基于限制位点相关的DNA(restriction site associated DNA,RAD)标记的测序方法是一种新型的测序技术.其优点是不仅节省传统测序的试验成本,而且能快速准确的定位出数以千计的基因标记,从而更加适合分子辅助育种的应用.该方法可应用于寻...基于限制位点相关的DNA(restriction site associated DNA,RAD)标记的测序方法是一种新型的测序技术.其优点是不仅节省传统测序的试验成本,而且能快速准确的定位出数以千计的基因标记,从而更加适合分子辅助育种的应用.该方法可应用于寻找DNA多态性,鉴别SNP,构建未知基因组序列生物的遗传图谱,定位目的性状基因等.本文主要综述了RAD标记和RAD测序的研究进展及其在分子育种中的应用.展开更多
The next generation sequencing enables generation of high resolution and high throughput data for structure sequence of any genome at a fast declining cost. This opens opportunity for population based genetic and geno...The next generation sequencing enables generation of high resolution and high throughput data for structure sequence of any genome at a fast declining cost. This opens opportunity for population based genetic and genomic analyses. In many applications, whole genome sequencing or re-sequencing is unnecessary or prohibited by budget limits. The Reduced Representation Genome Sequencing （RRGS）, which sequences only a small proportion of the genome of interest, has been proposed to deal with the situations. Several forms of RRGS are proposed and implemented in the literature. When applied to plant or crop species, the current RRGS protocols shared a key drawback that a significantly high proportion （up to 60%） of sequence reads to be generated may be of non-genomic origin but attributed to chloroplast DNA or rRNA genes, leaving an exceptional low efficiency of the sequencing experiment. We recommended and discussed here the design of optimized simplified genomic DNA and bisulfite sequencing strategies, which may greatly improves efficiency of the sequencing experiments by bringing down the presentation of the undesirable sequencing reads to less than 10% in the whole sequence reads. The optimized RAD- seq and RRBS-seq methods are potentially useful for sequence variant screening and genotyping in large plant/crop populations.展开更多
本研究通过简化基因组测序(2b-RAD)技术,对浙江省三门湾海域定居性优势无脊椎动物(哈氏仿对虾、口虾蛄、脊尾白虾、三疣梭子蟹、曼氏无针乌贼、棒锥螺和牡蛎)进行遗传结构和遗传多样性分析,以评估三门湾海域水生无脊椎动物资源现状,并...本研究通过简化基因组测序(2b-RAD)技术,对浙江省三门湾海域定居性优势无脊椎动物(哈氏仿对虾、口虾蛄、脊尾白虾、三疣梭子蟹、曼氏无针乌贼、棒锥螺和牡蛎)进行遗传结构和遗传多样性分析,以评估三门湾海域水生无脊椎动物资源现状,并为渔业可持续发展提供物种遗传资源监测依据。7个物种共获得12336~108139个SNP位点,变异位点比例为0.168%~1.571%。遗传分析结果显示,7个物种的平均核苷酸多样性(Pi)为0.147~0.306,平均观测杂合度(Ho)为0.142~0.289,多态信息含量(Polymorphism Information Content,PIC)为0.124~0.234,个体间平均遗传距离为0.118~0.246。本研究表明,三门湾水域7种代表性无脊椎动物中,生物群体变异位点比例较低,遗传多样性水平较低,且相同种群个体间的遗传分化较小,结合本次对三门湾海域渔业资源调查分析,这可能与人工增殖放流等因素有关。展开更多
文摘基于限制位点相关的DNA(restriction site associated DNA,RAD)标记的测序方法是一种新型的测序技术.其优点是不仅节省传统测序的试验成本,而且能快速准确的定位出数以千计的基因标记,从而更加适合分子辅助育种的应用.该方法可应用于寻找DNA多态性,鉴别SNP,构建未知基因组序列生物的遗传图谱,定位目的性状基因等.本文主要综述了RAD标记和RAD测序的研究进展及其在分子育种中的应用.
文摘The next generation sequencing enables generation of high resolution and high throughput data for structure sequence of any genome at a fast declining cost. This opens opportunity for population based genetic and genomic analyses. In many applications, whole genome sequencing or re-sequencing is unnecessary or prohibited by budget limits. The Reduced Representation Genome Sequencing （RRGS）, which sequences only a small proportion of the genome of interest, has been proposed to deal with the situations. Several forms of RRGS are proposed and implemented in the literature. When applied to plant or crop species, the current RRGS protocols shared a key drawback that a significantly high proportion （up to 60%） of sequence reads to be generated may be of non-genomic origin but attributed to chloroplast DNA or rRNA genes, leaving an exceptional low efficiency of the sequencing experiment. We recommended and discussed here the design of optimized simplified genomic DNA and bisulfite sequencing strategies, which may greatly improves efficiency of the sequencing experiments by bringing down the presentation of the undesirable sequencing reads to less than 10% in the whole sequence reads. The optimized RAD- seq and RRBS-seq methods are potentially useful for sequence variant screening and genotyping in large plant/crop populations.
文摘本研究通过简化基因组测序(2b-RAD)技术,对浙江省三门湾海域定居性优势无脊椎动物(哈氏仿对虾、口虾蛄、脊尾白虾、三疣梭子蟹、曼氏无针乌贼、棒锥螺和牡蛎)进行遗传结构和遗传多样性分析,以评估三门湾海域水生无脊椎动物资源现状,并为渔业可持续发展提供物种遗传资源监测依据。7个物种共获得12336~108139个SNP位点,变异位点比例为0.168%~1.571%。遗传分析结果显示,7个物种的平均核苷酸多样性(Pi)为0.147~0.306,平均观测杂合度(Ho)为0.142~0.289,多态信息含量(Polymorphism Information Content,PIC)为0.124~0.234,个体间平均遗传距离为0.118~0.246。本研究表明,三门湾水域7种代表性无脊椎动物中,生物群体变异位点比例较低,遗传多样性水平较低,且相同种群个体间的遗传分化较小,结合本次对三门湾海域渔业资源调查分析,这可能与人工增殖放流等因素有关。
