Exploring genetic diversity and population structure of a large grapevine (Vitis vinifera L.) germplasm collection in Türkiye

Abstract

Grapevine (Vitis Vinifera L.) has been one of the significant perennial crops in widespread temperate climate regions since its domestication around 6000 years ago. Grapevine and its products, particularly wine, table grapes, and raisins, have significant economic importance not only in grapevine-growing countries but also worldwide. Grapevine cultivation in Türkiye dates back to ancient times, and Anatolia is considered one of the main grapevine migration routes around the Mediterranean basin. Turkish germplasm collection, conserved at the Turkish Viticulture Research Institutes, includes cultivars and wild relatives mainly collected in Türkiye, breeding lines, rootstock varieties, and mutants, but also cultivars of international origin. Genotyping with high-throughput markers enables the investigation of genetic diversity, population structure, and linkage disequilibrium, which are crucial for applying genomic-assisted breeding. Here, we present the results of a high-throughput genotyping-by-sequencing (GBS) study of 341 genotypes from grapevine germplasm collection at Manisa Viticulture Research Institute. A total of 272,962 high-quality single nucleotide polymorphisms (SNP) markers on the nineteen chromosomes were identified using genotyping-by-sequencing (GBS) technology. The high‐density coverage of SNPs resulted in an average of 14,366 markers per chromosome, an average polymorphism information content (PIC) value of 0.23 and an expected heterozygosity (He) value of 0.28 indicating the genetic diversity within 341 genotypes. LD decayed very fast when r2 was between 0.45 and 0.2 and became flat when r2 was 0.05. The average LD decay for the entire genome was 30 kb when r2 = 0.2. The PCA and structure analysis did not distinguish the grapevine genotypes based on different origins, highlighting the occurrence of gene flow and a high amount of admixture. Analysis of molecular variance (AMOVA) results indicated a high level of genetic differentiation within populations, while variation among populations was extremely low. This study provides comprehensive information on the genetic diversity and population structure of Turkish grapevine genotypes.

Genetic Dissection of Diverse Seed Coat Patterns in Cowpea through a Comprehensive GWAS Approach

“…This observation aligns with the broader findings across multiple studies, where the LD decay distance can vary significantly across different organisms and even within different regions of the same genome [40,41]. For instance, in diverse populations or species, the average LD decay could be shorter due to higher historical recombination rates [42], or it could extend further in populations with low diversity or those that have undergone a bottleneck [43]. The complexity of genetic architecture highlighted by our analysis emphasizes the importance of applying established methods such as GWAS and genetic mapping in a comprehensive manner.…”

Crop Landraces and Indigenous Varieties: A Valuable Source of Genes for Plant Breeding

“…Over the last decades, a wealth of reports has been published concerning the genotyping of the indigenous grapevine reserves in the Mediterranean, either through SSR or SNP methodology [ 169 , 170 , 171 , 172 , 173 , 174 , 175 , 176 , 177 ]. In view of the drastic climate change and its impact on grapevine yield and quality, efforts have been undertaken to capitalize on the rapid advancements in genomic technologies to face current and future environmental challenges.…”