scholarly journals Inferring outcrossing in the homothallic fungus Sclerotinia sclerotiorum using linkage disequilibrium decay

Heredity ◽  
2014 ◽  
Vol 113 (4) ◽  
pp. 353-363 ◽  
Author(s):  
R N Attanayake ◽  
V Tennekoon ◽  
D A Johnson ◽  
L D Porter ◽  
L del Río-Mendoza ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Sclerotinia Sclerotiorum ◽  
Linkage Disequilibrium Decay

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

2018 ◽  
Vol 35 (10) ◽  
pp. 1786-1788 ◽  
Author(s):  
Chi Zhang ◽  
Shan-Shan Dong ◽  
Jun-Yang Xu ◽  
Wei-Ming He ◽  
Tie-Lin Yang
Keyword(s):  
Linkage Disequilibrium ◽  
Linkage Disequilibrium Decay ◽  
Variant Call Format ◽  
Variant Call

The population of Sclerotinia sclerotiorum in Brazil is structured by mycelial compatibility groups

Plant Disease ◽  
2021 ◽  
Author(s):  
Rhaphael Alves Silva ◽  
Camila Geovana Ferro ◽  
Miller da Silva Lehner ◽  
Trazilbo José Paula Júnior ◽  
Eduardo S. G. Mizubuti
Keyword(s):  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
Genetic Structure ◽  
Sclerotinia Sclerotiorum ◽  
Total Population ◽  
Random Mating ◽  
Genetic Groups ◽  
Close Relationship ◽  
Mycelial Compatibility ◽  
Variable Population

The genetic structure of the population of Sclerotinia sclerotiorum was analyzed using 238 individuals collected from different hosts. Individuals were characterized for microsatellite genotypes and mycelial compatibility groups (MCGs). A total of 22 MCGs and 64 multilocus lineages (MLLs) were identified. There was a close relationship between the MCGs and MLLs, but there was no association between MLLs and hosts or regions. At least 39 MCGs are present in Brazil and 68.5% of the isolates were assigned to either MCG 1 or 2. Eight new MCGs were found. Seven genetic groups were identified and associated with MCGs. Most genetic variation (70.0%) was due to differences among MCGs. High values of estimates of linkage disequilibrium among loci were more frequent in the total population (all MCGs). In contrast, there was evidence of random mating in subpopulations defined by MCGs 1 and 2. Additionally, there was evidence of outcrossing in the population of S. sclerotiorum in Brazil. The population was structured by MCGs, lineages originated from asexual reproduction or selfing prevail and are widely distributed in space, are persistent in time and affect many hosts, but there is evidence of some degree of outcrossing which may lead to a more genetically variable population in the future.

scholarly journals Rapid linkage disequilibrium decay in the Lr10 gene in wild emmer wheat (Triticum dicoccoides) populations

2010 ◽  
Vol 122 (1) ◽  
pp. 175-187 ◽  
Author(s):  
Hanan Sela ◽  
Caroline Loutre ◽  
Beat Keller ◽  
Alan Schulman ◽  
Eviatar Nevo ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Triticum Dicoccoides ◽  
Wild Emmer Wheat ◽  
Emmer Wheat ◽  
Wild Emmer ◽  
Linkage Disequilibrium Decay

scholarly journals Sources of genomic diversity in the self-fertile plant pathogen, Sclerotinia sclerotiorum, and consequences for resistance breeding

2020 ◽  
Author(s):  
Lone Buchwaldt ◽  
Harsh Garg ◽  
Krishna D. Puri ◽  
Jonathan Durkin ◽  
Jennifer Adam ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Point Mutation ◽  
Ssr Markers ◽  
Sclerotinia Sclerotiorum ◽  
Quantitative Resistance ◽  
Life Cycles ◽  
Genomic Diversity ◽  
Western Canada ◽  
Genomic Change ◽  
Over Time

