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

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.

Download Full-text

Quantitative Trait Locus Mapping of Yield-Related Components and Oligogenic Control of the Cap Color of the Button Mushroom, Agaricus bisporus

Applied and Environmental Microbiology ◽

10.1128/aem.07516-11 ◽

2012 ◽

Vol 78 (7) ◽

pp. 2422-2434 ◽

Cited By ~ 25

Author(s):

Marie Foulongne-Oriol ◽

Anne Rodier ◽

Thierry Rousseau ◽

Jean-Michel Savoie

Keyword(s):

Phenotypic Variation ◽

Quantitative Trait ◽

Agaricus Bisporus ◽

Agronomic Traits ◽

Wild Strain ◽

Pleiotropic Effect ◽

Average Weight ◽

Button Mushroom ◽

Content Type ◽

Beneficial Effects

ABSTRACTAs in other crops, yield is an important trait to be selected for in edible mushrooms, but its inheritance is poorly understood. Therefore, we have investigated the complex genetic architecture of yield-related traits inAgaricus bisporusthrough the mapping of quantitative trait loci (QTL), using second-generation hybrid progeny derived from a cross between a wild strain and a commercial cultivar. Yield, average weight per mushroom, number of fruiting bodies per m2, earliness, and cap color were evaluated in two independent experiments. A total of 23 QTL were detected for 7 yield-related traits. These QTL together explained between 21% (two-flushes yield) and 59% (earliness) of the phenotypic variation. Fifteen QTL (65%) were consistent between the two experiments. Four regions underlying significant QTL controlling yield, average weight, and number were detected on linkage groups II, III, IV, and X, suggesting a pleiotropic effect or tight linkage. Up to six QTL were identified for earliness. ThePPC1locus, together with two additional genomic regions, explained up to 90% of the phenotypic variation of the cap color. Alleles from the wild parent showed beneficial effects for some yield traits, suggesting that the wild germ plasm is a valuable source of variation for several agronomic traits. Our results constitute a key step toward marker-assisted selection and provide a solid foundation to go further into the biological mechanisms controlling productive traits in the button mushroom.

Download Full-text

Epigenome-Wide Study Identified Methylation Sites Associated with the Risk of Obesity

Nutrients ◽

10.3390/nu13061984 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1984

Author(s):

Majid Nikpay ◽

Sepehr Ravati ◽

Robert Dent ◽

Ruth McPherson

Keyword(s):

Quantitative Trait Locus ◽

Quantitative Trait ◽

Rare Variants ◽

Genome Wide ◽

A Genome ◽

Genome Wide Search ◽

Risk Snps ◽

Trait Locus ◽

Genomic Regions ◽

Eqtl Data

Here, we performed a genome-wide search for methylation sites that contribute to the risk of obesity. We integrated methylation quantitative trait locus (mQTL) data with BMI GWAS information through a SNP-based multiomics approach to identify genomic regions where mQTLs for a methylation site co-localize with obesity risk SNPs. We then tested whether the identified site contributed to BMI through Mendelian randomization. We identified multiple methylation sites causally contributing to the risk of obesity. We validated these findings through a replication stage. By integrating expression quantitative trait locus (eQTL) data, we noted that lower methylation at cg21178254 site upstream of CCNL1 contributes to obesity by increasing the expression of this gene. Higher methylation at cg02814054 increases the risk of obesity by lowering the expression of MAST3, whereas lower methylation at cg06028605 contributes to obesity by decreasing the expression of SLC5A11. Finally, we noted that rare variants within 2p23.3 impact obesity by making the cg01884057 site more susceptible to methylation, which consequently lowers the expression of POMC, ADCY3 and DNAJC27. In this study, we identify methylation sites associated with the risk of obesity and reveal the mechanism whereby a number of these sites exert their effects. This study provides a framework to perform an omics-wide association study for a phenotype and to understand the mechanism whereby a rare variant causes a disease.

