Multiregional origins of the domesticated tetraploid wheats

Abstract

We used genotyping-by-sequencing (GBS) to investigate the evolutionary history of domesticated tetraploid wheats. With a panel of 189 wild and domesticated wheats, we identified 1,172,469 single nucleotide polymorphisms (SNPs) with a read depth �3. Principal component analyses (PCAs) separated the Triticum turgidum and Triticum timopheevii accessions, as well as wild T. turgidum from the domesticated emmers and the naked wheats, showing that SNP typing by GBS is capable of providing robust information on the genetic relationships between wheat species and subspecies. The PCAs and a neighbourjoining analysis suggested that domesticated tetraploid wheats have closest affinity with wild emmers from the northern Fertile Crescent, consistent with the results of previous genetic studies on the origins of domesticated wheat. However, a more detailed examination of admixture and allele sharing between domesticates and different wild populations, along with genome-wide association studies (GWAS), showed that the domesticated tetraploid wheats have also received a substantial genetic input from wild emmers from the southern Levant. Taking account of archaeological evidence that tetraploid wheats were first cultivated in the southern Levant, we suggest that a pre-domesticated crop spread from this region to southeast Turkey and became mixed with a wild emmer population from the northern Fertile Crescent. Fixation of the domestication traits in this mixed population would account for the allele sharing and GWAS results that we report. We also propose that feralization of the component of the pre-domesticated population that did not acquire domestication traits has resulted in the modern wild population from southeast Turkey displaying features of both the domesticates and wild emmer from the southern Levant, and hence appearing to be the sole progenitor of domesticated tetraploids when the phylogenetic relationships are studied by methods that assume a treelike pattern of evolution.

Linkage disequilibrium patterns, population structure and diversity analysis in a worldwide durum wheat collection including Argentinian genotypes

“…However, some authors [ 17 ] have found a low or null decay in diversity from landraces to modern cultivars, although they observed an effect of breeding on the linkage disequilibrium (LD) patterns and allele’s frequency. Efforts in recovering genetic diversity and to capture beneficial alleles for specific traits have been made by exploring the genetic variability available in landraces [ 20 – 24 ] and wild relatives [ 25 – 27 ].…”

The History of Lentil (Lens culinaris subsp. culinaris) Domestication and Spread as Revealed by Genotyping-by-Sequencing of Wild and Landrace Accessions

“…Our filtering conditions produced widely different numbers of SNPs requiring decisions to be made between loose or more restrictive filtering conditions (more coverage, less missing data, higher MAFs) for different types of analyses. Nonetheless, it has been observed that filtering conditions do not, in general, affect determination of population structure or phylogenetic inference ( Loureiro et al, 2020a ; Oliveira et al, 2020 ). The clustering of accessions based on PCAs obtained from datasets with different numbers of SNPs was very similar ( Supplementary Figure 1 ), with the four basic groups in the Lens genus distinctively recovered time and again.…”

“…A study matching archaeobotanical findings with molecular data to determine how many times lentil may have been domesticated and pinpointing the place(s) where this domestication may have taken place is lacking, unlike for other major crops domesticated in the same area ( Heun et al, 1997 ; Pankin et al, 2018 ; Trněný et al, 2018 ; Oliveira et al, 2020 ). Likewise, the genetic basis of domestication syndrome traits in lentil has not been explored.…”

“…Next-generation sequencing coupled with complexity reduction methods such as genotyping-by-sequencing (GBS) allows for the detection of thousands of genome-wide genetic markers. This has been used to study crop domestication and evolution in rice ( Kim et al, 2016 ), common bean ( Rau et al, 2019 ), watermelon ( Nimmakayala et al, 2014 ), and emmer wheat ( Oliveira et al, 2020 ). GBS has also been used to elucidate the phylogeny of the Lens genus ( Wong et al, 2015 ) and the population structure of Mediterranean lentil varieties ( Pavan et al, 2019 ).…”

Identification of the Triticoid-type grains (Poaceae) from archaeobotanical assemblages in southwest Asia as Heteranthelium piliferum (Banks & Sol.) Hochst.

“…The fact that segetal habitats from which H. piliferum was collected during the 20th century also accumulate in northern Mesopotamia and the Zagros Mountains speaks against this possibility. However, only evidence from population genetics could rule out this scenario, as highlighted by recent DNA studies that demonstrate an anthropogenic movement of wild emmer populations out of the southern Levant and across the entire Fertile Crescent since the Early Neolithic (Civáň et al 2013;Oliveira et al 2020).…”