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 mays L. 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.KEYWORDS in vivo haploid induction; selective sweep; genome-wide association study; population structure; Zea mays L T HE double haploid (DH) technology based on in vivo haploid induction (HI) has become one of the most important tools in maize breeding during the past decade and is replacing the conventional method of line development by recurrent selfing . The success of this new technology became possible, because dozens of maize inducer lines have been developed worldwide (reviewed in Supplemental Material, File S1) which, when used as pollinators, trigger the production of seeds with haploid embryo at an acceptable rate, i.e., .2% . Double fertilization followed by elimination of the inducer chromosomes in the embryo at later developmental stages (Li et al. 2009;Xu et al. 2013) as well as parthenogenesis (Sarkar and Coe 1966;Beckert et al. 2008) HI in maize, but a proof of these hypotheses requires profound knowledge about the genetic and physiological factors underlying this phenomenon. All previous QTL mapping studies for unraveling the genetic architecture of HI detected a major QTL on chromosome 1 (Röber 1999;Beckert et al. 2008; Prigge et al. 2012). The most comprehensive study with four biparental populations (Prigge et al. 2012) mapped this QTL, termed qhir1, to bin 1.04 and hypothesized that it is required for HI, but QTL positions and 1-LOD support intervals differed substantially among populations. In another study with population 1680 3 UH400, Dong et al. (2013) fine mapped a 3.57-Mb region between markers umc1917 and bnlg1811, w...

Dissection of a major QTL qhir1 conferring maternal haploid induction ability in maize

“…The study clearly revealed that qhir11 is the only sub-region with a strong effect on HIR, whereas qhir12 had a negligible effect on HIR, in contrast to the hypothesis of Hu et al (2016) based on a selective sweep based GWAS approach. Furthermore, our study proved that qhir11 is more strongly associated than qhir12 with segregation distortion and kernel abortion, two traits that are associated with maternal haploid induction.…”

“…The qhir11 sub-region, also found significant in the study by Hu et al (2016), revealed two haplotypes, where the minor haplotype was shared by two non-inducer lines, which did not have HI ability. Additionally, Hu et al (2016) identified qhir12 as the most probable genomic segment carrying gene(s) responsible for HI, as this region had a single haplotype that was unchanged in all the inducers.…”

Loss of pollen‐specific phospholipase NOT LIKE DAD triggers gynogenesis in maize

“…In particular, lines EM1201 and Nys302, which have the same haplotype at the gim1/qhir1 locus as the inducer line PK6 except for the 4‐bp insertion, do not induce gynogenesis. This diagnostic indel is also absent in the lines Mo1W and TX303 used as non‐inducer controls in a GWAS study of gim1/qhir1 (Hu et al , ). This later result highlights the preponderant role of the sub‐region qhir11 (containing NLD ) compared to the sub‐region qhir12 (downstream of NLD ) in haploid induction phenotype.…”

Early diagnosis of ploidy status in doubled haploid production of maize by stomata length and flow cytometry measurements

“…During the past two decades, the traditional method of breeding homozygous inbreds by several generations of recurrent selfing has been complemented by the doubled haploid (DH) technology based on maternal in vivo haploid induction (Molenaar & Melchinger, ). This applies to both temperate and tropical maize, because meanwhile a wide variety of inducers adapted to different climatic zones has become available (Chaikam et al, ; Dong et al, ; Hu et al, ). In addition to the important advantages in breeding summarized by Molenaar and Melchinger (), DH line production is very appealing to breeders because it can be performed with relatively simple equipment and involves only four basic steps: (a) induction of maternal haploids by pollination with haploid inducers (genotypes triggering formation of seeds with haploid embryo), (b) discrimination of haploid seeds from normal crossing seeds, where the embryo contains paternal DNA, (c) chromosome doubling by treatment with chemical agents or occurring spontaneously and (d) selfing of fertile D 0 plants to produce D 1 ears with seed set.…”