scholarly journals Genomic regions associated with virulence in Setosphaeria turcica identified by linkage mapping in a biparental population

2021 ◽  
pp. 103655
Author(s):  
Pummi Singh ◽  
Shun-Yuan Huang ◽  
Alvaro G. Hernandez ◽  
Pragya Adhikari ◽  
Tiffany M. Jamann ◽  
...  
Keyword(s):  
Linkage Mapping ◽  
Setosphaeria Turcica ◽  
Biparental Population ◽  
Genomic Regions

Genetic Linkage Mapping of Genomic Regions Conferring Tolerance to High Aluminum in Slash Pine

1999 ◽  
Vol 10 (1-2) ◽  
pp. 69-78 ◽  
Author(s):  
T. L. Kubisiak ◽  
C. D. Nelson ◽  
J. Nowak ◽  
A. L. Friend
Keyword(s):  
Linkage Mapping ◽  
Genetic Linkage ◽  
Slash Pine ◽  
Genetic Linkage Mapping ◽  
Genomic Regions ◽  
High Aluminum

scholarly journals 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

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.

scholarly journals Population history of the Northern corn leaf blight fungal pathogen Setosphaeria turcica in Europe

2020 ◽  
Author(s):  
Mireia Vidal-Villarejo ◽  
Fabian Freund ◽  
Hendrik Hanekamp ◽  
Andreas von Tiedemann ◽  
Karl Schmid
Keyword(s):  
Genetic Diversity ◽  
Population Growth ◽  
Central Europe ◽  
Fungal Pathogen ◽  
Rapid Expansion ◽  
Setosphaeria Turcica ◽  
Northern Corn Leaf Blight ◽  
Maize Cultivation ◽  
Genomic Regions ◽  
Corn Leaf Blight

AbstractSetosphaeria turcica is a major fungal pathogen of maize and causes the foliar disease Northern corn leaf blight (NCLB). It originates from tropical regions and expanded into Central Europe since the 1980s, simultaneously with a rapid increase of maize cultivation area in this region. To investigate evolutionary processes influencing the rapid expansion of S. turcica we sequenced 121 isolates from Central Europe, Western Europe and Kenya. Population genetic inference revealed five genetically distinct clusters that differ by their geographic distribution and emergence dates. One genetically diverse cluster is restricted to Kenya, and the four European clusters consist of three distinct clonal lineages with low genetic diversity and one genetically diverse cluster with several clonal sublineages. A comparison of two different coalescent models for genetic diversity in the most frequent and geographically widespread clonal lineage in Europe supported a model of neutral, strongly exponential population growth over models accounting for different types of selection. In contrast to Kenyan isolates, European isolates did not show sexual recombination despite the presence of both mating types MAT1-1 and MAT1-2 in Europe. Within clonal lineages phenotypic variation in virulence to different monogenic resistances likely originated from repeated de novo mutations in virulence genes of S. turcica. k-mer based association mapping between genetic clusters did not identify genomic regions associated with pathogen races but few genomic regions that are significantly differentiated between two clonal lineages and contain putative effector genes. Our results suggest that the rapid colonization of Europe by different clonal lineages of S. turcica was not driven by selection of virulent races but reflects a neutral demographic process of fast pathogen population growth fostered by a rapid expansion of the maize cultivation area in this region.

scholarly journals A combined BSA-Seq and linkage mapping approach identifies genomic regions associated with Phytophthora root and crown rot resistance in squash

2020 ◽  
Author(s):  
Gregory Vogel ◽  
Kyle E. LaPlant ◽  
Michael Mazourek ◽  
Michael A. Gore ◽  
Christine D. Smart
Keyword(s):  
Disease Severity ◽  
Linkage Mapping ◽  
Prediction Models ◽  
Bulked Segregant Analysis ◽  
Phytophthora Capsici ◽  
Multiple Linear Regression Model ◽  
Crown Rot ◽  
Phenotypic Variance ◽  
Root And Crown Rot ◽  
Genomic Regions

