What is the effect of the MIKC MADS-box gene family on the growth and development of rye?
Foreword: Rye is a tertiary gene source of wheat and an important genetic resource in wheat breeding, and the development of flower organs will affect the yield and quality of rye, and the gene encoding MADS-box protein of MIKC type plays a central role in plant development.
In this study, a total of 47 genes encoding MADS-box protein encoding MIKC type were identified in the rye genome by bioinformatics methods.
The coding sequences of 47 MIKC transcription factors in rye were analyzed by bioinformatics software, and the protein physicochemical properties, phylogenetic tree, gene structure, conserved motif, collinearity and cluster analysis of each transcription factor in rye were obtained, which provided a theoretical basis for the sequence cloning and functional verification of rye MIKC gene family.
There are MIKC genes on 7 chromosomes of rye, and all the proteins of MIKC-type MADS-box in rye have both acidic proteins and alkaline proteins, all of which are hydrophilic proteins, among which 25 proteins have a fat-soluble index of more than 80, which belongs to thermophilic proteins, and the high fat-soluble index makes the proteins can better adapt to various environments.
In order to determine the relationship between the MIKC gene family of rye and the MIKC gene family of other species, a total of 174 MIKC protein sequences of three species of rye, wheat and Arabidopsis thaliana were constructed by NJ method, and then the MIKC gene encoding MIKC protein in rye was classified.
The results showed that the rye MIKC gene family was divided into 12 subfamilies, with the most genes encoding MIKC protein in the rye SEP/AGL2 subfamily, the least genes encoding MIKC protein in the AGL6 subfamily, and no FLC subfamily.
According to the phylogenetic relationship, the introns and exons of MIKC gene were compared, and the gene structure analysis showed that the gene structure of MIKC type encoding MADSbox protein was relatively conserved, and most of the MIKC family genes in rye contained exons and introns.
Most of the MIKC-type genes encoding MADS-box protein in plants are composed of 7 exons, and a few genes are composed of 8 exons.
The 10 genes in the rye MIKC gene family conform to the typical structure of the gene encoding the MADSbox protein in plants, i.e., 7 exons, each of which is of different length, which may be related to the exchange of chromosome fragments in rye during evolution.
The MADS-box family of genes is produced through gene repeat events during evolution.
According to the collinearity results between rye, wheat and rice, there were 35 pairs of collinearity genes between rye and rice, among which 4RL and 5RL had the most collinearity genes with rice.
There were 90 pairs of collinearity genes between rye and wheat, among which 4RL had the most collinearity genes with wheat 7A, 7B and 7DL, and 7RL had the most collinearity genes with wheat 4A, 4B and 4DL, indicating that rye 4RL was more closely related to wheat 7A, 7B and 7DL, and rye 7RL was more closely related to wheat 4A, 4B and 4DL.
Some studies have shown that the translocation between the chromosomes 4RL and 7RL of rye 4RL and 7RL is the main reason for the inverse correspondence between the chromosomes of rye 4RL and 7RL and wheat, and the number of collinearity genes of the three species shows that the relationship between rye and wheat is closer than that of rice.
The potential collinearity analysis of rye in species using TBtools software showed that the MIKC family genes were distributed on each chromosome and were unevenly distributed, and 5RL and 7RL contained the most genes encoding MIKC protein, with 9 genes in each and 3 homologous gene pairs.
These three pairs of genes belong to the same subfamily, namely SQUA/API, PI, and SOC, and the sequence similarity of these homologous genes suggests that they may have similar functions.
According to the characteristics expressed in tissues and organs and developmental periods, MIKC family genes can be divided into 11 subfamilies.
The genes encoding SEP/AGL2, AGL6, AG, CGM13 and ScMIKC17 were expressed at higher levels in spikes, and were also expressed in grains collected 10 and 20 days after flowering, but the expression levels were lower than those in spikes.
The expression levels of the four subfamily genes were higher in the panicle, but not in other parts, and the expression of four genes, ScMIKC09, ScMIKC35, ScMIKC31 and ScMIKC13, was high in the panicle, but not in other parts and growth periods.
RNA-seq data were used to analyze the expression patterns of different genes in rye, and a total of 18 differentially expressed genes were selected, among which 17 MIKC genes were up-regulated to varying degrees, 1 gene was down-regulated, and the other genes showed no obvious expression differences.
Conclusion:
Combined with intraspecific collinearity analysis, three pairs of homologous genes were found in rye, and each pair belonged to a subfamily, among which the ScMIKC31 gene was only expressed in panicles and the expression level was high.
The expression of ScMIKC31 gene was up-regulated, and the results of RNA-seq verification were consistent with the conclusions obtained by bioinformatics, and it was preliminarily speculated that the ScMIKC31 gene was a gene related to vernal flowering in rye.
