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

  • ️Fri Jan 01 2016

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

Hongwu Wang et al. BMC Plant Biol. 2016.

Abstract

Background: Plant 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.

Results: Acid 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.

Conclusions: Of 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.

Keywords: Digestibility; Forage quality; Genome-wide association; Maize.

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Figures

Fig. 1
Fig. 1

Distribution of forage quality traits in association panel. The frequency distribution of ADF, NDF, and IVDMD in association panel are shown in a, b and c, respectively

Fig. 2
Fig. 2

Phenotypic variation of forage quality traits in sub-groups of association panel. The phenotype distribution of ADF, NDF, and IVDMD in each sub-group are shown in a, b and c, respectively. Mixed: Mixed group; SS: Stiff stalk; NSS: Non-stiff stalk; TST: Tropical and sub-tropical

Fig. 3
Fig. 3

GWAS results for forage quality traits in a maize association panel. Manhattan plots for ADF, NDF, and IVDMD are shown in a, b and c, respectively. Grey and black dashed lines correspond to the thresholds of Bonferroni correction (P < 1.8 × 10−6) and P < 1 × 10−4. Red dots indicate significant SNPs (P < 1.0 × 10−4 and RMIP > 0.1) associated with each cell wall-related trait

Fig. 4
Fig. 4

Association and genomic location of known and new loci associated with forage quality traits. (a-c) Three identified genes were associated with forage quality traits. GRMZM2G140817 (ZmC3H2) (a) was associated with ADF, NDF, and IVDMD. GRMZM2G134752 (b) was associated with ADF and NDF. GRMZM2G042627 (c) was associated with ADF and IVDMD, with different leading SNPs. (Top) A 0.5-Mb region on each side of the leading SNP, which is denoted by a purple diamond. The color of the remaining SNPs reflects the r2 values with the most significantly associated SNP. Dashed horizontal lines depict the significance threshold (1 × 10−4). (Bottom) Gene structure according to the information from the B73 genome sequence in the GRAMENE database (

http://ensembl.gramene.org/Zea_mays/Info/Index

)

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