Salt stress severely constrains plant performance and global agricultural productivity.
5% of arable land, 20% of irrigated areas and 98% of water reserves worldwide are saline.
Improving the salt tolerance of major crop species could help attenuate yield losses and
expand irrigation opportunities and provide in situ relief in areas where poverty, food and
water scarcity are prevalent. Increasing the salt tolerance of crops with high commercial
and nutritional value, such as tomato (Solanum lycopersicum L.), would provide
particularly significant economic and health benefits. However, salt tolerance is a complex
trait with a limited genetic repertoire in domesticated crop varieties, including tomato,
frustrating attempts to breed and engineer tolerant crop varieties. Here, a genome-wide
association study (GWAS) was undertaken, leveraging the rich genetic diversity of the
wild, salt tolerant tomato Solanum pimpinellifolium and the latest phenotyping
technologies to identify traits that contribute to salt tolerance and the genetic basis for
variation in those traits. A panel of 220 S. pimpinellifolium accessions was phenotyped,
focusing on image-based high-throughput phenotyping over time in controlled and field
conditions in young and mature plants. Results reveal substantial natural variation in salt
tolerance over time across many traits. In particular, the use of unmanned aerial vehicle
(UAV)-based remote sensing in the field allowed high-resolution RGB, thermal and
hyperspectral mapping that offers new insights into plant performance in the field, over
time. To empower our GWAS and facilitate the identification of candidate genes, a new
S. pimpinellifolium reference genome was generated, 811Mb in size, N50 of ~76kb,
containing 25,970 annotated genes. Analysis of this reference genome highlighted
potential contributors to salt tolerance, including enrichments in genes with stress
response functions and a high copy number of the salt tolerance-associated gene inositol-
3-phosphate synthase (I3PS). A recently completed full genome re-sequencing of the
panel, along with a newly available pseudomolecule-level assembly of the S.
pimpinellifolium genome with N50 of ~11Mb, will serve to drive a GWAS to identify loci
associated with traits that contribute to salt tolerance. Further research including gene
validation, breeding, genetic modification and gene editing experiments will drive the
development of new salt tolerant tomato cultivars.
| Identifer | oai:union.ndltd.org:kaust.edu.sa/oai:repository.kaust.edu.sa:10754/662606 |
| Date | 10 1900 |
| Creators | Morton, Mitchell |
| Contributors | Tester, Mark A., Biological and Environmental Sciences and Engineering (BESE) Division, Krattinger, Simon G., McCabe, Matthew, Schafleitner, Roland |
| Source Sets | King Abdullah University of Science and Technology |
| Language | English |
| Detected Language | English |
| Type | Dissertation |
| Rights | 2021-04-21, At the time of archiving, the student author of this dissertation opted to temporarily restrict access to it. The full text of this dissertation will become available to the public after the expiration of the embargo on 2021-04-21. |
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