Diversity and genetic architecture of agro-morphological traits in a core collection of European traditional tomato

Abstract

European traditional tomato varieties have been selected by farmers given their consistent performance and adaptation to local growing conditions. Here we developed a multipurpose core collection, comprising 226 accessions representative of the genotypic, phenotypic and geographical diversity present in European traditional tomatoes, to investigate the basis of their phenotypic variation, G×E interactions and stability for 33 agro-morphological traits. Comparison of the traditional varieties with a modern reference panel revealed that some traditional varieties displayed excellent agronomic performance and high trait stability, as good as or better than that of their modern counterparts. We conducted genome-wide association and genome-wide environment interaction studies and detected 141 quantitative trait loci (QTLs). Out of those, 47 QTLs were associated with the phenotype mean (meanQTLs) and 41 with stability (stbQTLs) and 53 QTL-by-environment interactions (QTIs). Most QTLs displayed additive gene actions, with the exception of stbQTLs, which were mostly recessive and overdominant QTLs. Both common and specific loci controlled the phenotype mean and stability variation in traditional tomato; however, a larger proportion of specific QTLs was observed, indicating that the stability gene regulatory model is the predominant one. Developmental genes tended to map close to meanQTLs, while genes involved in stress response, hormone metabolism and signalling were found within regions affecting stability. A total of 137 marker trait associations for phenotypic means and stability were novel, and therefore our study enhances the understanding of the genetic basis of valuable agronomic traits and opens a new avenue for an exploitation of the allelic diversity available within European traditional tomato germplasm.

Meta-QTL and Candidate Gene Analyses of Agronomic Salt Tolerance and Related Traits in an RIL Population Derived from Solanum pimpinellifolium

“…A summary of coincidences is shown in Table 2 . Remarkable examples of frequent coincidences are MQTL2.2 [ 21 , 24 , 52 , 53 , 54 ], MQTL3 [ 23 , 54 , 55 ], MQTL4.1 [ 22 , 23 , 56 ], MQTL5 [ 23 , 24 , 56 ], and MQTL7.2 [ 56 , 57 , 58 ]. Such frequent coincidences seem to indicate that these MQTLs control tomato productivity across populations and cultivation conditions.…”

“…The development of marker technology has allowed both the saturation of genetic maps and their anchorage to the tomato physical map, which makes candidate gene analysis within QTL regions feasible. Nowadays, several genome-wide association studies (GWAS) using agronomically characterized tomato germplasm collections [ 21 , 22 , 23 , 24 ] have, theoretically, increased the resolution of QTL mapping relative to bi-parental populations. However, the evaluation of agronomic salt tolerance in wild germplasm seems too complex for this QTL methodology [ 3 , 16 ].…”

Impacte de la Reducció del Reg i de la Fertilització Nitrogenada en la Tomaca Valenciana

“…També s'observa que Valenciana III és més variable en la resposta per a la combinació dels dos caràcters que Valenciana II (Figura 2), indicant que Valenciana II és més estable per a aquesta combinació de caràcters. A aquest respecte, altres estudis han mostrat importants variacions en l'estabilitat de diferents materials de tomaca (Pons et al, 2023).…”

Identificació de marcadors genètics i fenotípics per a les tipologies de Tomata Valenciana utilitzant l' Atles de Tomata Tradicional Europea

“…En aquestes regions s'han desenvolupat un gran nombre de varietats locals de consum en fresc, llarga vida i processat adaptades al medi on es cultiven, amb fruits de diferents formes i colors. Estudis recents en una col•lecció de més de 1500 tomàquets tradicionals europeus (Blanca et al, 2022;Pons et al, 2023Pons et al, , 2022 han revelat una àmplia variabilitat gentica i fenotípica en la tomata tradicional Europa. Aquesta diversificació sembla que ha estat especialment dirigida per trets relacionats amb la forma i el tamany del fruit, principalment associats a l'ús culinari diferent en cada país i regió (Pons et al, 2022).…”