The allelic variation of the Wx gene in 50 non-glutinous rice varieties （lines） was analyzed by using the microsatellite marker RM190 [for （CT）n simple sequence repeat （SSR）] and cleaved amplified polymorphic se...The allelic variation of the Wx gene in 50 non-glutinous rice varieties （lines） was analyzed by using the microsatellite marker RM190 [for （CT）n simple sequence repeat （SSR）] and cleaved amplified polymorphic sequence（CAPS） marker 484/W2R-ACCⅠ[for G/T single nucleotide polymorphism （SNP）]. Six homozygous （CT）n types, namely （CT）20, （CT）19, （CT）18, （CT）17, （CT）16, （CT）14, （CT）11 and （CT）10, and a heterozygous genotype （CT）11/（CT）18 were detected for RM190, of which （CT）11 and （CT）18 were predominant. Two homozygous Wx genotypes （G/G and T/T） and one heterozygous （G/T） were detected using 484/W2R-ACC Ⅰ. Most of the materials with a RM190 of （CT）11 were G/G for SNP of 484/W2R-ACC Ⅰ, while T/T for SNP was predominantly appeared in materials with （CT）18. The materials tested could be grouped into 10 categories using the two markers together. Results indicated that 59.3% variance of amylose content was attributed to the polymorphism of Wx gene revealed by RM190, while 56.1% and 24.6% of the variances in amylose content and gel consistency were respectively to the polymorphism of Wx gene revealed by 484/W2R-ACC Ⅰ. Furthermore, with both SSR and CAPS markers, 72.4% of the variance in amylose content could be explained. In addition, the application prospects of the two markers in breeding were also discussed.展开更多
Mungbean （Vigna radiata （L.） Wilczek） is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptom...Mungbean （Vigna radiata （L.） Wilczek） is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptome sequencing. A total of 150 159 and 142 993 reads produced 5 254 and 6 374 large contigs （〉_500 bp） with an average length of 833 and 853 for Sunhwa and Jangan, respectively. Functional annotation to known sequences yielded 41.34% and 41.74% unigenes for Jangan and Sunhwa. A higher number of simple sequence repeat （SSR） motifs was identified in Jangan （1 630） compared with that of Sunhwa （1 334）. A similar SSR distribution pattern was observed in both varieties. A total of 8 249 single nucleotide polymorphisms （SNPs） and indels with 2 098 high-confidence candidates were identified in the two mungbean varieties. The average distance between individual SNPs was -860 bp. Our report demonstrates the utility of transcriptomic data for implementing a functional annotation and development of genetic markers. We also provide large resource sequence data for mungbean improvement programs.展开更多
【目的】蔗茅(Erianthus fulvus)是甘蔗重要的野生资源,可用于改良品种的抗逆性和产量。系统鉴定和开发蔗茅基因组中的简单重复序列(simple sequence repeat,SSR)位点,筛选可利用的多态性SSR标记,解析蔗茅资源的遗传多样性特征,开发重...【目的】蔗茅(Erianthus fulvus)是甘蔗重要的野生资源,可用于改良品种的抗逆性和产量。系统鉴定和开发蔗茅基因组中的简单重复序列(simple sequence repeat,SSR)位点,筛选可利用的多态性SSR标记,解析蔗茅资源的遗传多样性特征,开发重要性状关联分子标记,对于利用蔗茅基因资源改良品种性状具有重要意义。【方法】采用生物信息学软件TBtools中的SSRminer模块,对二倍体蔗茅全基因组序列进行系统性SSR位点挖掘,并对所得数据进行统计分析,揭示其在基因组中的分布模式及规律。利用Batch Target Region Primer Design功能批量设计SSR引物,并通过Primer check工具评估引物的特异性。在6个蔗茅种质中,通过对随机合成的50对SSR引物和14对来自甘蔗的SSR引物进行扩增效率和多态性比较分析,验证引物多态性。【结果】共鉴定出152707个蔗茅SSR位点,平均检测频率为5.64 kb/个,大部分分布在基因间区。SSR类型分布以单碱基、二碱基、三碱基为主。二核苷酸SSR类型中的基序重复次数变化最大,而五核苷酸的基序重复次数变异最低。共检测出883种不同的SSR基序重复类型,其中,A/T和AT/TA是最为丰富。共设计144692对SSR引物,其中85025对显示高特异性。这些特异性引物在基因组上呈现出两端密集、中间稀疏的分布特点。扩增试验显示,50对随机合成的SSR引物中,有42对在蔗茅中扩增出稳定清晰的条带,其中32对显示出多态性,多态率为64.0%。与甘蔗SSR引物相比,蔗茅SSR引物表现出更高的扩增效率和更好的多态性水平。经过筛选,从32对有效的蔗茅SSR引物中确定了16对多态性好且扩增条带清晰的引物。这16对引物共扩增出72条条带,多态性信息量(polymorphism information content,PIC)范围为0.63—0.83,平均PIC值为0.74,表明它们在蔗茅种质资源的多态性分析和分子标记研究中具有有效性和实用性。【结论】揭示了蔗茅基因组中高丰度和多样性的SSR分布特征。获得16对扩增效率高、多态性良好的SSR引物。展开更多
