比较基因组学解析月季皮刺发育的分子机制

	比较基因组学解析月季皮刺发育的分子机制; Comparative genomics reveals molecular mechanisms underlying stem prickle patterning in roses
	仲米财
导师	胡金勇
摘要	Roses are one of the most widely used groups of horticulture flower plants and have been extensively used for pharmaceuticals, cosmetics and food industry. And it simultaneously has crucial and typical biological characteristics, such as whether it is continuous blooming, flower type, flower color, floral scent, and whether it is prickly, etc. Those traits, which are not perfectly shared in any other model plant species, are of great value to botany and agricultural production research. However, due to frequent crosses leading to high heterozygosity and complexity of the genome, studies on the relationship and functional genomics of rose and its populations still face great challenges. In this study, the genome of Rosa wichuraiana ‘Basye’s Thornless’ (BT) was deeply sequenced and assembled, and compared with the haploOB genome, then combined with the quantitative trait location (QTL) analysis of prickle density. It revealed the molecular mechanism of the genetic differences between rose genomes and the development of rose prickles. The main results are as follows: 1. The chromosomal-level genome assembly of Rosa wichuraiana ‘Basye’s Thornless’（BT）was constructed using PacBio single-molucule real time (SMRT) sequencing technology, Hi-C technology and Illunima sequencing technology, and reached a golden reference level of LTR assembly index (LAI) indication. The final assembled genome size was 530.6 Mb, of which contigs N50 was 934 Kb. Based on Hi-C, the 493 Mb scafolds sequence is anchored to the BT chromosome, accounting for 92.5% of the total length of the assembled genome. The genetic map, BUSCO software and Illumina reads were used to verify the BT assembly. The results all showed that the BT genome assembly had a high accuracy. The BT genome contains 32,674 protein-coding-genes and 65.2% repeats, in which the Copia type LTR account for 43.4%, which was one of the species with the highest Copia/Gypsy ratio in the known genomes. 2. Through QTL analysis, we found that the inheritance of prickles density was regulated by two to three loci (QTLs); and the gene-regulatory-network (GRN) related to the development of prickle were identified by combining the genes related to the occurrence of prickles and the characteristics of QTL interval genes. The GRN was highly conserved in roses. The analysis of prickleless and prickly rose population diversity (Fst) revealed that the sequence diversity of QTL1 region located on chromosome three was significantly higher than that of surrounding regions and genome-wide sequence diversity; while the sequence diversity (Pi) of QTL1 region in the prickleless population was significantly reduced, namely a purifying selection occurred in the QTL1 region. These sequence variations have been fixed in the prickleless rose population, and this region is enriched in genes related to water use, in other words, prickle density of QTL1 and the genes related to water used regulation were co-localized.
	2020-05
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74225
专题	昆明植物所硕博研究生毕业学位论文
推荐引用方式 GB/T 7714	仲米财. 比较基因组学解析月季皮刺发育的分子机制, Comparative genomics reveals molecular mechanisms underlying stem prickle patterning in roses[D],2020.

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