Identification of Single Nucleotide Polymorphism Markers and Quantitative Trait Loci Conferring Drought Stress Tolerance in Maize
Rerenstradika Tizar Terryana *
Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Dani Satyawan
Research Center for Genetic Engineering, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Tri Joko Santoso
Research Center for Horticulture, Research Organization for Agricultural and Food, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Kristianto Nugroho
Research Center for Horticulture, Research Organization for Agricultural and Food, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Marcia Bunga Pabendon
Research Center for Food Crops, Research Organization for Agricultural and Food, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Tasliah
Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Lina Herlina
Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Muh. Dzulkifly Ashan
Department of Agricultural Production Technology, Pangkajene State Agricultural Polytechnic, South Sulawesi, Indonesia.
Muh. Aswad Ashan
Biology Doctoral Program, School of Life Science and Technology, Institut Teknologi Bandung, Bandung 40132, West Java, Indonesia.
Surya Diantina
Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Ifa Manzila
Research Center for Horticulture, Research Organization for Agricultural and Food, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Sigit Budi Santoso
Research Center for Food Crops, Research Organization for Agricultural and Food, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Nur Azizah
Indonesian Center for Agricultural Biotechnology and Genetic Resources Engineering and Modernization (ICABIOGREM), Jalan Tentara Pelajar 3A, Cimanggu 16111, Bogor, West Java, Indonesia.
Muhammad Azrai
Department of Agronomy, Faculty of Agriculture Hasanuddin University, Jalan Perintis Kemerdekaan KM 10, Makassar 90245, Indonesia.
Mastur
Politeknik Pembangunan Pertanian Yogyakarta-Magelang, Ministry of Agriculture Republic of Indonesia, Jalan Kusumanegara 2 Umbulharjo 55167, Yogyakarta, Indonesia.
Puji Lestari
Research Center for Horticulture, Research Organization for Agricultural and Food, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
Reflinur *
Research Center for Applied Botany, Research Organization for Life Sciences and Environment, National Research and Innovation Agency (BRIN), Cibinong, Bogor 16911, West Java, Indonesia.
*Author to whom correspondence should be addressed.
Abstract
Maize is one of the important food crops globally. However, its productivity is frequently affected by drought stress, particularly in tropical agro-climatic areas such as Indonesia. This study aimed to identify SNP markers and quantitative trait loci (QTL) associated with drought stress tolerance using a segregating F2:3 mapping population derived from a cross between MR13 (drought susceptible) and CML440 (drought tolerant). A total of 138 F2:3 lines were treated under normal irrigation and drought stress to evaluate five morphological traits: anthesis-silking interval (ASI), leaf rolling (LR), grain yield under stress (GYs), Grain yield potential (GYp), and drought sensitivity index (DSI). Genotyping produced 1,664 SNPs to construct a genetic linkage map spanning 4,173.4 cM across ten chromosomes, with an average marker interval of 2.51 cM. The results show that QTL mapping revealed nine loci associated with drought-related traits. A total of three QTLs were associated with ASI, two QTLs were associated with LR, GYs, and DSI, respectively, while no QTLs were linked to GYp. Major QTLs included qASI7a7 (15.53%), qLRb6 (15.87%), and qGYs4 (12.68%), while other QTLs contributed minor effects. Favourable alleles were contributed by both parents, which are MR13 alleles enhanced ASI, LR, and GYs traits, whereas CML440 alleles contributed strongly to ASI and LR traits. The identification of these QTLs, along with the discovery of SNP-derived SNAP markers, could provide valuable tools for marker-assisted selection related to drought stress in the maize breeding program.
Keywords: Drought tolerance, QTL mapping, SNP markers.