Genetic dissection of heat and drought stress QTLs in phenology-controlled synthetic-derived recombinant inbred lines in spring wheat


Abiotic stresses that affect wheat production—heat (H) and drought (D)—often occur concurrently. The genetic dissection of stress tolerance in a population with large range of phenology is difficult due to the confounding effects. We developed a recombinant inbred line (RIL) population of 276 entries with a narrow range of phenology, from a cross between a synthetic-derived parent (SYN-D: Croc 1/Aegilops squarrosa (224)//Opata) and an elite line (Weebill 1) to (a) understand the individual and combined effects of H and D stresses on yield and related traits, (b) identify the genetic basis of individual and combined stress tolerance, and (c) know the genetics of stress tolerance that can be explored from the line SYN-D. Phenotypic analysis indicated that the detrimental effect of combined stresses was greater than their individual effects. We constructed a genetic map—2771.5 cM—of the population with 569 SNPs (231 DArTseq and 338 Illumina bead chip 90 K array) and identified 71 QTLs, in which eight were common among stresses. We identified five QTL hotspots for yield and related traits under D, H, and H + D in chromosomes 2A (20.5 to 30.5 cM), 3D (92.5 to 108.5 cM), 6D (68.5 to 73.5 cM), 6D (125.5 to 135.5 cM), and 7B (40.5 to 61.5 cM). Among the 71 identified QTLs, SYN-D contributed 37 QTLs (52%) and Weebill 1 contributed 34 QTLs (48%). SYN-D also contributed the common thousand-grain weight QTL detected under H, D, and H + D, which can be used in molecular-assisted breeding.

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quantitative trait locus


recombinant inbred lines


grain yield m−2


thousand-grain weight


grain number m−2


days to heading


days to anthesis


days to maturity


plant height

CTvg, CTllg:

canopy temperature at vegetative and grain-filling stage, respectively

NDVIemg, NDVIvg, NDVIllg:

normalized difference vegetation index at emergence, vegetative, and grain-filling stage, respectively


single-nucleotide polymorphism


best linear unbiased prediction


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This work was implemented by the CIMMYT as part of the projects ARCADIA, MasAgro Trigo, and MasAgro Biodiversidad in collaboration with the CIMMYT, made possible by the generous support of SAGARPA MasAgro Trigo, MasAgro Biodiversidad, IWYP, and ARCADIA. Any opinions, findings, conclusion, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of SAGARPA and ARCADIA. Dr. Caiyun Liu’s stay at the CIMMYT is sponsored by the China Scholarship Council (CSC)—CIMMYT scholarship (

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C.L. and S.S. did the genetic and phenotypic analyses and drafted the manuscript; M.R. coordinated the phenotypic data collection; E.C. collected the phenotypic data; S.D. and C.S. did the genotyping; all authors reviewed and agreed on the manuscript.

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Correspondence to Sivakumar Sukumaran.

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Supplementary Figure 1

Pattern of variation in the traits (a) grain yield (YLD), (b) thousand-grain weight (TGW), (c) grain number (GN), (d) days to heading, (e) days to maturity (DTM), (f) plant height (PH), (g) canopy temperature at grain-filling stage (CTllg), and normalized difference vegetation index at vegetative stage (NDVIvg) of the SYN-D/Weebill 1 RILs population under drought stress in 2010 (D10), heat stress in 2010 (H10), head + drought in 2012 (HD12) and 2013 (HD13) environments. (PNG 187 kb)

Supplementary Figure 2

Genetic linkage map of chromosomes 1A to 4D showing the location of QTL detected in the SYN-D/Weebill 1 RILs population grown under different environments. (PNG 1973 kb)

Supplementary Figure 3

Genetic linkage map of chromosomes 5A to 7D showing the location of QTL detected in the SYN-D/Weebill 1 RILs population grown under different environments. (PNG 1287 kb)

Supplementary Figure 4

Yield advantage of the SYN-D/Weebill 1 RILs based on the presence of parental yield favorable QTL allele contribution. (PNG 34 kb)

High-resolution image (TIF 688 kb)

High-resolution image (TIF 6083 kb)

High-resolution image (TIF 2459 kb)

High-resolution image (TIF 202 kb)

Supplementary Table 1

Genotyping results of the major Rht, Ppd, Vrn, and Eps genes of the SYN-D/Weebill 1 RIL population (XLSX 21 kb)

Supplementary Table 2

Weather data of the experimental site during the crop growth season from 2010 to 2013 in Cd. Obregon, Mexico. (XLSX 8 kb)

Supplementary Table 3

Genetic data and linkage map of the SYN-D/Weebill 1 RIL population. (XLSX 554 kb)

Supplementary Table 4

QTL detected for traits of SYN-D/Weebill 1 RIL population under drought stress in 2010 season. (XLSX 11 kb)

Supplementary Table 5

QTL detected for traits of SYN-D/Weebill 1 RIL population under heat stress in 2010. (XLSX 11 kb)

Supplementary Table 6

QTL detected for traits of SYN-D/Weebill 1 RIL population under two H + D environments. (XLSX 15 kb)

Supplementary Table 7

QTL Located in the chromosome regions showing allele difference of high-yielding group and low-yielding group of SYN-D/Weebill 1 RIL population. (XLSX 11 kb)

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Liu, C., Sukumaran, S., Claverie, E. et al. Genetic dissection of heat and drought stress QTLs in phenology-controlled synthetic-derived recombinant inbred lines in spring wheat. Mol Breeding 39, 34 (2019).

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  • Synthetics
  • QTL
  • Heat and drought stress
  • Spring wheat