LK783 was found to be a good fertility restorer for K-type male sterility of wheat (Triticum aestivum L.). RAPD and ISSR (inter-simple sequence repeat polymorphism) markers were employed to map the major restoring gen...LK783 was found to be a good fertility restorer for K-type male sterility of wheat (Triticum aestivum L.). RAPD and ISSR (inter-simple sequence repeat polymorphism) markers were employed to map the major restoring gene in LK783. Maintainer and restorer DNA pools were established using the extreme sterile and fertile plants among KJ5418A//911289/LK783 F 1 population, respectively. Four hundred and eighteen RAPD primers and 33 ISSR primers were used for screening polymorphisms between the two pools, and amplification bands using a RAPD primer of OPK18 and an ISSR primer of UBC-845 were found polymorphic between the two pools. Linkage analysis showed that OPK18 450 and UBC-845 800 were linked to the restoring gene in LK783. The distance between the restoring gene and OPK18 450 was (15.07±6.28) cM (centiMorgan), with the distance between the restoring gene and UBC-845 800 being (8.20±4.85) cM. The marker of UBC-845 800 was located on chromosome 1BS by amplifying nulli-tetrasomics and 1B ditelosomics of Chinese Spring with the primer of UBC-845, indicating that the restoring gene in LK783 was located on 1BS. The breeding for new fertility restorer lines of K-type cytoplasmic male sterility of wheat would be facilitated by using the two markers.展开更多
短串联重复序列(short tandem repeat,STR)遗传标记在法庭科学DNA鉴定中占据绝对主导地位,包括中国在内的世界各国DNA数据库均基于STR遗传标记建立。STR遗传标记具有长度多态性和序列多态性。序列多态包括重复区和侧翼区序列的多态性。...短串联重复序列(short tandem repeat,STR)遗传标记在法庭科学DNA鉴定中占据绝对主导地位,包括中国在内的世界各国DNA数据库均基于STR遗传标记建立。STR遗传标记具有长度多态性和序列多态性。序列多态包括重复区和侧翼区序列的多态性。传统的基于毛细管电泳技术进行STR分型仅区分长度多态性,而深刻理解核心STR基因座的序列多态对于引物设计和DNA鉴定等方面至关重要。首先,STR扩增引物结合区的SNP、InDel可能干扰引物与DNA模板结合的亲和力,导致无法检测到某些等位基因或均衡性差,影响DNA鉴定准确性;其次,二代测序技术推动STR鉴定由长度多态分型向序列多态分型发展,显著提升了可检测的核心STR基因座多态信息含量,提高了其个体识别和亲缘关系分析效能;再者,不同人群具有不同的STR序列特征。近10年来,基于二代测序的STR序列多态性的研究逐渐增多,多个人群的序列多态性数据已经被报道,但以往的研究群体及数据较为零散,重复序列的数据格式不统一,导致核心STR基因座的序列多态性缺乏来自大数据的系统性总结和梳理。充分掌握核心STR基因座的序列特征对微量检材的个体识别、混合样本拆分、亲子鉴定中突变来源的确定等具有十分重要的意义。本文以19个常染色体核心STR为分析对象,整合了目前文献报道的群体数据和公开数据库中的中国人群变异频率数据,系统综述了这些STR的序列多态性,包括归纳STR基因座重复区的变异类型和分析变异规律,总结了中国人群中STR侧翼区的高频变异,并探讨了在STR序列检验中可能遇到的难点,以期为STR序列的应用解析、案件检验中稀有等位基因的判别以及STR试剂盒的研制等方面提供参考。展开更多
The present study investigated the genetic diversity of 24 germplasms of Polianthes tuberosa L.via 16 inter simple sequence repeat(ISSR)marker techniques.The research findings revealed that the ISSR markers presented ...The present study investigated the genetic diversity of 24 germplasms of Polianthes tuberosa L.via 16 inter simple sequence repeat(ISSR)marker techniques.The research findings revealed that the ISSR markers presented higher levels of band reproducibility andweremore efficient at clustering germplasms.Among the 16markers examined in this study,12 had a complete polymorphism rate of 100%.Themolecular analysis revealed a PICranging from0.079 to 0.373,with amean value of 0.30,whereas the range of themarker index was from0.0001 to 0.409,with an average value of 0.03,and the primer resolving power ranged from 0.173 to 4.173,with a mean value of 2.02.The UPGMA clustering dendrogram indicated that all 24 germplasms were grouped into three main clusters.The study revealed a variable range of tree distances between 0.185 and 0.621,with the highest tree distance(0.621)detected between germplasms BR-24 and BR-1.Through these studies,the dissimilarity among the germplasms was evaluated,and diverse parents were identified for further crop improvement programs.展开更多
