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QTL mapping for late leaf spot and rust resistance using an improved genetic map and extensive phenotypic data on a recombinant inbred line population in peanut (Arachis hypogaea L.)

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Abstract

The linkage map for the recombinant inbred line (RIL) mapping population derived from late leaf spot (LLS) and rust disease susceptible (TAG 24) and resistant (GPBD 4) varieties of peanut was improved by adding 139 new SSR and transposable element (TE) markers. The improved map now has 289 mapped loci with a total map distance of 1730.8 cM and average inter-marker distance of 6.0 cM across 20 linkage groups. Quantitative trait loci (QTL) analysis using improved genetic map with 289 markers and comprehensive phenotypic data for LLS and rust from 11 seasons could identify a region on linkage group AhXV (B03 linkage group of B genome) which contributed significantly towards LLS and rust resistance. Of the five QTL mapped in this region, three showed high phenotypic variance explained (PVE) for both LLS and rust, and two QTL showed high PVE for only rust. The QTL flanked by GM2009-IPAHM103 had very high PVE of 44.5 % and 53.7 %, respectively for LLS and rust response. Another genomic region on AhXII (B10 linkage group of B genome) contained a QTL flanked by GM1839-GM1009 which had a PVE of 14.1–35.2 % for LLS resistance. A new QTL with marker interval GM1989-AhTE0839 on AhV (A05 linkage group of A genome) showed a PVE of 10.2 % for rust resistance. The new markers, AhTE0498 and AhTE0928 linked to rust resistance were validated using another RIL population of TG 26 × GPBD 4. The marker AhTE0498 showed 49.3–52.3 % PVE, indicating a strong marker validation in the new population. The improved map, QTL and markers for LLS and rust resistance reported in this study will be of immense utility in peanut molecular breeding.

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References

  • Bhat RS, Sujay V, Mukri G, Khedikar YP, Sarvamangala C, Yeri SB, Jadhav SS, Pujer SB, Narasimhulu R, Varshakumari, Azharudheen TPM, Varshney RK, Nadaf HL, Gowda MVC (2012) Utility of peanut mapping populations developed at UAS Dharwad, India VI International Conference on Legume Genetics and Genomics (ICLGG), Hyderabad, India

  • Bromfield K, Bailey W (1972) Inheritance of resistance to Puccinia arachidis in peanut. Phytopathology 62:748

    Google Scholar 

  • Cuc LM, Mace ES, Crouch JH, Quang VD, Long TD, Varshney RK (2008) Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea). BMC Plant Biol 8:55

    Article  PubMed  PubMed Central  Google Scholar 

  • Dwivedi SL, Pande S, Rao JN, Nigam SN (2002) Components of resistance to late leaf spot and rust among interspecific derivatives and their significance in a foliar disease resistance breeding in groundnut (Arachis hypogaea L.). Euphytica 125:81–88

    Article  CAS  Google Scholar 

  • Gowda MVC, Motagi BN, Naidu GK, Diddimani SB, Sheshagiri R (2002) GPBD 4: a Spanish bunch groundnut genotype resistant to rust and late leaf spot. Int Arachis Newslet 22:29–32

    Google Scholar 

  • Gowda MVC, Bhat RS, Motagi BN, Sujay V, Varshakumari, Bhat S (2010) Association of high-frequency origin of late leaf spot resistant mutants with AhMITE1 transposition in peanut. Plant Breed 129:567–569

    CAS  Google Scholar 

  • Khedikar Y, Gowda MVC, Sarvamangala C, Patgar K, Upadhyaya H, Varshney R (2010) A QTL study on late leaf spot and rust revealed one major QTL for molecular breeding for rust resistance in groundnut (Arachis hypogaea L.). Theor Appl Genet 121:971–984

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Koilkonda P, Sato S, Tabata S, Shirasawa K, Hirakawa H, Sakai H, Sasamoto S, Watanabe A, Wada T, Kishida Y, Tsuruoka H, Fujishiro T, Yamada M, Kohara M, Suzuki S, Hasegawa M, Kiyoshima H, Isobe S (2012) Large-scale development of expressed sequence tag-derived simple sequence repeat markers and diversity analysis in Arachis spp. Mol Breed 30:125–138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mondal S, Badigannavar A, D’Souza S (2012) Development of genic molecular markers linked to a rust resistance gene in cultivated groundnut (Arachis hypogaea L.). Euphytica 188:163–173

