Akinlade Oluwaseun J, Robinson Hannah, Kang Yichen, Thudi Mahendar, Samineni Srinivasan, Gaur Pooran, Smith Millicent R, Voss-Fels Kai P, Costilla Roy, Varshney Rajeev K, Dinglasan Eric, Hickey Lee T
Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Queensland, Australia.
State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
Plant Genome. 2025 Sep;18(3):e70096. doi: 10.1002/tpg2.70096.
Multiparent populations are now widespread in crop genetic studies as they capture more genetic diversity and offer high statistical power for detecting quantitative trait loci (QTLs). To confirm the suitability of using a recently developed chickpea (Cicer arietinum L.) multi-parent advanced generation intercross (MAGIC) population for genetic studies, we characterized the diversity of the eight founder lines and explored the linkage disequilibrium decay, marker coverage, segregation distortion, allelic variation, and structure of the population. The MAGIC population was genotyped using whole-genome sequencing; following marker curation, a total of 4255 high-quality polymorphic single nucleotide polymorphism markers were used for genomic analyses. To demonstrate the effectiveness of the MAGIC population to dissect the genetics of key agronomic traits (days to 50% flowering and plant height), we employed both a genome-wide mapping approach using fixed and random model circulating probability unification and a haplotype-based mapping using the local genomic estimated breeding value approach. Our analyses confirmed the role of genomic regions previously reported in the literature and identified several new QTLs for days to 50% flowering and plant height. We also showed the potential for trait improvement through stacking the top 10 haploblocks to develop early flowering chickpea and selection of desirable haplotypes on chromosome 4 to improve plant height. Our results demonstrate the chickpea MAGIC population is a valuable resource for researchers and pre-breeders to study the genetic architecture of complex traits and allelic variation to accelerate crop improvement in chickpea.
多亲群体目前在作物遗传研究中广泛应用，因为它们能捕获更多的遗传多样性，并为检测数量性状基因座（QTL）提供强大的统计功效。为了确认最近开发的鹰嘴豆（Cicer arietinum L.）多亲高代杂交（MAGIC）群体用于遗传研究的适用性，我们对八个亲本系的多样性进行了表征，并探索了连锁不平衡衰退、标记覆盖范围、分离畸变、等位基因变异和群体结构。使用全基因组测序对MAGIC群体进行基因分型；经过标记筛选后，共4255个高质量的多态性单核苷酸多态性标记用于基因组分析。为了证明MAGIC群体在剖析关键农艺性状（50%开花天数和株高）遗传方面的有效性，我们采用了基于固定和随机模型循环概率统一的全基因组定位方法以及基于单倍型的局部基因组估计育种值定位方法。我们的分析证实了文献中先前报道的基因组区域的作用，并鉴定了几个与50%开花天数和株高相关的新QTL。我们还展示了通过堆叠前10个单倍型块来培育早花鹰嘴豆以及在4号染色体上选择理想单倍型来提高株高从而改良性状的潜力。我们的结果表明，鹰嘴豆MAGIC群体是研究人员和育种前人员研究复杂性状遗传结构和等位基因变异以加速鹰嘴豆作物改良的宝贵资源。
