Sequencing Analysis of Genetic Loci for Resistance for Late Leaf Spot and Rust in Peanut (Arachis hypogaea L.)
The aim of this study was to identify candidate resistance genes for late leaf spot (LLS) and rust diseases in peanut (Arachis hypogaea L.). We used a double-digest restriction-site associated DNA sequencing (ddRAD-Seq) technique based on next-generation sequencing (NGS) for genotyping analysis acro...
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| Format: | Article |
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Frontiers Media S.A.
2018-11-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2018.01727/full |
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| author | Kenta Shirasawa Ramesh S. Bhat Yogendra P. Khedikar Venkataswamy Sujay Rohini M. Kolekar Sharanabasappa B. Yeri Mallenahally Sukruth Sarvamangala Cholin Byregowda Asha Manish K. Pandey Rajeev K. Varshney Makanahally V. C. Gowda |
| author_facet | Kenta Shirasawa Ramesh S. Bhat Yogendra P. Khedikar Venkataswamy Sujay Rohini M. Kolekar Sharanabasappa B. Yeri Mallenahally Sukruth Sarvamangala Cholin Byregowda Asha Manish K. Pandey Rajeev K. Varshney Makanahally V. C. Gowda |
| author_sort | Kenta Shirasawa |
| collection | DOAJ |
| description | The aim of this study was to identify candidate resistance genes for late leaf spot (LLS) and rust diseases in peanut (Arachis hypogaea L.). We used a double-digest restriction-site associated DNA sequencing (ddRAD-Seq) technique based on next-generation sequencing (NGS) for genotyping analysis across the recombinant inbred lines (RILs) derived from a cross between a susceptible line, TAG 24, and a resistant line, GPBD 4. A total of 171 SNPs from the ddRAD-Seq together with 282 markers published in the previous studies were mapped on a genetic map covering 1510.1 cM. Subsequent quantitative trait locus (QTL) analysis revealed major genetic loci for LLS and rust resistance on chromosomes A02 and A03, respectively. Heterogeneous inbred family-derived near isogenic lines and the pedigree of the resistant gene donor, A. cardenasii Krapov. & W.C. Greg., including the resistant derivatives of ICGV 86855 and VG 9514 as well as GPBD 4, were employed for whole-genome resequencing analysis. The results indicated the QTL candidates for LLS and rust resistance were located in 1.4- and 2.7-Mb genome regions on A02 and A03, respectively. In these regions, four and six resistance-related genes with deleterious mutations were selected as candidates for LLS and rust resistance, respectively. These delimited genomic regions may be beneficial in breeding programs aimed at improving disease resistance and enhancing peanut productivity. |
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| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-23T21:24:43Z |
| publishDate | 2018-11-01 |
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| spelling | doaj.art-504a39d1af264175a4b6b70cc8ee67de2022-12-21T17:30:38ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-11-01910.3389/fpls.2018.01727417729Sequencing Analysis of Genetic Loci for Resistance for Late Leaf Spot and Rust in Peanut (Arachis hypogaea L.)Kenta Shirasawa0Ramesh S. Bhat1Yogendra P. Khedikar2Venkataswamy Sujay3Rohini M. Kolekar4Sharanabasappa B. Yeri5Mallenahally Sukruth6Sarvamangala Cholin7Byregowda Asha8Manish K. Pandey9Rajeev K. Varshney10Makanahally V. C. Gowda11Department of Frontier Research and Development, Kazusa DNA Research Institute (KDRI), Chiba, JapanDepartment of Biotechnology, University of Agricultural Sciences, Dharwad, IndiaDepartment of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, IndiaDepartment of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, IndiaDepartment of Biotechnology, University of Agricultural Sciences, Dharwad, IndiaDepartment of Biotechnology, University of Agricultural Sciences, Dharwad, IndiaDepartment of Biotechnology, University of Agricultural Sciences, Dharwad, IndiaDepartment of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, IndiaDepartment of Biotechnology, University of Agricultural Sciences, Dharwad, IndiaCenter of Excellence in Genomics and System Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, IndiaCenter of Excellence in Genomics and System Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, IndiaDepartment of Genetics and Plant Breeding, University of Agricultural Sciences, Dharwad, IndiaThe aim of this study was to identify candidate resistance genes for late leaf spot (LLS) and rust diseases in peanut (Arachis hypogaea L.). We used a double-digest restriction-site associated DNA sequencing (ddRAD-Seq) technique based on next-generation sequencing (NGS) for genotyping analysis across the recombinant inbred lines (RILs) derived from a cross between a susceptible line, TAG 24, and a resistant line, GPBD 4. A total of 171 SNPs from the ddRAD-Seq together with 282 markers published in the previous studies were mapped on a genetic map covering 1510.1 cM. Subsequent quantitative trait locus (QTL) analysis revealed major genetic loci for LLS and rust resistance on chromosomes A02 and A03, respectively. Heterogeneous inbred family-derived near isogenic lines and the pedigree of the resistant gene donor, A. cardenasii Krapov. & W.C. Greg., including the resistant derivatives of ICGV 86855 and VG 9514 as well as GPBD 4, were employed for whole-genome resequencing analysis. The results indicated the QTL candidates for LLS and rust resistance were located in 1.4- and 2.7-Mb genome regions on A02 and A03, respectively. In these regions, four and six resistance-related genes with deleterious mutations were selected as candidates for LLS and rust resistance, respectively. These delimited genomic regions may be beneficial in breeding programs aimed at improving disease resistance and enhancing peanut productivity.https://www.frontiersin.org/article/10.3389/fpls.2018.01727/fulllate leaf spot and rust diseasespeanutquantitative trait locusrestriction-site associated DNA sequencingwhole-genome resequencing analysis |
| spellingShingle | Kenta Shirasawa Ramesh S. Bhat Yogendra P. Khedikar Venkataswamy Sujay Rohini M. Kolekar Sharanabasappa B. Yeri Mallenahally Sukruth Sarvamangala Cholin Byregowda Asha Manish K. Pandey Rajeev K. Varshney Makanahally V. C. Gowda Sequencing Analysis of Genetic Loci for Resistance for Late Leaf Spot and Rust in Peanut (Arachis hypogaea L.) Frontiers in Plant Science late leaf spot and rust diseases peanut quantitative trait locus restriction-site associated DNA sequencing whole-genome resequencing analysis |
| title | Sequencing Analysis of Genetic Loci for Resistance for Late Leaf Spot and Rust in Peanut (Arachis hypogaea L.) |
| title_full | Sequencing Analysis of Genetic Loci for Resistance for Late Leaf Spot and Rust in Peanut (Arachis hypogaea L.) |
| title_fullStr | Sequencing Analysis of Genetic Loci for Resistance for Late Leaf Spot and Rust in Peanut (Arachis hypogaea L.) |
| title_full_unstemmed | Sequencing Analysis of Genetic Loci for Resistance for Late Leaf Spot and Rust in Peanut (Arachis hypogaea L.) |
| title_short | Sequencing Analysis of Genetic Loci for Resistance for Late Leaf Spot and Rust in Peanut (Arachis hypogaea L.) |
| title_sort | sequencing analysis of genetic loci for resistance for late leaf spot and rust in peanut arachis hypogaea l |
| topic | late leaf spot and rust diseases peanut quantitative trait locus restriction-site associated DNA sequencing whole-genome resequencing analysis |
| url | https://www.frontiersin.org/article/10.3389/fpls.2018.01727/full |
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