QTL Mapping for Haploid Inducibility Using Genotyping by Sequencing in Maize

Doubled haploid (DH) technology in maize takes advantage of in vivo haploid induction (HI) triggered by pollination of donors of interest with inducer genotypes. However, the ability of different donors to be induced—inducibility (IND), varies among germplasm and the underlying molecular mechanisms are still unclear. In this study, the phenotypic variation for IND in a mapping population of temperate inbred lines was evaluated to identify regions in the maize genome associated with IND. A total of 247 F2:3 families derived from a biparental cross of two elite inbred lines, A427 and CR1Ht, were grown in three different locations and Inclusive Composite Interval Mapping (ICIM) was used to identify quantitative trait loci (QTL) for IND. In total, four QTL were detected, explaining 37.4% of the phenotypic variance. No stable QTL was found across locations. The joint analysis revealed QTL × location interactions, suggesting minor QTL control IND, which are affected by the environment

A Comparison between Inbred and Hybrid Maize Haploid Inducers

The effectiveness of haploid induction systems is regarded not only for high haploid induction rate (HIR) but also resource savings. Isolation fields are proposed for hybrid induction. However, efficient haploid production depends on inducer traits such as high HIR, abundant pollen production, and tall plants. Seven hybrid inducers and their respective parents were evaluated over three years for HIR, seeds set in cross-pollinations, plant and ear height, tassel size, and tassel branching. Mid-parent heterosis was estimated to quantify how much inducer traits improve in hybrids in comparison to their parents. Heterosis benefits hybrid inducers for plant height, ear height, and tassel size. Two hybrid inducers, BH201/LH82-Ped126 and BH201/LH82-Ped128, are promising for haploid induction in isolation fields. Hybrid inducers offer convenience and resource-effectiveness for haploid induction by means of improving plant vigor without compromising HIR.This article is published as Trentin HU, Yavuz R, Dermail A, Frei UK, Dutta S, Lübberstedt T. A Comparison between Inbred and Hybrid Maize Haploid Inducers. Plants. 2023; 12(5):1095. https://doi.org/10.3390/plants12051095. Posted with permission. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/)

QTL mapping of spontaneous haploid genome doubling using genotyping-by-sequencing in maize (Zea mays L.)

Genome doubling of haploids is one of the major constraints of large-scale doubled haploid (DH) technology. Improving spontaneous haploid genome doubling (SHGD) is an alternative to overcome this limitation. In this study, we aimed to construct a high-density linkage map based on genotyping by sequencing (GBS) of Single Nucleotide Polymorphism (SNPs), to detect QTL and QTL by environment (Q by E) interactions affecting SHGD, and to identify the best trait for mapping and selection of haploid male fertility (HMF). To this end, a bi-parental population of 220 F2:3 families was developed from a cross between A427 (high HMF) and CR1Ht (moderate HMF) to be used as donor. A high-density linkage map was constructed containing 4,171 SNP markers distributed over 10 chromosomes with an average distance between adjacent markers of 0.51 cM. QTL mapping for haploid fertile anther emergence (AE), pollen production (PP), tassel size (TS), and HMF, identified 27 QTL across three environments, and Q by E interactions were significant. A major QTL was identified on chromosome 5. This QTL explained over 45% of the observed variance for all traits across all environments. The introgression of this major QTL, using marker-assisted backcrossing, has great potential to overcome the need of using colchicine in DH line development.This is a manuscript of an article published asTrampe, B., dos Santos, I.G., Frei, U.K. et al. QTL mapping of spontaneous haploid genome doubling using genotyping-by-sequencing in maize (Zea mays L.). Theor Appl Genet (2020). doi: 10.1007/s00122-020-03585-1.</p

QTL mapping of spontaneous haploid genome doubling using genotyping-by-sequencing in maize (Zea mays L.)