AbstractThe ascomycete, Sclerotinia sclerotiorum, has a broad host range and causes yield loss in dicotyledonous crops world wide. Genomic diversity and aggressiveness were determined in a population of 127 isolates from individual canola (Brassica napus) fields in western Canada. Genotyping with 39 simple sequence repeat (SSR) markers revealed each isolate was an unique haplotype. Analysis of molecular variation showed 97% was due to isolate and 3% to geographical location. Testing of mycelium compatibility identified clones of mutually compatible isolates, and stings of pairwise compatible isolates not seen before. Importantly, mutually compatible isolates had similar SSR haplotype, in contrast to high diversity among incompatible isolates. Isolates from the Province of Manitoba had higher allelic richness and higher mycelium compatibility (61%) than Alberta (35%) and Saskatchewan (39%). All compatible Manitoba isolates were interconnected in clones and strings, which can be explained by wetter growing seasons and more susceptible crops species both favouring more mycelium interaction and life cycles. Analysis of linkage disequilibrium rejected random recombination, consistent with a self-fertile fungus and restricted outcrossing due to mycelium incompatibility, and only one meiosis per lifecycle. More probable sources of genomic diversity is slippage during DNA replication and point mutation affecting single nucleotides, not withstanding the high mutation rate of SSRs compared to genes. It seems accumulation of these polymorphisms lead to increasing mycelium incompatibility in a population over time. A phylogenetic tree grouped isolates into 17 sub-populations. Aggressiveness was tested by inoculating one isolate from each sub-population onto B. napus lines with quantitative resistance. Results were significant for isolate, line, and isolate by line interaction. These isolates represent the genomic and pathogenic diversity in western Canada, and are suitable for resistance screening in canola breeding programs. Since the S. sclerotiorum life cycle is universal, conclusions on sources of genomic diversity extrapolates to populations in other geographical areas and host crops.Author summarySclerotinia sclerotiorum populations from various plant species and geographical areas have been studied extensively using mycelium compatibility tests and genotyping with a shared set of 6-13 SSR markers published in 2001. Most conclude the pathogen is clonally propagated with some degree of outcrossing. In the present study, a population of S. sclerotiorum isolates from 1.5 million km2 area in western Canada were tested for mycelium compatibility, and genotyped with 9 published and 30 newly developed SSR markers targeting all chromosomes in the dikaryot genome (8+8). A new way of visualizing mycelium compatibility results revealed clones of mutual compatible isolates, as well as long and short strings of pairwise compatible isolates. Importantly, clonal isolates had similar SSR haplotype, while incompatible isolates were highly dissimilar; a relationship difficult to discern previously. Analysis of population structure found a lack of linkage disequilibrium ruling out random recombination. Outcrossing, a result of alignment of non-sister chromosomes during meiosis, is unlikely in S. sclerotiorum, since mycelium incompatibility prevents karyogamy, and compatibility only occur between isolates with similar genomic composition. Instead, genomic diversity comprise transfer of nuclei through hyphal anastomosis, allelic modifications during cell division and point mutation. Genomic polymorphisms accumulate over time likely result in gradual divergence of individuals, which seems to resemble the ‘ring-species’ concept. We are currently studying whether nuclei in microconidia might also contribute to diversity. A phylogenetic analysis grouped isolates into 17 sub-populations. One isolate from each sub-population showed different level of aggressiveness when inoculated onto B. napus lines previously determined to have quantitative resistance to a single isolate. Seed of these lines and S. sclerotiorum isolates have been transferred to plant breeders, and can be requested from the corresponding author for breeding purposes. Quantitative resistance is likely to hold up over time, since the rate of genomic change is relatively slow in S. sclerotiorum.

scholarly journals Genetic ancestry, admixture, and population structure in rural Dominica

PLoS ONE ◽  
2021 ◽  
Vol 16 (11) ◽  
pp. e0258735
Author(s):  
Monica H. Keith ◽  
Mark V. Flinn ◽  
Harly J. Durbin ◽  
Troy N. Rowan ◽  
Gregory E. Blomquist ◽  
...  
Keyword(s):  
Population Structure ◽  
Linkage Disequilibrium ◽  
Clustering Algorithm ◽  
African Ancestry ◽  
Genetic Ancestry ◽  
Linkage Disequilibrium Decay ◽  
Eastern Coast ◽  
Population Genetic Study ◽  
Post Colonial ◽  
Family Based

The Caribbean is a genetically diverse region with heterogeneous admixture compositions influenced by local island ecologies, migrations, colonial conflicts, and demographic histories. The Commonwealth of Dominica is a mountainous island in the Lesser Antilles historically known to harbor communities with unique patterns of migration, mixture, and isolation. This community-based population genetic study adds biological evidence to inform post-colonial narrative histories in a Dominican horticultural village. High density single nucleotide polymorphism data paired with a previously compiled genealogy provide the first genome-wide insights on genetic ancestry and population structure in Dominica. We assessed family-based clustering, inferred global ancestry, and dated recent admixture by implementing the fastSTRUCTURE clustering algorithm, modeling graph-based migration with TreeMix, assessing patterns of linkage disequilibrium decay with ALDER, and visualizing data from Dominica with Human Genome Diversity Panel references. These analyses distinguish family-based genetic structure from variation in African, European, and indigenous Amerindian admixture proportions, and analyses of linkage disequilibrium decay estimate admixture dates 5–6 generations (~160 years) ago. African ancestry accounts for the largest mixture components, followed by European and then indigenous components; however, our global ancestry inferences are consistent with previous mitochondrial, Y chromosome, and ancestry marker data from Dominica that show uniquely higher proportions of indigenous ancestry and lower proportions of African ancestry relative to known admixture in other French- and English-speaking Caribbean islands. Our genetic results support local narratives about the community’s history and founding, which indicate that newly emancipated people settled in the steep, dense vegetation along Dominica’s eastern coast in the mid-19th century. Strong genetic signals of post-colonial admixture and family-based structure highlight the localized impacts of colonial forces and island ecologies in this region, and more data from other groups are needed to more broadly inform on Dominica’s complex history and present diversity.

scholarly journals Linkage Disequilibrium Decay and Haplotype Block Structure in the Pig

