Sylvie Cloutier
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Quantitative Traits ◽  
Snp Markers ◽  
Genetic Maps ◽  
Genome Wide ◽  
Trait Loci ◽  
Ssr And Snp Markers ◽  
Gene Scanning ◽  
Genomic Regions

Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits in a population. To date, a total of 267 QTL for 29 quantitative traits have been reported in 13 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, scaffold sequences, or pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but were mainly based on simple sequence repeat (SSR) or single nucleotide polymorphism (SNP) markers. This article provides methods with software tools and database files to uniquely map SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules. Using these methods, 195 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters. Mapping of QTL from different studies to the same reference enables comparisons and facilitates genome-wide QTL analysis, candidate gene scanning, and breeding applications.

Comparative analysis of QTLs affecting plant height and flowering among closely-related diploid and polyploid genomes

Genome ◽  
2002 ◽  
Vol 45 (5) ◽  
pp. 794-803 ◽  
Author(s):  
Ray Ming ◽  
Terrye A. Del Monte ◽  
Eduardo Hernandez ◽  
Paul H Moore ◽  
James E Irvine ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Plant Height ◽  
Dna Markers ◽  
Quantitative Trait ◽  
Saccharum Officinarum ◽  
Genetic Maps ◽  
Interspecific Crosses ◽  
Number Of Genes ◽  
Trait Loci ◽  
Genomic Regions

Quantitative trait loci (QTLs) affecting plant height and flowering were studied in the two Saccharum species from which modern sugarcane cultivars are derived. Two segregating populations derived from interspecific crosses between Saccharum officinarum and Saccharum spontaneum were genotyped with 735 DNA markers. Among the 65 significant associations found between these two traits and DNA markers, 35 of the loci were linked to sugarcane genetic maps and 30 were unlinked DNA markers. Twenty-one of the 35 mapped QTLs were clustered in eight genomic regions of six sugarcane homologous groups. Some of these could be divergent alleles at homologous loci, making the actual number of genes implicated in these traits much less than 35. Four QTL clusters controlling plant height in sugarcane corresponded closely to four of the six plant-height QTLs previously mapped in sorghum. One QTL controlling flowering in sugarcane corresponded to one of three flowering QTLs mapped in sorghum. The correspondence in locations of QTLs affecting plant height and flowering in sugarcane and sorghum reinforce the notion that the simple sorghum genome is a valuable "template" for molecular dissection of the much more complex sugarcane genome.Key words: DNA markers, genetic map, quantitative trait loci, Saccharum.

Sign in / Sign up

Export Citation Format

Share Document