| Whole genome duplications(WGDs)are widely exist in plants and contribute to the formation of new organs or new characters,the synthesis and accumulation of secondary metabolites and the improvement of the adaptability to the environment.The ancestor of grasses underwent a WGD(ρWGD)about 98 million years ago,and then differentiated to existing grasses.Most grasses,especially crops,have a large endosperm and it is rich in nutrients such as starch and proteins,so the development of endosperm determines the yield and quality of crops.The contribution of ρWGD to the production of grain-specific expression genes or key genes and the development of grain is still unclear.Therefore,we used four crops including rice,millet,sorghum and maize as the research objects,combined with genomic and transcriptome data to identify ρWGD genes through comparative genomic analysis.And analyzed the sequence and expression differentiation characteristics of ρWGD genes which expressed and specifically expressed in grains,and then constructed the regulatory networks of grain to explore the genetic contribution ofρWGD.Then explored the ρWGD-hub-TFs and other potential key genes that affect the development of grain to provide genetic resources for the improvement of yield and quality of crops.The main results are as follows:1.The ρWGD genes tended to expressed in grain in four crops.Through intragenome homology alignment,collinear analysis and Ks analysis,the ρWGD gene pairs in four crops were identified:there were 2732 pairs in rice,2472 pairs in sorghum,2417 pairs in millet and 2382 pairs in maize(5000 pairs of m WGD).Combined with transcriptome data,we found that more than 75% of the ρWGD gene pairs in four crops were expressed in the grain,and some evolved into the grain-specific expression genes.The functional enrichment analysis of ρWGD genes expressed in grain showed that these genes were mainly involved in transcription factors,signal transduction and environmental adaptation,and the genes retained by m WGD were more significantly enriched into protein synthesis,processing and degradation.2.There were sequence differences between grain expression/specific expressionρWGD gene pairs,and the sequence differences between ρWGD gene pairs with expression differentiation were greater.WGCNA was used to analyze the expression differentiation of ρWGD gene pairs that expressed and specifically expressed in grain.It was found that the expression differentiation(76%-80%)of the ρWGD genes expressed in the grain was overwhelming,and the differentiation degree of the specific expression gene pairs in the grain was higher(79%-87%).m WGD gene pairs also underwent expression differentiation,and the differentiation ratios of grain expression and specific expression gene pairs were 64% and 73%,respectively,and the degree of expression differentiation was slightly lower than that of ρWGD gene pairs.Sequence characterization analysis showed that the protein sequence consistency of the differentiated gene pairs was lower,and the GC content was more different,and both the expression differentiation and similar expression gene pairs were subject to purification selection(ka/ks<1).The ρWGD genes in four crops showed negative selection(kn/ks<1)in the promoter region,while the m WGD genes showed positive selection(kn/ks>1)and the sequence of promoter region changed rapidly.3.ρWGD produced a large number of hub-TFs,and some ρWGD-hub-TFs were retained in multiple crops,which had an important impact on the grain development regulatory networks.The GENIE3 software package was used to construct the regulatory networks for grain expressed genes.Among rice,millet,sorghum and maize,there were68,95,114 and 121 hub-TFs,while ρWGD retained 22,28,33 and 31 hub-TFs,m WGD retained 46 hub-TFs,and ρWGD retained a high proportion of hub-TFs.Homologous analysis found that there were two groups of ρWGD-hub-TFs retained in four crops,indicating that the contribution of ρWGD to the four crops had certain commonalities.Further analysised of the core network of hub-TFs regulatory networsk,we found that there were other TFs and genes produced by ρWGD in the core networks,indicating thatρWGD helped to reshape and complicate the regulatory networks.4.ρWGD expanded the key enzyme genes and the TFs that regulated these enzymes in the starch pathway of rice,indicating that ρWGD promoted the biosynthesis of grain starch and had an important impact on crop yield and quality.In summary,these hub-TFs and ρWGD-hub-TFs,as well as important node TFs and genes in their regulatory networks,may be key genes affecting grain development and synthesis and accumulation of stored substances,and can be used as potential genes to improve the yield and quality of crops. |