Download Full-text

Transcriptomic profiling of wheat near-isogenic lines reveals candidate genes on chromosome 3A for pre-harvest sprouting resistance

BMC Plant Biology ◽

10.1186/s12870-021-02824-x ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Xingyi Wang ◽

Hui Liu ◽

Kadambot H. M. Siddique ◽

Guijun Yan

Keyword(s):

Candidate Genes ◽

Quantitative Trait ◽

Genomic Region ◽

Nucleotide Polymorphisms ◽

Near Isogenic Lines ◽

Gene Effects ◽

Isogenic Lines ◽

Trait Locus ◽

Grain Yield And Quality ◽

Sprouting Resistance

Abstract Background Pre-harvest sprouting (PHS) in wheat can cause severe damage to both grain yield and quality. Resistance to PHS is a quantitative trait controlled by many genes located across all 21 wheat chromosomes. The study targeted a large-effect quantitative trait locus (QTL) QPhs.ccsu-3A.1 for PHS resistance using several sets previously developed near-isogenic lines (NILs). Two pairs of NILs with highly significant phenotypic differences between the isolines were examined by RNA sequencing for their transcriptomic profiles on developing seeds at 15, 25 and 35 days after pollination (DAP) to identify candidate genes underlying the QTL and elucidate gene effects on PHS resistance. At each DAP, differentially expressed genes (DEGs) between the isolines were investigated. Results Gene ontology and KEGG pathway enrichment analyses of key DEGs suggested that six candidate genes underlie QPhs.ccsu-3A.1 responsible for PHS resistance in wheat. Candidate gene expression was further validated by quantitative RT-PCR. Within the targeted QTL interval, 16 genetic variants including five single nucleotide polymorphisms (SNPs) and 11 indels showed consistent polymorphism between resistant and susceptible isolines. Conclusions The targeted QTL is confirmed to harbor core genes related to hormone signaling pathways that can be exploited as a key genomic region for marker-assisted selection. The candidate genes and SNP/indel markers detected in this study are valuable resources for understanding the mechanism of PHS resistance and for marker-assisted breeding of the trait in wheat.

Download Full-text

Genetic dissection of partial resistance to race 6 of Venturia inaequalis in apple

Genome ◽

10.1139/g02-127 ◽

2003 ◽

Vol 46 (2) ◽

pp. 224-234 ◽

Cited By ~ 60

Author(s):

C E Durel ◽

L Parisi ◽

F Laurens ◽

W E Van de Weg ◽

R Liebhard ◽

...

Keyword(s):

Resistance Gene ◽

Malus Domestica ◽

Quantitative Trait ◽

Partial Resistance ◽

Venturia Inaequalis ◽

Genetic Dissection ◽

Resistance Breakdown ◽

Trait Locus ◽

New Races ◽

Genomic Regions

Scab, caused by the fungus Venturia inaequalis, is one of the most important diseases of apple (Malus × domestica). The major resistance gene, Vf, has been widely used in apple breeding programs, but two new races of the fungus (races 6 and 7) are able to overcome this gene. A mapped F1 progeny derived from a cross between the cultivars Prima and Fiesta has been inoculated with two monoconidial strains of race 6. These strains originated from sporulating leaves of 'Prima' and a descendant of 'Prima' that were grown in an orchard in northern Germany. 'Prima' carries the Vf resistance gene, whereas 'Fiesta' lacks Vf. A large variation in resistance and (or) susceptibility was observed among the individuals of the progeny. Several quantitative trait loci (QTLs) for resistance were identified that mapped on four genomic regions. One of them was located in the very close vicinity of the Vf resistance gene on linkage group LG-1 of the 'Prima' genetic map. This QTL is isolate specific because it was only detected with one of the two isolates. Two out of the three other genomic regions were identified with both isolates (LG-11 and LG-17). On LG-11, a QTL effect was detected in both parents. The genetic dissection of this QTL indicated a favourable intra-locus interaction between some parental alleles.Key words: Malus × domestica, partial resistance, Venturia inaequalis, resistance breakdown, quantitative trait locus.

Download Full-text

Linkage mapping of quantitative trait loci for fiber yield and its related traits in the population derived from cultivated ramie and wild B. nivea var. tenacissima

Scientific Reports ◽

10.1038/s41598-019-53399-5 ◽

2019 ◽

Vol 9 (1) ◽

Author(s):

Zheng Zeng ◽

Yanzhou Wang ◽

Chan Liu ◽

Xiufeng Yang ◽

Hengyun Wang ◽

...

