2010年前后,随着各大作物模式品种基因组测序的完成,拟南芥、水稻、玉米等的重测序研究,突破了分子标记数量的限制,带动作物科学研究全面进入基因组时代,大量代表性品种、种质资源完成了重测序工作,数以百万甚至千万计的SNP标记,全基因...2010年前后,随着各大作物模式品种基因组测序的完成,拟南芥、水稻、玉米等的重测序研究,突破了分子标记数量的限制,带动作物科学研究全面进入基因组时代,大量代表性品种、种质资源完成了重测序工作,数以百万甚至千万计的SNP标记,全基因组关联分析(GWAS,genome-wide association study)广泛应用于遗传资源研究,使近10年成为种质资源研究的黄金期,通过GWAS解析一些复杂重要农艺性状的遗传基础,成为Cell、Nature和Science及其子刊这一时期的主要内容,推动种质资源学迈入一个崭新时代。20世纪,遗传育种学的发展和完善推动了种质资源学科的萌芽和初步形成,而21世纪基因组学的发展和广泛应用,逐步形成了种质资源学推动育种学发展的新局面,一些长期困扰育种家的问题,通过GWAS分析得到了重要启示或答案(如番茄的驯化、育种史,品质与产量矛盾问题,小麦骨干亲本等)。而泛基因组研究的迅速发展,突破了单一参考基因组的局限性,使我们认识到品种间基因组结构变异的普遍性,为深度解析重大品种、骨干亲本的形成及突破性资源的创制提供了更加宽广的视野。巢式关联作图群体(NAM,nested association mapping)、多亲本互交群体(MAGIC,multi-parent advanced generation intercross)及以此为基础衍生的构建多亲本遗传群体的思路和实践,使研究群体的遗传背景水平达到同期育种要求,不仅加快了基因的精细定位,并为组装育种提供了平台,推动着种质资源学、基因组学和育种学的融合与互动,开启了以基因组信息为支撑的基因资源和分子设计育种新时代,也预示着大学科融合与调整时代的到来。展开更多
Starch is the most important component in the endosperm, and its synthesis is regulated by multiple transcription factors(TFs) in cereals. However, whether the functions of these TFs are conserved among cereals remain...Starch is the most important component in the endosperm, and its synthesis is regulated by multiple transcription factors(TFs) in cereals. However, whether the functions of these TFs are conserved among cereals remains unclear. In this study,we cloned a B3 family TF in wheat, named TaABI19, based on its orthologous sequence in maize(Zea mays L.). Alignment of the DNA and protein sequences showed that ABI19 is conserved in maize and wheat(Triticum aestivum L.). We found that TaABI19 is highly expressed in young spikes and developing grains, and encodes a nucleus-localized transcriptional activator in wheat. The taabi19-b1 null mutants obtained by EMS exhibited a down-regulation of starch synthesis, shorter grain length and lower thousand-grain weight(TGW). Furthermore, we proved that TaABI19 could bind to the promoters of TaPBF homologous genes and enhance their expression. Haplotype association showed that TaABI19-B1 is significantly associated with TGW. We found that Hap2 and Hap3 were favored and had undergone positive selection in China’s wheat breeding programs. Less than 50% of the modern cultivars convey the favored haplotypes, indicating that TaABI19 still can be considered as a target locus for marker-assisted selection breeding to increase TGW in China.展开更多
Stress associated proteins(SAPs) are the A20/AN1 zinc-finger proteins which confer to abiotic stresses in plants. In this study, TaSAP7-B, including two AN1 domains, was isolated from B genome of wheat(Triticum aestiv...Stress associated proteins(SAPs) are the A20/AN1 zinc-finger proteins which confer to abiotic stresses in plants. In this study, TaSAP7-B, including two AN1 domains, was isolated from B genome of wheat(Triticum aestivum L.). Sequencing analysis on TaSAP7-B illustrated one In Del(insertion-deletion) and one SNP(single nucleotide polymorphism) in the promoter region while no diversity was observed in the coding region. On the basis of SNP in the promoter region(–260 bp), a dCAPS(derived cleaved amplified polymorphic sequences) marker SNP-260 was developed for TaSAP7-B. Using a natural population consisting of 262 wheat accessions, significant associations were detected between the marker SNP-260 and agronomic traits, such as plant height(PH), peduncle length(PL), length of penultimate internode(LPI), number of spike per plant(NSP), and 1 000-grain weight(TGW). Two genotypes were identified using marker SNP-260 in the natural population. Among them, the genotypes possessing C allele exhibited a higher TGW and shorter PH than the T genotypes. Hence, base C was considered as the superior allele. The dCAPS marker of TaSAP7-B can be instrumental for marker-assisted selection for high grain size and short plant height.展开更多
