scholarly journals Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm

2016 ◽  
Vol 6 (12) ◽  
pp. 3803-3815 ◽  
Author(s):  
Jiafa Chen ◽  
Rosemary Shrestha ◽  
Junqiang Ding ◽  
Hongjian Zheng ◽  
Chunhua Mu ◽  
...  
Keyword(s):  
Disease Resistance ◽  
Association Study ◽  
Candidate Genes ◽  
Genome Wide Association Study ◽  
Physical Map ◽  
Genome Wide Association ◽  
Fusarium Ear Rot ◽  
Ear Rot ◽  
Tropical Maize ◽  
Genome Wide

Abstract Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance. Each associated SNP locus had relatively small additive effects on disease resistance and accounted for 1–4% of trait variation. These SNPs and haplotypes were located within or adjacent to 38 candidate genes, 21 of which were candidate genes associated with plant tolerance to stresses, including disease resistance. Linkage mapping in four biparental populations to validate GWAS results identified 15 quantitative trait loci (QTL) associated with F. verticillioides resistance. Integration of GWAS and QTL to the maize physical map showed eight colocated loci on chromosomes 2, 3, 4, 5, 9, and 10. QTL on chromosomes 2 and 9 are new. These results reveal that FER resistance is a complex trait that is conditioned by multiple genes with minor effects. The value of selection on identified markers for improving FER resistance is limited; rather, selection to combine small effect resistance alleles combined with genomic selection for polygenic background for both the target and general adaptation traits might be fruitful for increasing FER resistance in maize.

scholarly journals Linkage Mapping and Genome-Wide Association Study Reveals Conservative QTLs and Candidate Genes for Fusarium Rot Resistance in Maize

2020 ◽  
Author(s):  
Yabin Wu ◽  
Zijian Zhou ◽  
Chaopei Dong ◽  
Jiafa Chen ◽  
Junqiang Ding ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Phenotypic Variation ◽  
Linkage Mapping ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Genome Wide Association ◽  
Ear Rot ◽  
Genome Wide

Abstract 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.

scholarly journals A Genome-Wide Association Study Reveals Genes Associated with Fusarium Ear Rot Resistance in a Maize Core Diversity Panel

2013 ◽  
Vol 3 (11) ◽  
pp. 2095-2104 ◽  
Author(s):  
Charles T. Zila ◽  
L. Fernando Samayoa ◽  
Rogelio Santiago ◽  
Ana Butrón ◽  
James B. Holland
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Fusarium Ear Rot ◽  
Ear Rot ◽  
Diversity Panel ◽  
Genome Wide ◽  
A Genome

scholarly journals Linkage Mapping and Genome-Wide Association Study Reveals Conservative QTLs and Candidate Genes for Fusarium Rot Resistance in  Maize

2019 ◽  
Author(s):  
Yabin Wu ◽  
Zijian Zhou ◽  
Chaopei Dong ◽  
Jiafa Chen ◽  
Junqiang Ding ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Phenotypic Variation ◽  
Linkage Mapping ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Genome Wide Association ◽  
Ear Rot ◽  
Genome Wide

Abstract Fusarium ear rot (FER) caused by Fusarium verticillioides is a major disease of maize that reduces grain yield and quality globally. 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). 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.

scholarly journals Genome-wide association study of Fusarium ear rot disease in the U.S.A. maize inbred line collection

2014 ◽  
Vol 14 (1) ◽  
Author(s):  
Charles T Zila ◽  
Funda Ogut ◽  
Maria C Romay ◽  
Candice A Gardner ◽  
Edward S Buckler ◽  
...  
Keyword(s):  
Association Study ◽  
Inbred Line ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Maize Inbred Line ◽  
Fusarium Ear Rot ◽  
Ear Rot ◽  
Genome Wide ◽  
Rot Disease

scholarly journals Linkage Mapping and Genome-Wide Association Study Reveals Conservative QTLs and Candidate Genes for Fusarium Rot Resistance in Maize

2020 ◽  
Author(s):  
Yabin Wu ◽  
Zijian Zhou ◽  
Chaopei Dong ◽  
Jiafa Chen ◽  
Junqiang Ding ◽  
...  
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Phenotypic Variation ◽  
Linkage Mapping ◽  
Genome Wide Association Study ◽  
Recombinant Inbred Lines ◽  
Inbred Lines ◽  
Genome Wide Association ◽  
Ear Rot ◽  
Genome Wide

Abstract 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.

scholarly journals Genome-Wide Association Study Reveals the Genetic Basis of Cold Tolerance in Rice at the Seedling Stage

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 318
Author(s):  
Tae-Ho Ham ◽  
Yebin Kwon ◽  
Yoonjung Lee ◽  
Jisu Choi ◽  
Joohyun Lee
Keyword(s):  
Association Study ◽  
Candidate Genes ◽  
Cold Tolerance ◽  
Genome Wide Association Study ◽  
Seedling Stage ◽  
Genome Wide Association ◽  
Matrix Analysis ◽  
Rice Seedlings ◽  
Genome Wide ◽  
A Genome

We conducted a genome-wide association study (GWAS) of cold tolerance in a collection of 127 rice accessions, including 57 Korean landraces at the seedling stage. Cold tolerance of rice seedlings was evaluated in a growth chamber under controlled conditions and scored on a 0–9 scale, based on their low-temperature response and subsequent recovery. GWAS, together with principal component analysis (PCA) and kinship matrix analysis, revealed four quantitative trait loci (QTLs) on chromosomes 1, 4, and 5 that explained 16.5% to 18.5% of the variance in cold tolerance. The genomic region underlying the QTL on chromosome four overlapped with a previously reported QTL associated with cold tolerance in rice seedlings. Similarly, one of the QTLs identified on chromosome five overlapped with a previously reported QTL associated with seedling vigor. Subsequent bioinformatic and haplotype analyses revealed three candidate genes affecting cold tolerance within the linkage disequilibrium (LD) block of these QTLs: Os01g0357800, encoding a pentatricopeptide repeat (PPR) domain-containing protein; Os05g0171300, encoding a plastidial ADP-glucose transporter; and Os05g0400200, encoding a retrotransposon protein, Ty1-copia subclass. The detected QTLs and further evaluation of these candidate genes in the future will provide strategies for developing cold-tolerant rice in breeding programs.

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