A Genetic Map and Linkage Panel for the Large-fruited Fresh-market Tomato

Bhandari, Prashant; Lee, Tong Geon

doi:10.21273/jashs04999-20

Cited by 10 publications

(14 citation statements)

References 28 publications

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“…For the raw reads, the quality controls were as follows: i) all positions having average Phred quality scores 30 or higher, ii) read without adapter sequence(s), and iii) read with ambiguous nucleotides (i.e., Ns) < 10%. In addition to the sequence reads we generated in this study, 63 raw read datasets of contemporary U.S. fresh-market tomatoes, which were generated by using the same technical conditions and quality control as described here, were obtained from our previous studies [ 23 , 97 ].…”

Section: Methodsmentioning

confidence: 99%

Genetic architecture of fresh-market tomato yield

2023

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Background The fresh-market tomato (Solanum lycopersicum) is bred for direct consumption and is selected for a high yield of large fruits. To understand the genetic variations (distinct types of DNA sequence polymorphism) that influence the yield, we collected the phenotypic variations in the yields of total fruit, extra-large-sized fruit, small-sized fruit, or red-colored fruit from 68 core inbred contemporary U.S. fresh-market tomatoes for three consecutive years and the genomic information in 8,289,741 single nucleotide polymorphism (SNP) positions from the whole-genome resequencing of these tomatoes. Results Genome-wide association (GWA) mapping using the SNP data with or without SNP filtering steps using the regularization methods, validated with quantitative trait loci (QTL) linkage mapping, identified 18 significant association signals for traits evaluated. Among them, 10 of which were not located within genomic regions previously identified as being associated with fruit size/shape. When mapping-driven association signals [558 SNPs associated with 28 yield (component) traits] were used to calculate genomic estimated breeding values (GEBVs) of evaluated traits, the prediction accuracies of the extra-large-sized fruit and small-sized fruit yields were higher than those of the total and red-colored fruit yields, as we tested the generated breeding values in inbred tomatoes and F2 populations. Improved accuracy in GEBV calculation of evaluated traits was achieved by using 364 SNPs identified using the regularization methods. Conclusions Together, these results provide an understanding of the genetic variations underlying the heritable phenotypic variability in yield in contemporary tomato breeding and the information necessary for improving such economically important and complex quantitative trait through breeding.

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Section: Methodsmentioning

confidence: 99%

Genetic architecture of fresh-market tomato yield

2023

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“…WGS of tomato accessions obtained from the Tomato Genetics Resource Center and Fla. lines was conducted using an Illumina HiSeq instrument as described in our previous study (Bhandari & Lee, 2021 ). The sequencing libraries were sequenced on average of 23 Gb for each tomato.…”

Section: Methodsmentioning

confidence: 99%

“…Resource Center and Fla. lines was conducted using an Illumina HiSeq instrument as described in our previous study (Bhandari & Lee, 2021).…”

Section: Wgs Of Tomato Accessions Obtained From the Tomato Geneticsmentioning

confidence: 99%

“…In particular, large‐fruited fresh‐market tomatoes cultivated in the United States (also called round tomatoes or beefsteak tomatoes) represent a unique type (fruit class) of tomato that is bred for direct consumption (Bhandari & Lee, 2021 ). These tomatoes account for more than $600 million per year in farm cash receipts (Florida Tomato Exchange, 2022 ).…”

Section: Introductionmentioning

confidence: 99%

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A mutant allele of the flowering promoting factor 1 gene at the tomato BRACHYTIC locus reduces plant height with high quality fruit

et al. 2022

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Reduced plant height due to shortened stems is beneficial for improving crop yield potential, better resilience to biotic/abiotic stresses, and rapid crop producer adoption of the agronomic and management practices. Breeding tomato plants with a reduced height, however, poses a particular challenge because this trait is often associated with a significant fruit size (weight) reduction. The tomato BRACHYTIC (BR) locus controls plant height. Genetic mapping and genome assembly revealed three flowering promoting factor 1 ( FPF1 ) genes located within the BR mapping interval, and a complete coding sequence deletion of the telomere proximal FPF1 ( Solyc01g066980 ) was found in the br allele but not in BR . The knock‐out of Solyc01g066980 in BR large‐fruited fresh‐market tomato reduced the height and fruit yield, but the ability to produce large size fruits was retained. However, concurrent yield evaluation of a pair of sister lines with or without the br allele revealed that artificial selection contributes to commercially acceptable yield potential in br tomatoes. A network analysis of gene‐expression patterns across genotypes, tissues, and the gibberellic acid (GA) treatment revealed that member(s) of the FPF1 family may play a role in the suppression of the GA biosynthesis in roots and provided a framework for identifying the responsible molecular signaling pathways in br ‐mediated phenotypic changes. Lastly, mutations of br homologs also resulted in reduced height. These results shed light on the genetic and physiological mechanisms by which the br allele alters tomato architecture.

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“…In this study, we used the R environment (version 4.1.1; [ 21 ]) with the R/qtl package (version 1.50; [ 22 ]) on both a stand-alone Windows operating PC and the UF/Research Computing Linux server, HiPerGator 3.0 [ 23 ]. A genetic map created for tomato ( Solanum lycopersicum ) [ 24 ] was used to simulate two different sized F 2 populations using the R/qtl function sim.cross(): F 2 individuals with 1000 (hereafter referred to as population #1) and 100 (hereafter referred to as population #2) to mimic mapping populations or breeding studies. Four simulated QTL were positioned at 5 cM on each of chromosomes 1, 5, 7, and 12, and simulated to have additive effect sizes of 1.0, 0.5, 0.2, and 0.2, respectively (Additional file 1 ).…”

Section: Methodsmentioning

confidence: 99%

postQTL: a QTL mapping R workflow to improve the accuracy of true positive loci identification

Bhandari

Lee

2022

BMC Res Notes

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Objective The determination of the location of quantitative trait loci (QTL) (i.e., QTL mapping) is essential for identifying new genes. Various statistical methods are being incorporated into different QTL mapping functions. However, statistical errors and limitations may often occur in a QTL mapping, implying the risk of false positive errors and/or failing to detect a true positive QTL effect. We simulated the power to detect four simulated QTL in tomato using cim() and stepwiseqtl(), widely adopted QTL mapping functions, and QTL.gCIMapping(), a derivative of the composite interval mapping method. While there is general agreement that those three functions identified simulated QTL, missing or false positive QTL were observed, which were prevalent when more realistic data (such as smaller population size) were provided. Results To address this issue, we developed postQTL, a QTL mapping R workflow that incorporates (i) both cim() and stepwiseqtl(), (ii) widely used R packages developed for model selection, and (iii) automation to increase the accuracy, efficiency, and accessibility of QTL mapping. QTL mapping experiments on tomato F2 populations in which QTL effects were simulated or calculated showed advantages of postQTL in QTL detection.

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A Genetic Map and Linkage Panel for the Large-fruited Fresh-market Tomato

Cited by 10 publications

References 28 publications

Genetic architecture of fresh-market tomato yield

Genetic architecture of fresh-market tomato yield

A mutant allele of the flowering promoting factor 1 gene at the tomato BRACHYTIC locus reduces plant height with high quality fruit

postQTL: a QTL mapping R workflow to improve the accuracy of true positive loci identification

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