Assessment of inducibility and spontaneous haploid genome doubling in maize (Zea mays L.)

Maize is a staple food, fuel, and feed crop grown around the world. Doubled haploid technology allows for the quick of development of inbred lines for hybrid development. The maternal in vivo doubled haploid system has gained rapid adoption by the maize breeding sector within the last 10 years. There have been significant improvements in the doubled haploid technology, which made it commercially viable. Within the doubled haploid system, there is limited genetic information about the two important traits that control the ability of generating doubled haploids, which are inducibility and spontaneous haploid genome doubling. Better understanding of these two traits could drastically improve the efficiencies and reduce labor needs for producing doubled haploid lines. In this dissertation, the genetic control of both inducibility and spontaneous haploid genome doubling were studied. A Quantitative Trait Loci (QTL) mapping study was conducted for both traits using an F2:3 population derived from inbred A427 and CR1Ht. Inducibility QTL were identified and the improvement of inducibility is examined. A major QTL was found for spontaneous haploid genome doubling and its application to doubled haploid breeding is discussed

Novel technologies in doubled haploid line development

haploid inducer line can be transferred (DH) technology can not only shorten the breeding process but also increase genetic gain. Haploid induction and subsequent genome doubling are the two main steps required for DH technology. Haploids have been generated through the culture of immature male and female gametophytes, and through inter- and intraspecific via chromosome elimination. Here, we focus on haploidization via chromosome elimination, especially the recent advances in centromere-mediated haploidization. Once haploids have been induced, genome doubling is needed to produce DH lines. This study has proposed a new strategy to improve haploid genome doubling by combing haploids and minichromosome technology. With the progress in haploid induction and genome doubling methods, DH technology can facilitate reverse breeding, cytoplasmic male sterile (CMS) line production, gene stacking and a variety of other genetic analysis

Mapping of QTL and Identification of Candidate Genes Conferring Spontaneous Haploid Genome Doubling in Maize (Zea mays L.)

In vivo doubled haploid (DH) technology is widely used in commercial maize (Zea mays L.) breeding. Haploid genome doubling is a critical step in DH breeding. In this study, inbred lines GF1 (0.65), GF3(0.29), and GF5 (0) with high, moderate, and poor spontaneous haploid genome doubling (SHGD), respectively, were selected to develop mapping populations for SHGD. Three QTL, qshgd1, qshgd2, and qshgd3, related to SHGD were identified by selective genotyping. With the exception of qshgd3, the source of haploid genome doubling alleles were derived from GF1. Furthermore, RNA-Seq was conducted to identify putative candidate genes between GF1 and GF5 within the qshgd1 region. A differentially expressed formin-like protein 5 transcript was identified within the qshgd1 region

Novel technologies in doubled haploid line development

haploid inducer line can be transferred (DH) technology can not only shorten the breeding process but also increase genetic gain. Haploid induction and subsequent genome doubling are the two main steps required for DH technology. Haploids have been generated through the culture of immature male and female gametophytes, and through inter- and intraspecific via chromosome elimination. Here, we focus on haploidization via chromosome elimination, especially the recent advances in centromere-mediated haploidization. Once haploids have been induced, genome doubling is needed to produce DH lines. This study has proposed a new strategy to improve haploid genome doubling by combing haploids and minichromosome technology. With the progress in haploid induction and genome doubling methods, DH technology can facilitate reverse breeding, cytoplasmic male sterile (CMS) line production, gene stacking and a variety of other genetic analysis.This article is published as Ren, Jiaojiao, Penghao Wu, Benjamin Trampe, Xiaolong Tian, Shaojiang Chen, and Thomas Lübberstedt. "Novel technologies in doubled haploid line development." Plant Biotechnology Journal (2017). 10.1111/pbi.12805. Posted with permission.</p

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

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

A Diallel Analysis of a Maize Donor Population Response to In Vivo Maternal Haploid Induction I: Inducibility

The maize in vivo maternal doubled haploid (DH) system is an important tool used by maize breeders and geneticists around the world. The ability to rapidly produce DH lines of maize for breeding allows breeders to quickly respond to new selection criteria based on the ever changing biotic and abiotic stresses that maize is subjected to across its growing area. There are two important steps in the generation of DH lines using the in vivo maternal DH system: 1) the production and identification of haploid progeny, and 2) the doubling of genomes to create fertile, diploid inbred lines that can be used for topcross and per se evaluation. For this study, the focus is the first step, the production and identification of haploid progeny. A diallel mating between six inbred lines of maize, three highly inducible lines (CR1HT, PA91HT1, WF9) and three lines with low inducibility (NK778, A427, A637) was produced to study the genetic makeup of inducibility in temperate maize germplasm. A maximum estimated rate of inducibility was found in A427/A637 at 14.6%. Significant general combining ability (GCA) specific combining ability (SCA), reciprocal (REC), environmental (ENV), as well as GCA by ENV and SCA by ENV interactions were found. Misclassification rates ranged from 0-45.2% in the 30 hybrids considered. This study supports the use of germplasm with improved inducibility for breeding to improve rates of inducibility in germplasm which has low induction rates.This is a manuscript of an article published as Gerald N. De La Fuente, Ursula K. Frei, Benjamin Trampe, Daniel Nettleton, Wei Zhang, and Thomas Lubberstedt. A Diallel Analysis of a Maize Donor Population Response to In Vivo Maternal Haploid Induction I: Inducibility. Crop Science (2018), doi: 10.2135/cropsci2017.05.0285</p

Mapping of QTL and Identification of Candidate Genes Conferring Spontaneous Haploid Genome Doubling in Maize (Zea mays L.)

In vivo doubled haploid (DH) technology is widely used in commercial maize (Zea mays L.) breeding. Haploid genome doubling is a critical step in DH breeding. In this study, inbred lines GF1 (0.65), GF3(0.29), and GF5 (0) with high, moderate, and poor spontaneous haploid genome doubling (SHGD), respectively, were selected to develop mapping populations for SHGD. Three QTL, qshgd1, qshgd2, and qshgd3, related to SHGD were identified by selective genotyping. With the exception of qshgd3, the source of haploid genome doubling alleles were derived from GF1. Furthermore, RNA-Seq was conducted to identify putative candidate genes between GF1 and GF5 within the qshgd1 region. A differentially expressed formin-like protein 5 transcript was identified within the qshgd1 region.This is a manuscript of an article published as Ren, Jiaojiao, Nicholas Boerman, Ruixiang Liu, Penghao Wu, Benjamin Trampe, Kimberly Vanous, Ursula K. Frei, Shaojiang Chen, and Thomas Lübberstedt. "Mapping of QTL and Identification of Candidate Genes Conferring Spontaneous Haploid Genome Doubling in Maize (Zea mays L.)." Plant Science (2019). doi: 10.1016/j.plantsci.2019.110337. Posted with permission.</p