Tomato genomic prediction for good performance under high-temperature and identification of loci involved in thermotolerance response

Cappetta, Elisa; Andolfo, Giuseppe; Guadagno, Anna; Matteo, Antonio Di; Barone, Amalia; Frusciante, Luigi; Ercolano, Maria Raffaella

doi:10.1038/s41438-021-00647-3

Cited by 26 publications

(17 citation statements)

References 93 publications

(73 reference statements)

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“…A comprehensive understanding of the molecular mechanisms that determine the relationships between important agronomic traits will help further promote breeding techniques and research to shape tomato plasticity under high temperature stress [ 13 ]. The frequent occurrence of global temperature extremes has also greatly upset the balance of carbon dioxide metabolism.…”

Section: Discussionmentioning

confidence: 99%

“…Cappetta et al evaluated the phenotypic characteristics of quantitative and qualitative traits by applying heat stress treatment to self-crossing F4 segregated populations of heat tolerant tomato varieties, and predicted several potential loci that may be involved in high temperature response by calculating the effect of a single nucleotide polymorphism (SNP)-dependent variation and combining with quantitative trait locus (QTL) analysis. This, to some extent, reveals a genome-selective (GS)-dependent approach that can control interactions between plants and high temperatures [ 13 ]. Lu and colleagues then found that after exposure to extreme heat and moderate warming, mutation rates of single-nucleotide variations (SNVs) and small indoles were increased in Arabidopsis thaliana multigenerational accumulation plants, which is associated with changes in epigenetic modifications, such as DNA methylation levels [ 18 ].…”

Section: Emerging Strategies In Vegetable Practice Managementmentioning

confidence: 99%

“…These studies and advances provide insights and guidance on genetic and epigenetic structures as well as correlations between different biological traits (i.e., yield and growth-dependent biomass) under high temperature stress. The optimized genetic prediction model is plausible as a valuable strategy to accelerate the development of heat tolerance in tomato fruits with high yield and soluble solids content [ 13 ], which is superposed with the potential impact of epigenetic improvement of breeding resources to further enrich vegetable food traits through the crop practice management [ 19 , 20 ].…”

Section: Emerging Strategies In Vegetable Practice Managementmentioning

confidence: 99%

“…Epigenetic modification enriches the diversity of genetic information in vegetable crops [ 19 ]. The evolution of heat-induced SNPs accumulation is dynamically regulated by DNA methylation [ 18 ], suggesting that epigenetic modification and environmentally induced SNP-dependent genetic selection should be considered synergistically [ 13 ].…”

Section: Emerging Strategies In Vegetable Practice Managementmentioning

confidence: 99%

“…chinensis ) [ 9 ] and a significant reduction in flower number and seed production per plant [ 10 ]. Moreover, it affects the leaf pigmentation and quality of Brassica oleracea L. [ 11 ], the yield of potato [ 12 ], as well as fruit setting rate in Solanum lycopersicum [ 13 ].…”

Section: Introductionmentioning

confidence: 99%

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Emerging Strategies Mold Plasticity of Vegetable Plants in Response to High Temperature Stress

Nie

Xing

Wang

et al. 2022

Plants

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As a result of energy consumption and human activities, a large amount of carbon dioxide emissions has led to global warming, which seriously affects the growth and development of plants. Vegetables are an indispensable part of people’s diet. In the plant kingdom, a variety of vegetables are highly sensitive to climate change. For them, an increase of just a few degrees above their optimum temperature threshold can result in a loss of yield and quality. Emerging strategies such as practice management and breeding varieties in response to above-optimal temperatures are critical for abiotic stress resistance of vegetable crops. In this study, the function and application of multiple strategies, including breeding improvement, epigenetic modification directed generation of alleles, gene editing techniques, and accumulation of mutations in multigenerational adaptation to abiotic stress, were discussed in vegetable crops. It is believed to be meaningful for plants to build plasticity under high temperature stress, thus generating more genetic structures for heat resistant traits in vegetable products.

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Section: Discussionmentioning

confidence: 99%

Section: Emerging Strategies In Vegetable Practice Managementmentioning

confidence: 99%

Section: Emerging Strategies In Vegetable Practice Managementmentioning

confidence: 99%

Section: Emerging Strategies In Vegetable Practice Managementmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Emerging Strategies Mold Plasticity of Vegetable Plants in Response to High Temperature Stress

Nie

Xing

Wang

et al. 2022

Plants

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Genomic prediction of seasonal forage yield in perennial ryegrass

Konkolewska,

Phang,

Conaghan

et al. 2023

Grassland Research

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BackgroundGenomic selection has the potential to accelerate genetic gain in perennial ryegrass breeding, provided complex traits such as forage yield can be predicted with sufficient accuracy.MethodsIn this study, we compared modelling approaches and feature selection strategies to evaluate the accuracy of genomic prediction models for seasonal forage yield production.ResultsOverall, model selection had limited impact on predictive ability when using the full data set. For a baseline genomic best linear unbiased prediction model, the highest mean predictive accuracy was obtained for spring grazing (0.78), summer grazing (0.62) and second cut silage (0.56). In terms of feature selection strategies, using uncorrelated single‐nucleotide polymorphisms (SNPs) had no impact on predictive ability, allowing for a potential decrease of the data set dimensions. With a genome‐wide association study, we found a significant SNP marker for spring grazing, located in the genic region annotated as coding for an enzyme responsible for fucosylation of xyloglucans—major components of the plant cell wall. We also presented an approach to increase interpretability of genomic prediction models with the use of Gene Ontology enrichment analysis.ConclusionsApproaches for feature selection will be relevant in development of low‐cost genotyping platforms in support of routine and cost‐effective implementation of genomic selection.

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