Zero hunger and good health could be realized by 2030 through effective conservation, characterization and utilization of germplasm resources¹. So far, few chickpea (Cicer arietinum) germplasm accessions have been characterized at the genome sequence level². Here we present a detailed map of variation in 3,171 cultivated and 195 wild accessions to provide publicly available resources for chickpea genomics research and breeding. We constructed a chickpea pan-genome to describe genomic diversity across cultivated chickpea and its wild progenitor accessions. A divergence tree using genes present in around 80% of individuals in one species allowed us to estimate the divergence of Cicer over the last 21 million years. Our analysis found chromosomal segments and genes that show signatures of selection during domestication, migration and improvement. The chromosomal locations of deleterious mutations responsible for limited genetic diversity and decreased fitness were identified in elite germplasm. We identified superior haplotypes for improvement-related traits in landraces that can be introgressed into elite breeding lines through haplotype-based breeding, and found targets for purging deleterious alleles through genomics-assisted breeding and/or gene editing. Finally, we propose three crop breeding strategies based on genomic prediction to enhance crop productivity for 16 traits while avoiding the erosion of genetic diversity through optimal contribution selection (OCS)-based pre-breeding. The predicted performance for 100-seed weight, an important yield-related trait, increased by up to 23% and 12% with OCS- and haplotype-based genomic approaches, respectively.

通过种质资源的有效保护、鉴定和利用，到 2030 年可以实现零饥饿和良好健康¹。到目前为止，很少有鹰嘴豆 ( Cicer arietinum ) 种质资源在基因组序列水平上得到表征²。在这里，我们展示了 3,171 个栽培种质和 195 个野生种质的详细变异图谱，为鹰嘴豆基因组学研究和育种提供公开可用的资源。我们构建了一个鹰嘴豆泛基因组来描述栽培鹰嘴豆及其野生祖先种质的基因组多样性。使用存在于一个物种中大约 80% 的个体中的基因的分歧树使我们能够估计Cicer的分歧在过去的 2100 万年里。我们的分析发现染色体片段和基因在驯化、迁移和改良过程中显示出选择特征。在优良种质中确定了导致遗传多样性有限和适应性下降的有害突变的染色体位置。我们确定了地方品种中改良相关性状的优良单倍型，这些性状可以通过基于单倍型的育种渗入到精英育种系中，并找到了通过基因组学辅助育种和/或基因编辑清除有害等位基因的目标。最后，我们提出了三种基于基因组预测的作物育种策略，以提高 16 个性状的作物生产力，同时通过基于最优贡献选择 (OCS) 的预育种避免遗传多样性的侵蚀。