Wild relatives of tomato are a valuable source of natural variation in tomato breeding, as many can be hybridized to the cultivated species (
- Award ID(s):
- 1855585
- NSF-PAR ID:
- 10321890
- Date Published:
- Journal Name:
- Plant Physiology
- Volume:
- 186
- Issue:
- 4
- ISSN:
- 0032-0889
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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SUMMARY Solanum lycopersicum ). Several, includingSolanum lycopersicoides , have been crossed toS. lycopersicum for the development of ordered introgression lines (ILs), facilitating breeding for desirable traits. Despite the utility of these wild relatives and their associated ILs, few finished genome sequences have been produced to aid genetic and genomic studies. Here we report a chromosome‐scale genome assembly forS. lycopersicoides LA2951, which contains 37 938 predicted protein‐coding genes. With the aid of this genome assembly, we have precisely delimited the boundaries of theS. lycopersicoides introgressions in a set ofS. lycopersicum cv. VF36 × LA2951 ILs. We demonstrate the usefulness of the LA2951 genome by identifying several quantitative trait loci for phenolics and carotenoids, including underlying candidate genes, and by investigating the genome organization and immunity‐associated function of the clusteredPto gene family. In addition, syntenic analysis of R2R3MYB genes sheds light on the identity of theAubergine locus underlying anthocyanin production. The genome sequence and IL map provide valuable resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance. We present a new genome resource for the wild speciesS. lycopersicoides , which we use to shed light on theAubergine locus responsible for anthocyanin production. We also provide IL boundary mappings, which facilitated identifying novel carotenoid quantitative trait loci of which one was likely driven by an uncharacterized lycopene β‐cyclase whose function we demonstrate. -
Wild cotton species can contribute to a valuable gene pool for genetic improvement, such as genes related to salt tolerance. However, reproductive isolation of different species poses an obstacle to produce hybrids through conventional breeding. Protoplast fusion technology for somatic cell hybridization provides an opportunity for genetic manipulation and targeting of agronomic traits. Transcriptome sequencing analysis of callus under salt stress is conducive to study salt tolerance genes. In this study, calli were induced to provide materials for extracting protoplasts and also for screening salt tolerance genes. Calli were successfully induced from leaves of Gossypium sturtianum (C 1 genome) and hypocotyls of G. raimondii (D 5 genome), and embryogenic calli of G. sturtianum and G. raimondii were induced on a differentiation medium with different concentrations of 2, 4-D, KT, and IBA, respectively. In addition, embryogenic calli were also induced successfully from G. raimondii through suspension cultivation. Transcriptome sequencing analysis was performed on the calli of G. raimondii and G. sturtianum , which were treated with 200 mM NaCl at 0, 6, 12, 24, and 48 h, and a total of 12,524 genes were detected with different expression patterns under salt stress. Functional analysis showed that 3,482 genes, which were differentially expressed in calli of G. raimondii and G. sturtianum , were associated with biological processes of nucleic acid binding, plant hormone (such as ABA) biosynthesis, and signal transduction. We demonstrated that DEGs or TFs which related to ABA metabolism were involved in the response to salt stress, including xanthoxin dehydrogenase genes ( ABA2 ), sucrose non-fermenting 1-related protein kinases ( SnRK2 ), NAM, ATAT1 / 2 , and CUC2 transcription factors ( NAC ), and WRKY class of zinc-finger proteins ( WRKY ). This research has successfully induced calli from two diploid cotton species and revealed new genes responding to salt stress in callus tissue, which will lay the foundation for protoplast fusion for further understanding of salt stress responses in cotton.more » « less
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Abstract Background Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations.
Results Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce’s disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes.
Conclusions This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.
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Abstract Accelerating biomass improvement is a major goal of
Miscanthus breeding. The development and implementation of genomic‐enabled breeding tools, like marker‐assisted selection (MAS) and genomic selection, has the potential to improve the efficiency ofMiscanthus breeding. The present study conducted genome‐wide association (GWA) and genomic prediction of biomass yield and 14 yield‐components traits inMiscanthus sacchariflorus . We evaluated a diversity panel with 590 accessions ofM. sacchariflorus grown across 4 years in one subtropical and three temperate locations and genotyped with 268,109 single‐nucleotide polymorphisms (SNPs). The GWA study identified a total of 835 significant SNPs and 674 candidate genes across all traits and locations. Of the significant SNPs identified, 280 were localized in mapped quantitative trait loci intervals and proximal to SNPs identified for similar traits in previously reportedMiscanthus studies, providing additional support for the importance of these genomic regions for biomass yield. Our study gave insights into the genetic basis for yield‐component traits inM. sacchariflorus that may facilitate marker‐assisted breeding for biomass yield. Genomic prediction accuracy for the yield‐related traits ranged from 0.15 to 0.52 across all locations and genetic groups. Prediction accuracies within the six genetic groupings ofM. sacchariflorus were limited due to low sample sizes. Nevertheless, the Korea/NE China/Russia (N = 237) genetic group had the highest prediction accuracy of all genetic groups (ranging 0.26–0.71), suggesting that with adequate sample sizes, there is strong potential for genomic selection within the genetic groupings ofM. sacchariflorus . This study indicated that MAS and genomic prediction will likely be beneficial for conducting population‐improvement ofM. sacchariflorus . -
Traits in wild relatives of crop species can help breed sustainable crop varieties that produce more food with fewer resources. To make use of this variation, we need to find the genetic regions that allow wild species to use water and nutrients more efficiently. Leaf anatomy has a major effect on photosynthesis by determining rates of carbon gain and water loss. However, finding the genetic regions underlying leaf anatomical evolution has been limited by low-throughput and low-resolution trait measurements. 3D imaging using X-ray microcomputed tomography (μCT) may overcome these obstacles by providing high-throughput, high-resolution data on leaf anatomy. Compared to traditional 2D methods for leaf anatomy, 3D imaging captures physiologically important volumetric traits, is less biased, and encompasses a larger leaf area. We used synchrotron μCT to measure leaf anatomy on two tomato species Solanum lycopersicum (cultivated tomato) and S. pennellii (wild, drought-tolerant species), and four introgression lines containing loci that alter leaf anatomy. We measured stomatal density, size, and 3D arrangement, as well as leaf thickness and mesophyll porosity. Preliminary analyses show that synchrotron μCT can identify previously described quantitative trait loci for stomatal traits and leaf thickness and show how those traits are related to 3D leaf anatomy. We will use finite element models to show how these anatomical differences may contribute to genetic variation leaf CO2 and water vapour exchange.more » « less
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/plphys/kiab230
