Shapes of edible plant organs vary dramatically among and within crop plants. To explain and ultimately employ this variation towards crop improvement, we determined the genetic, molecular and cellular bases of fruit shape diversity in tomato. Through positional cloning, protein interaction studies, and genome editing, we report that OVATE Family Proteins and TONNEAU1 Recruiting Motif proteins regulate cell division patterns in ovary development to alter final fruit shape. The physical interactions between the members of these two families are necessary for dynamic relocalization of the protein complexes to different cellular compartments when expressed in tobacco leaf cells. Together with data from other domesticated crops and model plant species, the protein interaction studies provide possible mechanistic insights into the regulation of morphological variation in plants and a framework that may apply to organ growth in all plant species.
Motivation The investigation of quantitative trait loci (QTL) is an essential component in our understanding of how organisms vary phenotypically. However, many important crop species are polyploid (carrying more than two copies of each chromosome), requiring specialised tools for such analyses. Moreover, deciphering meiotic processes at higher ploidy levels is not straightforward, but is necessary to understand the reproductive dynamics of these species, or uncover potential barriers to their genetic improvement. Results Here we present polyqtlR, a novel software tool to facilitate such analyses in (auto)polyploid crops. It performs QTL interval mapping in F1 populations of outcrossing polyploids of any ploidy level using identity-by-descent (IBD) probabilities. The allelic composition of discovered QTL can be explored, enabling favourable alleles to be identified and tracked in the population. Visualisation tools within the package facilitate this process, and options to include genetic co-factors and experimental factors are included. Detailed information on polyploid meiosis including prediction of multivalent pairing structures, detection of preferential chromosomal pairing and location of double reduction events can be performed. Availability polyqtlR is freely available from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/package=polyqtlR. Supplementary information Supplementary data are available at Bioinformatics online.
Valorisation of tuber protein is relevant for the potato starch industry to create added-value and reduce impact on the environment. Hence, protein content has emerged as a key quality trait for innovative potato breeders. In this study, we estimated trait heritability, explored the relationship between protein content and tuber under-water weight (UWW), inferred haplotypes underlying quantitative trait loci (QTLs) and pinpointed candidate genes. We used a panel of varieties (N = 277) that was genotyped using the SolSTW 20 K Infinium single-nucleotide polymorphism (SNP) marker array. Protein content data were collected from multiple environments and years. Our genome-wide association study (GWAS) identified QTLs on chromosomes 3, 5, 7 and 12. Alleles of StCDF1 (maturity) were associated with QTLs found on chromosome 5. The QTLs on chromosomes 7 and 12 are presented here for the first time, whereas those on chromosomes 3 and 5 co-localized with loci reported in earlier studies. The candidate genes underlying the QTLs proposed here are relevant for functional studies. This study provides resources for genomics-enabled breeding for protein content in potato.
Tuber shape is an intriguing morphological trait, which displays continuous trait variation ranging from flat, round to oval and long. Initially a single locus model was proposed to explain tuber shape, where multiple alleles rather than multiple loci were proposed to explain quantitative variation (van Eck et al. 1994). Besides this major-effect QTL on chromosome 10 another minor effect QTL has been published on chromosome 2, explaining 8% of the variance (Prashar et al. 2014). To obtain a better overview on the loci contributing to variation in tuber shape a comprehensive genome wide association study (GWAS) was performed in a panel of 537 commercial potato cultivars. This confirmed that the Ro locus is the major-effect QTL, but also the minor effect QTL on chromosome 2 was found. In addition, on chromosome 10, colocalization of the major effect QTL for tuber shape and a major QTL for eye depth was observed. For the Ro locus, most significant associations were found to localize on superscaffold PGSC0003DMB000000385 on chromosome 10. To refine this region we performed a recombinant screening in a diploid population (C×E). Recombinant analysis resulted in the identification of 104 recombinants originating from the female meiosis and 27 recombinants from the male meiosis. Recombinant analysis with additional SNPs within the selected region allowed us to confine the Ro locus to a 280 kb region, located on superscaffold DMB546 (323kb). Within this region a cluster of cell wall III peroxidase genes is found. Based on the putative role of peroxidases, this gene family cluster of repeats is likely to be implicated in mediating differences in tuber shape. Keywords Solanum tuberosum, organ morphology, high resolution mapping, GWAS, haplotypes Conclusion: We present a scalable approach that accurately reconstructs haplotypes in polyploid crops. The resulting haplotypes are instrumental for analysing the haplotype composition of the potato gene pool, and haplotype based QTL discovery.
Potato OFP20 is associated with the regulation of tuber shape. To further characterise the role of this gene in tuber shape, a panel of 136 potato varieties was re-sequenced to identify variants in the coding region of StOFP20. These SNPs were assembled into haplotypes and their allelic dosage was determined. Haplotype StOFP20.1 is the most common allele (65%) which in quadruplex condition results in long tubers. StOFP20.3 represents the second most common haplotype (22%) and is recognized as a dominant allele that is associated with round tubers in a dosage dependent manner. StOFP20.4 represents the third common haplotype (5%) and encodes a non-functional gene. The remaining haplotypes represent rare alleles and their phenotypic effect is unclear. We developed reliable DNA markers that distinguish between the long and round alleles for marker-assisted selection of tuber shape in a diverse collection of varieties. We also demonstrate that we can genetically engineer the tuber shape of two commercial tetraploid varieties and the diploid clone DM. Knock down of StOFP20 in the variety Atlantic using the RNAi strategy changed the tubers from round to oval and long-oval shapes. Conversely, overexpression of StOFP20 in Spunta changed tuber shape from long to round. The most dramatic change from very long into round tubers was achieved by overexpression of StOFP20 in DM. Our results demonstrate that engineering potato tuber shape is readily achieved by modulating StOFP20 gene expression in a dose dependent manner, either by traditional breeding or by using genetic engineering methods.
scite is a Brooklyn-based organization that helps researchers better discover and understand research articles through Smart Citations–citations that display the context of the citation and describe whether the article provides supporting or contrasting evidence. scite is used by students and researchers from around the world and is funded in part by the National Science Foundation and the National Institute on Drug Abuse of the National Institutes of Health.
hi@scite.ai
10624 S. Eastern Ave., Ste. A-614
Henderson, NV 89052, USA
Copyright © 2024 scite LLC. All rights reserved.
Made with 💙 for researchers
Part of the Research Solutions Family.