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）指农业价值极低的土地，因在该区域种植作物的收益甚至低于土地使用权的租金。助力非洲此类区域的开发，是欧盟资助的EWA-BELT项目的核心目标之一。
该项目旨在东非与西非六个国家的38个研究区域内，推动有机农业、农林业以及农牧混合生产系统下农业生产的可持续集约化。
项目将深化当前关于不同农业生态系统中新型及改良传统作物的适应性，以及传统农业实践对土壤健康影响的科学认知。
这份基于R语言的基因组数据分析入门教程，由欧盟“地平线2020”（H2020）框架下的EWA-BELT项目开发（资助协议编号：862848）。
该培训模块面向测序分型（genotyping by sequencing, GBS）数据集，介绍了各类群体基因组学分析方法，内容涵盖单核苷酸多态性（single-nucleotide polymorphism, SNP）调用与过滤方案、实验设计与各类应用场景、群体基因组学统计分析（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）。
课程主体为实操性R语言课程，旨在让学员获得上述分析的实操经验。
课程涵盖的核心主题与内容如下：
课程1：种质资源护照数据与生物信息学分析
课程2：VCF文件过滤
课程3：遗传多样性与群体结构
课程4：全基因组关联研究（GWAS）
每节课均包含核心概念简介（PDF格式）、R语言脚本（HTML/PDF格式）及配套数据集。