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Background The cell wall plays crucial roles in establishing the morphology of plant cells and defense response to biotic and abiotic stresses. The plant COBRA protein family plays an important role in secondary cell wall biosynthesis and the orientation of cell expansion, which have been extensively studied in Arabidopsis thaliana, maize, rice, etc., but no systematic studies were conducted in wheat. Methods and Results In this study, the full-length sequence of TaCOBLs was obtained by homology cloning from wheat, and a conserved motif analysis confirmed that TaCOBLs belonged to the COBRA protein family. qRT-PCR results showed that the TaCOBL transcripts were induced by abiotic stresses, including cold, drought, salinity, and abscisic acid (ABA). Two haplotypes of TaCOBL-5B (Hap5B-a and Hap5B-b), harboring one indel (----/TATA) in the 5’ flanking region (-550 bp), were found on chromosome 5BS. A co-dominant marker, Ta5BF/Ta5BR, was developed based on the polymorphism of the two TaCOBL-5B haplotypes. Significant correlations between the two TaCOBL-5B haplotypes and cold resistance were observed under four environmental conditions. Conclusion Hap5B-a, a favored haplotype acquired during wheat polyploidization, may positively contribute to enhanced cold resistance in wheat. Based on the promoter activity analysis, the Hap5B-a promoter containing a TATA-box was more active than that of Hap5B-b without the TATA-box under low temperature. Our study provides valuable information indicating that the TaCOBL genes are associated with cold response in wheat.

Seed dormancy evaluated by germination index (GI) is often regarded as a main and pivotal component of observed genetic variation for pre-harvest sprouting (PHS). Improving seed dormancy can decrease or avoid PHS damage to wheat before harvest. However, it is difficult to accurately evaluate seed dormancy under field conditions. In this study, 4 simple sequence repeat markers ( Xbarc57 , Xbarc294 , Xbarc310 , and Xbarc321 ) on the short arm of chromosome 3A and a gene-based marker ( Vp1-b2 ) on 3BL were used for genotyping 138 micro-core collections of Chinese wheat and landraces. Rich alleles were detected using these markers, and most of them were significantly correlated with GI value. A significant association between the 5 markers and seed dormancy was found according to General Linear Model. Vp1-b2 and Xbarc294 had larger effects on seed dormancy than other markers, which accounted for 65.8% and 61.2% of phenotypic variation, respectively. Combination of the 5 marker gave the largest estimation of GI variation in the 138 wheat genotypes (95.9%), followed by marker combination Vp1-b2 / Xbarc294 (89.1%), and marker combination Vp1-b2 / Xbarc321 had the smallest effect (79.4%). This result indicated that seed dormancy of tested genotypes was mainly associated with 2 loci on 3AS and 3BL.