Development of highly validated SNP markers for genetic analyses of chestnut species

Larue, Clément; Guichoux, Erwan; Laurent, Benoit; Barreneche, Teresa; Robin, Cécile; Massot, Marie; Delcamp, Adline; Petit, Rémy J.

doi:10.1007/s12686-021-01220-9

Cited by 6 publications

(11 citation statements)

References 28 publications

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“…Briefly, in May 2018, we collected one or two young leaves from all trees. We isolated DNA from 50 mg of leaves using a custom‐made CTAB protocol with 1.4 M NaCl lysis buffer (Larue, Guichoux, et al, 2021). We then assigned each tree to a species (Larue, Guichoux, et al, 2021).…”

Section: Methodsmentioning

confidence: 99%

“…All samples were stored at −20°C until DNA isolation. We isolated DNA from 50 mg of chestnut tissue using CTAB custom DNA isolation protocol for 96 well plate format with 2.4 M NaCl lysis buffer (Larue, Guichoux, et al, 2021). We checked the quality of isolated DNA with a spectrophotometer Thermo Scientific NanoDrop 8000.…”

Section: Fruit Sampling and Dna Isolationmentioning

confidence: 99%

“…We characterized all individuals at 79 SNP using Agena MassARRAY Platform (Larue, Guichoux, et al, 2021) and checked the raw data using MassARRAY Typer Analyser 4.0.26.75 (Agena Biosciences).…”

Section: Snp Genotypingmentioning

confidence: 99%

“…By focusing on an exhaustively sampled isolated chestnut population (Larue, Barreneche, & Petit, 2021a), we hope to source most fruits to their corresponding pollen donor using powerful genotyping techniques (Larue, Guichoux, et al, 2021). This should provide detailed description of the pollen pool sampled by each mother tree.…”

Section: Introductionmentioning

confidence: 99%

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Sexual interference revealed by joint study of male and female pollination success in chestnut

2022

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Most seed plants produce both pollen and ovules. In principle, pollen export could interfere with pollen import through self‐pollination, resulting in ovule usurpation and reduced fruit set. Evidence for such interference exists under experimental settings but its importance under natural conditions is unknown. To test for sexual interference in nature, it is necessary to study together mating system, through paternity analyses, and fruit set, the proportion of flowers giving seeds or fruits. We developed a new model combining both processes, using chestnut (Castanea) as case study. We carried out a paternity analysis in an intensively studied plot of 273 trees belonging to three interfertile chestnut species and including a range of individuals with more or less functional stamens, resulting in a large data set of 1924 mating events. We then measured fruit set on 216 of these trees. Fruit set of male‐fertile trees was much lower than that of male‐sterile trees. Our process‐based model shows that pollen is not limiting in the study site and hence cannot account for reduced fruit set. It also indicates that self‐pollination is high (74%) but selfing rate is low (4%). Self‐pollen is less competitive than cross‐pollen, reducing sexual interference, but not sufficiently, as many ovules end up being self‐fertilized, 95% of which abort before fruit formation, resulting in the loss of 46% of the fruit crop. These results suggest that the main cause of reduced reproductive potential in chestnut is sexual interference by self‐pollen, raising questions on its evolutionary origins.

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Section: Methodsmentioning

confidence: 99%

Section: Fruit Sampling and Dna Isolationmentioning

confidence: 99%

Section: Snp Genotypingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Sexual interference revealed by joint study of male and female pollination success in chestnut

2022

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“…Genes involved in adaptation have been linked to precipitations, indicating that drought resistance plays a role in species survival in given areas. In conclusion, our work will be of great use in the future as it lays the foundations for the development of specific markers that could be used to identify adaptive genetic variation and further develop SNPs, as was commenced by Larue et al [50].…”

Section: Discussionmentioning

confidence: 92%

Assessing the Genetic Identity of Tuscan Sweet Chestnut (Castanea sativa Mill.)

Cavallini

Lombardo

Binelli

et al. 2022

Forests

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The sweet chestnut (Castanea sativa Mill.) is an important species of European trees, studied for both ecological and economic reasons. Its cultivation in the Italian peninsula can be linked to the Roman period and has been documented, especially in the Tuscan region, for centuries. We sampled 131 grafted trees from three separate areas to determine the genetic variability between populations and assess genetic identity for different varieties of trees, which is useful for future breeding programs and propagation efforts. Molecular analyses were performed using eight microsatellite loci. A total of 98 alleles was detected with an average of 12.3 alleles per locus. We found high levels of genetic diversity within the varieties of the same area, ranging between He = 0.682–0.745. Of the eight loci, seven were found to be at Hardy-Weinberg equilibrium. (FST values Differentiation between cultivation areas was significant between 0.052–0.147) with the two Southern Tuscan areas showing the closest relationship as also indicated by Bayesian inference of the population structure, which revealed the existence of three ancestral gene pools of origin. Demographic events were detected by a coalescent-based approximate Bayesian computation in two of the homogeneous clusters. This work is a step forward for the conservation of this iconic species, albeit at a regional level, as chestnut varieties have never received the full attention of breeders.

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An intensive study plot to investigate chestnut tree reproduction

Larue

Barreneche

Petit

2021

Annals of Forest Science

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Key message Pollination is a key step for fruit production. To provide a tool for future in-depth analysis of pollination in chestnut, we describe in detail a chestnut orchard (location, genotype, phenotype and seed-set of all trees). Context Chestnuts, which are insect-pollinated trees, have been massively planted around the world for nut production. Orchards are planted with clonal varieties selected from crosses between the European chestnuts (Castanea sativa) and Japanese chestnuts (C. crenata) or Chinese chestnuts (C. mollissima) because these two last species are tolerant to blight and ink diseases. Aims To characterize chestnut genetic resources and accurately model male and female fitness as well as pollen exchanges in orchards, we characterized all chestnuts of the INRAE chestnut germplasm collection located near Bordeaux (France). Methods All chestnut trees were geolocated and genotyped using 79 SNP and 98 SSR loci. We scored their flowering phenology using chestnut BBCH scale and precisely described their phenotype (height, diameter a breast height (DBH), canopy diameter…), their capacity to produce pollen (flower type, catkins length…) and their fruit production (number of burrs, seed-set…). Results We geolocated 275 trees and genotyped 273 of them. We identified 115 unique genotypes and assigned each genotype to species. To assess phenology, we evaluated 244 trees twice a week, for 6 weeks from early June to mid-July. We also described tree phenotypes with 11 variables, pollen production with 5 variables and fruit production with 3 variables. All measures were recorded in 2018 except seed set that was measured two consecutive years, in 2018 and 2019. Conclusion The data collected is very detailed and allows modelling precisely pollen exchanges between trees. Parts of this data have been successfully published in scientific articles. Data are available at: https://data.inrae.fr/dataset.xhtml?persistentId=doi:10.15454/GSJSWW Associated metadata are available at:https://metadata-afs.nancy.inra.fr/geonetwork/srv/fre/catalog.search#/metadata/02c5ca07-1536-4f89-9a0c-9e8d44a91287

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Development of highly validated SNP markers for genetic analyses of chestnut species

Cited by 6 publications

References 28 publications

Sexual interference revealed by joint study of male and female pollination success in chestnut

Sexual interference revealed by joint study of male and female pollination success in chestnut

Assessing the Genetic Identity of Tuscan Sweet Chestnut (Castanea sativa Mill.)

An intensive study plot to investigate chestnut tree reproduction

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