Genome-wide association study identifies QTL for eight fruit traits in cultivated tomato (Solanum lycopersicumL.)

Abstract

Genome-wide association study (GWAS) is effective in identifying favorable alleles for traits of interest with high mapping resolution in crop species. In this study, we conducted GWAS to explore quantitative trait loci (QTL) for eight fruit traits using 162 tomato accessions with diverse genetic backgrounds. The eight traits included fruit weight, fruit width, fruit height, fruit shape index, pericarp thickness, locule number, fruit firmness, and brix. Phenotypic variations of these traits in the tomato collection were evaluated with three replicates in field trials over three years. We filtered 34,550 confident SNPs from the 51 K Axiom® tomato array based on < 10% of missing data and > 5% of minor allele frequency for association analysis. The 162 tomato accessions were divided into seven clusters and their membership coefficients were used to account for population structure along with a kinship matrix. To identify marker-trait associations (MTAs), four phenotypic data sets representing each of three years and combined were independently analyzed in the multilocus mixed model (MLMM). A total of 30 significant MTAs was detected over data sets for eight fruit traits at P < 0.0005. The number of MTA per trait ranged from one (brix) to seven (fruit weight and fruit width). Two SNP markers on chromosomes 1 and 2 were significantly associated with multiple traits, suggesting pleiotropic effects of QTL. Furthermore, 16 of 30 MTAs suggest potential novel QTL for eight fruit traits. These results facilitate genetic dissection of tomato fruit traits and provide a useful resource to develop molecular tools for improving fruit traits via marker-assisted selection and genomic selection in tomato breeding programs.

Quantitative trait loci mapping reveals important genomic regions controlling root architecture and shoot biomass under nitrogen, phosphorus, and potassium stress in rapeseed (Brassica napus L.)

“…Out of 18 QTL clusters, 12 QTL clusters exhibited a negative additive effect, indicating the significant contribution of ZS11 toward the investigated traits. We then divided the detected QTL clusters into common and specific clusters ( Kim et al, 2021 ). Based on this, we detected two NPK-common clusters, three K-specific clusters, four N-specific clusters, four PK-specific clusters, three NK-specific clusters, and two NP-specific clusters ( Table 2 and Figure 4 ), suggesting that key loci associated with these traits under multiple environments or treatments.…”

Genome-Wide Association Study for Agro-Morphological Traits in Eggplant Core Collection

“…In this study, 20 SNPs significantly associated with fruit width were found. In a previous study, seven SNPs were identified on Ch01 (1), Ch02 (2), Ch03 (1), Ch09 (1), and Ch12 (1) that were linked with tomato fruit width (two) [ 61 ]. Some of the most significantly associated SNPs with flower size were found in genes encoding pentatricopeptide repeat-containing protein At5g14770, probable histone chaperone ASF1A, Ultraviolet-B receptor UVR8, MACPF domain-containing protein At1g14780, G2/mitotic-specific cyclin-1, two-component response regulator ORR21, and adenosine triphosphatase (ARSA1 ATPase) ( Table 6 ).…”

Epigenetics and its role in effecting agronomical traits

“…Tomatoes ( Solanum lycopersicum L.) are a globally important crop cultivated worldwide and are one of the most consumed vegetables ( Kim et al, 2021 ). The silencing of the MutS HOMOLOG1 ( MSH1 ) gene by RNAi affects growth and development.…”