QTL Mapping For Heading Date Using Single Segment Substitution Line In Rice

Heading date of rice (Oryza sativa L.) is a key agronomic trait for adaption to cultivatedareas and seasons in order to attain an ideal grain yield, and it is also one of the leadingobjectives of rice improvement programs. Studies on genetic regulatory mechanism forheading date are useful for rice breeding and productive practice. The objectives of thisstudy were to detect QTLs for heading date and analyze their interaction effects using singlesegment substitution lines (SSSLs) with consistent genetic background. This result for QTLanalysis will be more accurate and useful for QTL cloning and molecular marker assistedbreeding. The main results were following:(1) Development of secondary SSSLs (S-SSSLs)Twenty homozygous S-SSSLs were obtained from segregation populations derived fromfour crosses between primary SSSLs (P-SSSLs): S1×S2， S1×S3，S1×S4and S1×S5.Among them, eight S-SSSLs contained the substituted segments on the short arm ofchromosome3derived from the same donor ‘Lemont’ and others contained substitutedsegments on the short arm of chromosome6derived from four different donors,‘Tetep’,‘BG367’,‘IR58025B’ and ‘Lemont’, respectively. The length of substituted segments inS-SSSL had been greatly shortened compared with the corresponding P-SSSL.(2) QTL identification with SSSLsTwo QTLs, qHD3and qHD6on the short arm of chromosome3and the short arm ofchromosome6, respectively, were identified with twenty SSSLs under natural long-day(NLD). Both qHD3and qHD6had pleiotropic effects. qHD3early allele not only promotedheading, but also decreased plant height and the number of grains main panicle and affectedgrain shape and weight. qHD6affected heading date and plant height, but had no significanteffect on the other agronomic traits.(3) Fine mapping of qHD3and candidate gene analysisWith substitution lines segregating population, qHD3was located between SSR markersRM14314and RM14320, the distance between the two markers was62.4Kb. Based oncandidate gene analysis, we found a transcription factor, MADS-box gene OsMADS50(heading date gene) was in qHD3target chromosomal region. Sequence alignment ofOsMADS50derived from SSSL with qHD3early heading allele and recipient HJX74 showed that the code region sequence of OsMADS50existed a nucleotide substitution andits intron sequence existed two variants,20nucleotides delete/insert and a nucleotidesubstitution. However, we did not found the differential expression at transcription level forOsMADS50from SSSL with qHD3early heading allele and recipient HJX74. This resultsuggested that the phenotypic variation of SSSLs with different qHD3alleles is not relatedto the expression of OsMADS50at transcription level.(4) Fine mapping of qHD6and candidate gene analysisWith a F2segregating population derived from the cross between SSSLs which containeddifferent qHD6allele, qHD6was located on the short arm of chromosome6and betweenSSR markers RM587and RM204, the distance between the two markers was876.6Kb. Inthis chromosomal region existed two heading date gene, RFT1and Hd3a. Both RFT1andHd3a showed variations in gene sequence and expression at transcription level betweenSSSLs with different qHD6allele. Therefore, it is still unknown which gene was the targetgene of qHD6.(5) Analysis for interaction between qHD3and qHD6Analysis of double segments pyramid lines (DSPLs) and F2populations showed theexistence of epistatic interactions between qHD3and qHD6. Furthermore, qHD3wasepistatic to qHD6under NLD conditions.