Exploiting Wild Emmer Wheat Diversity to Improve Wheat A and B Genomes in Breeding for Heat Stress Adaptation

Abstract

Wheat is highly sensitive to temperature beyond the optimum. To improve wheat adaptation to heat stress, the best option is to exploit the diversity of wild wheat progenitors. This study aimed to identify germplasm and quantitative trait loci associated with heat stress tolerance from wild emmer wheat diversity. We evaluated a diverse set of multiple derivative lines harboring chromosome segments from nine wild emmer wheat parents under four environments: two optimum environments at Tottori, Japan and Dongola, Sudan, one moderate heat stress environment, and one severe heat stress environment at Wad Medani, Sudan. Genome-wide association analysis was conducted with 13,312 SNP markers. Strong marker-trait associations (MTAs) were identified for chlorophyll content at maturity on chromosomes 1A and 5B: these MTAs explained 28.8 and 26.8% of the variation, respectively. A region on chromosome 3A (473.7-638.4 Mbp) contained MTAs controlling grain yield, under optimum and severe heat stress. Under severe heat stress, regions on chromosomes 3A (590.4-713.3 Mbp) controlled grain yield, biomass, days to maturity and thousand kernel weight, and on 3B (744.0-795.2 Mbp) grain yield and biomass. Heat tolerance efficiency (HTE) was controlled by three MTAs, one each on chromosomes 2A, 2B, and 5A under moderate heat stress and one MTA on chromosome 3A under severe heat stress. Some of the MTAs found here were previously reported, but the new ones originated from the wild emmer wheat genomes. The favorable alleles identified from wild emmer wheat were absent or rare in the elite durum wheat germplasm being bred for heat stress tolerance. This study provides potential genetic materials, alleles, MTAs, and quantitative trait loci for enhancing wheat adaptation to heat stress. The derivative lines studied here could be investigated to enhance other stress tolerance such as drought and salinity.

Keywords: durum wheat; genome-wide association study; heat; multiple-derivative lines; wild emmer wheat.

Figure 1

Daily maximum and minimum air temperatures of the four environments used to evaluate the multiple derivative lines (MDLs): (A) Tottori (TOT); (B) Dongola (DON); (C) Wad Medani first sowing date (MED/SD1); and (D) Wad Medani second sowing date (MED/SD2).

Figure 2

Average grain yield of the MDLs in Wad Medani for the second sowing date (MED/SD2) versus that in Wad Medani for the first sowing date (MED/SD1). The dashed blue lines intersect on the recurrent parent “Miki 3” (yellow circle). A few MDLs showed higher grain yield than their recurrent parent ‘Miki 3’ for both MED/SD1 and MED/SD2.

Figure 3

Grain yield (GY) versus heat tolerance efficiency (HTE). (A) GY at Dongola (DON) versus HTE calculated using the GY of DON as the cool environment and that of Wad Medani for the first sowing date (MED/SD1) as the hot environment (referred to as HTE1 in the text). (B) GY at MED/SD1 and HTE calculated using the GY of MED/SD1 as the cool environment and that of Wad Medani for the second sowing date MED/SD2 as the hot environment (referred to as HTE2 in the text). The yellow dot indicates the values for ‘Miki 3’. Black dots denote MDLs with HTE less than that of ‘Miki 3’. Red dots denote MDLs with HTE higher than that of ‘Miki 3’. Dashed blue lines intersect on ‘Miki 3’. Vertical black line marks HTE = 100. Horizontal grey arrows denote the ranges of heat tolerance and heat preference.

Figure 4

Physical positions of markers associated with evaluated traits in the four environments; Tottori (TOT); Dongola (DON); Wad Medani first sowing date (MED/SD1); and Wad Medani second sowing date (MED/SD1). BIO, biomass; CHLD, chlorophyll degradation; CHLH, chlorophyll at heading; CHLM, chlorophyll at maturity; CTH, canopy temperature at heading; DH, days to heading; DM, days to maturity; GFD, grain filling duration; GY, grain yield; HI, harvest index; HTE1, heat tolerance efficiency evaluated in MED/SD1; HTE2, heat tolerance efficiency evaluated in MED/SD2; PHT, plant height; SN, seed number/spike; TKW, thousand kernel weight. Symbol size corresponds to the allelic effect of each MTA.

Figure 5

Representative Manhattan plots for grain yield of the genome-wide analysis showing marker-trait association in the four environments; Tottori (TOT), Dongola (DON), Wad Medani first sowing date (MED/SD1) and Wad Medani second sowing date (MED/SD2). Frequency distributions and quantile−quantile plots for grain yield are shown for each environment.

Figure 6

Markers associated with multiple traits (see color key legend in the figure) identified under favored environment at Dongola (circles) or severe heat stress environment at Wad Medani (MED/SD2; diamonds). BIO, biomass; CHLD, chlorophyll degradation; CHLH, chlorophyll at heading; CTH, canopy temperature at heading; DH, days to heading; DM, days to maturity; GY, grain yield; HI, harvest index; TKW, thousand kernel weight.

Figure 7

Effect of selected marker-trait associations for different traits evaluated at Dongola (DON), Wad Medani first sowing date (MED/SD1) or Wad Medani second sowing date (MED/SD2). BIO, biomass; CHLD, chlorophyll degradation; CHLM, chlorophyll at maturity; DH, days to heading; DM, days to maturity; HTE1, heat tolerance efficiency evaluated in MED/SD1; HTE2, heat tolerance efficiency evaluated in MED/SD2; TKW, thousand kernel weight. Boxes show median and interquartile range and whiskers show the range. Significant marker and chromosome identified for each trait are displayed on the top box. Red dots indicate genotypes with ‘Miki 3’ allele. A, adenine; C, cytosine; T, thymine; G, guanine; N, unknown.

Figure 8

Effect of different allele combinations of significant marker-trait associations on grain yield performance at Wad Medani under late sowing date. The MDLs were divided into three classes based on haplotype diversity analysis for three significant MTAs. Black circles indicate average grain yield by each genotype. “+” marks indicate positive alleles, “–” marks indicate negative alleles. rs9724899, rs1017738, and rs3955557 denote significant MTAs for grain yield on chromosomes 2A, 3A, and 3B, respectively.