Data-driven, participatory characterization of traditional farmer varieties discloses teff (Eragrostis tef) adaptive and breeding potential under current and future climates

In smallholder farming systems, traditional farmer varieties of neglected and underutilized crops species (NUS) support the livelihoods of millions of growers and consumers. NUS combine cultural and agronomic value with local adaptation, and call for transdisciplinary methods to evaluate their breeding potential. Here, we combined farmers' traditional knowledge, genomics, and climate science to characterize 366 Ethiopian teff (Eragrostis tef) farmer varieties and breeding materials. We found that teff genetic diversity in Ethiopia could be organized in six genetic clusters associated to climate variation on the landscape. A participatory evaluation conducted in collaboration with local farmers could consistently identify best performing varieties and inform a genome wide association study to identify candidate genes for farmers' appreciation, phenology, yield, and local adaptation. By modelling the genomic adaptation of teff to current and projected climates, we identified an area around lake Tana where teff cropping will be most vulnerable to climate change. Our results show that transdisciplinary approaches may efficiently propel untapped NUS farmer varieties into modern breeding to foster more resilient and sustainable cropping systems

Targeted Sequencing Suggests Wild-Crop Gene Flow Is Central to Different Genetic Consequences of Two Independent Pumpkin Domestications

Studies of domestication genetics enrich our understanding of how domestication shapes genetic and morphological diversity. We characterized patterns of genetic variation in two independently domesticated pumpkins and their wild progenitors to assess and compare genetic consequences of domestication. To compare genetic diversity pre- and post-domestication and to identify genes targeted by selection during domestication, we analyzed ∼15,000 SNPs of 48 unrelated accessions, including wild, landrace, and improved lines for each of two pumpkin species, Cucurbita argyrosperma and Cucurbita maxima. Genetic diversity relative to its wild progenitor was reduced in only one domesticated subspecies, C. argyrosperma ssp. argyrosperma. The two species have different patterns of genetic structure across domestication status. Only 1.5% of the domestication features identified for both species were shared between species. These findings suggest that ancestral genetic diversity, wild-crop gene flow, and domestication practices shaped the genetic diversity of two similar Cucurbita crops in different ways, adding to our understanding of how genetic diversity changes during the processes of domestication and how trait improvement impacts the breeding potential of modern crops.

Breeding Potential of Maize Germplasm Line GEMS-0067 for High Amylose Proportion

Maize varieties with high amylose proportion are more valuable for starch industry. The SBEⅡb gene encodes one of the starch branching isozymes (SBEⅠ, SBEⅡa, and SBEⅡb). Its recessive mutant amylose-extender (ae/sbe2b) decreases the total activities of SBEs and increases amylose proportion up to 60%. Here, the breeding potential of introduced germplasm line GEMS-0067 was evaluated by genotyping and phenotyping. The deletion of the ninth exon of the SBEⅡb gene, high amylose proportion, and the typical irregular granules suggested that this germplasm line was derived from the same resource of high amylose line AE11. The gelatinization and thermal properties, and degree of polymerization of starch chain showed its advantages used for high amylose breeding. However, the negative correlation between amylose proportion and starch content, as well as ker-nel filling characteristics should be overcome during breeding process.