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

Verzegnazzi, Anderson Luiz; Santos, Iara Gonçalves dos; Krause, Matheus Dalsente; Hufford, Matthew B.; Frei, Ursula; Campbell, Jacqueline; Almeida, Vinícius Costa; Zuffo, Leandro Tonello; Boerman, Nicholas A.; Lübberstedt, Thomas

doi:10.1007/s00122-021-03780-8

Cited by 14 publications

(10 citation statements)

References 49 publications

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“…Absence of significant differences between BS39xA427_DH and BS39xA427_SSD lines for all traits in individual environments or across locations (Tables 2 and 3) suggest that spontaneous haploid genome doubling was not associated with undesirable linkage drag effects. Verzegnazzi et al (2021) found a significant enrichment of the A427 haplotype in the spontaneous haploid genome doubling QTL region on chromosome 5, which is consistent with strong selection for the major spontaneous haploid genome doubling QTL from A427 (Ren et al 2020;Trampe et al 2020) in this region.…”

supporting

confidence: 69%

“…This may lead to selection and perhaps fixation of particular 383 haplotypes in genome regions contributing to DH line development, and thus narrow the diversity among DH lines compared to SSD lines. Based on allele frequencies, genetic differentiation, and heterozygosity, Verzegnazzi et al (2021) showed that both SSD and DH breeding methods capture most of the genetic variability present in the BS39 population.…”

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confidence: 99%

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Usefulness of Adapted Exotic Maize Lines Developed By Doubled Haploid and Single Seed Descent Methods

Santos

Verzegnazzi

Edwards

et al. 2021

Preprint

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Adapted exotic maize (Zea mays L.) germplasm, such as BS39, provides a unique opportunity for broadening the genetic base of U.S. Corn Belt germplasm. In vivo doubled haploid (DH) technology has been used to efficiently exploit exotic germplasm. It can help to purge deleterious recessive alleles. The objectives of this study were to determine the usefulness of BS39-derived inbred lines using both SSD and DH methods, to determine the impact of spontaneous as compared to artificial haploid genome doubling on genetic variance among BS39-derived DH lines, and to identify SNP markers associated with agronomic traits among BS39 inbreds monitored at testcross level. We developed two sets of inbred lines directly from BS39 by DH and SSD methods, named BS39_DH and BS39_SSD. Additionally, two sets were derived from a cross between BS39 and A427 (SHGD donor) by DH and SSD methods, named BS39×A427_DH and BS39×A427_SSD, respectively. Grain yield, moisture, plant height, ear height, stalk lodging, and root lodging were measured to estimate genetic parameters. For genome-wide association (GWAS) analysis, inbred lines were genotyped using Genotype-by-Sequencing (GBS) and Diversity Array Technology Sequencing (DArTSeq). Some BS39-derived inbred lines performed better than elite germplasm inbreds and all sets showed significant genetic variance. The presence of spontaneous haploid genome doubling genes did not affect performance of inbred lines. Five SNPs were significant and three of them located within genes related to plant development or abiotic stresses. These results demonstrate the potential of BS39 to add novel alleles to temperate elite germplasm.

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confidence: 69%

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confidence: 99%

Usefulness of Adapted Exotic Maize Lines Developed By Doubled Haploid and Single Seed Descent Methods

Santos

Verzegnazzi

Edwards

et al. 2021

Preprint

Self Cite

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“…If so, this represents a remarkable case of parallel evolution of regulatory sequences [45][46][47] . Although both species are within the Cichorioideae subfamily of the Asteraceae, they occur in different subtribes that split between 13.5 and 20.8 million years ago 30,34 . They also differ fundamentally in the way female meiosis is avoided to achieve functional apomixis (Supplementary Note 1).…”

Section: Discussionmentioning

confidence: 99%

“…The observed twin seedlings grew slowly and either they died before true leaf formation, or those that did finally form true leaves were diploid. These diploid twins could be of sexual or parthenogenetic origin, in the latter case followed by spontaneous haploid genome doubling, which is often observed in crop species 34 .…”

