Genome-Wide Association Analysis of Senescence-Related Traits in Maize

Abstract

Senescence is a programmed process that involves the destruction of the photosynthesis apparatus and the relocation of nutrients to the grain. Identifying senescence-associated genes is essential to adapting varieties for the duration of the cultivation cycle. A genome-wide association study (GWAS) was performed using 400 inbred maize lines with 156,164 SNPs to study the genetic architecture of senescence-related traits and their relationship with agronomic traits. We estimated the timing of senescence to be 45 days after anthesis in the whole plant and specifically in the husks. A list of genes identified in a previous RNAseq experiment as involved in senescence (core senescence genes) was used to propose candidate genes in the vicinity of the significant SNPs. Forty-six QTLs of moderate to high effect were found for senescence traits, including specific QTLs for husk senescence. The allele that delayed senescence primarily increased grain yield and moisture. Seven and one significant SNPs were found in the coding and promoter regions of eight core senescence genes, respectively. These genes could be potential candidates for generating a new variation by genome editing for functional analysis and breeding purposes, particularly Zm00001d014796, which could be responsible for a QTL of senescence found in multiple studies.

Keywords: QTL; candidate gene; genome-wide association study (GWAS); maize; senescence.

Figure 1

(a) Evaluation of STRUCTURE outputs; (b) estimated population structure. (a) The change in log probability of ΔK value (K); (b) the estimations of population structure at K = 6 for 400 inbred lines. Each inbred line is represented as a vertical segment, which is partitioned into 6 colored segments to denote estimated membership to the K cluster.

Figure 2

Comparison of early senescence and late senescence genotypes with agronomical traits. GM—grain moisture in grams/plant; GDW—grain dry weight in grams/plant; VSP1—genotypes correspond to a visual scale of plant value 1 (completely dry) at 45 DAA; VSP2—genotypes correspond to a visual scale of plant value 2 (partial green) at 45 DAA; VSP3—genotypes correspond to a visual scale of plant value 3 (intermediate green, intermediate dry) at 45 DAA; VSP4—genotypes corresponds to a visual scale of plant value 4 (partial dry) at 45 DAA; VSP5—genotypes corresponds to a visual scale of plant value 5 (complete green) at 45 DAA; Red circle—exceptional genotypes to the relationship between plant visual scale and grain moisture and yield.

Figure 3

Correlation of traits with significance of p > 0.05. (a) Phenotypic correlation; (b) genotypic correlation. Trait: VSP—visual scale of the plant at 45 DAA; VSH—visual scale of husk leaves at 45 DAA; PHVDIF—the difference between the visual scale of plant and husk at 45 DAA; PA—photosynthesis activity at 45 DAA; SC—stomatal conductance at 45 DAA; GDW—grain dry weight; RDW—residual dry weight; GM—grain moisture; RM—residual moisture.

Figure 4

Circular Manhattan Plot. Red dots are significant SNPs for corresponding senescence traits. From inside to out: VSH—visual scale of husk leaves at 45 DAA; VSP—visual scale of plant at 45 DAA; SC—stomatal conductance; PHVDIF—the difference between the visual scale of plant and husk at 45 DAA; PA—photosynthesis activity at 45 DAA.

Figure 5

Gene expression levels during senescence, data from [20]. FC_15—RNA-seq performed 15 days after flowering (RPKM—reads per kilobase million); FC_30—RNA-seq performed 30 days after flowering (RPKM—reads per kilobase million); FC_45—RNA-seq performed 45 days after flowering (RPKM—reads per kilobase million); FC_60—RNA-seq performed 60 days after flowering (RPKM—reads per kilobase million); FC_75—RNA-seq performed 75 days after flowering (RPKM—reads per kilobase million); FC_90—RNA-seq performed 90 days after flowering (RPKM—reads per kilobase million). PHBB3, NC292—early senescence genotypes (ES). PHT10, PHW52, PA8637—optimum senescence genotypes (OS). PHBB9, PHW79—late senescence genotypes (LS). (a) Zm00001d026501; (b) Zm00001d005814; (c) Zm00001d014642; (d) Zm00001d014796; (e) Zm00001d016802; (f) Zm00001d017204; (g) Zm00001d039155; (h) Zm00001d038911.