| Heading date,one of the most important agronomic traits,enables rice to adapt to different seasons and growing regions.It also can influence growth stages and associated with yield,quality and tolerance to stresses.Study for heading date would have a significant impotance on guiding breeding,varietal improvement and cultivar popularization.In the last two decades,scientists have made a great progress in molecular analysis of rice heading date regulation and located lots of heading date associated QTLs on the rice genome.Even some QTLs were cloned and the detailed genetic mechanism was analyzed.However,in most studies the mapping accuracy are not fine,and the findings still need to be verified.Moreover,most of the located QTLs are difficult to applied in breeding.In present study,a recombination inbred lines?RILs?population including 192 lines derived from an inter-subspecific cross between indica rice‘Yuzhenxiang'and japonica rice‘02428'was generated.Two parent varieties and RILs population were separately sequenced by Whole Genome Sequencing?WGS?and Genotyping-By-Sequencing?GBS?to construct a genetic linkage map with 2711 recombination Bin markers.By using the software‘WinQTL Cartographer 2.5',we detected QTLs associated with heading date in 4 different environments.In addition,232 inbred lines were used to the Genome-wide Association Study?GWAS?with 427 polymorphic KASP-SNP markers which are distributed evenly in the whole genom of rice.Following are the results:1?The F8F11 generations of RILs population,which is derived from‘YZX'and‘02428',were planted in four different environments in two years.Phenotype values of heading date showed a continuous variation and fitted normal distribution.It indicated that heading date QTLs mapping is feasible in our study.A total of 14 QTLs,which were located on chromosomes 1,2,3,7,8,9 and 10,were detected in the four environments.Among them,qHD2.2 and qHD10.2,which explained 5.14%-11.15%and 5.35%-16.97%of the total phenotypic variation for the heading date separately,could be detected in three environments and shortened the heading date about 1.66 days and 1.55 days on average.2?After comparing with the physical positions of QTLs reported previously,it found that 11 of 14 QTLs were located in the same or near position.Moreover,qHD1.1,qHD2.2and qHD9.1 were newly reported,two cloned genes DTH8 and Ehd1 were repeatable in our study.Then the confidence interval of qHD2.2 was analyzed detailly:three annotated genes,LOCOs02g46450,LOCOs02g46710 and LOCOs02g46940,were found associated with the flower development.DNA sequence comparison between YZX and 02428 revealed all the three annotated genes could be candidate genes for further study.3?qHD2.2 and qHD10.2 were stably expressed in three environments and had highest PVE?Phenotype variation effection?values to decrease heading date.9 lines of the RILs which both carried the 2 favorable QTLs,were selected as germplasms for shortening heading date.Besides,the line named G55 was the best one for further studis such as fine mapping of qHD2.2 and breeding of early-maturing varities.4?Genome-wide Association Study in two different environments detected 16 markers associated with heading date,and R-square values ranging from 3.64%to 14.05%.Two loci associated with heading date were detectable in the two environments,and the R-square values are 10.64%and 10.32%respectively in average.Comparing with previous study,4markers were newly found.The two markers,SK0716957375 and SK1127982276,were both detectable in two environments,located on chromosomes 7 and 11 respectively.Combining genotype of favorable alleles of these two loci,10 germplasms were screened out from 232 varieties.These 10 germplasms carried two favorable alleles with effect on shortening heading date.In conclusion,some valueable QTLs and candidate genes we got in present study are referenceable for leaning of genetic mechanism of rice heading date;And the germplasms carried several favorable alleles we screened are useful for rice breeding. |
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