Abstract
Translational genomics can enable a quicker improvement of orphan crops toward novel agricultural applications, including the advancement of orphan biomass species for cultivation on marginal lands. In this sense, cell wall quality is a preeminent breeding target. However, tools to efficiently project genetic data on target traits across large sets of species are currently missing. This study aimed at closing this gap by developing a strategy to project a set of cell wall QTLs across a large group of plants by using genome synteny. This strategy is suited for large-scale analyses and detected 362 syntenic cell wall QTLs (SQTLs) across 74 angiosperms, including several (orphan) biomass species. SQTLs analyses revealed that they span large portions of the initial cell wall QTLs and are extensively conserved across diverse species. Moreover, numerous QTLs cell wall genes were conserved through SQTLs, including genes displaying allelic variation associated with cell wall composition. Functional analyses showed that highly conserved genes of SQTLs include important cell wall transcription factors and genes involved in the remodeling of cell wall polymers. For some of these gene families, SQTLs indicated the presence of differentially conserved genomic contexts for different gene members, highlighting their utility as a tool to pinpoint gene targets that maximize the likelihood of functional gene conservation. Overall, the results of this study can facilitate “universal” approaches for breeding (orphan) biomass crops, while the strategy for QTLs translation can be applied to other sets of traits and species, helping to unlock the potential of orphan species.
Highlights
A key challenge faced by modern plant breeding is the effective valorization of the genetic resources of orphan crops (Kamei et al, 2016)
To develop an effective methodology for projecting cell wall QTLs across a wide set of plants with the use of gene synteny, 610 cell wall QTLs previously mapped in arabidopsis (Brassicaceae), soybean (Fabaceae), poplar (Salicaceae), eucalyptus (Myrtaceae), miscanthus, maize, sorghum, and rice (Poaceae) were collected from scientific literature (Section “Collection of Cell Wall Quantitative Trait Loci” and Supplementary Table 1)
Since some of the 610 cell wall QTL intervals retrieved from scientific literature referred to genetic maps, the QTLs were first translated to physical genomic positions (Section “Collection of Cell Wall Quantitative Trait Loci” and Supplementary Table 1), and the gene content of the genomic QTL regions was analyzed
Summary
A key challenge faced by modern plant breeding is the effective valorization of the genetic resources of orphan crops (Kamei et al, 2016) These crops are currently underutilized in agriculture, despite being relevant for the subsistence of many local and regional communities, being promising for emerging agricultural markets, and carrying valuable traits (Kamei et al, 2016; Tadele, 2019). Syntenic QTL’s for Cell Wall are native of areas that face adverse climatic conditions (Pancaldi and Trindade, 2020) Their advancement could contribute to diversify agricultural markets, improve food diets, as well as mine useful traits to adapt staple crops to climate change (Kamei et al, 2016; Tadele, 2019). One of the main reasons for the underutilization of orphan crops in agriculture is the scarcity of genetic tools available for their improvement (Pancaldi and Trindade, 2020) This aspect, together with the niche markets currently shared by most of these crops, hampers their effective utilization for the purposes just discussed
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