Sari Duygu
Department of Field Crops, Faculty of Agriculture, Akdeniz University, 07070 Antalya, Turkey.
Plants (Basel). 2024 Sep 9;13(17):2530. doi: 10.3390/plants13172530.
Enhancing the marker repository and the development of breeder-friendly markers in chickpeas is important in relation to chickpea genomics-assisted breeding applications. Insertion-deletion (InDel) markers are widely distributed across genomes and easily observed with specifically designed primers, leading to less time, cost, and labor requirements. In light of this, the present study focused on the identification and development of InDel markers through the use of double-digest restriction site-associated DNA sequencing (ddRADSeq) data from 20 chickpea accessions. Bioinformatic analysis identified 20,700 InDel sites, including 15,031 (72.61%) deletions and 5669 (27.39%) insertions, among the chickpea accessions. The InDel markers ranged from 1 to 25 bp in length, while single-nucleotide-length InDel markers were found to represent the majority of the InDel sites and account for 79% of the total InDel markers. However, we focused on InDel markers wherein the length was greater than a single nucleotide to avoid any read or alignment errors. Among all of the InDel markers, 96.1% were less than 10 bp, 3.6% were between 10 and 20 bp, and 0.3% were more than 20 bp in length. We examined the InDel markers that were 10 bp and longer for the development of InDel markers based on a consideration of the genomic distribution and low-cost genotyping with agarose gels. A total of 29 InDel regions were selected, and primers were successfully designed to evaluate their efficiency. Annotation analysis of the InDel markers revealed them to be found with the highest frequency in the intergenic regions (82.76%), followed by the introns (6.90%), coding sequences (6.90%), and exons (3.45%). Genetic diversity analysis demonstrated that the polymorphic information content of the markers varied from 0.09 to 0.37, with an average of 0.20. Taken together, these results showed the efficiency of InDel marker development for chickpea genetic and genomic studies using the ddRADSeq method. The identified markers might prove valuable for chickpea breeders.
对于鹰嘴豆基因组辅助育种应用而言，加强鹰嘴豆标记库建设以及开发对育种者友好的标记非常重要。插入缺失（InDel）标记广泛分布于基因组中，使用专门设计的引物即可轻松观察到，从而减少了时间、成本和劳动力需求。有鉴于此，本研究聚焦于通过利用20份鹰嘴豆种质的双酶切简化基因组测序（ddRADSeq）数据来鉴定和开发InDel标记。生物信息学分析在鹰嘴豆种质中鉴定出20,700个InDel位点，其中包括15,031个（72.61%）缺失和5,669个（27.39%）插入。InDel标记的长度在1至25 bp之间，而单核苷酸长度的InDel标记占InDel位点的大多数，占InDel标记总数的79%。然而，为避免任何读取或比对错误，我们重点关注长度大于单核苷酸的InDel标记。在所有InDel标记中，96.1%的长度小于10 bp，3.6%在10至20 bp之间，0.3%的长度大于20 bp。基于基因组分布和琼脂糖凝胶低成本基因分型的考虑，我们研究了长度为10 bp及更长的InDel标记以用于InDel标记开发。总共选择了29个InDel区域，并成功设计了引物来评估其效率。对InDel标记的注释分析表明，它们在基因间区域的出现频率最高（82.76%），其次是内含子（6.90%）、编码序列（6.90%）和外显子（3.45%）。遗传多样性分析表明，这些标记的多态信息含量在0.09至0.37之间，平均为0.20。综上所述，这些结果表明了使用ddRADSeq方法开发InDel标记用于鹰嘴豆遗传和基因组研究的效率。所鉴定的标记可能对鹰嘴豆育种者具有重要价值。
