Mapping Minor-effect QTL For Grain Weight And Shape And Validation Of Five QTL In Rice

Grain weight and grain shape are important factors influencing grain yield and quality in rice.There are quantitative traits controlled by a large number of quantitative trait loci?QTL?that vary greatly in effect,but not much attention has been paid to minor QTL.This study was conducted to detect minor QTL for grain weight and shape in the absence of major-QTL segregation.In a previous QTL mapping study,the QTL,qGL3.2 and qGW5,were detected in the regions of GS3 on chromosome3 and qSW5/GW5/GSE5 on chromosome 5,respectively,and exhibited major effects in recombinant inbred line population derived from indica rice crosses Teqing/IRBB lines.In this study,minor-effect QTL for grain weight and shape were indentified and validated using four segregating rice populations.The two populations derived from residual heterozygotes were first performed to detect QTL for grain weight and shape in the exclusion of these two major loci.Then,based mapping results,two secondary populations with a more homogenous genetic background were developed to validate the QTL effects of the five regions.The main results are summarized as the following:1.Two F₇ plants of indica rice crosses Teqing/IRBB52,homozygous at the major loci of GS3 and qSW5/GW5/GSE5 were selected.They were selfed to produce two S₁ populations,Ti52-2 and Ti52-3.The Ti52-2 population carried 13 segregating regions of 80.7-Mb in total length and consisted of 251individuals.The Ti52-3 population carried 17 segregating regions of 102.3-Mb in total length and consisted of 250 individuals.The S_1:2 and S_1:3 families of each population were planted in the Hangzhou,Zhejiang and Lingshui,Hainan.Thousand-grain weight,grain length and grain width were tested and used for QTL analysis using Windows QTL Cartographer 2.5.A total of 22 QTL were detected in Ti52-2 population,distributing on 12 intervals of 10 chromosomes.Ten of them were significant in both locations,and the other two were detected in Hangzhou only.A total of 23 QTL were detected in Ti52-3population,distributing on 14 intervals of all 12 rice chromosomes.Eight of them were significant in both locations,and the other six were detected in Hangzhou only.2.One plant that was only heterozygous in intervals of RM20731 on chromosome 6,RM22755-RM210 on chromosome 8,RM6100-RM7300 on chromosome 10 and RM3246-RM511 on chromosome 12 was selected from the Ti52-2 population.All of these intervals were detected QTL for grain weight and grain shape in Ti52-2.This plant was selfed to construct one new population designated ZC8.The QTL effects of the four regions were well validated in ZC8 population.Compared with Ti52-2 population,the traits affected and directions of allelic effect were consistent across populations with R² increased.3.One plant,which carried a heterozygous region of RM107 on chromosome 9 but was homozygous at other genomic regions,was selected from Ti52-3 population.This plant was selfed to a new S₁ population.Assayed DNA markers,homozygous plants with no recombination in the corresponding segregating region were identified.Selfing progenies of these plants resulted in a set of near isogenic line?NIL?,which consisted of 35 Teqing homozygous lines and 35 IRBB52 homozygous lines that differed in the target interval RM107.The NIL population was planted in Hangzhou and thousand-grain weight,grain length,grain width,ratio of length to width and heading date were tested.The results of SAS procedure general linear model showed that significant variations between the two homozygous genotypic groups were found for grain width,ratio of length to width and heading date.The IRBB52 allele acted to increase grain width and heading date by 0.011 cm and 0.29 d,and decrease ratio of length to width by 0.009,with R² of 22.97%,5.86%and 18.27%,respectively.In summary,our results indicate that the power of detecting minor QTL could be efficiently increased by eliminating the influence of major-QTL segregation,and minor QTL could have a stable effect though it is believed that they are generally subjected to large influence of the genetic background and environmental conditions.Our results also lay a foundation for fine mapping,cloning and marker-assisted selection of minor QTL for grain weight and grain shape in rice.