Genome wide association study of 5 agronomic traits in olive (Olea europaea L.)

Abstract

Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs.

Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.)

“…Remarkably, we did not find any gene related to fatty acid metabolism and accumulation, although this has presumably been one of the most important characters under selection in olive domestication. Moreover, a recent study found 19 genes associated with five important agronomic traits in olive [ 61 ], and despite 14 of them being found in cv. Farga (see Additional file 2 : Table S16), only five were found in the gene set with negative Tajima’s D, and none was present in the detected selective sweep regions or the genes under positive selection according to MK test.…”

“…In general, genes positively selected in cultivated olives were associated with a response to biotic and abiotic stresses. Interestingly, five genes detected with negative Tajima’s D are related to genes recently described as important for fruit weight and stone weight [ 61 ]. However, further analyses are needed to ascertain whether they indeed play a role in trait selection during domestication (see [ 74 ] for secondary compounds).…”

Genomic evidence for recurrent genetic admixture during domestication mediterranean olive trees (Olea europaea)

“…Remarkably, we did not find any gene related to fatty acid metabolism and accumulation, although this has presumably been one of the most important characters under selection in olive domestication. Moreover, a recent study found 19 genes associated with 5 important agronomic traits in olive (59) and despite 14 of them being found in Farga (see Additional file 2: Table S8), none was present in the detected selective sweep regions. Similarly, a study based on transcriptomes of 68 different wild and cultivated samples using statistical approaches (PCAdapt (60) and BayeScan (61)) failed to identify candidate genes under selection associated with oil content or fruit size (11).…”

iQSPR in XenonPy: A Bayesian Molecular Design Algorithm

“…Other studies have also shown promising applications of transfer learning in materials informatics. [18,[34][35][36][37][38][39][40][41] In this study, we applied a specific type of transfer learning using pre-trained neural networks. For a target property, a neural network pre-trained on proxy properties is available in the library, where the source datasets are sufficiently large.…”