Chromosome 3A harbors several pleiotropic and stable drought-responsive alleles for photosynthetic efficiency selected through wheat breeding

Abstract

Water deficit is the most severe stress factor in crop production threatening global food security. In this study, we evaluated the genetic variation in photosynthetic traits among 200 wheat cultivars evaluated under drought and rainfed conditions. Significant genotypic, treatments, and their interaction effects were detected for chlorophyll content and chlorophyll fluorescence parameters. Drought stress reduced the effective quantum yield of photosystem II (YII) from the anthesis growth stage on. Leaf chlorophyll content measured at anthesis growth stages was significantly correlated with YII and non-photochemical quenching under drought conditions, suggesting that high throughput chlorophyll content screening can serve as a good indicator of plant drought tolerance status in wheat. Breeding significantly increased the photosynthetic efficiency as newer released genotypes had higher YII and chlorophyll content than the older ones. GWAS identified a stable drought-responsive QTL on chromosome 3A for YII, while under rainfed conditions, it detected another QTL on chromosome 7A for chlorophyll content across both growing seasons. Molecular analysis revealed that the associated alleles of AX-158576783 (515.889 Mbp) on 3A co-segregates with the NADH-ubiquinone oxidoreductase (TraesCS3A02G287600) gene involved in ATP synthesis coupled electron transport and is proximal to WKRY transcription factor locus. This allele on 3A has been positively selected through breeding and has contributed to increasing the grain yield.

Keywords: GWAS; breeding progress; chlorophyll content; chlorophyll fluorescence; drought; effective quantum yield of photosystem II; photosynthesis; wheat.

FIGURE 1

Drought stress effect on the photosynthesis‐related traits across growth stages. (a) Chlorophyll content in 2017; (b) effective quantum yield of PSII under drought (red and large curve) versus control (green and thin curve), in 2017 (circle‐shaped) and 2018 (squared‐shaped). (c) Diffusion porometer‐based leaf stomatal conductance in 2018. (d) Drought stress effect on photosynthetic rate (stars filled barplot) and leaf stomatal conductance (full colored barplot). The significance between both water regimes is given above the graphs and in Table S3. In sub‐panel (b), the first line of significance level is for 2017, whereas the second line is for 2018. The error bars of the curves represent the standard deviation. The thicker error bars are for drought conditions in sub‐panels (a)–(c).

FIGURE 2

Relationship between photosynthetic rate versus (a) stomatal conductance and (b) transpiration rate after anthesis growth stage in 2018 growing season. Red diamond‐shape and green circle‐shape indicate the genotypes data points under drought and rainfed conditions, respectively. (c) Principal component analysis biplot using 11 photosynthesis‐related variables and 4 visual scored developmental traits under prolonged drought stress conditions. Cosines square of the variables contributing to the newly constructed principal components (d). The size of the circle in sub‐panel (d) indicates the intensity of the variables. The abbreviations of traits name are listed in Table S2.

FIGURE 3

(a) Pearson correlation coefficient of photosynthetic traits vs aboveground yield (grain yield and plant biomass weight) under rainfed conditions (up panel) and drought conditions (lower panel). The legend on the right indicates the correlation coefficients. (b) Relationship between GY versus YII and F_V/F_M. The abbreviations of traits name are listed in Tables S2 and S3. The correlation coefficients significance level (p < .05) is indicated by *.

FIGURE 4

(a) Regression plots showing temporal trends in effective quantum yield of PSII among 20 winter wheat cultivars in relation to the year of cultivar registration under two contrasted water regimes. The slopes of the linear regression lines (orange line for drought and green line for rainfed) are referred to as absolute breeding progress. Boxplots of oldest versus newest released cultivars under rainfed and drought conditions for (b) YII and (C) SPAD values screened at heading/anthesis for the whole population; (D) heatmap representation of the average of visual scores of developmental traits screened over both experimental years showing a gradient of cultivars with lower relative scores in red (sensitive cultivars) to high relative scores in blue (tolerant cultivars). The error bars in panels (b) and (c) represent the standard deviations from the mean. The Mean in panel (d) represents the average of the scores of the four developmental traits.

