Based on the identification of DUF668 family genes, what is the impact of DUF668 on barley stress resistance breeding?
Foreword: Barley is the fourth most important cereal in the world and one of the earliest domesticated crops in the world, not only an important food and fodder crop, but also a valuable diploid model grain, which faces many stress stresses in the process of growth and development, and the evolution, function and classification of the DUF668 family in barley have not been systematically studied.
In this study, we planned to systematically identify the members of the DUF668 family in barley, and use bioinformatics methods to analyze the chromosome distribution, gene structure, and cis-acting elements of the identified members, so as to reveal their possible biological functions and provide a reference for barley stress resistance breeding.
Nine DUF668 genes were identified from barley, with a length of 1187~11490 bp and a corresponding CDS length of 888~2007 bp, which were named HvDUF668-01~HvDUF668-09 according to their positions on chromosomes.
The 9 genes were unevenly distributed on the 5 chromosomes of barley, the HvDUF668 gene was distributed on the chromosomes, and there was no clustered distribution, the protein length was 475~680aa, and the hydrophilic index (GRAVY) was negative, indicating that the DUF668 protein in barley was a hydrophilic basic protein (pI>7), but the degree of hydrophilicity was different.
The secondary structure of most proteins showed α-helix> random coil>β-folding>β-turn, and only HvDUF668-06 protein showed α-helix> random coiling>β-turn>β-folding, and the sum of the α-helix and random coil of the nine proteins was greater than 90%.
The tertiary structure of HvDUF668 protein showed a certain regularity, and there were great similarities in the same subgroup, and there were some differences among different subgroups.
The results of transmembrane domain prediction showed that none of the 9 HvDUF668 proteins contained transmembrane domains, suggesting that HvDUF668 protein would not undergo transmembrane transport after synthesis, and the subcellular localization prediction results showed that all 9 proteins were localized in the nucleus.
According to the phylogenetic tree, the 9 HvDUF668 genes were divided into 3 subgroups, and there were differences in Motif composition among different subgroups, and it was speculated that the HvDUF668 protein in the same subgroup had similar functions, while the HvDUF668 in different subgroups had functional differences.
The results showed that there were 266 cis-acting elements in the upstream initiation region of 9 barley HvDUF668 genes, which were divided into four types according to their functions: plant growth, stress response, plant hormone response and light response.
Among them, the number of cis-acting elements involved in the response of plant hormones was the largest, followed by the light-responsive cis-acting elements, including AAA motif (light-responsive element) and AE-box (part of the light-responsive module).
Among the four types, the number of hormone response elements and light response elements was larger, and HvDUF668 should play an important role in the response of barley to hormones, and the transcription of its genes may be regulated by photoperiod.
There were 57 response elements to stress stress, suggesting that the genes of this family played an important role in the face of abiotic stress in barley, and the number of response elements in plant growth was the least, indicating that the genes of this family also played a certain role in the growth process of barley.
The expression of barley DUF668 gene in 8 different tissues had obvious tissue specificity, and its expression levels were also different at different developmental stages, and the remaining 8 genes were also expressed in barley tissues, which further confirmed that HvDUF668 gene plays a specific role in the growth and development of barley.
Conclusion:
In this study, it was found that although there were collinear blocks between the genomes of barley, Arabidopsis thaliana and cotton, no collinearity gene pairs were found, but collinearity gene pairs existed between barley and rice.
HvDUF668-04, HvDUF668-05 and HvDUF668-08 were highly expressed in barley under yellow dwarf virus infection, indicating that these three genes could help improve the defense of barley against pathogenic bacteria, and may also contain Avr9/Cr-9, which mediates the biological defense response of barley.
