The cis-acting element DRE/CRT plays an important role in activating gene expression responsive to osmotic stress, low temperature and high-salinity. DREB1/CBF genes encode DRE-binding proteins with the function as transcript activators. TaDREB1 was also found to be induced by osmotic stress. The dates of osmotic stress was assessed by seed germination drought resistance index; the full-length cDNA sequences of TaDREB1 gene were downloaded from NCBI datebase; identification of allelic variation and transcript expression were assessed by PCR and semi-quantitive RT-PCR analysis, respectively. Total 13 new allele variations of TaDREB1 were identified in the germplasms tested in the paper, including 5 TaDREB1-A on chromosome 3AL, 4 TaDREB1-B on chromosome 3BL and 4 TaDREB1-D on chromosome 3DL. In each variety, there existed two loci of TaDREB1-D genes, named TaDREB1-D1 and TaDREB1-D2, both of which had the similar nucleotide sequence except an 11 bp insertion in the former. In wheat seeds under osmotic stress, we did not detect the transcript expression level of TaDREB1-A and TaDREB1-B, but that of TaDREB1-D. The capacity of osmotic stress tolerance was closely correlated with the expression level and tendency of TaDREB1-D.

Wheat grain color does not only affect the brightness of flour but also seed dormancy and pre-harvest sprouting (PHS) tolerance. The transcription factor Tamyb10 is an important candidate for R-1 gene, and the expression of its homologs determines wheat seed coat color. In the present study, the allelic variations of Tamyb10 were explored in a set of Chinese bread wheat varieties and advanced lines with different PHS tolerance, and a sequenced-tagged site (STS) marker for Tamyb10-D1 gene was developed, designated as Tamyb10D, which could be used as an efficient and reliable marker to evaluate the depth dormancy of wheat seeds. Using the marker Tamyb10D, 1629- and 1178-bp PCR fragments were amplified from the tolerant varieties, whereas a 1178-bp fragment was from the susceptible ones. Of the Chinese bread wheat varieties and advanced lines, 103 were used to validate the relationship between the polymorphic fragments of Tamyb10D and PHS tolerance. Statistical analysis indicated that Tamyb10D was significantly (P < 0.001) associated with depth of seed dormancy in these germplasms. To further confirm the association between allelic variants of Tamyb10-D1 and PHS tolerance, 200 recombinant inbred lines (RILs) from the cross between Zhongyou 9507 (1178-bp fragment) and Yangxiaomai (1178- and 1629-bp fragments) were genotyped using the marker Tamyb10D. General linear model analysis indicated that variation in Tamyb10-D1 had a significant (P < 0.001) association with the germination index (GI) values, explaining 13.7, 4.7, and 9.8 % of the phenotypic variation in GI in Shijiazhuang, Beijing, and the averaged data from those environments, respectively. In addition, among the 103 wheat varieties, 8 Tamyb10 genotypes (Tamybl0-A1, Tamybl0-B1, and Tamyb10-D1 loci) were detected, namely, aaa, aab, aba, abb, baa, bab, bba, and bbb, and these were significantly associated with GI value.

AFP is a negative regulator of ABA signaling that promotes ABI5 protein degradation and weakens regulation of ABA signaling by targeting upstream genes of ABI5, and TaABI5 gene was seed-specific, and accumulated during wheat grain maturation and dormancy acquisition, which played an important role in seed dormancy; TaAFP has a conserved domain with AFP, so TaAFP may also play an important role in seed dormancy in wheat. Two allelic variants of TaAFP were identified on chromosome 2BS in common wheat, and designated as TaAFP-B1a and TaAFP-B1b. Sequence analysis showed a 4-bp deletion in the 5’UTR region of TaAFP-B1b compared with TaAFP-B1a. Based on the 4-bp deletion, a co-dominant functional marker of TaAFP-B was developed and designated as AFPB. The genotype generating a 203-bp fragment (TaAFP-B1b) was more resistant to pre-harvest sprouting than the genotype producing a 207-bp fragment (TaAFP-B1a) in a test of 91 white-grained Chinese wheat cultivars and advanced lines. The average germination index(GI) values of TaAFP-B1a and that of TaAFP-B1b were 45.18 and 30.72%, respectively, indicating a significant difference (P < 0.001). Moreover, the 4-bp deletion located in the 5’UTR not only affected the transcription level of TaAFP-B but also affected the mRNA decay, reduced the translation level of GUS and tdTomatoER and GUS activity in wheat leaves of transient expression. The transcript expression and the mRNA half-life value of TaAFP-B1a in developing seeds and mature seeds were much higher than those of TaAFP-B1b. We identified a 4-bp InDel in the 5’UTR of TaAFP-B, which affected the mRNA transcription level, mRNA decay, translation levels of GUS and tdTomatoER, GUS activity, and was significantly associated with seed dormancy in common wheat. A functional marker was developed and validated based on this InDel.

As an important cereal crop, common oat, has attracted more and more attention due to its healthy nutritional components and bioactive compounds. Here, high-depth resequencing of 115 oat accessions and closely related hexaploid species worldwide was performed. Based on genetic diversity and linkage disequilibrium analysis, it was found that hulled oat (Avena sativa) experienced a more severe bottleneck than naked oat (Avena sativa var. nuda). Combined with the divergence time of ∼51,200 years ago, the previous speculation that naked oat was a variant of hulled oat was rejected. It was found that the common segments that hulled oat introgressed to naked oat cultivars contained 444 genes, mainly enriched in photosynthetic efficiency-related pathways. Selective sweeps during environmental adaptation and breeding improvement were identified in the naked oat genome. Candidate genes associated with smut resistance and the days to maturity phenotype were also identified. Our study provides genomic resources and new insights into naked oat domestication and breeding.