GBS-Based SNP Map Pinpoints the QTL Associated With Sorghum Downy Mildew Resistance in Maize (Zea mays L.)

Kashmiri Prakash Jadhav; Gajanan R Saykhedkar; Pandiampalayam Marappan Tamilarasi; Subramani Devasree; Rajagopalan Veera Ranjani; Chandran Sarankumar; Pukalenthy Bharathi; Adhimoolam Karthikeyan; Soosai Arulselvi; Esvaran Vijayagowri; Kalipatty Nalliappan Ganesan; Vaikuntavasan Paranidharan; Sudha K Nair; Raman Babu; Jegadeesan Ramalingam; Muthurajan Raveendran; Natesan Senthil

doi:10.3389/fgene.2022.890133

GBS-Based SNP Map Pinpoints the QTL Associated With Sorghum Downy Mildew Resistance in Maize (Zea mays L.)

Front Genet. 2022 Jul 20:13:890133. doi: 10.3389/fgene.2022.890133. eCollection 2022.

Authors

Kashmiri Prakash Jadhav¹, Gajanan R Saykhedkar², Pandiampalayam Marappan Tamilarasi³, Subramani Devasree⁴, Rajagopalan Veera Ranjani¹, Chandran Sarankumar⁵, Pukalenthy Bharathi⁵, Adhimoolam Karthikeyan⁶, Soosai Arulselvi⁷, Esvaran Vijayagowri¹, Kalipatty Nalliappan Ganesan⁸, Vaikuntavasan Paranidharan⁹, Sudha K Nair², Raman Babu¹⁰, Jegadeesan Ramalingam¹, Muthurajan Raveendran¹, Natesan Senthil^{6

11}

Affiliations

¹ Department of Plant Biotechnology, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India.
² Asian Regional Maize Program, International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, India.
³ Department of Crop Improvement, Kumaraguru Institute of Agriculture, Erode, India.
⁴ Department of Millets, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India.
⁵ Department of Plant Breeding and Genetics, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India.
⁶ Department of Biotechnology, Centre of Innovation, Agricultural College and Research Institute, Tamil Nadu Agricultural University, Madurai, India.
⁷ Agricultural College and Research Institute, Thanjavur, Tamil Nadu Agricultural University, Thanjavur, India.
⁸ Department of Forage Crops, Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, India.
⁹ Department of Plant Pathology, Centre for Plant Protection Studies, Tamil Nadu Agricultural University, Coimbatore, India.
¹⁰ Corteva Agrisciences, Multi Crop Research Centre, Hyderabad, India.
¹¹ Department of Plant Molecular Biology and Bioinformatics, Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, India.

Abstract

Sorghum downy mildew (SDM), caused by the biotrophic fungi Peronosclerospora sorghi , threatens maize production worldwide, including India. To identify quantitative trait loci (QTL) associated with resistance to SDM, we used a recombinant inbred line (RIL) population derived from a cross between resistant inbred line UMI936 (w) and susceptible inbred line UMI79. The RIL population was phenotyped for SDM resistance in three environments [E1-field (Coimbatore), E2-greenhouse (Coimbatore), and E3-field (Mandya)] and also utilized to construct the genetic linkage map by genotyping by sequencing (GBS) approach. The map comprises 1516 SNP markers in 10 linkage groups (LGs) with a total length of 6924.7 cM and an average marker distance of 4.57 cM. The QTL analysis with the phenotype and marker data detected nine QTL on chromosome 1, 2, 3, 5, 6, and 7 across three environments. Of these, QTL namely qDMR1.2, qDMR3.1, qDMR5.1, and qDMR6.1 were notable due to their high phenotypic variance. qDMR3.1 from chromosome 3 was detected in more than one environment (E1 and E2), explaining the 10.3% and 13.1% phenotypic variance. Three QTL, qDMR1.2, qDMR5.1, and qDMR6.1 from chromosomes 1, 5, and 6 were identified in either E1 or E3, explaining 15.2%-18% phenotypic variance. Moreover, genome mining on three QTL (qDMR3.1, qDMR5.1, and qDMR6.1) reveals the putative candidate genes related to SDM resistance. The information generated in this study will be helpful for map-based cloning and marker-assisted selection in maize breeding programs.

Keywords: QTL; genotyping by sequencing; maize; single nucleotide polymorphism; sorghum downy mildew.