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Whole Genome Re-sequencing of Soybean Accession EC241780 Providing Genomic Landscape of Candidate Genes Involved in Rust Resistance

[ Vol. 21 , Issue. 7 ]

Author(s):

Milind Balkrishna Ratnaparkhe*, Niharika Marmat, Giriraj Kumawat, Maranna Shivakumar, Viraj Gangadhar Kamble, Vennampally Nataraj, Shunmugiah Veluchamy Ramesh, Milind Panjabrao Deshmukh, Ajay Kumar Singh, Humira Sonah, Rupesh Kailasrao Deshmukh, Manoj Prasad, Suresh Chand and Sanjay Gupta   Pages 504 - 511 ( 8 )

Abstract:


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.

Keywords:

Soybean, whole genome re-sequencing, disease resistance, rust, Phakopsora pachyrhizi, single nucleotide polymorphisms (SNPs).

Affiliation:

ICAR-Indian Institute of Soybean Research, Indore-452001, MP, ICAR-Indian Institute of Soybean Research, Indore-452001, MP, ICAR-Indian Institute of Soybean Research, Indore-452001, MP, ICAR-Indian Institute of Soybean Research, Indore-452001, MP, ICAR-Indian Institute of Soybean Research, Indore-452001, MP, ICAR-Indian Institute of Soybean Research, Indore-452001, MP, ICAR-Indian Institute of Soybean Research, Indore-452001, MP, Agricultural Research Station, (MPKV), Kasbe Digraj, Sangli, MS, ICAR-National Institute of Abiotic Stress Management, Baramati, MS, National Agri-Food Biotechnology Institute, Mohali, National Agri-Food Biotechnology Institute, Mohali, National Institute of Plant Genome Research, New Delhi, School of Life Sciences, Devi Ahilya University, Indore, MP, ICAR-Indian Institute of Soybean Research, Indore-452001, MP

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