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Research article
Linkage Mapping and Genome-Wide Association Study Reveals Conservative QTLs and Candidate Genes for Fusarium Rot Resistance in Maize
Jianyu Wu
Henan Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-0487-8609
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Fusarium ear rot (FER) caused by Fusarium verticillioides is a major disease of maize that reduces grain yield and quality globally. However, there have been few reports of major loci for FER were verified and cloned.
Result: To gain a comprehensive understanding of the genetic basis of natural variation in FER resistance, a recombinant inbred lines (RIL) population and one panel of inbred lines were used to map quantitative trait loci (QTL) for resistance. As a result, a total of 10 QTL were identified by linkage mapping under four environments, which were located on six chromosomes and explained 1.0%-7.1% of the phenotypic variation. Epistatic mapping detected four pairs of QTL that showed significant epistasis effects, explaining 2.1%-3.0% of the phenotypic variation. Additionally, 18 single nucleotide polymorphisms (SNPs) were identified across the whole genome by genome-wide association study (GWAS) under five environments. Compared linkage and association mapping revealed five common intervals located on chromosomes 3, 4, and 5 associated with FER resistance, four of which were verified in different near-isogenic lines (NILs) populations. GWAS identified three candidate genes in these consistent intervals, which belonged to the Glutaredoxin protein family , actin-depolymerizing factors (ADFs), and AMP-binding proteins. In addition, two verified FER QTL regions were found consistent with Fusarium cob rot (FCR) and Fusarium seed rot (FSR).
Conclusions: These results revealed that multi pathways were involved in FER resistance, which was a complex trait that was controlled by multiple genes with minor effects, and provided important QTL and genes, which could be used in molecular breeding for resistance.
Keywords
maize, ear rot, disease resistance, QTL, GWAS, candidate gene
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CURRENT STATUS: Under Review
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Posted 16 Apr, 2020
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Submission checks complete
On 14 Apr, 2020
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Editorial decision: Minor revision
On 09 Apr, 2020
Review #1 received
Received 07 Apr, 2020
Reviewers invited
Invitations sent on 02 Apr, 2020
Reviewer #1 agreed
On 02 Apr, 2020
Editor assigned
On 25 Mar, 2020
Submission checks complete
On 24 Mar, 2020
Editor invited
On 24 Mar, 2020
No comments provided
Editorial decision: Minor revision
On 12 Mar, 2020
Review #2 received
Received 10 Mar, 2020
Reviewer #2 agreed
On 18 Feb, 2020
Review #1 received
Received 18 Dec, 2019
Reviewer #1 agreed
On 09 Dec, 2019
Reviewers invited
Invitations sent on 03 Oct, 2019
Submission checks complete
On 20 Aug, 2019
Editor invited
On 20 Aug, 2019
Editor assigned
On 16 Aug, 2019
First submitted
On 13 Aug, 2019
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This preprint is under consideration at BMC Genomics. A preprint is a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Learn more about In Review
Research article
Linkage Mapping and Genome-Wide Association Study Reveals Conservative QTLs and Candidate Genes for Fusarium Rot Resistance in Maize
Jianyu Wu
Henan Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-0487-8609
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
Prescreen
Peer Review Timeline
CURRENT STATUS: Under Review
Version 3
Posted 16 Apr, 2020
No community comments so far
Submission checks complete
On 14 Apr, 2020
No comments provided
Editorial decision: Minor revision
On 09 Apr, 2020
Review #1 received
Received 07 Apr, 2020
Reviewers invited
Invitations sent on 02 Apr, 2020
Reviewer #1 agreed
On 02 Apr, 2020
Editor assigned
On 25 Mar, 2020
Submission checks complete
On 24 Mar, 2020
Editor invited
On 24 Mar, 2020
No comments provided
Editorial decision: Minor revision
On 12 Mar, 2020
Review #2 received
Received 10 Mar, 2020
Reviewer #2 agreed
On 18 Feb, 2020
Review #1 received
Received 18 Dec, 2019
Reviewer #1 agreed
On 09 Dec, 2019
Reviewers invited
Invitations sent on 03 Oct, 2019
Submission checks complete
On 20 Aug, 2019
Editor invited
On 20 Aug, 2019
Editor assigned
On 16 Aug, 2019
First submitted
On 13 Aug, 2019
Metrics
Comments: 0
PDF Downloads: ...
HTML Views: ...
License:
This work is licensed under a CC BY 4.0 License. Read Full License
Background: Fusarium ear rot (FER) caused by Fusarium verticillioides is a major disease of maize that reduces grain yield and quality globally. However, there have been few reports of major loci for FER were verified and cloned.
Result: To gain a comprehensive understanding of the genetic basis of natural variation in FER resistance, a recombinant inbred lines (RIL) population and one panel of inbred lines were used to map quantitative trait loci (QTL) for resistance. As a result, a total of 10 QTL were identified by linkage mapping under four environments, which were located on six chromosomes and explained 1.0%-7.1% of the phenotypic variation. Epistatic mapping detected four pairs of QTL that showed significant epistasis effects, explaining 2.1%-3.0% of the phenotypic variation. Additionally, 18 single nucleotide polymorphisms (SNPs) were identified across the whole genome by genome-wide association study (GWAS) under five environments. Compared linkage and association mapping revealed five common intervals located on chromosomes 3, 4, and 5 associated with FER resistance, four of which were verified in different near-isogenic lines (NILs) populations. GWAS identified three candidate genes in these consistent intervals, which belonged to the Glutaredoxin protein family , actin-depolymerizing factors (ADFs), and AMP-binding proteins. In addition, two verified FER QTL regions were found consistent with Fusarium cob rot (FCR) and Fusarium seed rot (FSR).
Conclusions: These results revealed that multi pathways were involved in FER resistance, which was a complex trait that was controlled by multiple genes with minor effects, and provided important QTL and genes, which could be used in molecular breeding for resistance.
Figure 1
Figure 2
Figure 3