QTL Mapping linked to downy mildew resistance genes in maize (Zea mays)
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Abstract. Ashan MD, Miftahudin, Reflinur, Pabendon MB, Santoso SB, Salim A. 2020. QTL Mapping linked to downy mildew resistance genes in maize (Zea mays). Biodiversitas 21: 3735-3743. Downy Mildew (DM) caused by Peronosclerospora spp. is one of the most destructive diseases and problems in yield losses of maize production worldwide. Identification of molecular marker-linked to the DM resistance genes is considered as an important step in the improvement of the DM resistance nature in maize breeding program. The objective of the study was to identify molecular markers linked to the DM resistance genes in maize. A total of 198 F3 maize lines generated from a cross between R10-4430 and Kandora was used in microsatellite genetic map construction and the corresponding F3: 4 families were used in phenotypic evaluation to identify quantitative trait loci (QTLs) responsible for DM resistance-related trait. The entire genetic linkage map constructed with 28 SSR markers resulted in 460.3 cM with an average distance between markers of 26.85 cM. Seven main-effect QTLs controlling the DM resistance genes were identified in the entire genome map of F3 population with the phenotypic variation explained (PVE) values ranged from 43.35 to 53.71%. Among detected QTLs, three QTLs, qDM-Pp1a, qDM-Pp1b1, and qDM-Pp1b2 were detected on chromosome 1, one QTL, qDM-Pp5 was on chromosome 5, two QTLs, qDM-Pp6b1 and qDM-Pp6b2 were on chromosome 6 and one QTL, qDM-Pp10 was on chromosome 10. The effect of detected QTLs responsible for DM resistance trait ranged from 43.35 to 53.71% and those will be potential to be further used as molecular aided selection in maize breeding for DM resistance.
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References
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De Almeida JE, Guimarães JFR, Silva FFE, De Resende MDV, Muñoz P, Kirst M, Resende MFR. 2016. The contribution of dominance to phenotype prediction in a pine breeding and simulated population. Heredity (Edinb). 117(1):33–41.
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Gedil M, Menkir A. 2019. An integrated molecular and conventional breeding scheme for enhancing genetic gain in Maize in Africa. Front. Plant Sci. 10(1430):1–17.
George ML, Regalado E, Warburton M, Vasal S, Hoisington D. 2004. Genetic diversity of maize inbred lines in relation to downy mildew. Euphytica 135(2):145–155.
George MLC, Prasanna BM, Rathore RS, Setty TAS, Kasim F, Azrai M, Vasal S, Balla O, Hautea D, Canama A, Regalado E, Vargas M, Khairallah M, Jeffers D, Hoisington D. 2003. Identification of QTLs conferring resistance to downy mildews of maize in Asia. Theor. Appl. Genet. 107(3):544–551.
Khan IA, Awan FS, Ahmad A, Khan AA. 2004. A modified mini-prep method for economical and rapid extraction of genomic DNA in plants. Plant Mol. Biol. Report. 22(1):624892.
Kosambi DD. 1943. The estimation of map distances from recombination values. Ann. Eugen. 12(1):172–175.
Li WH, Liu W, Liu L, You MS, Liu GT, Li BY. 2011. QTL mapping for Wheat flour color with additive, epistatic, and QTL×environmental interaction effects. Agric. Sci. China 10(5):651–660.
Lohithaswa HC, Jyothi K, Sunil KKR, Puttaramanaik, Hittalmani S. 2015. Identification and introgression of QTLs implicated in resistance to sorghum downy mildew (Peronosclerospora sorghi (Weston and Uppal) C. G. Shaw) in maize through marker-assisted selection. J. Genet. 94(4):741–748.
Muis A, Nonci N, Pabendon MB. 2015. Skrining ketahanan galur S1 Jagung terhadap penyakit bulai dan pembentukan galur S2 tahan penyakit bulai. Bul. Plasma Nutfah 21(1):17–24.