Genetics ◽  
2008 ◽  
Vol 179 (1) ◽  
pp. 569-579 ◽  
Author(s):  
Andreia J. Amaral ◽  
Hendrik-Jan Megens ◽  
Richard P. M. A. Crooijmans ◽  
Henri C. M. Heuven ◽  
Martien A. M. Groenen
Keyword(s):  
Linkage Disequilibrium ◽  
Haplotype Block ◽  
Block Structure ◽  
Linkage Disequilibrium Decay ◽  
Haplotype Block Structure

Persistence of modern varieties and hybrids of carrots and its dependence on the biochemical composition

2020 ◽  
pp. 16-19
Author(s):  
Е.В. Янченко
Keyword(s):  
Botrytis Cinerea ◽  
Sclerotinia Sclerotiorum ◽  
Dry Matter ◽  
Inverse Correlation ◽  
Dry Weight ◽  
Matter Content ◽  
White Rot ◽  
Dry Matter Content ◽  
Important Indicator ◽  
Modern Varieties

Цель исследований – дать оценку сохраняемости и болезнеустойчивости современных сортов и гибридов моркови столовой и определить корреляционные зависимости влияния биохимических показателей качества на сохраняемость и степень поражения моркови столовой различными видами болезней в процессе хранения. Исследования проводились в 2011–2016 годах во ВНИИО – филиале ФГБНУ ФНЦО по общепринятым методикам. В биохимической лаборатории отдела земледелия и агрохимии содержание сухого вещества определяли высушиванием до абсолютно сухого веса, общего сахара – по Бертрану, аскорбиновой кислоты – по Мурри, нитраты – ионоселективным методом. При характеристике моркови столовой важнейший показатель, определяющий его качество – количество сухого вещества и сахаров. В процессе хранения были выявлены следующие болезни моркови: серая гниль (Botrytis cinerea Pers. ex Fr.), белая гниль (Sclerotinia sclerotiorum (Lib.)), белая парша (Rhizoctonia carotae Rad.), альтернариоз (Alternaria radicina M., Dr. et E.). В большей степени сортообразцы моркови столовой поражались серой гнилью. Лучшими по сохраняемости сортообразцами были Корсар (94,6%), F1Берлин (94,5%), Берликум Роял (94,1%) и F1 Звезда (94%). Сохраняемость у зарубежных сортов и гибридов моркови столовой была немного выше, чем у отечественных (на 0,4%) как за счет меньшей величины убыли массы (6,3% против 6,4%), так и потерь от болезней (1,6% против 1,9%). Сохраняемость корнеплодов моркови находится в прямой корреляционной зависимости от содержания сухого вещества (r=+0,41), каротиноидов (r=+0,39), моносахаров (r­=+0,30) и суммы сахаров (r=+0,27). Проявление серой гнили находится в обратной корреляционной связи с содержанием сухого вещества и каротиноидов (r=-0,37 и r=-0,35 соответственно), белой парши – в прямой корреляции с содержанием сухого вещества , моносахаров и дисахаров (r= +0,21; r= +0,39; r= -0,41 соответственно), белой гнили в обратной корреляционной связи с содержанием сухого вещества, моносахаров и дисахаров. The purpose of the research is to assess the persistence and disease resistance of modern varieties and hybrids of carrots and to determine the correlation between the influence of biochemical quality indicators on the persistence and degree of damage to carrots by various types of diseases during storage. The research was conducted in 2011–2016 at ARRIVG – branch of FSBSI FSVC, according to generally accepted methods. In the biochemical laboratory of the Department of Agriculture and Agrochemistry, the dry matter content was determined by drying to absolutely dry weight, total sugar – by Bertran, ascorbic acid – by Murri, nitrates – by the ion-selective method. When describing carrots, the most important indicator that determines its quality is the amount of dry matter and sugars. During storage, the following diseases of carrots were detected: gray rot (Botrytis cinerea Pers. ex Fr.), white rot (Sclerotinia sclerotiorum (Lib.), white scab (Rhizoctonia carotae Rad.), alternariasis (Alternaria radicina M., Dr. et E.). To a greater extent, varieties of table carrots were affected by gray rot. The best preserved varieties were Corsar (94.6%), F1 Berlin (94.5%), Berlicum Royal (94.1%) and F1 Zvezda (94%). The persistence of foreign varieties and hybrids of table carrots was slightly higher than that of domestic ones by 0.4%. both due to a smaller amount of weight loss (6.3% vs. 6.4%) and losses from diseases (1.6% vs. 1.9%). The persistence of carrot root crops is directly correlated with the content of dry matter (r=+0.41), carotenoids (r=+0.39), monosaccharides (r=+0.30) and the amount of sugars (r=+0.27). The manifestation of gray rot is in inverse correlation with the content of dry matter and carotenoids (r=-0.37 and r=-0.35, respectively), white scab is in direct correlation with the content of dry matter (r= +0.21; r= +0.39; r= –0.41, respectively), white rot is in inverse correlation with the content of dry matter, monosaccharides and disaccharides.

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