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Whole Genome Re-sequencing of Soybean Accession EC241780 Providing Genomic Landscape of Candidate Genes Involved in Rust Resistance
Current Genomics ( IF 1.8 ) Pub Date : 2020-10-22 , DOI: 10.2174/1389202921999200601142258 Milind Balkrishna Ratnaparkhe 1 , Niharika Marmat 1 , Giriraj Kumawat 1 , Maranna Shivakumar 1 , Viraj Gangadhar Kamble 1 , Vennampally Nataraj 1 , Shunmugiah Veluchamy Ramesh 1 , Milind Panjabrao Deshmukh 1 , Ajay Kumar Singh 1 , Humira Sonah 1 , Rupesh Kailasrao Deshmukh 1 , Manoj Prasad 1 , Suresh Chand 1 , Sanjay Gupta 1
Current Genomics ( IF 1.8 ) Pub Date : 2020-10-22 , DOI: 10.2174/1389202921999200601142258 Milind Balkrishna Ratnaparkhe 1 , Niharika Marmat 1 , Giriraj Kumawat 1 , Maranna Shivakumar 1 , Viraj Gangadhar Kamble 1 , Vennampally Nataraj 1 , Shunmugiah Veluchamy Ramesh 1 , Milind Panjabrao Deshmukh 1 , Ajay Kumar Singh 1 , Humira Sonah 1 , Rupesh Kailasrao Deshmukh 1 , Manoj Prasad 1 , Suresh Chand 1 , Sanjay Gupta 1
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Background
In this study, whole genome re-sequencing of rust resistant soybean genotype EC241780 was performed to understand the genomic landscape involved in the resistance mechanism. Methods
A total of 374 million raw reads were obtained with paired-end sequencing performed with Illumina HiSeq 2500 instrument, out of which 287.3 million high quality reads were mapped to Williams 82 reference genome. Comparative sequence analysis of EC241780 with rust susceptible cultivars Williams 82 and JS 335 was performed to identify sequence variation and to prioritise the candidate genes. Results
Comparative analysis indicates that genotype EC241780 has high sequence similarity with rust resistant genotype PI 200492 and the resistance in EC241780 is conferred by the Rpp1 locus. Based on the sequence variations and functional annotations, three genes Glyma18G51715, Glyma18G51741 and Glyma18G51765 encoding for NBS-LRR family protein were identified as the most prominent candidate for Rpp1 locus. Conclusion
The study provides insights of genome-wide sequence variation more particularly at Rpp1 loci which will help to develop rust resistant soybean cultivars through efficient exploration of the genomic resource.
中文翻译：
大豆登记号 EC241780 的全基因组重测序提供了参与锈病抗性的候选基因的基因组图谱
背景 在本研究中，对抗锈病大豆基因型 EC241780 进行全基因组重测序，以了解抗性机制中涉及的基因组景观。方法利用Illumina HiSeq 2500仪器进行双端测序，共获得3.74亿条原始reads，其中2.873亿条高质量reads映射到Williams 82参考基因组。对 EC241780 与锈病敏感品种 Williams 82 和 JS 335 进行比较序列分析，以识别序列变异并确定候选基因的优先顺序。结果比较分析表明，基因型EC241780与抗锈病基因型PI 200492具有较高的序列相似性，EC241780的抗性是由Rpp1位点赋予的。基于序列变异和功能注释，编码NBS-LRR家族蛋白的三个基因Glyma18G51715、Glyma18G51741和Glyma18G51765被确定为Rpp1基因座最突出的候选基因。结论 该研究提供了全基因组序列变异的见解，尤其是 Rpp1 位点的序列变异，这将有助于通过有效探索基因组资源来开发抗锈病大豆品种。
更新日期：2020-10-22
中文翻译：
大豆登记号 EC241780 的全基因组重测序提供了参与锈病抗性的候选基因的基因组图谱
背景 在本研究中，对抗锈病大豆基因型 EC241780 进行全基因组重测序，以了解抗性机制中涉及的基因组景观。方法利用Illumina HiSeq 2500仪器进行双端测序，共获得3.74亿条原始reads，其中2.873亿条高质量reads映射到Williams 82参考基因组。对 EC241780 与锈病敏感品种 Williams 82 和 JS 335 进行比较序列分析，以识别序列变异并确定候选基因的优先顺序。结果比较分析表明，基因型EC241780与抗锈病基因型PI 200492具有较高的序列相似性，EC241780的抗性是由Rpp1位点赋予的。基于序列变异和功能注释，编码NBS-LRR家族蛋白的三个基因Glyma18G51715、Glyma18G51741和Glyma18G51765被确定为Rpp1基因座最突出的候选基因。结论 该研究提供了全基因组序列变异的见解，尤其是 Rpp1 位点的序列变异，这将有助于通过有效探索基因组资源来开发抗锈病大豆品种。
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