Nair SK, Prasanna BM, Garg A, Rathore RS, Setty TAS, Singh NN. 2005. Identification and validation of QTLs conferring resistance to sorghum downy mildew (Peronosclerospora sorghi) and Rajasthan downy mildew (P. heteropogoni) in maize. Theor. Appl. Genet. 110(8):1384–1392.
Rashid Z, Zaidi PH, Vinayan MT, Sharma SS, Srirama Setty TA. 2013. Downy mildew resistance in maize (Zea mays L.) across Peronosclerospora species in lowland tropical Asia. Crop Prot. 43:183–191.
Rashid Z, Singh PK, Vemuri H, Zaidi PH, Prasanna BM, Nair SK. 2018. Genome-wide association study in Asia-adapted tropical maize reveals novel and explored genomic regions for sorghum downy mildew resistance. Sci. Rep. 8(1):1–12.
Reflinur B, Lestari P. 2015. Determination of gene locus in plant chromosomes with DNA marker. J. Litbang Pert. 34(4):177–186.
Roberdi, Aswidinnoor H, Setiawan A, Sutrisno, Pabendon MB, Azrai M. 2010. Keterpautan 23 marka mikrosatelit pada kromosom 6 dan 7 dengan karakter ketahanan populasi jagung terhadap penyakit bulai (Peronosclerospora maydis ). J. AgroBiogen 6(1):10–17.
Ruswandi D, Hautea DM, Carpena AL, Lantican RM, Salazar AM, Raymundo AD. 2015. Quantitative trait loci mapping of Philippine downy mildew resistance gene in maize (Zea Mays L.). Zuriat 13(1):27–34.
Sabry A, Jeffers D, Vasal SK, Frederiksen R, Magill C. 2006. A region of maize chromosome 2 affects response to downy mildew pathogens. Theor. Appl. Genet. 113(2):321–330.
Shah L, Si H, Wang S, Zhu Y, Jiang H, Cao J, Ali A, Ma C. 2017. Quantitative trait loci associated to Fusarium head blight resistance in wheat populations containing Annong–1124 and Zhoumai–27. Physiol. Mol. Plant Pathol. 100(2017):67–74.
Sukhwinder-Singh, Hernandez M V., Crossa J, Singh PK, Bains NS, Singh K, Sharma I. 2012. Multi-trait and multi-environment QTL analyses for resistance to wheat diseases. PLoS One 7(6):e38008.
Talanca AH. 2013. Status penyakit bulai pada tanaman jagung dan pengendaliannya. Semin. Nas. Inov. Teknol. Pertan.:76–87.
Wang S, Basten CJ, Zeng Z-B. 2010. Windows QTL Cartographer V2.5_011, Department of Statistics, North Carolina State University, Raleigh.
De Almeida JE, Guimarães JFR, Silva FFE, De Resende MDV, Muñoz P, Kirst M, Resende MFR. 2016. The contribution of dominance to phenotype prediction in a pine breeding and simulated population. Heredity (Edinb). 117(1):33–41.
Ashkani S, Rafii MY, Shabanimofrad M, Miah G, Sahebi M, Azizi P, Tanweer FA, Akhtar MS, Nasehi A. 2015. Molecular breeding strategy and challenges towards improvement of blast disease resistance in rice crop. Front. Plant Sci. 6(11):1–14.
Daryono BS, Parazulfa A, Purnomo P. 2018. Uji Ketahanan Tujuh Kultivar Jagung (Zea mays L.) Terhadap Penyakit Bulai (Peronosclerospora spp.). Biog. J. Ilm. Biol. 6(1):11–17.
Gedil M, Menkir A. 2019. An integrated molecular and conventional breeding scheme for enhancing genetic gain in Maize in Africa. Front. Plant Sci. 10(1430):1–17.
George ML, Regalado E, Warburton M, Vasal S, Hoisington D. 2004. Genetic diversity of maize inbred lines in relation to downy mildew. Euphytica 135(2):145–155.
George MLC, Prasanna BM, Rathore RS, Setty TAS, Kasim F, Azrai M, Vasal S, Balla O, Hautea D, Canama A, Regalado E, Vargas M, Khairallah M, Jeffers D, Hoisington D. 2003. Identification of QTLs conferring resistance to downy mildews of maize in Asia. Theor. Appl. Genet. 107(3):544–551.