Keyword(s):

Quantitative Trait ◽

Linkage Mapping ◽

Genetic Basis ◽

Natural Fiber ◽

Stem Bark ◽

High Yield ◽

Fiber Yield ◽

Wild Allele ◽

Trait Locus ◽

Genomic Regions

AbstractRamie is an important natural fiber crop, and the fiber yield and its related traits are the most valuable traits in ramie production. However, the genetic basis for these traits is still poorly understood, which has dramatically hindered the breeding of high yield in this fiber crop. Herein, a high-density genetic map with 6,433 markers spanning 2476.5 cM was constructed using a population derived from two parents, cultivated ramie Zhongsizhu 1 (ZSZ1) and its wild progenitor B. nivea var. tenacissima (BNT). The fiber yield (FY) and its four related traits—stem diameter (SD) and length (SL), stem bark weight (BW) and thickness (BT)—were performed for quantitative trait locus (QTL) analysis, resulting in a total of 47 QTLs identified. Forty QTLs were mapped into 12 genomic regions, thus forming 12 QTL clusters. Among 47 QTLs, there were 14 QTLs whose wild allele from BNT was beneficial. Interestingly, all QTLs in Cluster 10 displayed overdominance, indicating that the region of this cluster was likely heterotic loci. In addition, four fiber yield-related genes underwent positive selection were found either to fall into the FY-related QTL regions or to be near to the identified QTLs. The dissection of FY and FY-related traits not only improved our understanding to the genetic basis of these traits, but also provided new insights into the domestication of FY in ramie. The identification of many QTLs and the discovery of beneficial alleles from wild species provided a basis for the improvement of yield traits in ramie breeding.

Download Full-text

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

International Journal of Molecular Sciences ◽

10.3390/ijms21113960 ◽

2020 ◽

Vol 21 (11) ◽

pp. 3960 ◽

Cited By ~ 1

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.

Download Full-text

Explaining the heritability of an ecologically significant trait in terms of individual quantitative trait loci

Biology Letters ◽

10.1098/rsbl.2011.0409 ◽

2011 ◽

Vol 7 (6) ◽

pp. 896-898 ◽

Cited By ~ 13

Author(s):

Alison G. Scoville ◽

Young Wha Lee ◽

John H. Willis ◽

John K. Kelly

Keyword(s):

Qtl Mapping ◽

Quantitative Trait ◽

Complex Traits ◽

Genetic Variance ◽

Balancing Selection ◽

Natural Populations ◽

Population Based ◽

Population Variation ◽

Trait Locus ◽

Genomic Regions

Most natural populations display substantial genetic variation in behaviour, morphology, physiology, life history and the susceptibility to disease. A major challenge is to determine the contributions of individual loci to variation in complex traits. Quantitative trait locus (QTL) mapping has identified genomic regions affecting ecologically significant traits of many species. In nearly all cases, however, the importance of these QTLs to population variation remains unclear. In this paper, we apply a novel experimental method to parse the genetic variance of floral traits of the annual plant Mimulus guttatus into contributions of individual QTLs. We first use QTL-mapping to identify nine loci and then conduct a population-based breeding experiment to estimate V Q , the genetic variance attributable to each QTL. We find that three QTLs with moderate effects explain up to one-third of the genetic variance in the natural population. Variation at these loci is probably maintained by some form of balancing selection. Notably, the largest effect QTLs were relatively minor in their contribution to heritability.

Download Full-text

Further mapping of quantitative trait loci for female sterility in wheat (Triticum aestivum L.)

Genetics Research ◽

10.1017/s0016672310000054 ◽

2010 ◽

Vol 92 (1) ◽

pp. 63-70 ◽

Cited By ~ 4

Author(s):

BINGDE DOU ◽

BEIWEI HOU ◽

FANG WANG ◽

JINBIN YANG ◽

ZHONGFU NI ◽

...

