Hidden variation in polyploid wheat drives local adaptation

Gardiner, Laura‐Jayne; Joynson, Ryan; Omony, Jimmy; Rusholme‐Pilcher, Rachel; Olohan, Lisa; Lang, Daniel; Bai, Chen; Hawkesford, Malcolm J.; Salt, David E.; Spannagl, Manuel; Mayer, Klaus; Kenny, John; Bevan, Michael W.; Hall, Neil; Hall, Anthony

doi:10.1101/gr.233551.117

Cited by 46 publications

(33 citation statements)

References 49 publications

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“…Although the known population structure of the selected accessions in this study was recapitulated with methylation data, the level of methylation variation was linked to the overall genetic distance between any given samples. This result is similar to reports of natural Arabidopsis thaliana populations [6,12,25] and across a landrace Wheat collection [26]. Methods as described here, can dissect this confounding between genetics and epigenomics, to capture an additional piece of the missing heritability.…”

Section: Discussionsupporting

confidence: 87%

Extending the genotype inBrachypodiumby including DNA methylation reveals a joint contribution with genetics on adaptive traits

Eichten

Srivastava

Reddiex

et al. 2019

Preprint

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Epigenomic changes have been considered a potential missing link underlying phenotypic variation in quantitative traits but is potentially confounded with the underlying DNA sequence variation. Although the concept of epigenetic inheritance has been discussed in depth, there have been few studies attempting to directly dissect the amount of epigenomic variation within inbred natural populations while also accounting for genetic diversity. By using known genetic relationships between Brachypodium lines, multiple sets of nearly identical accession families were selected for phenotypic studies and DNA methylome profiling to investigate the dual role of (epi)genetics under simulated natural seasonal climate conditions. Despite reduced genetic diversity, appreciable phenotypic variation was still observable in the measured traits (height, leaf width and length, tiller count, flowering time, ear count) between as well as within the inbred accessions. However, with reduced genetic diversity there was diminished variation in DNA methylation within families. Mixed-effects linear modelling revealed large genetic differences between families and a minor contribution of epigenomic variation on phenotypic variation in select traits. Taken together, this analysis suggests a limited but significant contribution of DNA methylation towards heritable phenotypic variation relative to genetic differences.Recently, there has been great excitement investigating the role of possible epigenomic sources of variation, in the form of stable DNA or histone modifications, which may act alongside, or independently, of traditional genetic variation. A range of population-level studies have reported substantial diversity between different genetic backgrounds [4][5][6][7][8][9]. In certain cases, measures of DNA methylation were combined with genetic variation identifying genetic factors that can influence chromatin between populations and geographical locations [6,[10][11][12]. Results often highlight the covariation of genetic variation with chromatin state, transposable element (TE) methylation, and differential cytosine methylation among accessions. Nonetheless, a small portion of geneticallyindependent methylation variation, often in the CG context and in promoter regions, may contribute to phenotypic variance [6,[13][14][15].

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Section: Discussionsupporting

confidence: 87%

Extending the genotype inBrachypodiumby including DNA methylation reveals a joint contribution with genetics on adaptive traits

Eichten

Srivastava

Reddiex

et al. 2019

Preprint

View full text Add to dashboard Cite

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“…In the last decades, exotic parents have been used in breeding programmes with the aim of introducing greater diversity into elite gene pools (Singh et al, 2018). The exotic parents that are most frequently used are those from the primary gene pool represented by germplasm that share a common genome but that have become isolated from mainstream gene pools such as landraces (Reynolds et al, 2009a,b), which have been shown to be not only genetically, but epigenetically diverse (Gardiner et al, 2018). The secondary gene pool that has also been used is represented by closely related genomes that can be utilised through inter-specific hybridisation, and would include the development of so-called 'synthetic' or 're-synthesised' wheat, where a tetraploid durum wheat has been hybridised with Aegilops tauschii, the ancestral donor of the D genome, to recreate hexaploid bread wheat (Mujeeb-Kazi et al, 1996).…”

