Theoretical and Applied Genetics

, Volume 131, Issue 3, pp 581–595 | Cite as

Genetic dissection of early-season cold tolerance in sorghum: genome-wide association studies for seedling emergence and survival under field and controlled environment conditions

  • Sebastian Parra-Londono
  • Karin Fiedler
  • Mareike Kavka
  • Birgit Samans
  • Silke Wieckhorst
  • Arndt Zacharias
  • Ralf Uptmoor
Original Article


Key message

A QTL on sorghum chromosome SBI-06 putatively improves field emergence under low-temperature conditions.


Low temperatures decisively limit seedling emergence and vigor during early growth of sorghum and, thus, strongly impair geographical expansion. To broaden sorghum cultivation to temperate regions, the establishment of cold-tolerant genotypes is a prioritized breeding goal. The present study aims at the quantification of seedling emergence and survival under chilling temperatures and the detection of marker–trait associations controlling temperature-related seedling establishment. A diversity set consisting of 194 biomass sorghum lines was subjected to extensive phenotyping comprising field trials and controlled environment experiments. The final emergence percentage (FEP) under field conditions was significantly reduced under cold stress. Broad-sense heritability was h 2 = 0.87 for FEP in the field and h 2 = 0.93 for seedling survival rate (SR) under controlled conditions. Correlations between FEP in the field and under controlled conditions were low; higher correlations were observed between field FEP and SR in controlled environments. Genome-wide association studies (GWAS) were conducted using 44,515 single nucleotide polymorphisms (SNPs) and revealed eight regions with suggestive marker–trait associations for FEP and SR on chromosomes SBI-01, -02, -03, -06, -09, and -10 (p < 5.7 × 10−5) and a significant association on SBI-06 for field FEP (p < 2.9 × 10−6). Although not significant under controlled conditions, SR of genotypes carrying the minor allele on the field FEP quantitative trait loci (QTL) on SBI-06 was on average 13.1% higher, while FEP under controlled conditions was on average 9.7% higher with a linearly decreasing effect with increasing temperatures (R 2 = 0.82). Promising candidate genes putatively conferring seedling cold tolerance were identified.



Financial support from the German Federal Ministry of Education and Research (BMBF), ERA-net Bioenergy and the Fachagentur Nachwachsende Rohstoffe e.V. is gratefully acknowledged. Technical assistance provided by Katharina Meyer and contributions to the main text body by Claudia Matschegewski are greatly appreciated.

Compliance with ethical standards


KF and parts of the study (phenotyping) were funded by the German Federal Ministry of Education and Research (BMBF, BioEnergie 2021, Project no. 03154211). Genotyping, SPL and BS were funded by ERA-net Bioenergy and the Fachagentur Nachwachsende Rohstoffe e.V. (FKZ 22001213).

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

122_2017_3021_MOESM1_ESM.docx (2.9 mb)
Supplementary material 1 (DOCX 2973 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2017

Authors and Affiliations

  1. 1.Chair of AgronomyUniversity of RostockRostockGermany
  2. 2.KWS SAAT SEEinbeckGermany
  3. 3.Department of Plant BreedingJustus Liebig University GießenGießenGermany

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