High throughput genetic diversity analyses of neglected crops: training data, codes and materials (Africa)

Marginal land is land that is of little agricultural value because crops produced there would be worth less than any rent paid for access to the area. Helping to develop such zones in Africa is a key goal for the EU-funded EWA-BELT project. The aim is to promote the sustainable intensification of agricultural production in organic, agroforestry and mixed crop and livestock farming systems in 38 study areas of six countries belonging to East and West Africa. The project will enhance current scientific knowledge on the adaptation of new and improved traditional crops in different agroecosystems and the impacts of traditional agricultural practices on soil health. This initiation to genomic data analysis with R was designed within the EWA-BELT H2020 EU project (grant agreement ID 862848). The training module introduced to a variety of population genomics analyses for genotyping by sequencing (GBS) datasets. It included an introduction to single-nucleotide polymorphism (SNP) calling and filtering options, experimental design and various applications, population genomics statistics (genetic diversity and structure, Fst-based analyses) and genome-wide association studies (GWAS). The majority of the course consisted of practical R sessions to give hands-on experience of these analyses. Main topic and contents treated during the courses : Session 1. Passport data and Bioinformatics analysis Session 2. VCF filtering Session 3. Genetic diversity and structure Session 4. Genome-Wide Association Studies (GWAS) Each session includes a short introduction outlining the core concepts (PDF), R scripts (HTLM/PDF) and associated datasets.

边际土地（marginal land）指农业利用价值极低的土地，其产出农作物的经济价值低于使用该地块所需支付的租金。
助力非洲此类边际土地的开发，是欧盟资助的EWA-BELT项目的核心目标之一。
该项目旨在推动东非与西非6个国家共计38个研究区域内，有机农业、农林业以及农牧混合种植体系下农业生产的可持续集约化发展。
本项目将深化现有科学认知，涵盖新型及改良传统作物在不同农业生态系统中的适应性，以及传统农业耕作实践对土壤健康的影响。
这份基于R语言的基因组数据分析入门教程，由欧盟H2020框架下的EWA-BELT项目（资助协议编号：862848）开发完成。
本培训模块围绕测序分型（genotyping by sequencing, GBS）数据集的各类群体基因组学分析展开入门教学。
教程涵盖单核苷酸多态性（single-nucleotide polymorphism, SNP）的基因型检测与过滤方案、实验设计及各类应用场景、群体基因组学统计分析（包括遗传多样性与群体结构、基于Fst的分析），以及全基因组关联研究（genome-wide association studies, GWAS）。
课程主体以实操性R语言课程为主，旨在让学员获得上述分析流程的亲身体验。
课程涵盖的核心主题与内容如下：
1. 种质资源护照数据与生物信息学分析
2. VCF文件过滤
3. 遗传多样性与群体结构分析
4. 全基因组关联研究（GWAS）
每个教学单元均配有核心概念简介文档（PDF格式）、R语言脚本文件（HTML/PDF格式）及配套数据集。