Decoupling the molecular regulation of perenniality and flowering in bulbous barley (Hordeum bulbosum)

Abstract

Global crop production is being challenged by rapid population growth, declining natural resources, and dramatic climatic turnovers. These challenges have prompted plant breeders to explore new ventures to enhance adaptation and sustainability in crops. One intriguing approach to make agriculture more sustainable is by turning annual systems into perennial which offers many economic and biodiversity-friendly benefits. Previous attempts to develop a perennial cereal crop employed a classical breeding approach and extended over a long period with limited success. Thus, elucidating the genetic basis of perenniality at the molecular level can accelerate the breeding process.Here, we investigated the genetic basis of bulb formation in the barley congener species Hordeum bulbosum by elucidating the transcripts presence/absence variation compared with other annual species in the Poaceae, and a differential expression analysis of meristem tissues. The PAV analysis recaptured the expected phylogeny and indicated that H. bulbosum is enriched with developmental and disease responsive genes that are absent among annual species. Next, the abundance of transcripts was quantified and allowed to identify differentially expressed genes that are associated with bulb formation pathways in addition to major circadian clock genes that regulate flowering. A first model for the bulb formation pathway is suggested and include developmental and starch biosynthesis genes. To the best of our knowledge this is the first transcriptome developed for H. bulbosum and the first attempt to describe the regulation of bulb initiation in cereals at the molecular level.

A haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum

“…Bulbous barley has also been proposed as a target for de novo domestication 50 . With genome sequences in hand and enough knowledge about domestication genes in barley 51 , it should to edit their homologs in crop wild relatives so as to abolish seed shattering, adapt owering times to farmers' needs and increase seed set 50,52,53 . Still, the new domesticates might not contribute as much to human sustenance as hoped for 54 , but they would be valuable tools for plant scientists and evolutionary geneticists.…”

Perennials as Future Grain Crops: Opportunities and Challenges

“…In barley, genome sequencing of perennial H. bulbosum and annual H. vulgare is facilitating such research. As an alternative to the creation of interspecific annual-perennial crosses, presence and absence variant (PAV) analysis has been conducted between the two species to identify genetic differences (Fuerst et al, 2021). Within the H. bulbosum genome, Fuerst et al (2021) identified a significant enrichment of developmental and disease resistance genes absent among annual Poaceae species, alongside those associated with bulb formation relating to starch biosynthesis.…”

“…As an alternative to the creation of interspecific annual-perennial crosses, presence and absence variant (PAV) analysis has been conducted between the two species to identify genetic differences (Fuerst et al, 2021). Within the H. bulbosum genome, Fuerst et al (2021) identified a significant enrichment of developmental and disease resistance genes absent among annual Poaceae species, alongside those associated with bulb formation relating to starch biosynthesis. These findings, and further interrogation of this PAV dataset, should help identify the genes and processes responsible for perennial-to-annual conversion, making them available for reverse engineering.…”

“…Concurrently, genotyping-by-sequencing was used to create high-density genetic maps of H. bulbosum, in addition to a partial de novo genome assembly for H. bulbosum, for which gene models were predicted (Wendler et al, 2017). Notably, the H. bulbosum genome is enriched with developmental and diseaseresponsive genes absent among annual Poaceae species (Fuerst et al, 2021).…”