Genotyping by Sequencing of Cultivated Lentil (Lens culinaris Medik.) Highlights Population Structure in the Mediterranean Gene Pool Associated With Geographic Patterns and Phenotypic Variables

Abstract

Cultivated lentil (Lens culinaris Medik.) is one of the oldest domesticated crops and one of the most important grain legumes worldwide. The Mediterranean Basin holds large part of lentil biodiversity; however, no genetic structure was defined within the Mediterranean gene pool. In this study, we used high-throughput genotyping by sequencing to resolve the genetic structure of the Mediterranean ex situ lentil collection held at the Italian National Research Council. Sequencing of a 188-plex genotyping-by-sequencing library and bioinformatics treatment of data yielded 6,693 single nucleotide polymorphisms. Analysis of nonredundant genotypes with nonparametric and parametric methods highlighted the occurrence of five highly differentiated genetic clusters. Clustering could be related to geographic patterns and phenotypic traits, indicating that post-domestication routes introducing cultivation in Mediterranean countries and selection were major forces shaping lentil population structure. The estimation of the fixation index FST at individual single nucleotide polymorphism loci allowed the identification of distinctive alleles across clusters, suggesting the possibility to set up molecular keys for the assignment of lentil germplasm to specific genetic groups. Finally, significant associations between markers and phenotypic data were identified. Overall, the results of this study are of major importance for lentil conservation genetics and breeding and provide insights on the lentil evolutionary history.

Almond diversity and homozygosity define structure, kinship, inbreeding, and linkage disequilibrium in cultivated germplasm, and reveal genomic associations with nut and seed weight

“…Information on the genetic structure of crop species is pivotal for the correct management of ex situ germplasm collections and the efficient implementation of breeding programs, which should be based on the hybridization of genetically diverse individuals 2 . In addition, geographic patterns in the genetic structure may reveal key events, including routes of dissemination, associated with crop cultivation histories 3,4 . So far, studies aiming at the characterization of the almond genetic structure used a few simple sequence repeat (SSR) markers [5][6][7][8][9] .…”

Recommendations for Choosing the Genotyping Method and Best Practices for Quality Control in Crop Genome-Wide Association Studies

“…Another advantage of these RRS methods is their scalability, meaning that different combinations of restriction enzymes may be used to customize the percentage of the genome captured. The number of SNPs identified by RRS genotyping typically varies from a few to several thousands (Pavan et al, 2018(Pavan et al, , 2019Colonna et al, 2019), depending on the amount of genome sequenced and population diversity. As discussed above, this output can be largely sufficient in GWAS experiments whose main aim is to implement marker-assisted selection, and for crops displaying slow LD decay ( Table 1).…”

“…Many studies have used IBS/IBD thresholds of 95 or 99% to declare samples as identical (Myles et al, 2011). The examination of the IBS/IBD distribution associated with a few known identical samples, included on purpose in the GWAS population, might also be used to set up a threshold to estimate identity (Pavan et al, 2019).…”

“…Therefore, a crucial step in the QC procedure is the characterization of ancestry within the GWAS population. Genetic structure (i.e., the occurrence of sub-populations with different allele frequencies) reflects remote differences in ancestry; in crops, it often originates from physical barriers to random mating and anthropic selection for specific traits, such as seed/fruit size and phenological features (Pavan et al, 2017(Pavan et al, , 2019Siol et al, 2017). Instead, kinship reflects recent ancestry, often related to pedigree connections among modern cultivars (Taranto et al, 2020).…”

Serendipitous In Situ Conservation of Faba Bean Landraces in Tunisia: A Case Study

“…Moreover, recent breeding efforts are directed towards the development of new cultivars with low anti-nutritional compounds (vicine and convicine), to improve the quality and utilization efficiency of faba in human diet and for livestock feed [13]. Different molecular tools were used to investigate genetic diversity in grain legume species [14][15][16][17]. Some attempts to evaluate genetic variability have also been made for Tunisian faba bean germplasm.…”