AbstractPhytophthora root and crown rot, caused by the soilborne oomycete pathogen Phytophthora capsici, leads to severe yield losses in squash (Cucurbita pepo). To identify quantitative trait loci (QTL) involved in resistance to this disease, we crossed a partially resistant squash breeding line with a susceptible zucchini cultivar and evaluated over 13,000 F2 seedlings in a greenhouse screen. Bulked segregant analysis with whole genome resequencing (BSA-Seq) resulted in the identification of five genomic regions – on chromosomes 4, 5, 8, 12, and 16 – featuring significant allele frequency differentiation between susceptible and resistant bulks in each of two independent replicates. In addition, we conducted linkage mapping using a population of 176 F3 families derived from individually genotyped F2 individuals. Variation in disease severity among these families was best explained by a four-QTL model, comprising the same loci identified via BSA-Seq on chromosomes 4, 5, and 8 as well as an additional locus on chromosome 19, for a combined total of six QTL identified between both methods. Loci, whether those identified by BSA-Seq or linkage mapping, were of small to moderate effect, collectively accounting for 28-35% and individually for 2-10% of the phenotypic variance explained. However, a multiple linear regression model using one marker in each BSA-Seq QTL could predict F2:3 disease severity with only a slight drop in cross-validation accuracy compared to genomic prediction models using genome-wide markers. These results suggest that marker-assisted selection could be a suitable approach for improving Phytophthora crown and root rot resistance in squash.

scholarly journals Combining QTL-seq and linkage mapping to uncover the genetic basis of single vs. paired spikelets in the advanced populations of two-ranked maize×teosinte

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhengjie Chen ◽  
Dengguo Tang ◽  
Kun Hu ◽  
Lei Zhang ◽  
Yong Yin ◽  
...  
Keyword(s):  
Fine Mapping ◽  
Linkage Mapping ◽  
Genetic Basis ◽  
Recurrent Selection ◽  
Epistatic Effect ◽  
Phenotypic Variance ◽  
Epistatic Qtl ◽  
Maize Domestication ◽  
Genomic Regions ◽  
Mapping Populations

Abstract Background Teosinte ear bears single spikelet, whereas maize ear bears paired spikelets, doubling the number of grains in each cupulate during maize domestication. In the past 20 years, genetic analysis of single vs. paired spikelets (PEDS) has been stagnant. A better understanding of genetic basis of PEDS could help fine mapping of quantitative trait loci (QTL) and cloning of genes. Results In this study, the advanced mapping populations (BC3F2 and BC4F2) of maize × teosinte were developed by phenotypic recurrent selection. Four genomic regions associated with PEDS were detected using QTL-seq, located on 194.64–299.52 Mb, 0–162.80 Mb, 12.82–97.17 Mb, and 125.06–157.01 Mb of chromosomes 1, 3, 6, and 8, respectively. Five QTL for PEDS were identified in the regions of QTL-seq using traditional QTL mapping. Each QTL explained 1.12–38.05% of the phenotypic variance (PVE); notably, QTL qPEDS3.1 with the average PVE of 35.29% was identified in all tests. Moreover, 14 epistatic QTL were detected, with the total PVE of 47.57–66.81% in each test. The QTL qPEDS3.1 overlapped with, or was close to, one locus of 7 epistatic QTL. Near-isogenic lines (NILs) of QTL qPEDS1.1, qPEDS3.1, qPEDS6.1, and qPEDS8.1 were constructed. All individuals of NIL-qPEDS6.1(MT1) and NIL-qPEDS8.1(MT1) showed paired spikelets (PEDS = 0), but the flowering time was 7 days shorter in the NIL-qPEDS8.1(MT1). The ratio of plants with PEDS > 0 was low (1/18 to 3/18) in the NIL-qPEDS1.1(MT1) and NIL-qPEDS3.1(MT1), maybe due to the epistatic effect. Conclusion Our results suggested that major QTL, minor QTL, epistasis and photoperiod were associated with the variation of PEDS, which help us better understand the genetic basis of PEDS and provide a genetic resource for fine mapping of QTL.

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