陆地棉×黄褐棉种间全基因组SSR高密度遗传图谱的构建
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摘要
基因组庞大的棉花是世界上重要的农作物,传统育种结合DNA分子标记和分子育种技术在作物改良中逐步发挥核心作用。相对于利用形态学和地理学鉴定棉花种质资源的传统方法,分子途径在加速搜集遗传信息上更具潜力。
变异与遗传是作物改良的重要手段。大部分的棉种间存在生殖隔离,种间杂交如不克服这种隔离则难以成功。利用传统育种方法,把野生资源中优良农艺和品质性状基因转移到栽培作物中已被证明难以凑效。如果克服棉种间的生殖隔离,则可以拓宽商业棉种的遗传基础。为了加强拓宽棉花的遗传基础,多种不同的棉种被用来杂交,以得到拥有最大产量和优异性状潜力的栽培棉种。通常来说亲本间遗传距离越远,杂种优势越强。
近年来分子标记技术的发展为高密度遗传图谱的构建提供了基础,高密度遗传图谱有助于基因组测序、序列组装、基因定位和目标基因标记,它能更好解析棉花遗传信息,从而达到改良棉花的目的。
本研究,构建了一张完全基于SSR标记的陆地棉x黄褐棉种间高密度遗传图谱。该图谱覆盖棉花基因组大部分区域,其中2029个SSR标记覆盖4026.10cM的遗传距离,位点间平均距离为2.20cM,染色体上的标记数在23-127之间,染色体的平均长度在154.85cM; SSR标记在A基因组(51.70%)明显高于D基因组(48.30%),标记的遗传距离A基因组的2096.71cM也多于D基因组的1929.39cM。
图谱中最长的染色体为209.96cM,最短为99.52cM。其中最大同源染色体对是Chr.19(D05)和Chr.05(A05),最小的同源染色体对&Chr.20(D10)。在构建的高密度遗传图谱中566个位点表现出偏分离,占27.89%。26条染色体中共发现55个SDRs。其中27个SDRs分布在A基因组中,28个在D基因组中。A基因组中的偏分离位点多于D基因组,所有大的SDRs偏向杂合子,SDR内的所有位点偏分离方向一致。在24号染色体(D08)中可以观察到一个独特的染色体内复制,其中4ON_CGR5433, MON_CGR0152和MON CGR5423这3个标记扩增出双位点,平均重组率为10cM。本研究中构建的完全基于SSR标记的高密度遗传图谱在对重要的数量性状的遗传分析、分子标记辅助育种、结构基因组学以及比较基因组学上都具有重要作用。此外,这张高密度遗传图谱可为高通量分子标记辅助选择,构建黄褐棉染色体片段置换系奠定基础,有助于将黄褐棉中优良基因转育到陆地棉种质资源中,特别是抗虫性。
Cotton, with large genome, is an important crop throughout the world. Conventional breeding has great potential and will play a central role in sustained genetic improvement by incorporating DNA marker technology and molecular breeding. The application of molecular methods to cotton germplasm which have been classified on the basis of morphology and geography has the potential to accelerate the accumulation of genetic information as compared to traditional methods.
Extensive genetic variability and large effective breeding populations are essential bases for the crop improvement. Most of the Gossypium species being sexually incompatible, new interspecific hybrids are difficult to develop, unless sterility barrier is overcome. The conventional methods of plant breeding for the transference of desirable agronomic and quality traits of wild species to the commercial cotton have not been proved much helpful. The genetic basis of the commercial cotton can considerably be broadened by overcoming the incompatibility among various species of Gossypium. To enhance the wide genetic basis of cotton genotypes the most diversed cotton genotypes were crossed to develop genetically diverse cultivars having maximum potential for yield and having desireable traits. Genetically more distinct parents will produce maximum hybrid vigor.
Recent advances in molecular technology provide a base to construct a high density genetic map which can facilitate genome sequencing, sequence assembly, gene mapping and the design of targeted genetic markers for better understanding and improvement of the cotton plant.
In this study, an entire microsatellite (Simple sequence repeat, SSR) PCR-based high density genetic map was constructed using the interspecific cross of G.hirsutum x G.mustelinum and covering a large region of cotton genome. This high density genetic map constitutes of2029SSR mapped markers covering4026.10cM with an average inter-marker distance of2.20cM. Number of marker anchored on the chromosomes varied from23to127with an average of154.85cM. More markers were anchored on At sub-genome (51.70%) than Dt-subgenome (48.30%).The At-subgenome span more distance (2096.71cM) than the Dt-subgenome (1929.39cM).
The maximum length of chromosome was209.96cM and the minimum was99.52cM. The largest homeologous chromosome pair was Chr.19(D05) and05(A05) smallest is Chr.20(D10) as far mapped loci are concerned. In this map566loci showed segregation distortion and accounting for27.89%. A total of55segregating hotspot (SDRs) were found on the26cotton chromosomes with27SDRs on the At subgenome and28on the Dt subgenome. More distorted loci were located on the At subgenome than the Dt sub-genome. All the large SDRs revealed skewness toward the heterozygous allele and all the skewed alleles within the SDR segregate in the same direction. A unique intra-chromosomal duplications observed in chromosome24(D08), where3markers viz MON_CGR5433, MON_CGR0152and MON_CGR5423each revealed duplicate loci and their recombination rates on an average is lOcM respectively. The SSR-based map constructed in this study will be useful for further genetic analysis of important quantitative traits, marker assisted selection and genome organization architecture in cotton as well as for comparative genomics between cotton and other species. Moreover this map will lay the foundation for developing chromosome segment substitution lines (CSSLs) from G. mustelinum in an upland cotton background by marker-assisted high throughput selection and also enrich the cotton germplasm by incorporating superior genes especially insect resistance from wild genetic resources.
