bims-plasge 2020-10-04 papers

Issue of 2020–10–04
two papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Nat Genet. 2020 Oct;52(10): 1111-1121

Analysis of wild tomato introgression lines elucidates the genetic basis of transcriptome and metabolome variation underlying fruit traits and pathogen response.

Jędrzej Szymański, Samuel Bocobza, Sayantan Panda, Prashant Sonawane, Pablo D Cárdenas, Justin Lashbrooke, Avinash Kamble, Nir Shahaf, Sagit Meir, Arnaud Bovy, Jules Beekwilder, Yury Tikunov, Irene Romero de la Fuente, Dani Zamir, Ilana Rogachev, Asaph Aharoni.

Wild tomato species represent a rich gene pool for numerous desirable traits lost during domestication. Here, we exploited an introgression population representing wild desert-adapted species and a domesticated cultivar to establish the genetic basis of gene expression and chemical variation accompanying the transfer of wild-species-associated fruit traits. Transcriptome and metabolome analysis of 580 lines coupled to pathogen sensitivity assays resulted in the identification of genomic loci associated with levels of hundreds of transcripts and metabolites. These associations occurred in hotspots representing coordinated perturbation of metabolic pathways and ripening-related processes. Here, we identify components of the Solanum alkaloid pathway, as well as genes and metabolites involved in pathogen defense and linking fungal resistance with changes in the fruit ripening regulatory network. Our results outline a framework for understanding metabolism and pathogen resistance during tomato fruit ripening and provide insights into key fruit quality traits.

DOI: https://doi.org/10.1038/s41588-020-0690-6

Sci Rep. 2020 Sep 28. 10(1): 15925

Meta-analysis of QTL reveals the genetic control of yield-related traits and seed protein content in pea.

Anthony Klein, Hervé Houtin, Céline Rond-Coissieux, Myriam Naudet-Huart, Michael Touratier, Pascal Marget, Judith Burstin.

Pea is one of the most important grain legume crops in temperate regions worldwide. Improving pea yield is a critical breeding target. Nine inter-connected pea recombinant inbred line populations were evaluated in nine environments at INRAE Dijon, France and genotyped using the GenoPea 13.2 K SNP array. Each population has been evaluated in two to four environments. A multi-population Quantitative Trait Loci (QTL) analysis for seed weight per plant (SW), seed number per plant (SN), thousand seed weight (TSW) and seed protein content (SPC) was done. QTL were then projected on the multi-population consensus map and a meta-analysis of QTL was performed. This analysis identified 17 QTL for SW, 16 QTL for SN, 35 QTL for TSW and 21 QTL for SPC, shedding light on trait relationships. These QTL were resolved into 27 metaQTL. Some of them showed small confidence intervals of less than 2 cM encompassing less than one hundred underlying candidate genes. The precision of metaQTL and the potential candidate genes reported in this study enable their use for marker-assisted selection and provide a foundation towards map-based identification of causal polymorphisms.

DOI: https://doi.org/10.1038/s41598-020-72548-9