Construction Of The High-Density Genetic Linkage Map Of Salvia Miltiorrhiza Using SLAF-seq

Salvia miltiorrhiza, belonging to Labiatae family, is an important medicinal crop in traditional Chinese medicine(TCM), and its toot and rhizome has been traditionally used for centuries to treat cardiovascular diseases. S. miltiorrhiza breeding methods mainly based on introduction and selective. The demand of S. miltiorrhiza is very huge, but its process of genetic improvement is slow and excellent varieties is limited. S. miltiorrhiza agronomic trait deeply affect quality and economic benefit. S. miltiorrhiza agronomic trait is quantitative trait controlled by the number of genes Also it is the main factor that influence efficiency of breeding. Genetic linkage map, particularly high-density genetic map, is one of the most valuable tools in meeting the requirement of high-throughput superior trait selection among various germplasms, including plants and animals. The genetic map of S. miltiorrhiza, even though as model medicinal plant, was only recently constructed in our laboratory, and has just begun to be studied. It is very important to build a high density genetic linkage map of S. miltiorrhiza, and position the genes of controlling agronomic traits.In this study, an F1 population consisting of 98 individuals was derived from an cross of S. miltiorrhiza ?BH18?(male parent) and S. miltiorrhiza f. alba ?ZH74?(female parent) SLAF-seq was used for the rapid discovery of SLAFs in the F1 population. Subsequently, a high-density genetic map of S. miltiorrhiza was constructed. On this bases, the quantitative trait loci(QTLs) for agronomic traits were also detected. The main results of this dissertation are indicated as follows:1?A total of 155.96 Mb of data containing 155,958,181 pair-end reads were obtained after preprocessing. The average coverage of each SLAF marker was 83.43-fold for the parents compared with 10.36-fold for the F1 offspring. Among the 151,035 high-quality SLAFs, 62,834 were polymorphic, resulting in a polymorphism rate of 41.60%. For the F1 population, five segregation patterns(ab × cd, ef × eg, hk × hk, lm × ll, nn × np) were used for genetic map construction, and 23,890 SLAFs fell into these classes(a ratio of 15.82%). The genotyping quality scores were used to select the qualified markers. A total of 5,198 SLAFs were used for map construction.2?The final linkage map consists of 5,164 SLAFs in 8 linkage groups(LGs) and spans 1,516.43 c M, with an average distance of 0.29 c M between adjacent markers. There was a total of 2,966 BH18(male) markers, 3,038 ZH74(female) markers, and 5,164 SLAFs(7,554 SNPs), which fell into 8 LGs, for the integrated map. The largest LG, LG8, harbored 830 markers covering a length of 297.25 c M; the largest average inter-marker distance was 0.36 c M. LG1 was the most saturated, comprising 559 markers with an average marker density of 0.24 c M, and the smallest LG, LG5, contained 478 markers with a length of 130.64 c M and an average inter-marker distance of 0.27 c M. The largest LG in the parental map was the same as that of the integrated map, LG8, with 468 markers covering 297.244 c M for the male and 511 markers covering 293.022 c M for the female. However, the smallest LG varied widely, corresponding to LG1 for BH18(107.028 c M) and LG7 for ZH74(115.325 c M).3?According to constructed integrated maps, we took interval mapping(Logarithm of odds, LOD>2.5) to detect our quantitative trait. A total of 13 QTLs were detected foragronomic traits, which located on LG1?LG2?LG4?LG7 and LG8. Of them, two for the length of acervate petiole, one for the number of acervate leaflet, one for the length of cauline petiole, one for the length of cauline leaf, one for the length of Inflorescenc, one for the number of floower per ring, one for the length of Footstalk length, one for the number of roots, one for the range of root.