, 215:188 | Cite as

Genome wide association studies for yield and its component traits under terminal heat stress in Indian mustard (Brassica juncea L.)

  • Surinder K. SandhuEmail author
  • Lalit Pal
  • Jasneet Kaur
  • Dharminder Bhatia


Breeding for terminal heat stress (THS) in Brassica juncea L. Czern & Coss is recognized as an imperative objective for sustained productivity in contemporary climatic changes. A fixed diversity stock of 491 genotypes was documented for wide range of variations for seed yield under natural terminal heat stress. A set of top 20 genotypes comprising introgression lines from wild species Erucastrum cardaminoides and B. tournefortii; derived B. juncea lines using B. carinata and B. napus; land races;, commercial cultivars and breeding lines, having the lowest heat susceptibility index and the least yield reduction under heat stress, have been identified as potential heat tolerant donors. A panel of 96 genotypes was constituted from this stock on the basis of their differential response to heat susceptibility index and seed yield reduction under natural THS. The constituted panel was evaluated for validation under controlled conditions for ten seed yield-related traits. Moderate to low correlations between SY and its related traits were observed in NS and THS conditions. Double digest restriction site associated DNA sequencing of 71 genotypes identified 18,258 SNPs after filtration. Least square means of all the traits under NS and THS conditions and the best linear unbiased predictors along with identified SNPs were used for genome-wide association study. A total of 34 SNPs under NS, 24SNPs under THS and 30SNPs using BLUP values were found to be associated with all seed yield-related traits. Chromosome B05 harbored the maximum number of SNPs (nine) followed by chromosomes A07 and A09 (eight SNPs each). SNPs under NS conditions could not be associated with THS. This is the first report on the identification of 24 marker-traits associations detected for SY and its component traits under THS conditions. It may be possible to develop the molecular markers for significant SNPs after due validation. The constituted panel may also serve as a source of allelic diversity for genes controlling various economic traits. The derived introgression lines as potential heat tolerant donors indicated the possibility of using wild species to breed for abiotic stress tolerance in Indian mustard.


Brassica juncea GWAS BLUP SNPs Yield Terminal heat stress 



The Indian mustard germplasm, used in this study, was collected/developed and maintained by ICAR National Professor Dr. S. S. Banga. The authors duly acknowledge the receipt of germplasm and his inputs for the preparation of the manuscript.

Supplementary material

10681_2019_2489_MOESM1_ESM.tiff (88 kb)
Supplementary Figure 1. Frequency distribution of 491 genotypes: a Heat susceptibility index (HSI), b Percent yield reduction (YD%). *Number of genotypes selected from each interval (HSI) to constitute diversity panel are given in parenthesis. (TIFF 88 kb)
10681_2019_2489_MOESM2_ESM.tiff (229 kb)
Supplementary Figure 2. 2D plot of first two Principle Components (PCs). Figure in parenthesis represents the explained variation by that PC. (TIFF 229 kb)
10681_2019_2489_MOESM3_ESM.tiff (88 kb)
Supplementary Figure 3. Genome-wide linkage disequilibrium (LD) decay plot. Linkage disequilibrium, measured as r2, between pairs of polymorphic marker loci is plotted against the physical distance (Kbp). (TIFF 88 kb)
10681_2019_2489_MOESM4_ESM.tiff (639 kb)
Supplementary Figure 4. Seed yield component traits showing significant marker-trait associations for NS environment: a Plant height (PH), b Main shoot length (MSL), c Days to Maturity (DM), d Number of pods on main shoot (NPMS), e Pod length (PL), f Number of seeds per pod (NSP), g Thousand seed weight (TSW), h Seed yield (SY). *Chromosome 1 to 10 represents A genome mentioned as A01 to A10 and chromosome 11 to 18 represents B genome mentioned as B01 to B08 in manuscript. (TIFF 638 kb)
10681_2019_2489_MOESM5_ESM.tiff (2.2 mb)
Supplementary Figure 5. Seed yield component traits showing significant marker-trait associations for BLUP values: a Plant height (PH), b Main shoot length (MSL), c Days to Maturity (DM), d Number of pods on main shoot (NPMS), e Pod length (PL), f Number of seeds per pod (NSP), g Thousand seed weight (TSW), h Seed yield (SY). *Chromosome 1 to 10 represents A genome mentioned as A01 to A10 and chromosome 11 to 18 represents B genome mentioned as B01 to B08 in manuscript. (TIFF 2258 kb)
10681_2019_2489_MOESM6_ESM.tiff (298 kb)
Supplementary Figure 6. Q-Q (Quantile-Quantile) plots of GWAS for NS environment: a Plant height (PH), b Main shoot length (MSL), c Days to Maturity (DM), d Number of pods on main shoot (NPMS), e Pod length (PL), f Number of seeds per pod (NSP), g Thousand seed weight (TSW), h Seed yield (SY). (TIFF 297 kb)
10681_2019_2489_MOESM7_ESM.tiff (297 kb)
Supplementary Figure 7. Q-Q (Quantile-Quantile) plots of GWAS for BLUP values: a Plant height (PH), b Main shoot length (MSL), c Days to Maturity (DM), d Number of pods on main shoot (NPMS), e Pod length (PL), f Number of seeds per pod (NSP), g Thousand seed weight (TSW), h Seed yield (SY). (TIFF 296 kb)
10681_2019_2489_MOESM8_ESM.tiff (288 kb)
Supplementary Figure 8. Q-Q (Quantile-Quantile) plots of GWAS for THS environment: a Plant height (PH), b Main shoot length (MSL), c Days to Maturity (DM), d Number of pods on main shoot (NPMS), e Pod length (PL), f Number of seeds per pod (NSP), g Thousand seed weight (TSW), h Seed yield (SY). (TIFF 287 kb)
10681_2019_2489_MOESM9_ESM.docx (30 kb)
Supplementary file9 (DOCX 29 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Surinder K. Sandhu
    • 1
    Email author
  • Lalit Pal
    • 1
  • Jasneet Kaur
    • 1
  • Dharminder Bhatia
    • 1
  1. 1.Department of Plant Breeding and GeneticsPunjab Agricultural UniversityLudhianaIndia

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