文摘The allelic variation of the Wx gene in 50 non-glutinous rice varieties （lines） was analyzed by using the microsatellite marker RM190 [for （CT）n simple sequence repeat （SSR）] and cleaved amplified polymorphic sequence（CAPS） marker 484/W2R-ACCⅠ[for G/T single nucleotide polymorphism （SNP）]. Six homozygous （CT）n types, namely （CT）20, （CT）19, （CT）18, （CT）17, （CT）16, （CT）14, （CT）11 and （CT）10, and a heterozygous genotype （CT）11/（CT）18 were detected for RM190, of which （CT）11 and （CT）18 were predominant. Two homozygous Wx genotypes （G/G and T/T） and one heterozygous （G/T） were detected using 484/W2R-ACC Ⅰ. Most of the materials with a RM190 of （CT）11 were G/G for SNP of 484/W2R-ACC Ⅰ, while T/T for SNP was predominantly appeared in materials with （CT）18. The materials tested could be grouped into 10 categories using the two markers together. Results indicated that 59.3% variance of amylose content was attributed to the polymorphism of Wx gene revealed by RM190, while 56.1% and 24.6% of the variances in amylose content and gel consistency were respectively to the polymorphism of Wx gene revealed by 484/W2R-ACC Ⅰ. Furthermore, with both SSR and CAPS markers, 72.4% of the variance in amylose content could be explained. In addition, the application prospects of the two markers in breeding were also discussed.
基金support of the "Cooperative Research Program for Agriculture Science & Technology Development (Project No. 200908FHT020609001)" Rural Development Administration (RDA),Republic of Korea
文摘Mungbean （Vigna radiata （L.） Wilczek） is a unique species in its ability to fix atmospheric nitrogen, with early maturity, and relatively good drought resistance. We used 454 sequencing technology for transcriptome sequencing. A total of 150 159 and 142 993 reads produced 5 254 and 6 374 large contigs （〉_500 bp） with an average length of 833 and 853 for Sunhwa and Jangan, respectively. Functional annotation to known sequences yielded 41.34% and 41.74% unigenes for Jangan and Sunhwa. A higher number of simple sequence repeat （SSR） motifs was identified in Jangan （1 630） compared with that of Sunhwa （1 334）. A similar SSR distribution pattern was observed in both varieties. A total of 8 249 single nucleotide polymorphisms （SNPs） and indels with 2 098 high-confidence candidates were identified in the two mungbean varieties. The average distance between individual SNPs was -860 bp. Our report demonstrates the utility of transcriptomic data for implementing a functional annotation and development of genetic markers. We also provide large resource sequence data for mungbean improvement programs.
文摘【目的】蔗茅(Erianthus fulvus)是甘蔗重要的野生资源,可用于改良品种的抗逆性和产量。系统鉴定和开发蔗茅基因组中的简单重复序列(simple sequence repeat,SSR)位点,筛选可利用的多态性SSR标记,解析蔗茅资源的遗传多样性特征,开发重要性状关联分子标记,对于利用蔗茅基因资源改良品种性状具有重要意义。【方法】采用生物信息学软件TBtools中的SSRminer模块,对二倍体蔗茅全基因组序列进行系统性SSR位点挖掘,并对所得数据进行统计分析,揭示其在基因组中的分布模式及规律。利用Batch Target Region Primer Design功能批量设计SSR引物,并通过Primer check工具评估引物的特异性。在6个蔗茅种质中,通过对随机合成的50对SSR引物和14对来自甘蔗的SSR引物进行扩增效率和多态性比较分析,验证引物多态性。【结果】共鉴定出152707个蔗茅SSR位点,平均检测频率为5.64 kb/个,大部分分布在基因间区。SSR类型分布以单碱基、二碱基、三碱基为主。二核苷酸SSR类型中的基序重复次数变化最大,而五核苷酸的基序重复次数变异最低。共检测出883种不同的SSR基序重复类型,其中,A/T和AT/TA是最为丰富。共设计144692对SSR引物,其中85025对显示高特异性。这些特异性引物在基因组上呈现出两端密集、中间稀疏的分布特点。扩增试验显示,50对随机合成的SSR引物中,有42对在蔗茅中扩增出稳定清晰的条带,其中32对显示出多态性,多态率为64.0%。与甘蔗SSR引物相比,蔗茅SSR引物表现出更高的扩增效率和更好的多态性水平。经过筛选,从32对有效的蔗茅SSR引物中确定了16对多态性好且扩增条带清晰的引物。这16对引物共扩增出72条条带,多态性信息量(polymorphism information content,PIC)范围为0.63—0.83,平均PIC值为0.74,表明它们在蔗茅种质资源的多态性分析和分子标记研究中具有有效性和实用性。【结论】揭示了蔗茅基因组中高丰度和多样性的SSR分布特征。获得16对扩增效率高、多态性良好的SSR引物。