Section: Introductionmentioning

confidence: 99%

Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential

Molero

Joynson

Piñera-Chávez

et al. 2019

Plant Biotechnology Journal

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Summary One of the major challenges for plant scientists is increasing wheat ( Triticum aestivum ) yield potential ( YP ). A significant bottleneck for increasing YP is achieving increased biomass through optimization of radiation use efficiency ( RUE ) along the crop cycle. Exotic material such as landraces and synthetic wheat has been incorporated into breeding programmes in an attempt to alleviate this; however, their contribution to YP is still unclear. To understand the genetic basis of biomass accumulation and RUE , we applied genome‐wide association study ( GWAS ) to a panel of 150 elite spring wheat genotypes including many landrace and synthetically derived lines. The panel was evaluated for 31 traits over 2 years under optimal growing conditions and genotyped using the 35K wheat breeders array. Marker‐trait association identified 94 SNP s significantly associated with yield, agronomic and phenology‐related traits along with RUE and final biomass ( BM _ PM ) at various growth stages that explained 7%–17% of phenotypic variation. Common SNP markers were identified for grain yield, BM _ PM and RUE on chromosomes 5A and 7A. Additionally, landrace and synthetic derivative lines showed higher thousand grain weight ( TGW ), BM _ PM and RUE but lower grain number ( GM 2) and harvest index ( HI ). Our work demonstrates the use of exotic material as a valuable resource to increase YP . It also provides markers for use in marker‐assisted breeding to systematically increase BM _ PM , RUE and TGW and avoid the TGW / GM 2 and BM _ PM / HI trade‐off. Thus, achieving greater genetic gains in elite germplasm while also highlighting genomic regions and candidate genes for further study.

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“…The recent study of these decoy F-box protein networks involved in circadian clock function strongly endorses the importance of such truncated F-Box microProteins in the regulation of plant development in response to environmental stimuli (Lee et al 2018). Equally, the inferred regulation of protein function and gene expression by methylation and other similar transient modifications are known to regulate development and stress adaptation in crops (Gardiner et al 2018;Wang et al 2011).…”

Section: Discussionmentioning

confidence: 96%

Global Analysis of Cereal microProteins Suggests Diverse Roles in Crop Development and Environmental Adaptation

Bhati

Kruusvee

Straub

et al. 2020

G3 Genes|Genomes|Genetics

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MicroProteins are class of small single-domain proteins that post-translationally regulate larger multidomain proteins from which they evolved or to which they relate. They disrupt the normal function of their targets by forming microProtein-target heterodimers through compatible protein-protein interaction (PPI) domains. Recent studies confirm the significance of microProteins in the fine-tuning of plant developmental processes such as shoot apical meristem maintenance and flowering time regulation. While there are a number of well-characterised microProteins in Arabidopsis thaliana, studies from more complex plant genomes are still missing. Our lab has previously developed miPFinder, a software for identifying microProteins from annotated genomes. Here we present an improved version, where we have updated the algorithm to increase its accuracy and speed, and used it to analyse five cereal crop genomes - wheat, rice, barley, maize and sorghum. We found 20,064 potential microProteins from a total of 258,029 proteins in these five organisms, of which approximately 2000 are high-confidence, i.e. likely to function as actual microProteins. Gene ontology analysis of these 2000 microProtein candidates revealed their roles in stress, light and growth responses, hormone signalling and transcriptional regulation. Using a recently developed rice gene co-expression database, we analysed 347 potential rice microProteins that are also conserved in other cereal crops and found over 50 of these rice microProteins co-regulated with their identified interaction partners. Overall, our study reveals a rich source of biotechnologically interesting small proteins that regulate fundamental plant processes such a growth and stress response that could be utilised in crop bioengineering.

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Hidden variation in polyploid wheat drives local adaptation

Cited by 46 publications

References 49 publications

Extending the genotype inBrachypodiumby including DNA methylation reveals a joint contribution with genetics on adaptive traits

Extending the genotype inBrachypodiumby including DNA methylation reveals a joint contribution with genetics on adaptive traits

Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential

Global Analysis of Cereal microProteins Suggests Diverse Roles in Crop Development and Environmental Adaptation

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