There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of geno...There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing （GBS） platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop mo- lecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype- phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of （a） rapid development in gene discovery of important traits, （b） deepened understanding of quantitative traits through new analytical models and population designs, （c） integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and （d） improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.展开更多
Restriction-site associated DNA sequencing(RAD-seq)技术是在二代测序基础上发展起来的一项基于全基因组酶切位点的简化基因组测序技术。该方法技术流程简单,不受有无参考基因组的限制,可大大简化基因组的复杂性,减少实验费用,通过...Restriction-site associated DNA sequencing(RAD-seq)技术是在二代测序基础上发展起来的一项基于全基因组酶切位点的简化基因组测序技术。该方法技术流程简单,不受有无参考基因组的限制,可大大简化基因组的复杂性,减少实验费用,通过一次测序就可以获得数以万计的多态性标记。目前,RAD-seq技术已成功应用于超高密度遗传图谱的构建、重要性状的精细定位、辅助基因组序列组装、群体基因组学以及系统发生学等基因组研究热点领域。文章主要介绍了RAD-seq的技术原理、技术发展及其在基因组研究中的广泛应用。鉴于RAD-seq方法的独特性,该技术必将在复杂基因组研究领域具有广泛的应用前景。展开更多
Based on the theory of constitution of Traditional Chinese Medicine （TCM）, the human population is divided into nine constitutions including one balanced constitution （Normality） and eight unbalanced constitutions...Based on the theory of constitution of Traditional Chinese Medicine （TCM）, the human population is divided into nine constitutions including one balanced constitution （Normality） and eight unbalanced constitutions （Yang-deficiency, Yin-deficiency, Phlegm-wetness, Qi-deficiency, Wetness-heat, Blood stasis, Depressed constitution, and Inherited special constitution）. Different constitutions have specific metabolic features and different susceptibility to certain diseases. However, whether a genetic basis accounts for such constitution classification is yet to be determined. Here we performed a genetic study to assess the association between genetic variations of metabolic genes including PPARD, PPARG and APM1 and the constitutions. A total of 233 individuals of the Han population in China were classified into four groups, Normality, Yang-deficiency, Yin-deficiency and Phlegm-wetness with whom 23 single nucleotide polymorphisms （SNPs） in the three genes were genotyped using polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP） method. Biased distribution of PPARD rs2267669 and rs2076167, APM1 rs7627128 and rs1063539 in Yang-deficiency, PPARG Prol2Ala in Yin-deficiency and PPARD rs2076167, APMI rs266729 and rs7627128 in Phlegm-wetness were observed. The frequencies of Haplotypel3 （Hapl3） of PPARG in Yin-deficiency, Hap25 of APM1 in Yang-deficiency and Hap2 of PPARD and Hapl4 of PPARG in Phlegm-wetness, were significantly different from those in Normality, suggesting those might be group-associated haplotypes. These results suggested that single SNP and haplotypes ofPPARD, PPARG and APM1 may underlie the genetic basis of the constitutions classified in TCM.展开更多
基金This study was supported by the National Key Research and Development Program of China （2016YFD0101802 and 2016YFE0108600） and National Natural Science Foundation of China （31550110212）.
文摘There is a rapidly rising trend in the development and application of molecular marker assays for gene map- ping and discovery in field crops and trees. Thus far, more than 50 SNP arrays and 15 different types of genotyping-by-sequencing （GBS） platforms have been developed in over 25 crop species and perennial trees. However, much less effort has been made on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. In this review, we discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategies to develop targeted platforms for crop mo- lecular breeding. We propose that future practical breeding platforms should adopt automated genotyping technologies, either array or sequencing based, target functional polymorphisms underpinning economic traits, and provide desirable prediction accuracy for quantitative traits, with universal applications under wide genetic backgrounds in crops. The development of such platforms faces serious challenges at both the technological level due to cost ineffectiveness, and the knowledge level due to large genotype- phenotype gaps in crop plants. It is expected that such genotyping platforms will be achieved in the next ten years in major crops in consideration of （a） rapid development in gene discovery of important traits, （b） deepened understanding of quantitative traits through new analytical models and population designs, （c） integration of multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and （d） improvement in cost effectiveness of large-scale genotyping. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate the development of cultivars with desired yield potential, quality, and enhanced adaptation to mitigate the effects of climate change.
文摘Restriction-site associated DNA sequencing(RAD-seq)技术是在二代测序基础上发展起来的一项基于全基因组酶切位点的简化基因组测序技术。该方法技术流程简单,不受有无参考基因组的限制,可大大简化基因组的复杂性,减少实验费用,通过一次测序就可以获得数以万计的多态性标记。目前,RAD-seq技术已成功应用于超高密度遗传图谱的构建、重要性状的精细定位、辅助基因组序列组装、群体基因组学以及系统发生学等基因组研究热点领域。文章主要介绍了RAD-seq的技术原理、技术发展及其在基因组研究中的广泛应用。鉴于RAD-seq方法的独特性,该技术必将在复杂基因组研究领域具有广泛的应用前景。
基金supported by the National Basic Research Program of China (973 Program) (No. 2005CB523501)
文摘Based on the theory of constitution of Traditional Chinese Medicine （TCM）, the human population is divided into nine constitutions including one balanced constitution （Normality） and eight unbalanced constitutions （Yang-deficiency, Yin-deficiency, Phlegm-wetness, Qi-deficiency, Wetness-heat, Blood stasis, Depressed constitution, and Inherited special constitution）. Different constitutions have specific metabolic features and different susceptibility to certain diseases. However, whether a genetic basis accounts for such constitution classification is yet to be determined. Here we performed a genetic study to assess the association between genetic variations of metabolic genes including PPARD, PPARG and APM1 and the constitutions. A total of 233 individuals of the Han population in China were classified into four groups, Normality, Yang-deficiency, Yin-deficiency and Phlegm-wetness with whom 23 single nucleotide polymorphisms （SNPs） in the three genes were genotyped using polymerase chain reaction-restriction fragment length polymorphism （PCR-RFLP） method. Biased distribution of PPARD rs2267669 and rs2076167, APM1 rs7627128 and rs1063539 in Yang-deficiency, PPARG Prol2Ala in Yin-deficiency and PPARD rs2076167, APMI rs266729 and rs7627128 in Phlegm-wetness were observed. The frequencies of Haplotypel3 （Hapl3） of PPARG in Yin-deficiency, Hap25 of APM1 in Yang-deficiency and Hap2 of PPARD and Hapl4 of PPARG in Phlegm-wetness, were significantly different from those in Normality, suggesting those might be group-associated haplotypes. These results suggested that single SNP and haplotypes ofPPARD, PPARG and APM1 may underlie the genetic basis of the constitutions classified in TCM.