变异与遗传是作物改良的重要手段。大部分的棉种间存在生殖隔离,种间杂交如不克服这种隔离则难以成功。利用传统育种方法,把野生资源中优良农艺和品质性状基因转移到栽培作物中已被证明难以凑效。如果克服棉种间的生殖隔离,则可以拓宽商业棉种的遗传基础。为了加强拓宽棉花的遗传基础,多种不同的棉种被用来杂交,以得到拥有最大产量和优异性状潜力的栽培棉种。通常来说亲本间遗传距离越远,杂种优势越强。
近年来分子标记技术的发展为高密度遗传图谱的构建提供了基础,高密度遗传图谱有助于基因组测序、序列组装、基因定位和目标基因标记,它能更好解析棉花遗传信息,从而达到改良棉花的目的。
本研究,构建了一张完全基于SSR标记的陆地棉x黄褐棉种间高密度遗传图谱。该图谱覆盖棉花基因组大部分区域,其中2029个SSR标记覆盖4026.10cM的遗传距离,位点间平均距离为2.20cM,染色体上的标记数在23-127之间,染色体的平均长度在154.85cM; SSR标记在A基因组(51.70%)明显高于D基因组(48.30%),标记的遗传距离A基因组的2096.71cM也多于D基因组的1929.39cM。
图谱中最长的染色体为209.96cM,最短为99.52cM。其中最大同源染色体对是Chr.19(D05)和Chr.05(A05),最小的同源染色体对&Chr.20(D10)。在构建的高密度遗传图谱中566个位点表现出偏分离,占27.89%。26条染色体中共发现55个SDRs。其中27个SDRs分布在A基因组中,28个在D基因组中。A基因组中的偏分离位点多于D基因组,所有大的SDRs偏向杂合子,SDR内的所有位点偏分离方向一致。在24号染色体(D08)中可以观察到一个独特的染色体内复制,其中4ON_CGR5433, MON_CGR0152和MON CGR5423这3个标记扩增出双位点,平均重组率为10cM。本研究中构建的完全基于SSR标记的高密度遗传图谱在对重要的数量性状的遗传分析、分子标记辅助育种、结构基因组学以及比较基因组学上都具有重要作用。此外,这张高密度遗传图谱可为高通量分子标记辅助选择,构建黄褐棉染色体片段置换系奠定基础,有助于将黄褐棉中优良基因转育到陆地棉种质资源中,特别是抗虫性。
Cotton, with large genome, is an important crop throughout the world. Conventional breeding has great potential and will play a central role in sustained genetic improvement by incorporating DNA marker technology and molecular breeding. The application of molecular methods to cotton germplasm which have been classified on the basis of morphology and geography has the potential to accelerate the accumulation of genetic information as compared to traditional methods.
Extensive genetic variability and large effective breeding populations are essential bases for the crop improvement. Most of the Gossypium species being sexually incompatible, new interspecific hybrids are difficult to develop, unless sterility barrier is overcome. The conventional methods of plant breeding for the transference of desirable agronomic and quality traits of wild species to the commercial cotton have not been proved much helpful. The genetic basis of the commercial cotton can considerably be broadened by overcoming the incompatibility among various species of Gossypium. To enhance the wide genetic basis of cotton genotypes the most diversed cotton genotypes were crossed to develop genetically diverse cultivars having maximum potential for yield and having desireable traits. Genetically more distinct parents will produce maximum hybrid vigor.
Recent advances in molecular technology provide a base to construct a high density genetic map which can facilitate genome sequencing, sequence assembly, gene mapping and the design of targeted genetic markers for better understanding and improvement of the cotton plant.
In this study, an entire microsatellite (Simple sequence repeat, SSR) PCR-based high density genetic map was constructed using the interspecific cross of G.hirsutum x G.mustelinum and covering a large region of cotton genome. This high density genetic map constitutes of2029SSR mapped markers covering4026.10cM with an average inter-marker distance of2.20cM. Number of marker anchored on the chromosomes varied from23to127with an average of154.85cM. More markers were anchored on At sub-genome (51.70%) than Dt-subgenome (48.30%).The At-subgenome span more distance (2096.71cM) than the Dt-subgenome (1929.39cM).
The maximum length of chromosome was209.96cM and the minimum was99.52cM. The largest homeologous chromosome pair was Chr.19(D05) and05(A05) smallest is Chr.20(D10) as far mapped loci are concerned. In this map566loci showed segregation distortion and accounting for27.89%. A total of55segregating hotspot (SDRs) were found on the26cotton chromosomes with27SDRs on the At subgenome and28on the Dt subgenome. More distorted loci were located on the At subgenome than the Dt sub-genome. All the large SDRs revealed skewness toward the heterozygous allele and all the skewed alleles within the SDR segregate in the same direction. A unique intra-chromosomal duplications observed in chromosome24(D08), where3markers viz MON_CGR5433, MON_CGR0152and MON_CGR5423each revealed duplicate loci and their recombination rates on an average is lOcM respectively. The SSR-based map constructed in this study will be useful for further genetic analysis of important quantitative traits, marker assisted selection and genome organization architecture in cotton as well as for comparative genomics between cotton and other species. Moreover this map will lay the foundation for developing chromosome segment substitution lines (CSSLs) from G. mustelinum in an upland cotton background by marker-assisted high throughput selection and also enrich the cotton germplasm by incorporating superior genes especially insect resistance from wild genetic resources.
引文
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