Optimization Of A High-Density Genetic Map For Chinese Jujube And QTL Mapping For Several Important Traits

Chinese jujube (Ziziphus jujuba Mill,2n=2x=24), belongs to the Rhamnaceae, which is an economically important Chinese fruit tree. Jujube production occupies an important position in China’s agriculture. Improved varieties are the basis for the healthy development of jujube production. Conventional genetic strategies, up to now, have been employed to jujube improvement work but with limited progress, such as laborious and time-consuming. Markerassisted selection (MAS) has been proven to be a promising solution for quickening breeding of fruit trees, but jujube lags behind other fruit crops in molecular genetic map construction and marker assisted selection. In this study,99 F1 progenies derived from the cross ’Dongzao’ x’Yingshanhong’ were used as mapping population. We detected SNP and InDel by restriction-site-associated DNA sequencing (RAD-seq) and alignment of short reads on a reference genome. Subsequently, we constructed a high-density linkage map of jujube using SNPs and InDels integrated with SSRs the laboratory has acquired. On this bases, the quantitative trait loci (QTLs) for Chilling Tolerance (CT), Plant Height (PH), Ground Diameter (GD) and Leaf Area (LA) were detected in the integrated map. The main results of this dissertation are as follows:1. Illumina sequencing of reduced-representation libraries generated a total of -98.76Gb clean reads from parents and 99 F1 progenies. A total number of 7939 markers (7026 SNPs and 913 InDels) that follow Mendel’s segregation ratio were identified through mapping the RAD reads to the reference genome of Z. ’Dongzao’.2. Genetic map was constructed based on pseudo-testcross theory combine with the SSR markers our laboratory has obtained. Finally, the linkage map consists of 4173 SNP markers,486 InDel markers and 46 SSRs,4669 markers in total, spanning 2643.79 cM, with an average marker distance of 0.57 cM. The integrated map contained 12 linkage groups (LGs), consistent with the haploid chromosome number of the two parents. Of the 4669 RAD markers,3919 were linked to the female genetic map,4184 to the male map.3. Based on this high-density integrated jujube linkage map, a total of 117 potential QTLs for 4 traits, including Chilling Tolerance (CT), Plant Height (PH), Ground Diameter (GD) and Leaf Area (LA), were identified and positioned on the genetic map by Kruskal-Wallis model method of MapQTL 6.0 software. The QTL for PH, GD and LA were focused on 48.18-85.23 cM region and 134.80-195.72 cM region on LG3, and QTL for CT mainly distributed in 0-45.41 cM region on LG7.In conclusion, we generated a high-density genetic linkage map for jujube by reduced representation genome sequencing approach and identified a range of chilling tolerance and growth-related QTLs. The results of this study are expected to provide important theoretical references for QTL detection, map-base gene cloning and molecular-assisted selection breeding. It may also serve to broaden our understanding of the jujube genome.