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ARS Home » Southeast Area » Tifton, Georgia » Crop Protection and Management Research » Research » Publications at this Location » Publication #336119
Title: QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.)

Author
item PANDEY, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item KHAN, AAMIR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item SINGH, VIKAS - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item VISHWAKARMA, MANISH - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item SHASIDHAR, YADURU - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item KUMAR, VINAY - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item GARG, VANIKA - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item BHAT, RAMESH - University Of Agricultural Sciences
item CHITIKINENI, ANU - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item JANILA, PASUPULETI - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item Guo, Baozhu
item VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/2/2016
Publication Date: 2/7/2017
Citation: Pandey, M.K., Khan, A.W., Singh, V.K., Vishwakarma, M.K., Shasidhar, Y., Kumar, V., Garg, V., Bhat, R.S., Chitikineni, A., Janila, P., Guo, B., Varshney, R.K. 2017. QTL-seq approach identified genomic regions and diagnostic markers for rust and late leaf spot resistance in groundnut (Arachis hypogaea L.). Plant Biotechnology Journal. 2017:1-15. Available: http://onlinelibrary.wiley.com/doi/10.1111/pbi.12686/full.

Interpretive Summary: Rust and late leaf spot (LLS) are the two major foliar fungal diseases in peanut, causing significant yield loss of peanut pods and quality reduction of peanut hay as a by-product. In order to breed peanut cultivars with resistance to both diseases, we applied the new next-generation sequencing technology to identify candidate genomic regions, using whole genome re-sequencing (WGRS) based approach, which regulate the resistance to rust and LLS for molecular marker-assisted selection in breeding programs. We identified and confirmed co-localization of genomic regions for resistance to both diseases on the chromosome A03. A total of 3,136 single nucleotide polymorphisms (SNPs) for rust and 66 SNPs for LLS were identified in the region. We found 30 non-synonymous SNPs affecting 25 candidate genes for rust resistance and 14 intronic and 3 synonymous SNPs for LLS resistance affecting 9 candidate genes. Further, we developed and validated three diagnostic markers which could be used as routine tool to select the resistance lines to both rust and LLS in breeding program. Genotyping of RIL population with these four diagnostic markers revealed higher phenotypic variation for these two diseases. These results suggest usefulness of WGRS approach in rapid and precise identification of candidate genomic regions and development of diagnostic markers for breeding applications.

Technical Abstract: Rust and late leaf spot (LLS) are the two major foliar fungal diseases in groundnut, and their co-occurrence leads to yield loss up to 50–70% in addition to the deterioration of fodder quality. To identify candidate genomic regions controlling rust and LLS resistance, we deployed whole genome re-sequencing (WGRS) based approach referred as ‘QTL-seq’. A total of 231.67 Gb raw and 192.10 Gb of clean sequence data were generated through WGRS of resistant parent, and resistance and susceptible bulks for rust and LLS. Analysis of bulks for rust and LLS with reference guided resistant parent assembly confirmed co-localization of QTLs for both the diseases between 131.60- 134.66 Mb on the pseudomolecule A03. A total of 3,136 single nucleotide polymorphisms (SNPs) for rust and 66 SNPs for LLS with the read depth of =7 were identified in the QTL region. We found 30 non-synonymous SNPs affecting 25 candidate genes for rust resistance and 14 intronic and 3 synonymous SNPs for LLS resistance affecting 9 candidate genes. Further, we developed and validated three allele-specific diagnostic markers for rust and one for LLS resistance to use in routine breeding program. Genotyping of RIL population with above mentioned four diagnostic markers revealed higher phenotypic variation. The above results suggest usefulness of QTL-seq approach in precise and rapid identification of candidate genomic regions and development of diagnostic markers for breeding applications.