Section: Functional Evidence That Par Induces Parthenogenesismentioning

confidence: 99%

A PARTHENOGENESIS allele from apomictic dandelion can induce egg cell division without fertilization in lettuce

et al. 2022

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This publication is made publicly available in the institutional repository of Wageningen University and Research, under the terms of article 25fa of the Dutch Copyright Act, also known as the Amendment Taverne. This has been done with explicit consent by the author.Article 25fa states that the author of a short scientific work funded either wholly or partially by Dutch public funds is entitled to make that work publicly available for no consideration following a reasonable period of time after the work was first published, provided that clear reference is made to the source of the first publication of the work.This publication is distributed under The Association of Universities in the Netherlands (VSNU) 'Article 25fa implementation' project. In this project research outputs of researchers employed by Dutch Universities that comply with the legal requirements of Article 25fa of the Dutch Copyright Act are distributed online and free of cost or other barriers in institutional repositories. Research outputs are distributed six months after their first online publication in the original published version and with proper attribution to the source of the original publication.

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“…Compared to linkage maps, the use of GWAS methodologies has advantages such as using genetically diverse populations with different rates of recombination and linkage disequilibrium (LD; Myles et al, 2009). Despite the observed GWAS efficiency in several crops (Warraich et al, 2020;Zhang et al, 2020;Verzegnazzi et al, 2021), this methodology still presents limitations related to the low proportion of phenotypic variance explained by the identified genomic regions (Manolio et al, 2009). As an alternative, the combination of GWAS results with other molecular methodologies, such as transcriptomics and proteomics analyses, can contribute to better knowledge of the genetic mechanisms involved in the definition of a trait (Tam et al, 2019), overcoming the statistical limitations on the characterization of a broad set of causal genomic regions.…”

Section: Introductionmentioning

confidence: 99%

Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches

et al. 2021

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Hevea brasiliensis (rubber tree) is a large tree species of the Euphorbiaceae family with inestimable economic importance. Rubber tree breeding programs currently aim to improve growth and production, and the use of early genotype selection technologies can accelerate such processes, mainly with the incorporation of genomic tools, such as marker-assisted selection (MAS). However, few quantitative trait loci (QTLs) have been used successfully in MAS for complex characteristics. Recent research shows the efficiency of genome-wide association studies (GWAS) for locating QTL regions in different populations. In this way, the integration of GWAS, RNA-sequencing (RNA-Seq) methodologies, coexpression networks and enzyme networks can provide a better understanding of the molecular relationships involved in the definition of the phenotypes of interest, supplying research support for the development of appropriate genomic based strategies for breeding. In this context, this work presents the potential of using combined multiomics to decipher the mechanisms of genotype and phenotype associations involved in the growth of rubber trees. Using GWAS from a genotyping-by-sequencing (GBS) Hevea population, we were able to identify molecular markers in QTL regions with a main effect on rubber tree plant growth under constant water stress. The underlying genes were evaluated and incorporated into a gene coexpression network modelled with an assembled RNA-Seq-based transcriptome of the species, where novel gene relationships were estimated and evaluated through in silico methodologies, including an estimated enzymatic network. From all these analyses, we were able to estimate not only the main genes involved in defining the phenotype but also the interactions between a core of genes related to rubber tree growth at the transcriptional and translational levels. This work was the first to integrate multiomics analysis into the in-depth investigation of rubber tree plant growth, producing useful data for future genetic studies in the species and enhancing the efficiency of the species improvement programs.

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

Cited by 14 publications

References 49 publications

Usefulness of Adapted Exotic Maize Lines Developed By Doubled Haploid and Single Seed Descent Methods

Usefulness of Adapted Exotic Maize Lines Developed By Doubled Haploid and Single Seed Descent Methods

A PARTHENOGENESIS allele from apomictic dandelion can induce egg cell division without fertilization in lettuce

Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches

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