Development and application of Single Primer Enrichment Technology (SPET) SNP assay for population genomics analysis and candidate gene discovery in lettuce

Frontiers in Plant Science

Plant Science

Ilias Kalfas¹  Rob van Treuren²  Pasquale Tripodi³  Sandra Goritschnig⁴  Anthony Laidet⁵  Gael Briand⁵  Davide Scaglione⁶  Massimiliano Beretta⁷  Damien Peltier⁸  Christos Vasilikiotis⁹  Charlotte Aichholz^1,10  Tizian Zollinger^1,11 

[1] American Farm School, Thessaloniki, Greece;Centre for Genetic Resources, the Netherlands (CGN), Wageningen University and Research, Wageningen, Netherlands;Council for Agricultural Research and Economics (CREA), Research Centre for Vegetable and Ornamental Crops, Pontecagnano Faiano, SA, Italy;European Cooperative Programme for Plant Genetic Resources (ECPGR) Secretariat c/o Alliance of Bioversity International and CIAT, Rome, Italy;Gautier Semences Route d’Avignon 13630, Eyragues, France;IGA Technology Services Srl, Udine, Italy;ISI Sementi SpA, Fidenza (PR), Italy;Limagrain - Vilmorin-Mikado, La Ménitré, France;Perrotis College, American Farm School, Thessaloniki, Greece;Sativa Rheinau AG, Rheinau, Switzerland;Zollinger Conseilles Sarl, Les Evouettes, Switzerland;

关键词: lettuce;    SPET;    high-throughput genotyping;    genomic diversity;    phenotyping;    GWAS;    candidate genes;   

DOI  :  10.3389/fpls.2023.1252777

 received in 2023-07-04, accepted in 2023-07-26,  发布年份 2023

来源: Frontiers

【 摘 要 】

Single primer enrichment technology (SPET) is a novel high-throughput genotyping method based on short-read sequencing of specific genomic regions harboring polymorphisms. SPET provides an efficient and reproducible method for genotyping target loci, overcoming the limits associated with other reduced representation library sequencing methods that are based on a random sampling of genomic loci. The possibility to sequence regions surrounding a target SNP allows the discovery of thousands of closely linked, novel SNPs. In this work, we report the design and application of the first SPET panel in lettuce, consisting of 41,547 probes spanning the whole genome and designed to target both coding (~96%) and intergenic (~4%) regions. A total of 81,531 SNPs were surveyed in 160 lettuce accessions originating from a total of 10 countries in Europe, America, and Asia and representing 10 horticultural types. Model ancestry population structure clearly separated the cultivated accessions (Lactuca sativa) from accessions of its presumed wild progenitor (L. serriola), revealing a total of six genetic subgroups that reflected a differentiation based on cultivar typology. Phylogenetic relationships and principal component analysis revealed a clustering of butterhead types and a general differentiation between germplasm originating from Western and Eastern Europe. To determine the potentiality of SPET for gene discovery, we performed genome-wide association analysis for main agricultural traits in L. sativa using six models (GLM naive, MLM, MLMM, CMLM, FarmCPU, and BLINK) to compare their strength and power for association detection. Robust associations were detected for seed color on chromosome 7 at 50 Mbp. Colocalization of association signals was found for outer leaf color and leaf anthocyanin content on chromosome 9 at 152 Mbp and on chromosome 5 at 86 Mbp. The association for bolting time was detected with the GLM, BLINK, and FarmCPU models on chromosome 7 at 164 Mbp. Associations were detected in chromosomal regions previously reported to harbor candidate genes for these traits, thus confirming the effectiveness of SPET for GWAS. Our findings illustrated the strength of SPET for discovering thousands of variable sites toward the dissection of the genomic diversity of germplasm collections, thus allowing a better characterization of lettuce collections.

【 授权许可】

Unknown   
Copyright © 2023 Tripodi, Beretta, Peltier, Kalfas, Vasilikiotis, Laidet, Briand, Aichholz, Zollinger, Treuren, Scaglione and Goritschnig