title: QTL mapping of agronomic waterlogging tolerance using recombinant inbred lines derived from tropical maize (Zea mays L) germplasm.
abstract: Waterlogging is an important abiotic stress constraint that causes significant yield losses in maize grown throughout south and south-east Asia due to erratic rainfall patterns. The most economic option to offset the damage caused by waterlogging is to genetically incorporate tolerance in cultivars that are grown widely in the target agro-ecologies. We assessed the genetic variation in a population of recombinant inbred lines (RILs) derived from crossing a waterlogging tolerant line (CAWL-46-3-1) to an elite but sensitive line (CML311-2-1-3) and observed significant range of variation for grain yield (GY) under waterlogging stress along with a number of other secondary traits such as brace roots (BR), chlorophyll content (SPAD), % stem and root lodging (S&RL) among the RILs. Significant positive correlation of GY with BR and SPAD and negative correlation with S&RL indicated the potential use of these secondary traits in selection indices under waterlogged conditions. RILs were genotyped with 331 polymorphic single nucleotide polymorphism (SNP) markers using KASP (Kompetitive Allele Specific PCR) Platform. QTL mapping revealed five QTL on chromosomes 1, 3, 5, 7 and 10, which together explained approximately 30% of phenotypic variance for GY based on evaluation of RIL families under waterlogged conditions, with effects ranging from 520 to 640 kg/ha for individual genomic regions. 13 QTL were identified for various secondary traits associated with waterlogging tolerance, each individually explaining from 3 to 14% of phenotypic variance. Of the 22 candidate genes with known functional domains identified within the physical intervals delimited by the flanking markers of the QTL influencing GY and other secondary traits, six have previously been demonstrated to be associated with anaerobic responses in either maize or other model species. A pair of flanking SNP markers has been identified for each of the QTL and high throughput marker assays were developed to facilitate rapid introgression of waterlogging tolerance in tropical maize breeding programs.
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT)-Asia, C/o International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India.
authors.forename: Pervez Haider
authors.initials: PH
authors.lastname: Zaidi
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT)-Asia, C/o International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India.
authors.forename: Zerka
authors.initials: Z
authors.lastname: Rashid
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT)-Asia, C/o International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India.
authors.forename: Madhumal Thayil
authors.initials: MT
authors.lastname: Vinayan
authors.affiliation: Monsanto Company, Uberlândia, Minas Gerais, Brazil.
authors.forename: Gustavo Dias
authors.initials: GD
authors.lastname: Almeida
authors.affiliation: Directorate of Maize Research (DMR), Pusa Campus, New Delhi, India.
authors.forename: Ramesh Kumar
authors.initials: RK
authors.lastname: Phagna
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT)-Asia, C/o International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India.
authors.forename: Raman
authors.initials: R
authors.lastname: Babu
mesh_terms: D002734:Chlorophyll / Q000378:metabolism; D032461:Chromosomes, Plant / Q000235:genetics; D005298:Fertility / Q000235:genetics; D017343:Genes, Plant; D056726:Genetic Association Studies; D008040:Genetic Linkage; D057166:High-Throughput Screening Assays; D007178:Inbreeding; D010641:Phenotype; D020161:Physical Chromosome Mapping; D018517:Plant Roots / Q000254:growth & development; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics; D011891:Rain; D000068098:Seed Bank; D013312:Stress, Physiological; D003313:Zea mays / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism
chemical_list: D002734:Chlorophyll