    Article  CAS  Google Scholar 

  • Mondal S, Hande P, Badigannavar AM (2013) Identification of transposable element markers for a rust (Puccinia arachidis Speg.) resistance gene in cultivated peanut. J Phytopathol 162:548–552

    Article  Google Scholar 

  • Pandey MK, Gautami B, Jayakumar T, Sriswathi M, Upadhyaya HD, Gowda MVC, Radhakrishnan T, Bertioli DJ, Knapp SJ, Cook DR, Varshney RK (2012) Highly informative genic and genomic SSR markers to facilitate molecular breeding in cultivated groundnut (Arachis hypogaea). Plant Breed 131:139–147

    Article  CAS  Google Scholar 

  • Paramasivam K, Jayasekhar M, Rajasekharan R, Veerabadhiran P (1990) Inheritance of rust resistance in groundnut (Arachis hypogaea L.). Madras Agric J 77:50–52

    Google Scholar 

  • Patil S, Kale D, Deshmukh S, Fulzele G, Weginwar B (1995) Semi-dwarf, early maturing and high yielding new groundnut variety, TAG-24. J Oilseeds Res 12:254–257

    Google Scholar 

  • Shirasawa K, Hirakawa H, Tabata S, Hasegawa M, Kiyoshima H, Suzuki S, Sasamoto S, Watanabe A, Fujishiro T, Isobe S (2012a) Characterization of active miniature inverted-repeat transposable elements in the peanut genome. Theor Appl Genet 124:1429–1438

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shirasawa K, Koilkonda P, Aoki K, Hirakawa H, Tabata S, Watanabe M, Hasegawa M, Kiyoshima H, Suzuki S, Kuwata C, Naito Y, Kuboyama T, Nakaya A, Sasamoto S, Watanabe A, Kato M, Kawashima K, Kishida Y, Kohara M, Kurabayashi A, Takahashi C, Tsuruoka H, Wada T, Isobe S (2012b) In silico polymorphism analysis for the development of simple sequence repeat and transposon markers and construction of linkage map in cultivated peanut. BMC Plant Biol 12:80

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shirasawa K, Bertioli DJ, Varshney RK, Moretzsohn MC, Leal-Bertioli SC, Thudi M, Pandey MK, Rami JF, Fonceka D, Gowda MV, Qin H, Guo B, Hong Y, Liang X, Hirakawa H, Tabata S, Isobe S (2013) Integrated consensus map of cultivated peanut and wild relatives reveals structures of the A and B genomes of Arachis and divergence of the legume genomes. DNA Res 20:173–184

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Singh AK, Mehan VK, Nigam SN (1997) Sources of resistance to groundnut fungal and bacterial diseases: an update and appraisal. Report No. 9290663677, ICRISAT, Patancheru, Andhra Pradesh

  • Sourdille P, Cadalen T, Guyomarc’h H, Snape J, Perretant M, Charmet G, Boeuf C, Bernard S, Bernard M (2003) An update of the Courtot × Chinese spring intervarietal molecular marker linkage map for the QTL detection of agronomic traits in wheat. Theor Appl Genet 106:530–538

    CAS  PubMed  Google Scholar 

  • Subbarao PV, Subramanyam P, Reddy PM (1990) A modified nine points diseases scale for assessment of rust and late leaf spot of groundnut Second International Congress of French Phytopathological Society. French Phyto-Pathological Society, France, p 25

    Google Scholar 

  • Subrahmanyam P, McDonald D, Waliar F, Reddy LJ, Nigam SN, Gibbons RW, Rao VR, Singh AK, Pande S, Reddy PM, Rao PVS (1995) Screening methods and sources of resistance to rust and late leaf spot of groundnut. ICRISAT, Patancheru, Andhra Pradesh

    Google Scholar 

  • Sujay V, Gowda MVC, Pandey MK, Bhat RS, Khedikar YP, Nadaf HL, Gautami B, Sarvamangala C, Lingaraju S, Radhakrishan T, Knapp SJ, Varshney RK (2012) QTL analysis and construction of consensus genetic map for foliar disease resistance based on two RIL populations in cultivated groundnut (Arachis hypogaea L.). Mol Breed 30:773–788

