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

AbstractHaploid genome doubling is a key limiting step of haploid breeding in maize. Spontaneous restoration of haploid male fertility (HMF) provides a method by which costs can be saved and which does not require the use of toxic chemicals, in contrast to the artificial doubling process. To reveal the genetic basis of HMF, haploids were obtained from the offspring of 285 F2:3 families, derived from the cross Zheng58× K22. The F2:3 families were used as female donor and YHI-1 as the male inducer line. The rates of HMF from each family line were evaluated at two field sites over two planting seasons. Quantitative trait loci (QTL) for HMF were identified using a genetic linkage map containing 157 simple sequence repeat (SSR) markers. QTL for HMF displayed incomplete dominance. Transgressive segregation of haploids from F2:3 families was observed relative to haploids derived from the two parents of the mapping population. A total of nine QTL were detected, which were distributed on chromosomes 1, 3, 4, 7, and 8. Three QTL, qHMF3b, qHMF7a, and qHMF7b were detected in both locations, respectively. In our mapping population, HMF was controlled by three major QTL. These QTL could be useful to predict the ability of spontaneous haploid genome doubling in related breeding materials, and to accelerate the haploid breeding process by introgression or aggregation of those QTL.

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Impact of Spontaneous Haploid Genome Doubling in Maize Breeding

Plants ◽

10.3390/plants9030369 ◽

2020 ◽

Vol 9 (3) ◽

pp. 369 ◽

Cited By ~ 4

Author(s):

Nicholas A. Boerman ◽

Ursula K. Frei ◽

Thomas Lübberstedt

Keyword(s):

Genome Editing ◽

Male Fertility ◽

Gene Pyramiding ◽

Haploid Genome ◽

Systematic Design ◽

Maize Breeding ◽

Genome Doubling ◽

New Methodologies ◽

Marker Assisted Backcrossing ◽

The Impact

Doubled haploid (DH) technology has changed the maize-breeding landscape in recent years. Traditionally, DH production requires the use of chemical doubling agents to induce haploid genome doubling and, subsequently, male fertility. These chemicals can be harmful to humans and the plants themselves, and typically result in a doubling rate of 10%–30%. Spontaneous genome doubling and male fertility of maize haploids, without using chemical doubling agents, have been observed to a limited extent, for nearly 70 years. Rates of spontaneous haploid genome doubling (SHGD) have ranged from less than 5% to greater than 50%. Recently, there has been increased interest to forgo chemical treatment and instead utilize this natural method of doubling. Genetic-mapping studies comprising worldwide germplasm have been conducted. Of particular interest has been the detection of large-effect quantitative trait loci (QTL) affecting SHGD. Having a single large-effect QTL with an additive nature provides flexibility for the method of introgression, such as marker-assisted backcrossing, marker-assisted gene pyramiding, and systematic design. Moreover, it allows implementation of new methodologies, such as haploid-inducer mediated genome editing (HI-edit) and promotion of alleles by genome editing. We believe the use of SHGD can further enhance the impact of DH technology in maize.

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Mapping of QTL and identification of candidate genes conferring spontaneous haploid genome doubling in maize (Zea mays L.)

Plant Science ◽

10.1016/j.plantsci.2019.110337 ◽

2020 ◽

Vol 293 ◽

pp. 110337 ◽

Cited By ~ 5

Author(s):

Jiaojiao Ren ◽

Nicholas A. Boerman ◽

Ruixiang Liu ◽

Penghao Wu ◽

Benjamin Trampe ◽

...

Keyword(s):

Zea Mays ◽

Candidate Genes ◽

Zea Mays L ◽

Haploid Genome ◽

Genome Doubling

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

Theoretical and Applied Genetics ◽

10.1007/s00122-020-03585-1 ◽

2020 ◽

Vol 133 (7) ◽

pp. 2131-2140 ◽

Cited By ~ 2

Author(s):

Benjamin Trampe ◽

Iara Gonçalves dos Santos ◽

Ursula Karoline Frei ◽

Jiaojiao Ren ◽

Shaojiang Chen ◽

...

Keyword(s):

Zea Mays ◽

Qtl Mapping ◽

Zea Mays L ◽

Genotyping By Sequencing ◽

Haploid Genome ◽

Genome Doubling

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

10.21203/rs.3.rs-799789/v1 ◽

2021 ◽

Author(s):

Iara Goncalves Santos ◽

Anderson L. Verzegnazzi ◽

Jode Edwards ◽

Ursula K. Frei ◽

Nicholas Boerman ◽

...

Keyword(s):

Doubled Haploid ◽

Genetic Variance ◽

Agronomic Traits ◽

Inbred Lines ◽

Snp Markers ◽

Haploid Genome ◽

Genome Doubling ◽

The Impact ◽

Elite Germplasm

Abstract 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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