Identification Of Genome-Wide SSRs And QTL Analysis Of Photoperiod Regulating Flowering In Kenaf(Hibiscus Cannabinus)

Kenaf（Hibiscus cannabinus L.）（2n=36）is an annual bast fiber crop of the Hibiscus genus of the Malvaceae family.When kenaf is transferred from vegetative growth to reproductive growth,its fiber quality and yield will decrease.The development of SSR primers and dissection of the genetic basis of flowering time can provide the reference information of kenaf molecular breeding.In this study,genome data from the research group were used to conduct genome-wide SSR identification and characterization,to evaluate SSR primer polymorphisms of key genes involved in photoperiodic flowering time using diverse germplasm,and to analyze QTL of flowering time using an existed high-density genetic map.The main results are as follows:1.301,525 and 14,269 SSRs were identified from kenaf genome and CDS sequences respectively,with an average density of 288.70 SSRs/Mb and 182.70 SSRs/Mb.Tri-and tetra-nuclueotide are dominant in the genome and CDS sequences,accounting for 57.64%and 92.84%of the total SSR.The predominance of AT-rich motifs was observed in both genomic and CDS sequences.2.The homologous genes involved in photoperiod in kenaf was performed using the Arabidopsis photoperiod related genes.A total of 71homologous genes were found,and 115 pairs of SSR markers（named Hc Ph01～Hc Ph115）were developed.Among these SSR primers,there are mainly tri-and tetranucleotide repeats,accounting for 35.7%and 30.4%,respectively.The repeat motif types are mainly AT-rich repeat motif.Polymorphism assessment and cluster analysis were performed on 24 kenaf germplasms with different growth stage time.And 98 pairs（89.3%）of the primers were amplified and could be to classify the varieties with different growth stage time.Hc Ph10 and Hc Ph48 primers were screened for their correlation with the growth stage time.The 24 kenaf germplasms were used to assess these SSR primers involved in photoperiod related genes.Using one-way analysis of variance and regression analysis,phenotypeic variation explained of growth stage time by the primers Hc Ph10 and Hc Ph48 reached 24.18%and 32.00%,respectively.Based on SSR involved in photoperiod related genes,cluster analysis showed that 24 varieties could be divided into different groups with the growth stage time.3.QTL mapping of flowering time in the F₂ population was performed using the high-density genetic map previously developed in this laboratory.Distribution of flowering time in the F₂ population showed a rich genetic and a normal distribution.There are 10 QTLs,located on chromosomes of chr6,chr11,chr12 and chr18 respectively,with a range of 3.53%to 16.16%phenotypic variation explained in the F₂ population using QTL Ici Mapping4.1 software.There are 10 QTLs,located on the chr6,chr10,chr16 and chr18 respectively,with a range of 11.21%to 24.55%phenotypic variation explained in the F_2:3 population.The parents and 22 individuals,including11 extreme early flowering and 11 extreme late flowering of the F₂population,were used to assess these SSR primers involved in photoperiod.And 2 markers of the Hc Ph10 and Hc Ph48 primers were correlated to flowering time.Furthermore,154 kenaf germplasm resources with different flowering times were used.The marker of Hc Ph48 reached a significant level（P<0.01）,and phenotypic variation explained is 4.88%by using one-way analysis of variance and regression analysis.This indicated that this marker might be correlated to the flowering time in kenaf.The gene sequence,Hca.07G0041660（Hc VIN3）,of this primer Hc Ph48 was located in the QTL of q FT18-1 with the amino acid similarity of 91%using local Blast.These results not only provide a theoretical basis for kenaf molecular marker assisted selection breeding,but also lay the foundation for dissection the genetic basis of flowering time in kenaf.