Stress-associated protein(SAP)has functions in maintaining plant cell elongation,embryo development and response to abiotic stresses.TaSAP1-A1,one of the Triticum aestivum SAP1(TaSAP1)members located on wheat chromoso...Stress-associated protein(SAP)has functions in maintaining plant cell elongation,embryo development and response to abiotic stresses.TaSAP1-A1,one of the Triticum aestivum SAP1(TaSAP1)members located on wheat chromosome 7A was isolated for polymorphism analysis.HapIII of TaSAP1-A1 was found significantly associated with thousand-grain weight(TGW)in multiple environments.In this study,HapIII also made a positive contribution to TGW in Population 2.The distribution of TaSAP1-A1HapIII was tracked among varieties released in different years and geographical environments of China.The frequency of HapIII showed an increasing trend during the breeding process in two different populations.The HapIII was gradually selected and applied from 6.36%in landraces to 13.50%in modern varieties.These results exhibited that TaSAP1-A1 HapIII was positively selected during wheat breeding,which is beneficial for grain-yield improvement.The preferred HapIII was initially selected and applied in the higher latitude areas of China in accord with the long day season and longer grain filling stage in these areas.Moreover,the frequency of HapIII in recent modern varieties was still quite low(19.29-26.67%).It indicated a high application potential of TaSAP1-A1 HapIII for improving grain yield in wheat breeding.展开更多
Besides the natural selection, the crops cultivated today have experienced two episodes of strong artificial selection, domestic and modern breeding. Domestication led to giant genetic structure differentiation betwee...Besides the natural selection, the crops cultivated today have experienced two episodes of strong artificial selection, domestic and modern breeding. Domestication led to giant genetic structure differentiation between cultivars and their wild species, while modern breeding made further genetic structure differentiation between the modern varieties and the landraces. In a population, diversity of the loci under strong selection is significantly lower than that of other loci. At the same time, diversity in the genomic regions flanking these selected loci also declines in the process of selection. This phenomenon is called hitchhiking effects or selection sweep in genetics. Genomic regions with selection sweep (haplotype block) could be detected after draft genome scanning (genome typing) with molecular markers in a number of released varieties or natural populations. Marker/trait association analysis in these regions would detect the loci (or QTLs) even the favored alleles (genes) in breeding or natural adaptation. Fine scanning of these genomic regions would help to determine the sizes of haplotype blocks and to discover the key genes, thereby providing very valuable information for isolation of the key genes and molecular design of new varieties. Establishment of high density genetic linkage maps in the major crops and availability of high throughput genotyping platform make it possible to discover agronomic important genes through marker/trait association analysis. On the basis of available publications, we give a brief introduction of the hitchhiking effect mapping approach in this paper using plant height, 1 000-grain weight, and phosphorus-deficiency tolerance as examples in wheat.展开更多
文摘2010年前后,随着各大作物模式品种基因组测序的完成,拟南芥、水稻、玉米等的重测序研究,突破了分子标记数量的限制,带动作物科学研究全面进入基因组时代,大量代表性品种、种质资源完成了重测序工作,数以百万甚至千万计的SNP标记,全基因组关联分析(GWAS,genome-wide association study)广泛应用于遗传资源研究,使近10年成为种质资源研究的黄金期,通过GWAS解析一些复杂重要农艺性状的遗传基础,成为Cell、Nature和Science及其子刊这一时期的主要内容,推动种质资源学迈入一个崭新时代。20世纪,遗传育种学的发展和完善推动了种质资源学科的萌芽和初步形成,而21世纪基因组学的发展和广泛应用,逐步形成了种质资源学推动育种学发展的新局面,一些长期困扰育种家的问题,通过GWAS分析得到了重要启示或答案(如番茄的驯化、育种史,品质与产量矛盾问题,小麦骨干亲本等)。而泛基因组研究的迅速发展,突破了单一参考基因组的局限性,使我们认识到品种间基因组结构变异的普遍性,为深度解析重大品种、骨干亲本的形成及突破性资源的创制提供了更加宽广的视野。巢式关联作图群体(NAM,nested association mapping)、多亲本互交群体(MAGIC,multi-parent advanced generation intercross)及以此为基础衍生的构建多亲本遗传群体的思路和实践,使研究群体的遗传背景水平达到同期育种要求,不仅加快了基因的精细定位,并为组装育种提供了平台,推动着种质资源学、基因组学和育种学的融合与互动,开启了以基因组信息为支撑的基因资源和分子设计育种新时代,也预示着大学科融合与调整时代的到来。
基金supported by the the Central Public-interest Scientific Institution Basal Research Fund,Chinese Academy of Agricultural Sciences(Y2017PT39).
