title: Fine mapping of Msv1, a major QTL for resistance to Maize Streak Virus leads to development of production markers for breeding pipelines.
abstract: Msv1 , the major QTL for MSV resistance was delimited to an interval of 0.87 cM on chromosome 1 at 87 Mb and production markers with high prediction accuracy were developed. Maize streak virus (MSV) disease is a devastating disease in the Sub-Saharan Africa (SSA), which causes significant yield loss in maize. Resistance to MSV has previously been mapped to a major QTL (Msv1) on chromosome 1 that is germplasm and environment independent and to several minor loci elsewhere in the genome. In this study, Msv1 was fine-mapped through QTL isogenic recombinant strategy using a large F 2 population of CML206 × CML312 to an interval of 0.87 cM on chromosome 1. Genome-wide association study was conducted in the DTMA (Drought Tolerant Maize for Africa)-Association mapping panel with 278 tropical/sub-tropical breeding lines from CIMMYT using the high-density genotyping-by-sequencing (GBS) markers. This study identified 19 SNPs in the region between 82 and 93 Mb on chromosome 1(B73 RefGen_V2) at a P < 1.00E-04, which coincided with the fine-mapped region of Msv1. Haplotype trend regression identified a haplotype block significantly associated with response to MSV. Three SNPs in this haplotype block at 87 Mb on chromosome 1 had an accuracy of 0.94 in predicting the disease reaction in a collection of breeding lines with known responses to MSV infection. In two biparental populations, selection for resistant Msv1 haplotype demonstrated a reduction of 1.03-1.39 units on a rating scale of 1-5, compared to the susceptible haplotype. High-throughput KASP assays have been developed for these three SNPs to enable routine marker screening in the breeding pipeline for MSV resistance.
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, Greater Hyderabad, 502324, India, Sudha.nair@cgiar.org.
authors.forename: Sudha K
authors.initials: SK
authors.lastname: Nair
authors.forename: Raman
authors.initials: R
authors.lastname: Babu
authors.forename: Cosmos
authors.initials: C
authors.lastname: Magorokosho
authors.forename: George
authors.initials: G
authors.lastname: Mahuku
authors.forename: Kassa
authors.initials: K
authors.lastname: Semagn
authors.forename: Yoseph
authors.initials: Y
authors.lastname: Beyene
authors.forename: Biswanath
authors.initials: B
authors.lastname: Das
authors.forename: Dan
authors.initials: D
authors.lastname: Makumbi
authors.forename: P
authors.initials: P
authors.lastname: Lava Kumar
authors.forename: Michael
authors.initials: M
authors.lastname: Olsen
authors.forename: Prasanna M
authors.initials: PM
authors.lastname: Boddupalli
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D060467:Disease Resistance / Q000235:genetics*; D005819:Genetic Markers; D006239:Haplotypes; D026762:Maize streak virus; D010641:Phenotype; D000069600:Plant Breeding; D010935:Plant Diseases / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D003313:Zea mays / Q000235:genetics* / Q000821:virology
chemical_list: D005819:Genetic Markers