Analysis On The Ovule Transcriptomes Of Apomictic Sorghum Line SSA-1 And The Apomixis Related Genes In Sorghum Bicolor

The seeds produced by apomixis are the maternal replicas containing the genetic information of the female parent.Apomixis has the potential to fix heterosis and is a potential way to break the traditional sorghum three-line cross breeding(male sterile line,maintainer line and restorer line).It can effectively solve the problem that the traditional breeding hybrids need to continuously breed the parents,which leads to the high price for the production of seeds.Sorghum is a typical C4 plants,specialized photosynthetic apparatus so that it has a high photosynthetic efficiency and high yield potential.It also has characteristics including resistance to drought,water logging and salinity.It is one of the major grain crops mainly grown in Africa,Asia,the arid and semi-arid areas of the America and Australia after three gramineous crops,wheat,corn and rice in the world.Studies on apomixis had focused on improving apomixis frequency and embryogenesis mechanisms,and there are a few reports on apomixis-related genes in sorghum.In this study,transcriptome sequencing of sorghum ovules and young seeds was performed using high-throughput sequencing technology and analysed using bioinformatics software.The specific results are as the following:1.The independent seed setting rate of sorghum apomictic line SSA-1 is 9.4 %,and the independent seed setting rate is not only affected by temperature single environmental factors,but also by precipitation.The apomixis frequency in SSA-1 is 37.5 %,which is a facultative apomixis type,and pollen may have a certain induction effect on apomixis.The frequency for distributions of plant height,flag leaf length,flag leaf width,ear length and stem diameter of sorghum 44A×SSA-1 hybrid F2 population were continuous and normal distribution,which is in accordance with the genetic characteristics of quantitative traits.2.By transcriptome sequencing of ovules and young seeds(pollination 10 d)of sorghum SSA-1,according to the reference genome analysis,a total of 26.41 Gb was obtained,and the effective data of each sample reached 7.98 Gb or more.The percentage of Q30 base content was between 93.48% and 94.23%,and the GC base content was between 55.36% and 57.51%.The effective data of each sample was compared with sorghum BTx623(transcriptome reference)by HISAT2.The alignment efficiency of each sample and reference was between 87.15% and 93.41%.After sequencing and annotating the sequencing gene data with NR,Swiss-Prot,GO,COG,KOG,Pfam and KEGG databases,2919 new genes were identified,in which 2008 have functional annotations;The DESeq method of FPKM values was used to analyse the differential expression of genes.A total of 6902 differentially expressed genes were identified,including 3238 up-regulated ones and 3664 down-regulated ones.A total of 12 genes related to apomixis were obtained based on differential expression analysis.Among them,small RNA genesis and gene silencing are involved: 4 ARGONAUTE(AGO)genes(Sobic.001G136000;Sobic.001G136150;Sobic.001G153600;Sobic.001G331800);1 DICER-LIKE(DCL)gene(Sobic.001G180000).Participation in embryogenesis: 1 SERK1 gene(Sobic.006G104500);4 LEC1/2 genes(Sobic.006G266400;Sobic.002G161600;Sobic.001G338700;Sobic.002G369800).Participation in meiosis: 1 WUS gene(Sobic.003G350900).Participation in endosperm production: 1 FIS gene(Sobic.006G160400).3.A total of 19 Sb AGOs genes were identified in the genome of S.bicolor,distributed on 8 chromosomes except SBI-05 and SBI-07,of which Sb AGO5b1,Sb AGO5b2,Sb AGO5 c,Sb AGO5 d,Sb AGO7 and Sb AGO18 b were all on SBI-01.The first two pairs are arranged in tandem and may be formed by local repetition.Phylogenetic tree analysis indicated that Sb AGOs could be divided into five groups: AGO1/10,AGO5,AGO4/9,AGO2/7,and AGO18;and they were more closely related to the corresponding Si AGOs and Zm AGOs proteins.Sb AGO1 a,Sb AGO1 b,Sb AGO1 d,Sb AGO4a2 and Sb AGO9 are highly expressed genes,and have higher expression levels in sexual organs or tissues than vegetative organs,indicating that Sb AGOs have a regulatory effect on sorghum reproductive development.4.A total of 6 Sb DCLs were identified in the genome of S.bicolor,distributed on three chromosomes: SBI-01,SBI-03 and SBI-06,of which Sb DCL2 a,Sb DCL2 b,Sb DCL3 b and Sb DCL1 were concentrated on SBI-01 with Sb DCL2 a and Sb DCL2 b are arranged in tandem.Phylogenetic tree analysis showed that Sb DCLs were divided into four subfamilies,namely DCL1,DCL2,DCL3 and DCL4,and were more closely related tothe corresponding maize genes in evolution.Sb DCL2 a,Sb DCL1 and Sb DCL3 a are highly expressed genes and have higher expression levels in sexual organs or tissues than vegetative organs,indicating that Sb DCLs have regulatory effects on sorghum vegetative growth and reproductive development.