文摘Starch is the most important component in the endosperm, and its synthesis is regulated by multiple transcription factors(TFs) in cereals. However, whether the functions of these TFs are conserved among cereals remains unclear. In this study,we cloned a B3 family TF in wheat, named TaABI19, based on its orthologous sequence in maize(Zea mays L.). Alignment of the DNA and protein sequences showed that ABI19 is conserved in maize and wheat(Triticum aestivum L.). We found that TaABI19 is highly expressed in young spikes and developing grains, and encodes a nucleus-localized transcriptional activator in wheat. The taabi19-b1 null mutants obtained by EMS exhibited a down-regulation of starch synthesis, shorter grain length and lower thousand-grain weight(TGW). Furthermore, we proved that TaABI19 could bind to the promoters of TaPBF homologous genes and enhance their expression. Haplotype association showed that TaABI19-B1 is significantly associated with TGW. We found that Hap2 and Hap3 were favored and had undergone positive selection in China’s wheat breeding programs. Less than 50% of the modern cultivars convey the favored haplotypes, indicating that TaABI19 still can be considered as a target locus for marker-assisted selection breeding to increase TGW in China.
基金supported by the National Key Research and Development Program of China (2016YFD0100605)the National Natural Science Foundation of China (31271720)
文摘Stress associated proteins(SAPs) are the A20/AN1 zinc-finger proteins which confer to abiotic stresses in plants. In this study, TaSAP7-B, including two AN1 domains, was isolated from B genome of wheat(Triticum aestivum L.). Sequencing analysis on TaSAP7-B illustrated one In Del(insertion-deletion) and one SNP(single nucleotide polymorphism) in the promoter region while no diversity was observed in the coding region. On the basis of SNP in the promoter region(–260 bp), a dCAPS(derived cleaved amplified polymorphic sequences) marker SNP-260 was developed for TaSAP7-B. Using a natural population consisting of 262 wheat accessions, significant associations were detected between the marker SNP-260 and agronomic traits, such as plant height(PH), peduncle length(PL), length of penultimate internode(LPI), number of spike per plant(NSP), and 1 000-grain weight(TGW). Two genotypes were identified using marker SNP-260 in the natural population. Among them, the genotypes possessing C allele exhibited a higher TGW and shorter PH than the T genotypes. Hence, base C was considered as the superior allele. The dCAPS marker of TaSAP7-B can be instrumental for marker-assisted selection for high grain size and short plant height.
基金supported by the National Basic Research Program of China(2010CB951501)the National High-Tech R&D Program of China(2011AA100501)
文摘Stress-associated protein(SAP)has functions in maintaining plant cell elongation,embryo development and response to abiotic stresses.TaSAP1-A1,one of the Triticum aestivum SAP1(TaSAP1)members located on wheat chromosome 7A was isolated for polymorphism analysis.HapIII of TaSAP1-A1 was found significantly associated with thousand-grain weight(TGW)in multiple environments.In this study,HapIII also made a positive contribution to TGW in Population 2.The distribution of TaSAP1-A1HapIII was tracked among varieties released in different years and geographical environments of China.The frequency of HapIII showed an increasing trend during the breeding process in two different populations.The HapIII was gradually selected and applied from 6.36%in landraces to 13.50%in modern varieties.These results exhibited that TaSAP1-A1 HapIII was positively selected during wheat breeding,which is beneficial for grain-yield improvement.The preferred HapIII was initially selected and applied in the higher latitude areas of China in accord with the long day season and longer grain filling stage in these areas.Moreover,the frequency of HapIII in recent modern varieties was still quite low(19.29-26.67%).It indicated a high application potential of TaSAP1-A1 HapIII for improving grain yield in wheat breeding.
文摘Besides the natural selection, the crops cultivated today have experienced two episodes of strong artificial selection, domestic and modern breeding. Domestication led to giant genetic structure differentiation between cultivars and their wild species, while modern breeding made further genetic structure differentiation between the modern varieties and the landraces. In a population, diversity of the loci under strong selection is significantly lower than that of other loci. At the same time, diversity in the genomic regions flanking these selected loci also declines in the process of selection. This phenomenon is called hitchhiking effects or selection sweep in genetics. Genomic regions with selection sweep (haplotype block) could be detected after draft genome scanning (genome typing) with molecular markers in a number of released varieties or natural populations. Marker/trait association analysis in these regions would detect the loci (or QTLs) even the favored alleles (genes) in breeding or natural adaptation. Fine scanning of these genomic regions would help to determine the sizes of haplotype blocks and to discover the key genes, thereby providing very valuable information for isolation of the key genes and molecular design of new varieties. Establishment of high density genetic linkage maps in the major crops and availability of high throughput genotyping platform make it possible to discover agronomic important genes through marker/trait association analysis. On the basis of available publications, we give a brief introduction of the hitchhiking effect mapping approach in this paper using plant height, 1 000-grain weight, and phosphorus-deficiency tolerance as examples in wheat.
