title: The Genetic Basis of Haploid Induction in Maize Identified with a Novel Genome-Wide Association Method.
abstract: In vivo haploid induction (HI) triggered by pollination with special intraspecific genotypes, called inducers, is unique to Zea maysL. within the plant kingdom and has revolutionized maize breeding during the last decade. However, the molecular mechanisms underlying HI in maize are still unclear. To investigate the genetic basis of HI, we developed a new approach for genome-wide association studies (GWAS), termed conditional haplotype extension (CHE) test that allows detection of selective sweeps even under almost perfect confounding of population structure and trait expression. Here, we applied this test to identify genomic regions required for HI expression and dissected the combined support interval (50.34 Mb) of the QTL qhir1, detected in a previous study, into two closely linked genomic segments relevant for HI expression. The first, termed qhir11(0.54 Mb), comprises an already fine-mapped region but was not diagnostic for differentiating inducers and noninducers. The second segment, termed qhir12(3.97 Mb), had a haplotype allele common to all 53 inducer lines but not found in any of the 1482 noninducers. By comparing resequencing data of one inducer with 14 noninducers, we detected in the qhir12 region three candidate genes involved in DNA or amino acid binding, however, none for qhir11 We propose that the CHE test can be utilized in introgression breeding and different fields of genetics to detect selective sweeps in heterogeneous genetic backgrounds.
authors.affiliation: Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany.
authors.forename: Haixiao
authors.initials: H
authors.lastname: Hu
authors.affiliation: Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany.
authors.forename: Tobias A
authors.initials: TA
authors.lastname: Schrag
authors.affiliation: Plant Breeding, School of Life Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany.
authors.forename: Regina
authors.initials: R
authors.lastname: Peis
authors.affiliation: Plant Breeding, School of Life Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany.
authors.forename: Sandra
authors.initials: S
authors.lastname: Unterseer
authors.affiliation: Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany.
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Schipprack
authors.affiliation: Beijing Key Laboratory of Crop Genetic Improvement and National Maize Improvement Center, China Agricultural University, 100193 Beijing, China.
authors.forename: Shaojiang
authors.initials: S
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, China Agricultural University, 100193 Beijing, China.
authors.forename: Jinsheng
authors.initials: J
authors.lastname: Lai
authors.affiliation: National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070 Wuhan, China.
authors.forename: Jianbing
authors.initials: J
authors.lastname: Yan
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), ICRAF House, United Nations Avenue, Gigiri, 00621 Nairobi, Kenya.
authors.forename: Boddupalli M
authors.initials: BM
authors.lastname: Prasanna
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), ICRISAT Campus, Patancheru, 502324 Greater Hyderabad, India.
authors.forename: Sudha K
authors.initials: SK
authors.lastname: Nair
authors.affiliation: International Maize and Wheat Improvement Center (CIMMYT), 06600 Mexico Federal District, Mexico.
authors.forename: Vijay
authors.initials: V
authors.lastname: Chaikam
authors.affiliation: Procera Genetics, Fundulea, 915200 Calarasi, Romania.
authors.forename: Valeriu
authors.initials: V
authors.lastname: Rotarenco
authors.affiliation: P. P. Luk'yanenko Krasnodar All-Russia Research and Development Institute of Agriculture, Russian Academy of Agricultural Sciences, 350012 Krasnodar-12, Russia.
authors.forename: Olga A
authors.initials: OA
authors.lastname: Shatskaya
authors.affiliation: Department of Genetics Faculty of Biology, Saratov State University, 410012, Russia.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Zavalishina
authors.affiliation: Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Scholten
authors.affiliation: Plant Breeding, School of Life Sciences Weihenstephan, Technische Universität München, 85354 Freising, Germany.
authors.forename: Chris-Carolin
authors.initials: CC
authors.lastname: Schön
authors.affiliation: Institute of Plant Breeding, Seed Science, and Population Genetics, University of Hohenheim, 70593 Stuttgart, Germany melchinger@uni-hohenheim.de.
authors.forename: Albrecht E
authors.initials: AE
authors.lastname: Melchinger
mesh_terms: D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D055106:Genome-Wide Association Study / Q000379:methods; D023281:Genomics / Q000379:methods; D005838:Genotype; D006238:Haploidy; D010641:Phenotype; D000069600:Plant Breeding; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D003313:Zea mays / Q000235:genetics*
keywords: Zea mays L; genome-wide association study; in vivo haploid induction; population structure; selective sweep