Genetic Analysis Of Transgressive Heading Date In A DH Population Derived From Indica×Japonica Crosses

In this study,we mapped heading date QTLs using high-density genetic maps constructed by 8940 SLAF markers in japonica rice ZYQ8,japonica rice JX17 and 102 stable strains from a DH population of their progeny.Sequence analysis was then applied on candidate genes which share structural similarities with cloned heading date genes within the predicted heading date QTLs.The association between the variant loci and heading date traits was investigated to determine the candidate genes controlling the heading date and to analyze the gene effects of the candidate genes.The main findings are as follows:1.The heading date of the DH population lines varied widely.The shortest heading line with the shortest heading date showed a 10-day shorter heading date than the shortheading dated parent JX17,while the line with the longest heading date 19-day longer compared with the short-heading dated parent ZYQ8,suggesting a prominent transgressive phenomenon.A bimodal distribution of the heading date in DH population indicates the presence of major genes in controlling rice heading date.2.In three independent tests,QTLs for heading date were detected on four rice chromosomes including chromosome 1,chromosome 3,chromosome 6,and chromosome 8.Among them,the QTLs located on a 3Mb～10Mb regions on chromosome 8 were mapped twice in two consecutive years,with LOD values above 6.0 and variation contribution rates ranging from 24.3% to 27.7%.3.Using bioinformatic methods,9 candidate genes with structrural similaries to plant growth period genes were screened out from the 4 QTL regions.Among them,5 were genes for rice heading date cloned and annotated previously and 4 were not reported.Sequence analyses of these 9 genes were performed in JX17,ZYQ8 and their DH lines.Non-synonymous SNP loci were identified in Hd16 on chromosome 3 and Hd18 and Os HAP5 F on chromosome 8.No difference between the parents was detected in the DNA sequences of DTH8,a reported major gene for heading date on chromosome 8.Association analysis showed extremely significant correlations between two rice genes and rice heading date,including Hd16 on chromosome 3,a flowering time related gene identified previously,and Os HAP5 F on chromosome 8,whose functions was not yet identified(P = 0.002 and 0.0001,respectively).4.The gene effect of Hd16 was 4.668 days and-6.393 days for Os HAP5 F.In the DH population,the average heading date of one line with recombinant genotype was shorter than that of the parent with shorter growth period,and the mean heading date of the other line with recombinant genotype was longer than that of the parent with longer growth period.The recombination between Os HAP5 F from japonica ZYQ8 with Hd16 from japonica JX17 could shorten the heading date in their offspring;On the other hand,the recombination between Hd16 from japonica ZYQ8 and Os HAP5 F from japonica JX17 could lengthen the heading date in offspring.We believe that OsHAP5F is likely to be a new major gene controlling the heading date.It possibly encodes a signaling molecule activated by other specific “signals”,which modulates the expression level of another heading date related gene via translocating to and interacting with the promoter of this gene,thereby regulating the heading date in rice.Further analyses are required.