Genome doubling of haploids is one of the major constraints of large-scale doubled haploid (DH) technology. Improving spontaneous haploid genome doubling (SHGD) is an alternative to overcome this limitation. In this study, we aimed to construct a high-density linkage map based on genotyping by sequencing (GBS) of Single Nucleotide Polymorphism (SNPs), to detect QTL and QTL by environment (Q by E) interactions affecting SHGD, and to identify the best trait for mapping and selection of haploid male fertility (HMF). To this end, a bi-parental population of 220 F2:3 families was developed from a cross between A427 (high HMF) and CR1Ht (moderate HMF) to be used as donor. A high-density linkage map was constructed containing 4,171 SNP markers distributed over 10 chromosomes with an average distance between adjacent markers of 0.51 cM. QTL mapping for haploid fertile anther emergence (AE), pollen production (PP), tassel size (TS), and HMF, identified 27 QTL across three environments, and Q by E interactions were significant. A major QTL was identified on chromosome 5. This QTL explained over 45% of the observed variance for all traits across all environments. The introgression of this major QTL, using marker-assisted backcrossing, has great potential to overcome the need of using colchicine in DH line development

Genetic basis of maize maternal haploid induction beyond MATRILINEAL and ZmDMP

In maize, doubled haploid (DH) lines are created in vivo through crosses with maternal haploid inducers. Their induction ability, usually expressed as haploid induction rate (HIR), is known to be under polygenic control. Although two major genes (MTL and ZmDMP) affecting this trait were recently described, many others remain unknown. To identify them, we designed and performed a SNP based (~9007) genome-wide association study using a large and diverse panel of 159 maternal haploid inducers. Our analyses identified a major gene near MTL, which is present in all inducers and necessary to disrupt haploid induction. We also found a significant quantitative trait loci (QTL) on chromosome 10 using a case-control mapping approach, in which 793 noninducers were used as controls. This QTL harbors a kokopelli ortholog, whose role in maternal haploid induction was recently described in Arabidopsis. QTL with smaller effects were identified on six of the ten maize chromosomes, confirming the polygenic nature of this trait. These QTL could be incorporated into inducer breeding programs through marker-assisted selection approaches. Further improving HIR is important to reduce the cost of DH line production.This article is published as Trentin HU, Krause MD, Zunjare RU, Almeida VC, Peterlini E, Rotarenco V, Frei UK, Beavis WD and Lübberstedt T (2023) Genetic basis of maize maternal haploid induction beyond MATRILINEAL and ZmDMP. Front. Plant Sci. 14:1218042. doi: 10.3389/fpls.2023.1218042.© 2023 Trentin, Krause, Zunjare, Almeida, Peterlini, Rotarenco, Frei, Beavis and Lübberstedt. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms

Major locus for spontaneous haploid genome doubling detected by a case–control GWAS in exotic maize germplasm

Temperate maize (Zea mays L.) breeding programs often rely on limited genetic diversity, which can be expanded by incorporating exotic germplasm. The aims of this study were to perform characterization of inbred lines derived from the tropical BS39 population using different breeding methods, to identify genomic regions showing segregation distortion in lines derived by the DH process using spontaneous haploid genome doubling (SHGD), and use case-control association mapping to identify loci controlling SHGD. Four different sets were used: BS39_DH and BS39_SSD were derived from the BS39 population by DH and single-seed descendent (SSD) methods, and BS39×A427_DH and BS39×A427_SSD from the cross between BS39 and A427. A total of 663 inbred lines were genotyped. The analyses of gene diversity and genetic differentiation for the DH sets provided evidence of the presence of a SHGD locus near the centromere of chromosome 5. The case-control GWAS for the DH set also pinpointed this locus. Haplotype sharing analysis showed almost 100% exclusive contribution of the A427 genome in the same region on chromosome 5 of BS39×A427_DH, presumably due to an allele in this region affecting SHGD. This locus enables DH line production in exotic populations without colchicine or other artificial haploid genome doubling.This is a manuscript of an article published as Verzegnazzi, A.L., dos Santos, I.G., Krause, M.D. et al. Major locus for spontaneous haploid genome doubling detected by a case–control GWAS in exotic maize germplasm. Theor Appl Genet (2021). doi: 10.1007/s00122-021-03780-8. Posted with permission.</p