    Article  PubMed  PubMed Central  Google Scholar 

  • Sukruth M, Paratwagh SA, Sujay V, Varshakumari, Gowda MVC, Nadaf HL, Motagi BN, Lingaraju S, Pandey MK, Varshney RK, Bhat RS (2015) Validation of markers linked to late leaf spot and rust resistance, and selection of superior genotypes among diverse recombinant inbred lines and backcross lines in peanut (Arachis hypogaea L.). Euphytica 204:343–351

    Article  CAS  Google Scholar 

  • Tiwari S, Ghewande M, Misra D (1984) Inheritance of resistance to rust and late leaf spot in groundnut (Arachis hypogaea L.). J Cytol Genet 19:97–101

    Google Scholar 

  • Van Ooijen J., (2006), JoinMap® 4, Software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen, Netherlands 33

  • Varshakumari, (2013), Introgression of foliar disease resistance using synthetic amphidiploids and identification of associated QTLs in groundnut (Arachis hypogaea L.). PhD. Thesis, University of Agricultural Sciences, Dharwad, India

  • Varshney RK, Pandey MK, Pasupuleti J, Nigam SN, Sudini H, Gowda MVC, Sriswathi M, Radhakrishan T, Manohar SS, Patne N (2014) Marker-assisted introgression of a QTL region to improve rust resistance in three elite and popular varieties of peanut (Arachis hypogaea L.). Theor Appl Genet 127:1771–1781

    Article  PubMed  PubMed Central  Google Scholar 

  • Wang S, Basten C, Zeng Z (2007), Windows QTL cartographer 2.5. North Carolina State University

  • Wessler SR (1998) Transposable elements associated with normal plant genes. Physiol Plant 103:581–586

    Article  CAS  Google Scholar 

  • Wessler SR (2001) Plant transposable elements. A hard act to follow. Plant Physiol 125:149–151

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wynne JC, Beute MK, Nigam SN (1991) Breeding for disease resistance in peanut (Arachis hypogaea L.). Annu Rev Phytopathol 29:279–303

    Article  Google Scholar 

  • Yeri SB, 2015, Validation of late leaf spot and rust resistance-linked markers and transfer of associated QTL to JL 24 in groundnut (Arachis hypogaea L.). PhD. Thesis, University of Agricultural Sciences, Dharwad, India

  • Yeri SB, Kolekar RM, Motagi BN, Nadaf HL, Lingaraju S, Gowda MVC, Bhat RS (2014a) Development of late leaf spot and rust tolerant genotypes from TMV 2 and JL 24 by marker assisted backcross breeding in groundnut AAGB 2014—7th International Conference on Advances in Arachis through Genomics & Biotechnology, Georgia, USA, p 45

  • Yeri SB, Shirasawa K, Pandey MK, Gowda MVC, Sujay V, Shriswathi M, Nadaf HL, Motagi BN, Lingaraju S, Bhat ARS, Varshney RK, Krishnaraj PU, Bhat RS (2014b) Development of NILs from heterogeneous inbred families for validating the rust resistance QTLs in peanut (Arachis hypogaea L.). Plant Breed 133:80–85

    Article  CAS  Google Scholar 

  • Zhang Q, Arbuckle J, Wessler SR (2000) Recent, extensive, and preferential insertion of members of the miniature inverted-repeat transposable element family Heartbreaker into genic regions of maize. Proc Natl Acad Sci 97:1160–1165

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhou X, Xia Y, Ren X, Chen Y, Huang L, Huang S, Liao B, Lei Y, Yan L, Jiang H (2014) Construction of a SNP-based genetic linkage map in cultivated peanut based on large scale marker development using next-generation double-digest restriction-site-associated DNA sequencing (ddRADseq). BMC Genomics 15:351

    Article  PubMed  PubMed Central  Google Scholar 

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Correspondence to R. S. Bhat.

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Supplementary Table 1—Map position of markers on the linkage groups

Supplementary Table 2—Comparative names of linkage groups

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Kolekar, R.M., Sujay, V., Shirasawa, K. et al. QTL mapping for late leaf spot and rust resistance using an improved genetic map and extensive phenotypic data on a recombinant inbred line population in peanut (Arachis hypogaea L.). Euphytica 209, 147–156 (2016). https://doi.org/10.1007/s10681-016-1651-0

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