文摘LK783 was found to be a good fertility restorer for K-type male sterility of wheat (Triticum aestivum L.). RAPD and ISSR (inter-simple sequence repeat polymorphism) markers were employed to map the major restoring gene in LK783. Maintainer and restorer DNA pools were established using the extreme sterile and fertile plants among KJ5418A//911289/LK783 F 1 population, respectively. Four hundred and eighteen RAPD primers and 33 ISSR primers were used for screening polymorphisms between the two pools, and amplification bands using a RAPD primer of OPK18 and an ISSR primer of UBC-845 were found polymorphic between the two pools. Linkage analysis showed that OPK18 450 and UBC-845 800 were linked to the restoring gene in LK783. The distance between the restoring gene and OPK18 450 was (15.07±6.28) cM (centiMorgan), with the distance between the restoring gene and UBC-845 800 being (8.20±4.85) cM. The marker of UBC-845 800 was located on chromosome 1BS by amplifying nulli-tetrasomics and 1B ditelosomics of Chinese Spring with the primer of UBC-845, indicating that the restoring gene in LK783 was located on 1BS. The breeding for new fertility restorer lines of K-type cytoplasmic male sterility of wheat would be facilitated by using the two markers.
文摘短串联重复序列(short tandem repeat,STR)遗传标记在法庭科学DNA鉴定中占据绝对主导地位,包括中国在内的世界各国DNA数据库均基于STR遗传标记建立。STR遗传标记具有长度多态性和序列多态性。序列多态包括重复区和侧翼区序列的多态性。传统的基于毛细管电泳技术进行STR分型仅区分长度多态性,而深刻理解核心STR基因座的序列多态对于引物设计和DNA鉴定等方面至关重要。首先,STR扩增引物结合区的SNP、InDel可能干扰引物与DNA模板结合的亲和力,导致无法检测到某些等位基因或均衡性差,影响DNA鉴定准确性;其次,二代测序技术推动STR鉴定由长度多态分型向序列多态分型发展,显著提升了可检测的核心STR基因座多态信息含量,提高了其个体识别和亲缘关系分析效能;再者,不同人群具有不同的STR序列特征。近10年来,基于二代测序的STR序列多态性的研究逐渐增多,多个人群的序列多态性数据已经被报道,但以往的研究群体及数据较为零散,重复序列的数据格式不统一,导致核心STR基因座的序列多态性缺乏来自大数据的系统性总结和梳理。充分掌握核心STR基因座的序列特征对微量检材的个体识别、混合样本拆分、亲子鉴定中突变来源的确定等具有十分重要的意义。本文以19个常染色体核心STR为分析对象,整合了目前文献报道的群体数据和公开数据库中的中国人群变异频率数据,系统综述了这些STR的序列多态性,包括归纳STR基因座重复区的变异类型和分析变异规律,总结了中国人群中STR侧翼区的高频变异,并探讨了在STR序列检验中可能遇到的难点,以期为STR序列的应用解析、案件检验中稀有等位基因的判别以及STR试剂盒的研制等方面提供参考。
基金funded by Uttar Banga Krishi Viswavidyalaya,IndiaBangladesh Wheat and Maize Research Institute,Dinajpur 5200,Bangladeshfunded by Taif University,Saudi Arabia,Project No.(TU-DSPP-2025-30).
文摘The present study investigated the genetic diversity of 24 germplasms of Polianthes tuberosa L.via 16 inter simple sequence repeat(ISSR)marker techniques.The research findings revealed that the ISSR markers presented higher levels of band reproducibility andweremore efficient at clustering germplasms.Among the 16markers examined in this study,12 had a complete polymorphism rate of 100%.Themolecular analysis revealed a PICranging from0.079 to 0.373,with amean value of 0.30,whereas the range of themarker index was from0.0001 to 0.409,with an average value of 0.03,and the primer resolving power ranged from 0.173 to 4.173,with a mean value of 2.02.The UPGMA clustering dendrogram indicated that all 24 germplasms were grouped into three main clusters.The study revealed a variable range of tree distances between 0.185 and 0.621,with the highest tree distance(0.621)detected between germplasms BR-24 and BR-1.Through these studies,the dissimilarity among the germplasms was evaluated,and diverse parents were identified for further crop improvement programs.