Keyword(s):

Quantitative Trait ◽

Triticum Aestivum L ◽

Female Sterility ◽

Phenotypic Variance ◽

Crop Breeding ◽

Main Effect ◽

Sterile Mutant ◽

Likelihood Approach ◽

Trait Locus ◽

Simple Sequence

SummaryEpistasis underlying fertility plays an important role in crop breeding. Although a new female sterile mutant in wheat, XND126, has been identified and a major quantitative trait locus (QTL), taf1, for the female sterility has been mapped, the genetic architecture of the female sterility needs to be further addressed. To identify the interaction involving the gene(s) controlling the female sterility, an investigation was carried out for the seed setting ratio in an F2 population derived from the cross between XND126 and Gaocheng 8901. Among 1250 simple sequence repeat (SSR) primer pairs in the whole genome, a total of 21 markers, obtained by recessive class approach, along with other ten tightly linked markers on reference maps in wheat, were used to survey 243 F2 individuals. As a result, 28 markers were mapped into five genetic linkage groups. The performance for female sterility for each F2 individual was evaluated simultaneously at the Urumqi and Huai'an experimental stations in 2006–2007. The two phenotypic datasets along with marker information were jointly analysed in the detection of QTL using penalized maximum likelihood approach. A total of six QTLs, including two main-effect QTLs, three epistatic QTLs and one environmental interaction and accounting for 0·67–24·55% of the total phenotypic variance, were identified. All estimated effects accounted for 53·26% of the total phenotypic variation. The taf1 detected in previous study was also located on the same marker interval on chromosome 2DS. These results enrich our understanding of the genetic basis of the female sterility.

Download Full-text

Quantitative Trait Locus Analysis Identifies Rat Genomic Regions Related to Amphetamine-Induced Locomotion and Gαi3 Levels in Nucleus Accumbens

Neuropsychopharmacology ◽

10.1038/sj.npp.1301667 ◽

2008 ◽

Vol 33 (11) ◽

pp. 2735-2746 ◽

Cited By ~ 4

Author(s):

Marc N Potenza ◽

Edward S Brodkin ◽

Bao-Zhu Yang ◽

Shari G Birnbaum ◽

Eric J Nestler ◽

...

Keyword(s):

Quantitative Trait Locus ◽

Nucleus Accumbens ◽

Quantitative Trait Locus Analysis ◽

Quantitative Trait ◽

Trait Locus ◽

Genomic Regions

Download Full-text

High-Density Genetic Linkage Map Construction and White Rot Resistance Quantitative Trait Loci Mapping for Genus Vitis Based on Restriction Site-Associated DNA Sequencing

Phytopathology ◽

10.1094/phyto-12-19-0480-r ◽

2021 ◽

pp. PHYTO-12-19-048

Author(s):

Kai Su ◽

Yinshan Guo ◽

Weihao Zhong ◽

Hong Lin ◽

Zhendong Liu ◽

...

Keyword(s):

Qtl Mapping ◽

Dna Sequencing ◽

Quantitative Trait ◽

Restriction Site ◽

Genetic Distances ◽

Snp Markers ◽

High Density ◽

White Rot ◽

Phenotypic Variance ◽

Trait Locus

Grape white rot (Coniothyrium diplodiella) is a major fungal disease affecting grape yield and quality. Quantitative trait locus (QTL) analysis is an important method for studying important horticultural traits of grapevine. This study was conducted to construct a high-density map and conduct QTL mapping for grapevine white rot resistance. A mapping population with 177 genotypes was developed from interspecific hybridization of a white rot-resistant cultivar (Vitis vinifera × V. labrusca ‘Zhuosexiang’) and white rot-susceptible cultivar (V. vinifera ‘Victoria’). Single-nucleotide polymorphism (SNP) markers were developed by restriction site-associated DNA sequencing. The female, male, and integrated maps contained 2,501, 4,110, and 6,249 SNP markers with average genetic distances of adjacent markers of 1.25, 0.77, and 0.50 cM, respectively. QTL mapping was conducted based on white rot resistance identification of 177 individuals in July and August of 2017 and 2018. Notably, one stable QTL related to white rot resistance was detected and located on linkage group LG14. The phenotypic variance ranged from 12.93 to 13.43%. An SNP marker (chr14_3929380), which cosegregated with white rot resistance, was discovered and shows potential for use in marker-assisted selection to generate new grapevine cultivars with resistance to white rot.

Download Full-text