Identification Of Residual Heterozygous Lines With QTL Of Heading Date And Plant Height Using The F₇ MAGIC Population In Rice

Residual heterozygous lines（RHLs）are single-plant-derived families that are basically homozygous for whole genome segments and heterozygous for individual segments during the construction of high-generation recombinant inbred lines.Generally,the number of alleles with functional variation in any two individuals is limited on a genome-wide scale,so the detection efficacy of RHLs derived from parental recombinant inbred lines is limited.The multiparent advanced generation inter-cross（MAGIC）population is recombined by multiple parents,and there are multiple allele separations.Therefore,there are multiple biallelic combinations in the heterozygous segment,and the RHLs derived from them have higher detection efficiency in theory.In this study,an eight-parent MAGIC population containing 1164 families was constructed with 3 kinds of indica rice,4 kinds of japonica rice and 1 kind of Aus rice,with 24 plants in each family in the F7generation,and the heading date and plant height phenotypes were investigated to determine the RHLs with phenotypic segregation from the progeny of F6 individual plants.Then the haplotype map was reconstructed by mixed sequencing to find the whole-genome heterozygous region,and the association analysis of genotype and phenotype was carried out in a population of 60 plants per family.Finally,the single-plant progeny heterozygous for the target QTL region will be used to construct the RHL-F2 population,which provided a genetic population for subsequent fine-mapping.The main results are as follows:1.In 1164 F7 families,the Residual heterozygous segments are expected to cover the whole genome 36 times.Therefore,there are theoretically a large number of RHLs in this population.The phenotypic investigation found that there were 72 and 40 RHLs segregating at heading date and plant height,respectively,of which 9 RHLs were segregated at both heading date and plant height,which could provide genetic materials for functional gene identification and genetic effect analysis of heading date and plant height.2.The population of 21 RHLs was expanded in Hainan,their haplotype maps were constructed,and their heterozygous segments were determined.A total of 7 RHLs were identified as QTLs:two RHLs at the heading date gene Ghd7 locus,two RHLs at the plant height gene SD1 locus,one RHLs at the heading date gene Ghd7.1 locus and a new RHLs at the new plant height QTL q PH5 locus.In addition,there may be a new QTL of plant height in the MG651 family.3.Based on the 8-parent genome,we determined the parental origin of the heterozygous segment of the target gene,completed the haplotype analysis of the target gene,and analyzed the genetic effects of Ghd7,Hd1,Ghd7.1,SD1 and q PH5 of 7 RHLs.Among the RHLs segregated at heading date,the heterozygous segments of Ghd7 in two RHLs（MG652 and MG670）were both derived from the parents:Aus449 and ZS97,and the Ghd7^Aus449allele delayed heading for 14 d and 18 d in two families,respectively.Ghd7 mainly showed additive effect in both backgrounds,reaching 7.1 d and 9.2 d,respectively;but the dominant effect of Ghd7 was significantly different,reaching 1.5 d and 5.1 d,respectively.The heterozygous segment of Ghd7.1 in the MG1072 family was derived from the parents:9311 and Mitak,and the additive effect of homozygous Ghd7.1^Mitakand Ghd7.1⁹³¹¹ was not significantly different.Ghd7.1 mainly showed negative overdominant in this background with a dominant degree of-2.6.The heterozygous segment of Hd1 in the MG700 family was derived from the parents:Aus449 and ZS97,and the Hd1^ZS97 allele delayed heading for about 8 d.Hd1 mainly showed negative overdominant in this background with a dominant degree of-2.9;Among the RHLs segregated at plant height,the heterozygous segments of SD1 in two RHLs（MG1081 and MG1115）were both derived from the parents:Aus449 and ZS97,and the SD1^Aus449 allele increased the plant height for 43.6 cm and 32.0 cm in two families,respectively.SD1 mainly showed an additive effect in both backgrounds,and the additive and dominant effects were basically the same.In the MG668 family:the heterozygous segment of q PH5 was derived from the parents:MH63 and XS134,q PH5 has no additive effect,its dominant effect is 7.3 cm,and the dominance degree reaches 4.5,which is over dominant.In this study,a collection of phenotypically segregating RHLs was identified from the F7 MAGIC population based on phenotype,which can be used to identify heterozygous segments of the genome that control trait variation,and compared the genetic effects of different parental alleles,providing advanced genetic materials for efficient gene isolation and accurate evaluation of the genetic effects of parental alleles.