Nucleotide diversity of the ZmPox3 maize peroxidase gene: Relationships between a MITE insertion in exon 2 and variation in forage maize digestibility

Guillet-Claude, Carine; Birolleau-Touchard, C.; Manicacci, Doménica; Rogowsky, Peter; Rigau, Joan; Murigneux, Alain; Martinant, Jean‐Pierre; Barrière, Yves

doi:10.1186/1471-2156-5-19

Cited by 62 publications

(8 citation statements)

References 28 publications

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“…The huge variations in association mapping population suggests that natural germplasm with a broad genetic base could be a potential resource for improving forage quality. The sample size and phenotypic variation in the current study are larger than in the previous studies of associations between lignin pathway genes and forage quality traits [ 57 – 60 ]. According to the population stratification, the association panel was divided into four sub-groups [ 53 ].…”

Section: Discussionmentioning

confidence: 93%

“…In previous candidate gene-based association studies, ten lignin biosynthetic genes were investigated to detect associations between polymorphisms and forage quality traits [ 57 – 60 ]. The results showed that polymorphisms within the PAL , ZmC3H1 and F5H were associated with forage quality traits.…”

Section: Discussionmentioning

confidence: 99%

“…However, these associations were affected by population structure and multiple tests. Only individual polymorphisms in the 4CL1 , CCoAOMT2 and ZmPox3 were stably associated with digestibility [ 57 , 59 , 60 ]. In the present study, we did not find any other gene involved in lignin biosynthesis in association with ADF, NDF or IVDMD with the exception of ZmC3H2 .…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide association analysis of forage quality in maize mature stalk

Wang

Xiu

et al. 2016

BMC Plant Biol

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BackgroundPlant digestibility of silage maize (Zea mays L.) has a large influence on nutrition intake for animal feeding. Improving forage quality will enhance the utilization efficiency and feeding value of forage maize. Dissecting the genetic basis of forage quality will improve our understanding of the complex nature of cell wall biosynthesis and degradation, which is also helpful for breeding good quality silage maize.ResultsAcid detergent fiber (ADF), neutral detergent fiber (NDF) and in vitro dry matter digestibility (IVDMD) of stalk were evaluated in a diverse maize population, which is comprised of 368 inbred lines and planted across seven environments. Using a mixed model accounting for population structure and polygenic background effects, a genome-wide association study was conducted to identify single nucleotide polymorphisms (SNPs) significantly associated with forage quality. Scanning 559,285 SNPs across the whole genome, 73, 41 and 82 SNPs were found to be associated with ADF, NDF, and IVDMD, respectively. Each significant SNP explained 4.2 %–6.2 % of the phenotypic variation. Underlying these associated loci, 56 genes were proposed as candidate genes for forage quality.ConclusionsOf all the candidate genes proposed by GWAS, we only found a C3H gene (ZmC3H2) that is directly involved in cell wall component biosynthesis. The candidate genes found in this study are mainly involved in signal transduction, stress resistance, and transcriptional regulation of cell wall biosynthetic gene expression. Adding high digestibility maize into the association panel would be helpful for increasing genetic variability and identifying more genes associated with forage quality traits. Cloning and functional validation of these genes would be helpful for understanding the molecular mechanism of the fiber content and digestibility. These findings provide us new insights into cell wall formation and deposition.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0919-9) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 93%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genome-wide association analysis of forage quality in maize mature stalk

Wang

Xiu

et al. 2016

BMC Plant Biol

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“…Two SNPs in the F5H gene, leading to a substitution from Proline to Arginine, were associated with dry matter yield (DMY) ). Finally, a miniature invertedrepeat transposable elements (MITE) insertion in the second exon of ZmPox3 was associated with cell wall digestibility in 56 inbreds (Guillet-Claude et al 2004b).…”

Section: Genes Controlling Forage Quality Of Maizementioning

confidence: 99%

Qualitative and Quantitative Trait Polymorphisms in Maize

Yang

2013

Diagnostics in Plant Breeding

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“…Lignin structure and cross-linking between cell wall components influence digestibility (Barrière et al, 2003). Analysis of allelic diversity in relation to cell wall digestibility revealed ZmPox3 peroxidase, a candidate gene for silage maize digestibility improvement (Guillet-Claude et al, 2004), as it is colocalized with a cell wall digestibility and lignification QTL (Barrière et al, 2003). GBSS, starch branching enzymes 1 (SBE1) and 3 (SBE3), are major enzymes involved in starch biosynthesis in rice endosperm.…”

Section: B Genomic Resources 1 Genetic Markersmentioning

confidence: 99%

The Molecularization of Public Sector Crop Breeding: Progress, Problems, and Prospects

Dwivedi

Crouch

Mackill

et al. 2007

Advances in Agronomy

135

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Molecular markers and genetic maps are available for most important food crops. Marker-trait associations have been established for a diverse array of traits in these crops, and research on marker/quantitative trait loci (QTL) validation and refinement is increasingly common. Researchers are now routinely using candidate gene-based mapping and genome-wide linkage disequilibrium and association analysis in addition to classical QTL mapping to identify markers broadly applicable to breeding programs. Marker-assisted selection (MAS) is practiced for enhancing various host plant resistances, several quality traits, and a number of abiotic stress tolerances in many wellresearched crops. Markers are also increasingly used to transfer yield or quality-enhancing QTL alleles from wild relatives to elite cultivars. Largescale MAS-based breeding programs for crops such as rice, maize, wheat, barley, pearl millet, and common bean have already been initiated worldwide. Advances in ''omics'' technologies are now assisting researchers to address complex biological issues of significant agricultural importance: modeling genotype-by-environment interaction; fine-mapping, cloning, and pyramiding of QTL; gene expression analysis and gene function elucidation; dissecting the genetic structure of germplasm collections to mine novel alleles and develop genetically structured trait-based core collections; and understanding the molecular basis of heterosis. The challenge now is to translate and integrate this knowledge into appropriate tools and methodologies for plant breeding programs. The role of computational tools in achieving this is becoming increasingly important. It is expected that harnessing the outputs of genomics research will be an important component in successfully addressing the challenge of doubling world food production by 2050.

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Nucleotide diversity of the ZmPox3 maize peroxidase gene: Relationships between a MITE insertion in exon 2 and variation in forage maize digestibility

Cited by 62 publications

References 28 publications

Genome-wide association analysis of forage quality in maize mature stalk

Genome-wide association analysis of forage quality in maize mature stalk

Qualitative and Quantitative Trait Polymorphisms in Maize

The Molecularization of Public Sector Crop Breeding: Progress, Problems, and Prospects

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