FIGURE 5

Circle Manhattan plot for YII under control (inside track) and drought (outside track) including significant marker‐trait associations (MTAs) in (a) 2017 and (b) 2018 showing drought inducible quantitative trait locus (QTL) on chromosome 3A. (c) Manhattan plot showing a hotspot of associated SNPs on 3A region of 22 Mbp length delimited from AX‐158597824 (510.691 Mbp) to wsnp_Ex_rep_c66865_65263145 (533.624 Mbp) associated with YII under drought stress in 2017 and 2018.

FIGURE 6

Circular plot showing the epistatic interactions SNPs with the corresponding positions on the genetic map of wheat. Wheat chromosomes 1A–7D are shown in a clockwise direction in the Circos diagram. Green‐colored connections represent epistatic loci on chromosome 3A controlling YII (left panel) and SPAD values (right panel). Gray‐colored connections represent epistatic interactions on other chromosomes. The first track line after the chromosome name track is showing the significant (10⁻⁴) epistatic loci detected under rainfed while the following track is showing the ones detected under drought conditions.

FIGURE 7

(a) Representation of most pleiotropic SNPs detected under drought, among which some are involved in breeding progress. (b) Chromosomic region of 5.847 Mbp length on 3A from RFL_Contig4399_956 (496.705 Mbp) to AX‐111076088 (503.027 Mbp) harbored six SNPs (gray square) associated with breeding progress and YII. Two haplotypes blocs were found in this region, pairwise D′ between SNPs of LD block are displayed.

FIGURE 8

Illustration of genomic region on chromosomes 3A harboring pleiotropic SNP for breeding progress (BP) and YII. The upper panel presents genome‐wide association studies (GWAS) –log₁₀ p values of significant SNPs between 495 and 503 Mbp associated with BP (red color) and YII (green color). The dotted line (−log₁₀ p value = 3) indicated the threshold considered to find significant marker‐trait associations (MTAs) with pleiotropic effect for BP and YII. The lower panel is the map positions of drought inducible SNPs associated with evaluated traits. Map distance (in base pairs) is shown on the upper part of the chromosome bar, and the SNP names are under the chromosome bar. “Underlined and bold” SNPs names are pleiotropic for YII and BP; the color of the SNPs names indicated the category of traits the SNP is associated with [“red” = BP; “green” = YII; “underlined purple” = BP + YII].

FIGURE 9

Allelic effect of the chromosome 3A SNP AX‐158576783 (515.889–516.804 Mbp) on YII under drought (a) and rainfed (b); and its effect on GY under drought (c) and rainfed (d); (e,f) The SNP AX‐158576783 alleles distribution by cultivars year of release in the wheat panel. Two‐sample t‐test p values show significant difference (* for p < .05; ** for p < .01; and *** for p < .001) between major (TT) and minor (CC) alleles.

FIGURE 10

(a) Representation of 20 drought‐tolerant (dark‐green) and 20 drought‐sensitive (dark‐red) cultivars groups based on their stress weighted performance (SWP) estimates; the p value indicates significant difference between both groups. (b) Bar plot of newer (dark‐green) and older (dark‐read) released cultivars based on SWP estimates. The dark‐green color showed that new released cultivars are prominent among the drought‐tolerant cultivars, whereas old ones in dark‐red color are mostly present in the drought‐sensitive group. The light‐green color showed some old‐released cultivars that are drought‐tolerant, whereas the light‐red indicated some new‐released that are drought‐sensitive. (c) Biplot of principal component analysis based on 28 marker‐trait associations (MTAs) of breeding progress (BP) separated 13 drought‐tolerant and new released (in green circle) and 10 drought‐sensitive and old cultivars (dark‐red square).