Khan IA, Awan FS, Ahmad A, Khan AA. 2004. A modified mini-prep method for economical and rapid extraction of genomic DNA in plants. Plant Mol. Biol. Report. 22(1):624892.
Kosambi DD. 1943. The estimation of map distances from recombination values. Ann. Eugen. 12(1):172–175.
Li WH, Liu W, Liu L, You MS, Liu GT, Li BY. 2011. QTL mapping for Wheat flour color with additive, epistatic, and QTL×environmental interaction effects. Agric. Sci. China 10(5):651–660.
Lohithaswa HC, Jyothi K, Sunil KKR, Puttaramanaik, Hittalmani S. 2015. Identification and introgression of QTLs implicated in resistance to sorghum downy mildew (Peronosclerospora sorghi (Weston and Uppal) C. G. Shaw) in maize through marker-assisted selection. J. Genet. 94(4):741–748.
Muis A, Nonci N, Pabendon MB. 2015. Skrining ketahanan galur S1 Jagung terhadap penyakit bulai dan pembentukan galur S2 tahan penyakit bulai. Bul. Plasma Nutfah 21(1):17–24.
Nair SK, Prasanna BM, Garg A, Rathore RS, Setty TAS, Singh NN. 2005. Identification and validation of QTLs conferring resistance to sorghum downy mildew (Peronosclerospora sorghi) and Rajasthan downy mildew (P. heteropogoni) in maize. Theor. Appl. Genet. 110(8):1384–1392.
Rashid Z, Zaidi PH, Vinayan MT, Sharma SS, Srirama Setty TA. 2013. Downy mildew resistance in maize (Zea mays L.) across Peronosclerospora species in lowland tropical Asia. Crop Prot. 43:183–191.
Rashid Z, Singh PK, Vemuri H, Zaidi PH, Prasanna BM, Nair SK. 2018. Genome-wide association study in Asia-adapted tropical maize reveals novel and explored genomic regions for sorghum downy mildew resistance. Sci. Rep. 8(1):1–12.
Reflinur B, Lestari P. 2015. Determination of gene locus in plant chromosomes with DNA marker. J. Litbang Pert. 34(4):177–186.
Roberdi, Aswidinnoor H, Setiawan A, Sutrisno, Pabendon MB, Azrai M. 2010. Keterpautan 23 marka mikrosatelit pada kromosom 6 dan 7 dengan karakter ketahanan populasi jagung terhadap penyakit bulai (Peronosclerospora maydis ). J. AgroBiogen 6(1):10–17.
Ruswandi D, Hautea DM, Carpena AL, Lantican RM, Salazar AM, Raymundo AD. 2015. Quantitative trait loci mapping of Philippine downy mildew resistance gene in maize (Zea Mays L.). Zuriat 13(1):27–34.
Sabry A, Jeffers D, Vasal SK, Frederiksen R, Magill C. 2006. A region of maize chromosome 2 affects response to downy mildew pathogens. Theor. Appl. Genet. 113(2):321–330.
Shah L, Si H, Wang S, Zhu Y, Jiang H, Cao J, Ali A, Ma C. 2017. Quantitative trait loci associated to Fusarium head blight resistance in wheat populations containing Annong–1124 and Zhoumai–27. Physiol. Mol. Plant Pathol. 100(2017):67–74.
Sukhwinder-Singh, Hernandez M V., Crossa J, Singh PK, Bains NS, Singh K, Sharma I. 2012. Multi-trait and multi-environment QTL analyses for resistance to wheat diseases. PLoS One 7(6):e38008.
Talanca AH. 2013. Status penyakit bulai pada tanaman jagung dan pengendaliannya. Semin. Nas. Inov. Teknol. Pertan.:76–87.
Wang S, Basten CJ, Zeng Z-B. 2010. Windows QTL Cartographer V2.5_011, Department of Statistics, North Carolina State University, Raleigh.
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