Hellwig, T. | Search bioRxiv

bioRxiv2022

Novel diversity panel facilitates genomic dissection of lodging in tef (Eragrostis tef)

RationalUnderutilized species that are not widely cultivated (known as orphan crops) present opportunities to increase crop diversity and food security. Tef [Eragrostis tef (Zucc.) Trotter] is known for its high-quality grain and forage. Root-borne lodging is a major devastating problem in tef cultivation, leading to large economic losses and limiting its widespread adoption. ObjectiveThe aim of this study was to identify genomic regions that are associated with tef lodging. MethodsA tef diversity panel (TDP-300) comprised of 297 lines was assembled, genotyped, and phenotyped across 4 field environments. This unique panel, the first of its kind in tef, has the potential to facilitate tef research and breeding. ResultsGenome-wide association study identified 29 sites associated with lodging; in all cases with a minor allele conferring reduced lodging. The eleven sites of prime interest were located in or near genes, 5 of them with a putative role, of which 3 were found to be involved root development. ConclusionsThe identification of lodging-related sites in the current study may advance understanding of the mechanisms underlying tef lodging and crop improvement. The identification of genes related to root development support the importance of root traits in tef lodging, which should be targeted in future breeding.

plant biology↗

bioRxiv2021

Drivers of genetic differentiation and recent evolutionary history of an Eurasian wild pea

Genetic diversity a major determinant for the capacity of species to persist and adapt to their environments. Unraveling the factors affecting genetic differentiation is crucial to understand how genetic diversity is shaped and species may react to changing environments. We employed genotyping by sequencing to test the influence of climate, space, latitude, altitude and land cover on genetic differentiation in a collection of 81 wild pea samples (Pisum sativum ssp. elatius) from across its distribution range from western Europe to central Asia. We also attempted to elucidate the species recent evolutionary history and its effect on the current distribution of genetic diversity. Association of single SNPs with climate variables were analyses to test for signatures of local adaptation. Genetic variation was geographically structured into six distinct genetic cluster. Two of which were associated with a taxonomic group (Pisum sativum ssp. humile) that according to some researchers does not qualify for a sub-species rank due to its alleged lack of genetic distinctness from other conspecific groups. The effect of the tested factors influencing genetic differentiation were rather variable among genetic clusters. The climate predictors were most important in all clusters. Land use was more important in clusters from areas strongly influenced by human land use, especially by agriculture. We found a statistically significant association of 3,623 SNPs (2.4 % of all SNPs) with one of the environmental predictors. Most of them were correlated with latitude followed by temperature, precipitation and altitude. Estimation of SNP effects of the candidates resulted in a missense to silent ratio of 0.45, suggesting many of the observed candidates SNPs may alter the encoded amino acid sequence. Wild peas went through a genetic bottleneck during the last glacial period followed by population recovery. Probably associated with this population recovery, we detected a range expansion, which may have led to an eastward range expansion of the European cluster to Turkey and thereof southwards and eastwards. Overall, the interplay of several environmental factors and the recent evolutionary history affected the distribution of genetic diversity in wild peas where each subpopulations were differently affected by those factors and processes.

evolutionary biology↗