1) 种质资源评估时期：主要是依赖分子标记来评估遗传多样性，筛选核心种质，增加种质资源开发的利用价值，提高效率；
2）基因定位时期：在种质资源评估时期获得一些遗传差异大，性状变异大的材料来构建资源群体和作图群体，通过GWAS或遗传作图方法来定位基因座；
3）基因组测序时期：控制性状基因座的定位只是得到一个标记区间，要想知道控制该性状的基因或者调控元件，需要进一步测序基因组，确定是哪个基因或者哪个调控元件发生变异导致性状变异；
4）基因功能机制研究时期：在确定了功能基因或者功能元件后，需要进一步确定该基因或调控元件是如何影响到最终的性状；
5）功能基因应用时期：确定了导致性状差异的遗传变异后，可以开发成诊断标记或者育种芯片应用于医学诊断和遗传育种。
通过SSR或RAD技术获得分型数据后，再对种质资源进行遗传多样性评估，对个体间的亲缘关系进行比较，获得个体间的遗传距离矩阵，进而构建进化树。再根据一定的阈值筛选有代表性的个体作为核心种质资源[4]。
1）对作图群体所有个体进行基因组分析和性状统计[5]；
2）利用BSA方法，将某一性状的极端个体混合，再找关联的分子标记，但条件是该物种已有参考基因组[6]；性状可以是传统的农艺性状（株高、产量、开花期、含油量、千粒重等），也可以是分子表型（基因RNA表达量[7]、代谢产物[8]、区域可及性[9]等）。
物种形成的过程也伴随着物种分化的过程，在不断经历着基因组加倍和二倍化的过程，通过比较基因组的分析，可以揭示基因组进化的痕迹，探索物种的性状形成的遗传基础。通过同一物种不同品种的基因组分析，可以挖掘出物种的核心基因和品种特有基因，为性状控制基因挖掘提供基础。
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