Detection of QTLs for genotype × environment interactions in tomato seeds and seedlings

Abstract

Seed quality and seedling establishment are the most important factors affecting successful crop development. They depend on the genetic background and are acquired during seed maturation and therefor, affected by the maternal environment under which the seeds develop. There is little knowledge about the genetic and environmental factors that affect seed quality and seedling establishment. The aim of this study is to identify the loci and possible molecular mechanisms involved in acquisition of seed quality and how these are controlled by adverse maternal conditions. For this, we used a tomato recombinant inbred line (RIL) population consisting of 100 lines which were grown under two different nutritional environmental conditions, high phosphate and low nitrate. Most of the seed germination traits such as maximum germination percentage (G max ), germination rate (t 50 ) and uniformity (U 8416 ) showed ample variation between genotypes and under different germination conditions. This phenotypic variation leads to identification of quantitative trait loci (QTLs) which were dependent on genetic factors, but also on the interaction with the maternal environment (QTL × E). Further studies of these QTLs may ultimately help to predict the effect of different maternal environmental conditions on seed quality and seedling establishment which will be very useful to improve the production of high‐performance seeds.

Genetic and maturation environmental modulation of tomato dry seed metabolites

“…A few mQTLs co-located with the phenotypic QTLs that have been detected in a previous study (Geshnizjani et al 2020). For instance, the QTLs on the middle of chromosome 10 affecting galactarate and malate colocated with ones influencing uniformity of germination (U 8416 ) at different germination conditions, such as high temperature, mannitol, water and NaCl.…”

“…Moneymaker (MM) × S. pimpinellifolium(PI) accession G1.1554 (Voorrips et al 2000) have been genotyped with 865 single nucleotide polymorphism (SNP) markers. The F 8 population was grown in two different nutritional maturation environments as previously described (Geshnizjani et al 2020). The fully ripened fruits were collected and the seeds were extracted and dried as previously reported (Chapter 2).…”

“…In order to assess the relationship between metabolites and seed phenotypic traits, seed performance phenotypes which were previously assessed for the same seeds (Geshnizjani et al 2020), were integrated into the metabolic correlation matrix (Figure 7 ). We found many positive and negative correlations between metabolites and phenotypic traits.…”

Plasticity of maternal environment dependent expression-QTLs of tomato seeds

“…More specifically, seed performance/germination in species such as tomato and the model plant Arabidopsis thaliana is determined during seed development and maturation, and depends on temperature [6][7][8], photoperiod [9,10], nutrient composition and levels [8,11,12]. Seed quality, germination and seedling establishment traits also have strong genetic determinants and (natural) genetic variation in quality traits, including Quantitative Trait Loci (QTLs), have been reported [8,[12][13][14][15][16][17].…”

“…For instance, wild cultivars have been used in genetic screens and genome wide association studies (GWAS) to discover genomic loci and genes involved in variation in metabolic traits [38][39][40][41][42], insect resistance [43], floral meristem identity [31], trichome formation [44], and fruit shape and size [28,34,45]. In addition to GWAS, Recombinant Inbred Line (RIL) populations, derived from experimental crossing between S. lycopersicum and S. pimpinellifolium, are frequently used to uncover the effect of genetic variation on tomato traits [46][47][48][49][50][51][52], including various seed quality traits [12,14,15,17,53,54].…”