Construction Of "Huang Huazhan / Basmati Surkb 89-15" Chromosome Segment Substitution Lines And Genetic Mapping And Analysis Of QTL For Important Agronomic Traits

Rice(Oryza sativa L.)was one of the main food crops in China,and more than half of the world’s population lives on rice.Therefore,the yield of rice directly affects the food security of China and even the world.The application of molecular breeding provides a strong guarantee for the safe production of rice.The research on functional genes and Quantitative Trait Loci(QTL)of rice has greatly enriched the resources for rice molecular breeding.Breeders have achieved gene and QTL transfer or polymerized multiple excellent genes through Marker Assisted Selection(MAS),so as to cultivate excellent rice varieties.However,many Quantitative Trait Genes(QTG)with molecular breeding value have not been cloned for a wide variety of rice.As a permanent isolated population,Chromosome Segment Substitution Lines(CSSLs)have been widely used in QTL mapping and functional gene cloning,and the single line can also be used as a conventional rice variety for grain production or hybrid rice seed production.In this study,an excellent indica rice cultivar Huanghuazhan developed by Chinese breeders was used as a recurring parent and a conventional rice variety Basmati Surkb 89-15(BAS)from Pakistan was used as a donor.A set of chromosome fragment replacement line population with Huanghuazhan as the background was constructed by means of multi generation backcross,MAS and High-throughput Genotyping based on Whole Genome Resequencing.QTL for important agronomic traits in rice were mapped using this population and some of them were further analyzed.The main results are as follows: 1.With Huanghuazhan as the recurrent parent,and BAS as a donor,a set of CSSLs with 117 lines was obtained through continuous backcross and selfing.Each line of the CSSLs contains only one chromosome fragment from the donor parent.The total length of 117 introduced fragments was 704.6 Mb,which was about 1.89 times the length of rice genome.The genome coverage of donor parents was about 99.78%.The length of a single imported fragment was between 0-24 Mb,of which 71.79% was less than 7 Mb,and the length of introduced fragments carried by 10 lines was no more than 1 Mb.2.Heading date(HD),plant height(PH),panicle length(PL),flag leaf angle(FLA),flag leaf length(FLL),flag leaf width(FLW)and tiller number(TN)and yield per plant(YPP)were investigated in Shanghai and Hangzhou,respectively.Using the Inclusive Composite Interval Mapping method and statistical analysis of genotype and phenotypic data,we mapped 19 and 18 QTLs related to the agronomic traits in Shanghai and Hangzhou,respectively,of which 5 QTLs(q PH1-1,q HD6-1,q HD8-1,q HD10-1 and q FLL6-1)were located from the data of both two places.In addition,one QTL q HD6-2 was detected in 84 CSSLs planted in Hainan in 2020.A total of 12 QTLs related to heading date were detected in BC3F1 population planted in Shanghai in 2019,of which 4 loci(q HD1-1,q HD6-1,q HD8-1,q HD10-1)were also detected in CSSLs planted in the same environment.It was found that the q PH1-1 locus interval included "Green Revolution" gene sd1,q HD6-1 and q FLL6-1 contained cloned rice flowering genes Hd3 a and RFT1,q HD8-1 contained Ghd8 which mainly regulates the heading date,and q HD10-1 contained the gene Ehd1 affecting the heading date.Polymorphisms were all found in alleles of those genes between two parents.3.Sequence alignment showed that RFT1 from BAS had a proline-to-serine change at amino acid 95(P95S)compared with Huanghuazhan and Nipponbare.Yeast two-hybrid assay showed that RFT1-BAS could not bind to 14-3-3 protein,which confirmed that RFT1-BAS lost the function of inducing heading and was a non-biological protein.4.Two major loci q HD6-1 and q HD8-1 related to heading date were located with the CSSLs.Near-isogenic lines CS066 and CS082 carried QTL q HD6-1 and q HD8-1 from BAS,respectively.The plant heights of CS066 and CS082 were significantly higher than Huanghuazhan under long-day and short-day.The heading date of CS066 under long-day and short-day was also significantly delayed than Huanghuazhan,while the heading date of CS082 was only significantly delayed than that of Huanghuazhan under long-day.The recurrent parents were hybridized with CS066 and CS082 to create hybrid F1 lines,and their agronomic traits were analyzed.It was found that the heterozygous q HD6-1 and homozygous q HD8-1 were better for production.5.According to the genome sequence alignment results of Huanghuazhan,BAS and Nipponbare,396 In Del(Insertion-Deletion)molecular markers with uniform coverage of rice genome were designed for genotype analysis and breeding research.